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Sticky Revision:

Revision 26435 - Directory Listing
Modified Tue Oct 10 17:19:13 2017 UTC (8 days, 3 hours ago) by jcfr
STYLE: qSlicerAppMainWindow: Use releaseType() instead of isRelease()

See https://www.slicer.org/wiki/Documentation/Nightly/Developers/Tutorials/MigrationGuide/Slicer#Slicer_4.8:_Application:_isRelease.28.29_function_not_available_or_deprecated

Revision 26434 - Directory Listing
Modified Tue Oct 10 14:45:58 2017 UTC (8 days, 5 hours ago) by pieper
BUG: fix Help menu urls

Old code didn't map version number to valid pages,
so now a non-release build is pointed to Nightly.

Also Publication Database link is fixed.

Revision 26380 - Directory Listing
Modified Wed Sep 20 17:13:25 2017 UTC (4 weeks ago) by jcfr
ENH: Integrate VTK plotting to support Interactive manipulation

This commit provides Plotting facilities that include a Plot View
that can be packed in the layout, similar to the Slice Views and 3D Views.

The architecture also includes nodes that represent the data to be displayed
in the plot as well as nodes to represent the display properties of the data
and the plot itself.

In Addition, the PlotView is connected with the Table Module and Views allowing
the plotting of arrays with a simple click.

References:
https://www.slicer.org/wiki/Documentation/Nightly/Developers/Plots
https://www.na-mic.org/wiki/Project_Week_25/Interactive_Manipulation_of_Plots_and_Graphs
https://www.slicer.org/wiki/Developer_Meetings/20170425

Reviewed-by: Andras Lasso <lasso@queensu.ca>
Reviewed-by: Andriy Fedorov <fedorov@bwh.harvard.edu>
Reviewed-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Reviewed-by: Steve Pieper <pieper@bwh.harvard.edu>

From: Davide Punzo <punzodavide@hotmail.it>

Revision 26351 - Directory Listing
Modified Wed Sep 6 02:54:53 2017 UTC (6 weeks ago) by jcfr
ENH: Extend application API adding environment()/startupEnvironment()

Thanks: Andras Lasso <lasso@queensu.ca>

Revision 26329 - Directory Listing
Modified Fri Sep 1 01:50:27 2017 UTC (6 weeks, 5 days ago) by jcfr
BUG: ScriptedModuleDiscoveryTest: Skip test using test output on windows

Waiting the approach used in SlicerStartupCompletedTest and SlicerRCTest tests
is generalized, this commit exclude the test on windows.

This is required because on windows, when the launcher is user
to start the Slicer application, the console output is disabled.

Revision 26328 - Directory Listing
Modified Thu Aug 31 23:47:57 2017 UTC (6 weeks, 5 days ago) by jcfr
ENH: Extend scripted module API adding support for cleanup() method

This allows to do some cleanup before a scripted module is effectively
unloaded. It is particularly useful to update objects or widgets and avoid
memory leaks due to complex interdependencies between C++ application and
python layer.

Reviewed-by: Steve Pieper <pieper@bwh.harvard.edu>

Revision 26320 - Directory Listing
Modified Wed Aug 30 16:26:32 2017 UTC (7 weeks ago) by lassoan
BUG: Made SlicerStartupCompletedTest not require console

These tests relied on having console (standard output) available:
py_startupcompleted_signal_emitted_without_mainwindow_test
py_startupcompleted_signal_emitted_with_mainwindow_test

When console was not enabled (it is optional on Windows) then these tests failed.

The solution was to use the same method as for testing slicerrc startup options: communicate with the test using an output file.

Revision 26317 - Directory Listing
Modified Tue Aug 29 16:10:44 2017 UTC (7 weeks, 1 day ago) by lassoan
BUG: Fixed multiple emits of startupCompleted signal

startupCompleted signal was emitted each time the main window was minimized and then restored, causing errors such as duplicate content in data probe widget.

Revision 26280 - Directory Listing
Modified Wed Aug 16 14:15:49 2017 UTC (2 months ago) by jcfr
ENH: SlicerApplication: Introduce "startupCompleted()" signal

This signal is emitted when the startup phase has been completed.

Startup is complete when all the modules have been
initialized and the main window is shown to the user.

Note: If the application is started without the mainwindow,
the signal is emitted after the modules are initialized.

Test checking that both cases work as expected is also added.

Suggested-by: Andras Lasso <lasso@queensu.ca>

Revision 26279 - Directory Listing
Modified Wed Aug 16 14:15:45 2017 UTC (2 months ago) by jcfr
BUG: Fix module updating mainwindow at load time when using Qt5

With Qt5, relying on "Qtimer::singleShow" with a time of 0ms is not
sufficient anymore to ensure the associated slot is called after the
main window is shown.

The following errors were reported at startup time:

```
Failed to obtain reference to 'FileMenu'
Failed to obtain reference to 'qSlicerAppMainWindow'
No Data Probe frame - cannot create DataProbe
Failed to obtain reference to 'qSlicerAppMainWindow'
Failed to obtain reference to 'FileMenu'
```

To ensure module can update the main window once it is shown, this
commit introduces the signal "qSlicerApplication::mainWindowShown()" that
can be connected when a scripted or loadable module is initialized.

Once the main window is shown, the signal "mainWindowShown()" ends up being
triggered.

Revision 26262 - Directory Listing
Modified Mon Aug 14 02:16:15 2017 UTC (2 months ago) by jcfr
ENH: Enable Qt high DPI scaling

From: Max Smolens <max.smolens@kitware.com>

Revision 26260 - Directory Listing
Modified Mon Aug 14 02:16:07 2017 UTC (2 months ago) by jcfr
ENH: Set default QSurfaceFormat for QVTKOpenGLWidget

Set default QSurfaceFormat for QVTKOpenGLWidget so that QVTKOpenGLWidget
receives the proper OpenGL core profile context.

From QOpenGLWidget documentation (http://doc.qt.io/qt-5/qopenglwidget.html):

    Note: Calling QSurfaceFormat::setDefaultFormat() before constructing
    the QApplication instance is mandatory on some platforms (for
    example, macOS) when an OpenGL core profile context is requested.
    This is to ensure that resource sharing between contexts stays
    functional as all internal contexts are created using the correct
    version and profile.

Client code uses QVTKOpenGLWidget when SlICer_VTK_USE_QVTKOPENGLWIDGET
is defined in vtkSlicerConfigure.h.

Multisampling is disabled to support volume rendering and other VTK
functionality that reads from the framebuffer. See
https://gitlab.kitware.com/vtk/vtk/issues/1709.

From: Max Smolens <max.smolens@kitware.com>

Revision 26255 - Directory Listing
Modified Mon Aug 14 02:15:31 2017 UTC (2 months ago) by jcfr
BUG: Fix deprecated use of QPixmap::grabWidget

Co-authored-by: Max Smolens <max.smolens@kitware.com>

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 26252 - Directory Listing
Modified Mon Aug 14 02:15:15 2017 UTC (2 months ago) by jcfr
ENH: Suport Qt5 integrating QCleanLooksStyle from qtstyleplugins

This commit integrates qtstyleplugins files based of commit 600c296
from git://code.qt.io/qt/qtstyleplugins.git

BUG: bug fixes for some compilation errors on Windows

Co-authored-by: Hina Shah <hina.shah@kitware.com>

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 26251 - Directory Listing
Modified Mon Aug 14 02:07:21 2017 UTC (2 months ago) by jcfr
ENH: Add preliminary support for Qt5

Support configuration using either Qt4 or Qt5

Based on preliminary work from Steve Pieper <pieper@bwh.harvard.edu>

* vtkSlicerConfigure: Introduced Slicer_HAVE_QT5 and Slicer_HAVE_WEBKIT_SUPPORT.
  This was needed to workaround limitation of "moc" compiler preventing it
  from expanding macro like "QT_VERSION_CHECK.

* Explicitly set QT_PLUGINS_DIR and QT_BINARY_DIR variables when using Qt5

* Update extension build system to propagate Qt version

Tested with Qt 5.7 and Qt 5.9 on Ubuntu

Remaining tasks:
* Port extension manager
* Update install/packaging rules to support Qt5
* SlicerStyle (based on CommonStyle) is disabled (see Main.cxx). Application crashes on Linux.
* Fix runtime errors:
 * libpng warning: iCCP: known incorrect sRGB profile
 * QPixmap::grabWidget is deprecated, use QWidget::grab() instead

Co-authored-by: Hina Shah <hina.shah@kitware.com>
Co-authored-by: Max Smolens <max.smolens@kitware.com>

COMP adding qt5 variables for extension testing

COMP Adding Qt5 build and plugin cmake variables

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 26235 - Directory Listing
Modified Fri Aug 11 07:27:21 2017 UTC (2 months, 1 week ago) by jcfr
BUG: Import CTK Python module

Fix the following error due the CTK module not being imported:

    NameError: global name 'ctk' is not defined

The error occurred in at least the following tests:
py_SlicerMRBMultipleSaveRestoreLoopTest
py_SlicerMRBSaveRestoreCheckPathsTest

From: Max Smolens <max.smolens@kitware.com>

Revision 26230 - Directory Listing
Modified Fri Aug 11 03:50:39 2017 UTC (2 months, 1 week ago) by lassoan
ENH: Made sitkUtils API more robust

Methods in sitkUtils were simple and usable for simple testing, but were not robust enough
for general use:
- Referring to nodes by ID is unreliable: several nodes may have the same node name;
  users may change node name at any time; node names may be changed when added to the scene
  if a node name is already used, etc.
- Old APIs are used. For example, adding of display nodes, showing volumes in certain views, adding nodes
  to the scene have simpler, more effective methods.
- Display options were mixed with data management (data pushed into Slicer was forced to be displayed)

Solution:

Existing methods were kept for backward compatibility but a warning is logged to inform the user that the methods
are deprecated and will be removed in the future.

Added new methods that are more robust, refer to nodes by node object, and use new APIs.
Method names are more specific (indicate that volume nodes are pushed/pulled, not transforms, etc).
Slice display management is removed from push/pull volume.

Updated tests. Tests cover both current and deprecated methods.

Revision 26199 - Directory Listing
Modified Fri Aug 4 03:35:37 2017 UTC (2 months, 2 weeks ago) by lassoan
ENH: Changed coded entry field order to (value, scheme, meaning)

This (value, scheme, meaning) order is more commonly used in the DICOM standard and DCMTK as the (scheme, value, meaning) order that was used in the original implementation of vtkCodedEntry.

Revision 26195 - Directory Listing
Modified Thu Aug 3 18:35:51 2017 UTC (2 months, 2 weeks ago) by jcfr
ENH: Volumes: Add test for Volumes with NaN. See #3851

From: Sumedha Singla <sumedha.singla@kitware.com>

Revision 26185 - Directory Listing
Modified Sat Jul 29 04:39:55 2017 UTC (2 months, 2 weeks ago) by lassoan
ENH: Added saving of DICOM scalar volume voxel quantity&unit in volume node

It implements functionality originally implemented in this commit (but later reverted due to regressions):
"ENH: init quantity/units in scalar volume plugin" (4ac23a026eac73f471c53383c9cd73cf30eabc79).

This commit is functionally equivalent (except CT quantity incorrect code value has been fixed in
mapSOPClassUIDToDICOMQuantityAndUnits).

Quantity and unit of voxel values of scalar volumes can be accessed in vtkMRMLScalarVolumeNode by using these methods:
  void SetVoxelValueQuantity(vtkCodedEntry*);
  vtkGetObjectMacro(VoxelValueQuantity, vtkCodedEntry);
  void SetVoxelValueUnits(vtkCodedEntry*);
  vtkGetObjectMacro(VoxelValueUnits, vtkCodedEntry);

vtkCodedEntry class was added that simplifies storage, printing, serialization of code scheme/value/meaning triplets
so that it can be easily added to other node types in the future.

DICOMScalarVolumePlugin sets these values when the data is loaded from DICOM.

Added test of setting quantity and unit in scalar volume node during DICOM import (py_DICOMReaders test).

Revision 26177 - Directory Listing
Modified Wed Jul 26 14:54:05 2017 UTC (2 months, 3 weeks ago) by pinter
ENH: Added subject hierarchy attribute filter test

A new test section has been added to SubjectHierarchyGenericSelfTest to test attribute filter. Also a bug was fixed that 

Revision 26163 - Directory Listing
Modified Fri Jul 21 21:06:09 2017 UTC (2 months, 4 weeks ago) by jcfr
ENH: Enable python bz2 module adding bzlib2 dependency

The bzip2 library is statically built and linked into the corresponding
python module.

Suggested-by: Michael Hardisty <m.hardisty@utoronto.ca>

Revision 26148 - Directory Listing
Modified Mon Jul 10 14:38:11 2017 UTC (3 months, 1 week ago) by lassoan
ENH: Added test for slicer.util.arrayFromModelPoints

Revision 26147 - Directory Listing
Modified Mon Jul 10 13:59:40 2017 UTC (3 months, 1 week ago) by lassoan
ENH: Added more numpy array conversions to slicer.util

Added arrayFromVolume() and arrayFromModelPoints(). These are more explicit MRML node -> numpy array
conversion functions than array(): they use a MRML node object as input and it is more clear
what part of the MRML node is retrieved as numpy array.

Added updateVolumeFromArray. It copies content of an existing numpy array into image data of a volume node.

Also added automatic tests to UtilTest.py.

Revision 26145 - Directory Listing
Modified Thu Jul 6 15:50:03 2017 UTC (3 months, 1 week ago) by lassoan
ENH: Make CLI output update more robust

After a CLI module is executed, nodes that have references to other nodes are updated:
their parent transform are set to the referenced transform node; and/or their subject hierarchy
parent item is set to be the same as the parent of the referenced node.

This scene updated relied on a Qt timer that performed the updates "right after" CLI execution
was completed. This mechanism was not reliable because the timer required the user to
force background event processing for a while after the CLI execution was reported to be completed,
but this workaround was not reliable (see for example this report:
https://discourse.slicer.org/t/issues-modifying-the-transform-tree/569/13).

Changed the mechanism to use the same event queue that is used for processing reading of results
back into the scene. This way it can be assured that by the time the CLI execution is reported
to be complete, all the scene updates are completed as well.

Revision 26129 - Directory Listing
Modified Fri Jun 23 00:27:44 2017 UTC (3 months, 3 weeks ago) by pieper
ENH: move comparison utility from test to plugin

This will make the utility available for use in the
plugin and also from other code that needs
the same functionality.

TODO: this could be moved to the vtkSlicerVolumesLogic
class for even greater applicability.

From: Steve Pieper <pieper@isomics.com>

Revision 26128 - Directory Listing
Modified Fri Jun 23 00:27:42 2017 UTC (3 months, 3 weeks ago) by pieper
ENH: add scalar type detection to DICOM reader compare

DCMTK imageIO is returning unsigned char data.
This detects the error that still needs to be fixed.

From: Steve Pieper <pieper@isomics.com>

Revision 26126 - Directory Listing
Modified Fri Jun 23 00:27:40 2017 UTC (3 months, 3 weeks ago) by pieper
ENH: add logic to detect test failures

If any of the techniques unexpectedly loads a volume
incorrectly the test will throw and exception and
print the mismatches.

From: Steve Pieper <pieper@isomics.com>

Revision 26124 - Directory Listing
Modified Fri Jun 23 00:27:37 2017 UTC (3 months, 3 weeks ago) by pieper
ENH: add extra test case (MRHead as DICOM)

This is a useful test because it is a sagittal acquisition
and revealed a difference between GDCM and DCMTK imageIOs.

From: Steve Pieper <pieper@isomics.com>

Revision 26120 - Directory Listing
Modified Fri Jun 23 00:25:05 2017 UTC (3 months, 3 weeks ago) by pieper
ENH: Add DCMTK as reader option for DICOMScalarVolumePlugin

Make the default loading strategy use gdcm for backwards
compatibility, but if that fails, try to load with DCMTK.

Also expose a preference panel that let's users choose the
preferred approach.  For example, this can be used by developers to see
if DCMTK is able to directly load data that GDCM can also load.

Added a test that confirms DCMTK can load data that GDCM cannot.

See discussions [1,2] for context.

[1] https://discourse.slicer.org/t/slicer-dicom-scalar-volume-plugin-relies-on-old-gdcm-why-do-we-not-use-dcmtk/354/14

[2] https://discourse.slicer.org/t/error-with-dce-mri-loading-in-dicom-browser/327/39

From: Steve Pieper <pieper@isomics.com>

Revision 26118 - Directory Listing
Modified Fri Jun 23 00:25:01 2017 UTC (3 months, 3 weeks ago) by pieper
BUG: fix incorrect reference to dicom dialog in rsna self test

From: Steve Pieper <pieper@isomics.com>

Revision 26059 - Directory Listing
Modified Tue May 30 18:39:17 2017 UTC (4 months, 2 weeks ago) by lassoan
BUG: Removed all iteratorless traverse of shared collections

Collections have convenience functions for traversing it without the need for creating an iterator,
using InitTraversal() and GetNextItemAsObject(). These functions use an internal iterator stored in the collection.

Problem:

When a collection is traversed using the internal iterator by multiple functions at the same time, the behavior will be incorrect.

For collections that can be accessed by multiple objects, it is almost impossible to make sure that only one function will use
the internal iterator at a time. Therefore, shared collections must be traversed using external iterators.

For example, this error caused a bug in View Controllers module: it only showed the first slice view controller (while there were three). The problem was that View Controllers module iterated through the nodes using the internal iterator and internally a method was called that asked for a list of nodes by classname, which used the same internal iterator.

Solution:

- Replaced all instances of shared collection traversal with internal iterator.
- Made vtkMRMLScene's InitTraversal, GetNextNode, and GetNextNodeByClass methods deprecated (they are still functional,
  but log a warning when they are called).
- Added vtkMRMLScene::GetFirstNodeByClass convenience function and modified functions that used InitTraversal/GetNextNodeByClass
  or GetNthNodeByClass(0, ...) to use this function.

Revision 26058 - Directory Listing
Modified Tue May 30 01:57:28 2017 UTC (4 months, 2 weeks ago) by lassoan
BUG: Fixed go to home module shortcut

The shortcut has to be added to a menu to make the shortcut action trigger signal connected to qSlicerAppMainWindow.

Revision 26050 - Directory Listing
Modified Fri May 26 15:07:04 2017 UTC (4 months, 3 weeks ago) by lassoan
BUG: Removed CLI tests from install package

They caused printing of these warning messages:
When loading module  "CLIEventTest" , the dependency "CLI4Test" failed to be loaded.
When loading module  "TwoCLIsInARowTest" , the dependency "CLI4Test" failed to be loaded.
When loading module  "TwoCLIsInParallelTest" , the dependency "CLI4Test" failed to be loaded.

The problem was that the testing CLI modules that they required was not included in the package. It makes the most sense to not include these low-level tests in the installation package at all.

Note that Slicer tests that are run with --disable-cli-modules may still print similar messages for scripted or loadable modules that rely on CLI modules.

Revision 26011 - Directory Listing
Modified Mon May 15 15:46:24 2017 UTC (5 months ago) by jcfr
ENH: Add support for MINC image IO

Issue #4085

This enables MINC Image IO via ITK. This currently supports MINC version 2
(HDF5-based).

Reviewed-by: Andriy Fedorov <fedorov@bwh.harvard.edu>
Reviewed-by: Andras Lasso <lasso@queensu.ca>
Reviewed-by: Johan Andruejol <johan.andruejol@kitware.com>
Reviewed-by: Gabriel A. Devenyi <gdevenyi@gmail.com>
Reviewed-by: Vladimir S. FONOV <vladimir.fonov@gmail.com>

Tested-by: Andras Lasso <lasso@queensu.ca>
Tested-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Matt McCormick <matt.mccormick@kitware.com>

Revision 25985 - Directory Listing
Modified Fri Apr 28 15:44:53 2017 UTC (5 months, 3 weeks ago) by jcfr
ENH: AppErrorReportDialog: Secure bugtracker link using https

Using the HTTPS version of the bugtracker avoids that login passwords are transferred in plain text.

Fixes #4368

From: Robert Pollak <robert.pollak@jku.at>

Revision 25980 - Directory Listing
Modified Thu Apr 27 16:53:47 2017 UTC (5 months, 3 weeks ago) by lassoan
ENH: Reduced false alarms in UtilTest

Reduced false alarms in UtilTest to make it easier to detect real errors on the dashboard.

Revision 25977 - Directory Listing
Modified Wed Apr 26 13:58:07 2017 UTC (5 months, 3 weeks ago) by pinter
BUG: Fixed SubjectHierarchyGenericSelfTest

Revision 25933 - Directory Listing
Modified Sat Apr 15 21:47:09 2017 UTC (6 months ago) by lassoan
ENH: Further tune error submission URL

Further tune error submission URL to improve text displayed in Firefox on Ubunutu 16.

Revision 25932 - Directory Listing
Modified Sat Apr 15 20:41:29 2017 UTC (6 months ago) by lassoan
ENH: Tuned Slicer forum link for error reporting

New-line characters cannot be reliable sent in URL on all platforms, therefore pre-populate form with single-line text only. For example:

Problem report for Slicer 4.7.0-2017-04-15 / win-amd64:
[please describe expected and actual behavior]

Revision 25930 - Directory Listing
Modified Sat Apr 15 02:18:06 2017 UTC (6 months ago) by lassoan
ENH: Updated error report dialog with Slicer forum links

slicer-users mailing list link is replaced by Slicer forum link.

Bug report link pre-populates submission form with operating system and Slicer version.

Revision 25896 - Directory Listing
Modified Mon Apr 3 15:23:15 2017 UTC (6 months, 2 weeks ago) by pinter
ENH: Removed explicit level member from subject hierarchy item

The reason for this is that level was somewhat confusing: all items for data nodes had series level by default, but it was not explicitly specified what it caused, and also the role of subseries level was unclear. Moreover as level was a member, it was expected to be non-empty, however in some cases it was not useful
Level is still available and used, but it's now a subject hierarchy item attribute, which is not mandatory. Convenience functions were preserved for level getting, setting, and checking, and added for creating patient, study, and folder items. So level argument was removed from functions where it was not useful, and the code is now a bit simpler

Revision 25799 - Directory Listing
Modified Sun Mar 12 19:43:43 2017 UTC (7 months, 1 week ago) by jcfr
COMP: Fix unused variable warnings

Revision 25777 - Directory Listing
Modified Fri Mar 10 16:46:19 2017 UTC (7 months, 1 week ago) by pinter
ENH: Changed invalid subject hierarchy item ID to 0 for easier checking

Revision 25775 - Directory Listing
Modified Thu Mar 9 22:21:20 2017 UTC (7 months, 1 week ago) by cpinter
ENH: Fixed subject hierarchy generic test on Mac/Linux

Revision 25757 - Directory Listing
Modified Tue Mar 7 20:51:07 2017 UTC (7 months, 1 week ago) by pinter
ENH: Added subject hierarchy CLI and segmentations tests

Revision 25752 - Directory Listing
Modified Tue Mar 7 20:47:00 2017 UTC (7 months, 1 week ago) by pinter
ENH: Implemented MRML scene save/import for subject hierarchy 2.0

-----------------------------------------------
Details:

STYLE: Removed commented-out items

Potentially useful code was left there commented with TODO comments. After implementing most subject hierarchy features and deciding they will not be needed, they were removed

ENH: DICOM export works

ENH: Updated subject hierarchy python tests

BUG: Fix various issues with segment handling in subject hierarchy

ENH: Merge subject hierarchies and resolve IDs after scene import

ENH: Subject hierarchy scene write added, MRML can be considered final


Revision 25720 - Directory Listing
Modified Thu Feb 23 12:50:07 2017 UTC (7 months, 3 weeks ago) by lassoan
BUG: Fixed incorrect baseline in SlicerBoundsTest

Baseline bounds for transformed Segmentation object was incorrect.

Revision 25698 - Directory Listing
Modified Wed Feb 8 18:30:22 2017 UTC (8 months, 1 week ago) by jcfr
ENH: Interaction for transform node

The transform will automatically be centered around whatever objects
it transforms at the moment when the TransformUpdateEditorBoundsEvent is
invoked. This is more intuitive to the user as it looks as if the object under
the transform itself is moved/scaled/translated.
When no object is present, the transform is just scaled to facilitate
interaction with it.

Testing is added to ensure that:
 - The widget holds correctly the objects it will transform. Furthermore this
test is perfomed with models to extend the coverage as transform interaction
can theoritically deal with any vtkMRMLDisplayableNode.
 - Testing for interacting with transforms with parents
 - Serialization and deserialization of the scene

The transform interaction is only valid linear transforms

From: Johan Andruejol <johan.andruejol@kitware.com>

Revision 25696 - Directory Listing
Modified Wed Feb 8 18:30:16 2017 UTC (8 months, 1 week ago) by jcfr
ENH: Add GetNodeBounds to return untransformed bounds of node

Also add a vtkSlicerTransformLogic method that get the bounds of a list of
nodes.

From: Johan Andruejol <johan.andruejol@kitware.com>

Revision 25617 - Directory Listing
Modified Wed Dec 21 13:07:46 2016 UTC (9 months, 3 weeks ago) by lassoan
ENH: Made py_CLIEventTest more robust

cli.Running event may or may not be fired. Ignore it to prevent random test failures.

Revision 25616 - Directory Listing
Modified Wed Dec 21 01:42:45 2016 UTC (9 months, 4 weeks ago) by lassoan
ENH: Turned on output testing for MRML logic tests

Output testing makes the test fail if any unexpected VTK errors or warnings are logged (and it also makes VTK logs visible on the dashboard).
Fixed test failures (they were all test errors).

Revision 25596 - Directory Listing
Modified Thu Dec 8 21:10:42 2016 UTC (10 months, 1 week ago) by johan.andruejol
ENH: Add util methods for easier programming of python widgets

LoadUI() allows to create a widget from a .ui file and findChild() allows
quick access to a particular widget by name.

Revision 25595 - Directory Listing
Modified Thu Dec 8 21:09:27 2016 UTC (10 months, 1 week ago) by johan.andruejol
ENH: Add util method to set and fit slice views in python

Also add testing for those methods.

Revision 25590 - Directory Listing
Modified Wed Dec 7 19:45:00 2016 UTC (10 months, 1 week ago) by lassoan
ENH: Moved clickAndDrag to slicer.util

It is more accessible there.
Removed duplicates of clickAndDrag in other modules, now all of them use the one in slicer.util.

Revision 25550 - Directory Listing
Modified Fri Nov 18 07:56:26 2016 UTC (10 months, 4 weeks ago) by jcfr
STYLE: Fix spelling 'additonal' -> 'additional'

From: Isaiah Norton <inorton@bwh.harvard.edu>

Revision 25419 - Directory Listing
Modified Fri Oct 7 18:23:11 2016 UTC (12 months, 1 week ago) by jcfr
COMP: remove vtkTeem/DMRI-related tests.

Tractography-related parts of vtkTeem were removed in commit
r25408 so tests using that functionality will be moved to SlicerDMRI:

  https://github.com/SlicerDMRI/SlicerDMRI

From: Isaiah Norton <inorton@bwh.harvard.edu>

Revision 25363 - Directory Listing
Modified Wed Sep 14 15:52:15 2016 UTC (13 months ago) by pinter
ENH: Make use of node combobox editing option from slice views

The nodeAboutToBeEdited signal was so far not used within Slicer core, however it was defined. This commit does not actually enable node editing in the slice view controllers, only allows it to happen later.

Revision 25353 - Directory Listing
Modified Mon Sep 12 22:37:59 2016 UTC (13 months ago) by johan.andruejol
BUG: Update CLISerialazation test expected JSON

Due to changes made to the ExecutionModelTour, the CLI serialization test
must be updated.
The changes were made in ed1da2a93ec1713a36752a32fa7b4a5a355fe793 (r25330)

Revision 25337 - Directory Listing
Modified Thu Sep 8 20:09:24 2016 UTC (13 months, 1 week ago) by johan.andruejol
ENH: Add ParameterSerializer Support

With the paramater serializer support, one can now serialize and
deserialize CLIs with the command line. The python test
CLISerializationTest is added to make sure it works as expected.

Revision 25331 - Directory Listing
Modified Sat Sep 3 02:25:13 2016 UTC (13 months, 2 weeks ago) by lassoan
BUG: Fixed module factoryManager loadModules

When trying to load an unregistered module, caused Slicer to crash
slicer.app.moduleManager().factoryManager().loadModules(['nonexisting'])

Replaced assert by pointer check and added some more checks.

Revision 25286 - Directory Listing
Modified Mon Aug 15 18:03:31 2016 UTC (14 months ago) by jcfr
BUG: Fixed node reference counting tests

MRMLCreateNodeByClassWithSetReferenceCountToOne: removed. This test performs a double-delete and expects to get a runtime error. However, result of double-delete is "undefined behavior", i.e., it is not guaranteed to generate run-time error (and in some cases it does not).

MRMLCreateNodeByClassWithSetReferenceCountMinusOne: comments clarified.
1. Decreasing the reference count is needed because Python variable takes ownership of the created object, so the additional reference that Create...() adds is not needed anymore.
2. To decrement reference count, UnRegister() or Delete() method has to be called (SetReferenceCount should never be called).

From: Andras Lasso <lasso@queensu.ca>

Revision 25285 - Directory Listing
Modified Sun Aug 14 19:34:43 2016 UTC (14 months ago) by lassoan
BUG: Fix py_nomainwindow_SlicerOptionIgnoreSlicerRCTest

Probably the test fails because there is no console output on Windows.
Instead of testing if rc file is loaded by checking the console output, check if an ouptut file is created.

Revision 25264 - Directory Listing
Modified Fri Aug 5 02:48:22 2016 UTC (14 months, 1 week ago) by lassoan
BUG: Restored toolbar list in View/Toolbars menu

It was a regression caused by recent View menu rework for Python interactor toggling.

Revision 25255 - Directory Listing
Modified Fri Jul 29 20:07:02 2016 UTC (14 months, 2 weeks ago) by lassoan
ENH: Made Python interactor dockable window optional

In application settings Python section the user can now choose betwen dockable/standalone window.
Also made the Python Interactor toolbar button and menu item checkable.

Revision 25252 - Directory Listing
Modified Fri Jul 29 13:41:12 2016 UTC (14 months, 2 weeks ago) by lassoan
ENH: Add back Python interactor button to toolbar

Revision 25250 - Directory Listing
Modified Thu Jul 28 13:55:40 2016 UTC (14 months, 3 weeks ago) by lassoan
ENH: Tuned Python interactor window display

Hide Python interactor by default.

Moved "Reset to default" to the main menu (from the Toolbars submenu) because it actually restores all windows positions and states (docked, visible, etc).

Revision 25248 - Directory Listing
Modified Wed Jul 27 21:29:57 2016 UTC (14 months, 3 weeks ago) by lassoan
ENH: Made Python interactor a docking widget

Problem:
 It was always necessary to rearrange windows after showing the Python interactor so that both the console and Slicer screen.
 This has to be repeated every time Slicer is started, since the Python interactor window's position was not saved.

Implemented solution:

1.Made Python interactor a docking widget (if Slicer starts with main window visible).
 For single-screen configuration this allows sharing of the screen between the Python interactor and other Slicer windows.
 On multi-screen configurations the interactor can be dragged to the second screen.

2.The position (which screen, where), size, and state (docked/undocked, shown/hidden) of the Python interactor window is now also saved,
 so there is no need for any repositioning of the windows between sessions.

3.Ctrl-3 shows/hides the interactor (not just shows as before) and when the interactor is shown it gets keyboard focus.
 It allows easy opening of the interactor, typing some text, and closing it, without the need of taking the mouse to reposition
 any windows.

Also cleaned up deletion of ctkPythonConsole. As the ctkPythonConsole widget can be owned by a widget (docking window), it is not
 possible to create it on the stack anymore. Instead, qSlicerApplication creates the ctkPythonConsole (similarly to qSlicerPythonManager)
 and destroys it if it is not owned by a widget.

Revision 25179 - Directory Listing
Modified Fri Jun 10 17:43:56 2016 UTC (16 months, 1 week ago) by msmolens
BUG: Fix py_nomainwindow_SlicerOptionIgnoreSlicerRCTest

This commit fixes an error when running py_nomainwindow_SlicerOptionIgnoreSlicerRCTest. On Windows the error message is similar to:

      File "C:/D/N/Slicer-0/Applications/SlicerApp/Testing/Python/SlicerOptionIgnoreSlicerRCTest.py", line 79, in <module>
	os.remove(slicerrc)
    WindowsError: [Error 32] The process cannot access the file because it is being used by another process: 'c:\\users\\slicer~1\\appdata\\local\\temp\\tmpqu7b2u'

The issue is that tempfile.mkstemp() returns an OS-level handle to an open file.
Using Python's open() function on the filename opens the file a second time.
Therefore, an error occurs when attempting to remove the file, because the
handle opened by tempfile.mkstemp() has not been closed.

Replacing open() with os.fdopen() is one way to fix the issue. In that case, the
file is opened only once.

From: Max Smolens <max.smolens@kitware.com>

Revision 25171 - Directory Listing
Modified Wed Jun 8 20:08:41 2016 UTC (16 months, 1 week ago) by jcfr
ENH: Add support for managing slice orientation presets

This commit generalizes the concept of slice orientation known as
Axial, Sagittal and Coronal so that it is possible to add, rename and
delete new ones.

Default presets (Axial, Sagittal and Coronal) are associated to a default
slice node in the application logic.

Handle orientation as 3x3 because maintaining sliceOrigin information
in matrices that are orientation presets is not relevant.

Notes:

(1) Mark Get/SetOrientationReference as protected: These methods are only
    used internally and could ultimately be removed by refactoring
    "RotateToVolumePlane()"

(2) Remove unused SetOrientationString: The method is not used in any Slicer
    extensions.

(3) Explicitly setting the orienation string to "Reformat" is
    not needed anymore because "GetOrientation()" or "GetOrientationString()"
    will return "Reformat" if the SliceToRAS matrix is not one of the preset.

(4) For sake of consistency, in the RenameSliceOrientationPreset, the
    orientation reference is also renamed.

(5) In "Copy()" method, Orientation and OrientationReference are set
    after the presets.

(6) Remove unused SetOrientationToReformat() function. At the time of this
    commit, it was used only in "SlicerRT/ExternalBeamPlanning/Logic/vtkSlicerExternalBeamPlanningModuleLogic"
    and the maintainer of the module planned on removing the call.

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Co-authored-by: Andras Lasso <lasso@queensu.ca>

From: Davide Punzo <punzodavide@hotmail.it>

Revision 25150 - Directory Listing
Modified Fri Jun 3 03:40:03 2016 UTC (16 months, 2 weeks ago) by jcfr
BUG: Fix LandmarkRegistration test updating slicer.util.getNode. See #4201

This commit fixes a regression introduced in r25140 (BUG: slicer.util.getNodes:
Return MRML nodes by default. Fixes #4201)

The method "getNode()" should *NOT* return a node if an empty pattern
is provided.

Revision 25149 - Directory Listing
Modified Thu Jun 2 06:49:25 2016 UTC (16 months, 2 weeks ago) by jcfr
ENH: Add option "--application-information"

By default, do not print application information to standard output, only
log it to file.

If the application is started with `--application-information`, information
will also be displayed in the terminal.

To remain consistent with existing option displaying information in
the terminal (e.g --home, --settings-path, ...), the option has been
named "--application-information".

Revision 25145 - Directory Listing
Modified Thu Jun 2 03:12:42 2016 UTC (16 months, 2 weeks ago) by jcfr
ENH: Add SlicerCreateRulerCrashIssue4199 test. See #4199

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 25144 - Directory Listing
Modified Thu Jun 2 03:12:40 2016 UTC (16 months, 2 weeks ago) by jcfr
ENH: Add SlicerRestoreSceneViewCrashIssue3445 test. See #3445

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 25140 - Directory Listing
Modified Wed Jun 1 16:28:14 2016 UTC (16 months, 2 weeks ago) by jcfr
BUG: slicer.util.getNodes: Return MRML nodes by default. Fixes #4201

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 25139 - Directory Listing
Modified Wed Jun 1 15:39:13 2016 UTC (16 months, 2 weeks ago) by jcfr
BUG: Fix SubjectHierarchy generic tests

This commit fixes a regression introduced in r25128 (STYLE: Simplify
import of Logic/MRML/DisplayableManager python modules)

$ ctest -R py_SubjectHierarchy
Test project /home/jcfr/Projects/Slicer-Release/Slicer-build
    Start 592: py_SubjectHierarchyGenericSelfTest
1/2 Test #592: py_SubjectHierarchyGenericSelfTest .......   Passed    7.27 sec
    Start 593: py_SubjectHierarchyCorePluginsSelfTest
2/2 Test #593: py_SubjectHierarchyCorePluginsSelfTest ...   Passed    5.37 sec

Revision 25133 - Directory Listing
Modified Tue May 31 06:11:45 2016 UTC (16 months, 2 weeks ago) by jcfr
PERF: Speedup loading of SlicerMRBTest removing unneeded EditorLib import

Improve the loading time of the SlicerMRBTest module by ~50%  (2.6s -> 1.2s, warm cache)

Revision 25132 - Directory Listing
Modified Tue May 31 06:11:43 2016 UTC (16 months, 2 weeks ago) by jcfr
ENH: MeasureStartupTimes: Add --display-slicer-output option

Revision 25131 - Directory Listing
Modified Tue May 31 06:11:41 2016 UTC (16 months, 2 weeks ago) by jcfr
ENH: MeasureStartupTimes: Add --reuse-module-list option

Add convenience option allowing to reuse existing 'Modules.json' file,
it allows to more quickly get feedback without having to wait for
the function "collect_modules" to complete.

Revision 25130 - Directory Listing
Modified Tue May 31 06:11:39 2016 UTC (16 months, 2 weeks ago) by jcfr
ENH: MeasureStartupTimes: Add option to load only specific modules

Revision 25129 - Directory Listing
Modified Tue May 31 06:11:38 2016 UTC (16 months, 2 weeks ago) by jcfr
ENH: MeasureStartupTimes: Add option to include one module at a time

Revision 25119 - Directory Listing
Modified Wed May 25 19:46:00 2016 UTC (16 months, 3 weeks ago) by jcfr
BUG: Fixes widget and logic python module loading regression

This commit fixes regressions introduced in r25115 and r25116.

* Ensure vtkSlicerCLIModuleLogic (in Base/QTCLI/) python wrapping is loaded.

* Update EMSegment to a version referencing python widget and logic
from the "slicer" namespace.

Reported-by: Andras Lasso <lasso@queensu.ca>

Revision 25112 - Directory Listing
Modified Mon May 23 06:13:56 2016 UTC (16 months, 3 weeks ago) by jcfr
ENH: MeasureStartupTimes: Add option to benchmark only regular startup

Revision 25111 - Directory Listing
Modified Mon May 23 06:13:54 2016 UTC (16 months, 3 weeks ago) by jcfr
ENH: MeasureStartupTimes: Add option to flush disk cache

This commit adds the option "--drop-cache" to the script.

See http://unix.stackexchange.com/questions/87908/how-do-you-empty-the-buffers-and-cache-on-a-linux-system

Only supported only on Linux. If the --drop-cache option is used on
other platform, an exception is raised.

Revision 25103 - Directory Listing
Modified Sat May 21 10:13:30 2016 UTC (16 months, 4 weeks ago) by jcfr
ENH: Improve MeasureStartupTimes script adding "--repeat" argument

timecall decorator learned how to repeat a run and compute the average time
across all runs.

Revision 25101 - Directory Listing
Modified Sat May 21 06:06:01 2016 UTC (16 months, 4 weeks ago) by jcfr
ENH: Improve MeasureStartupTimes script

collect_startup_times_overall:

 * Move existing code into "collect_startup_times_overall" function and
   save stats to a json file "StartupTimes.json" to facilitate analysis.

collect_startup_times_excluding_one_module:

 * Added "collect_startup_times_excluding_one_module" starting Slicer N
   times excluding each one of the N modules one by one. Stats are
   then saved to "StartupTimesExcludingOneModule.json".

 * List of module names (and their type) is also saved to "Modules.json"

 * This allows to check if there are modules impacting the startup
   time more than the average.

Revision 25100 - Directory Listing
Modified Sat May 21 05:44:14 2016 UTC (16 months, 4 weeks ago) by jcfr
BUG: Fix regression: python code "exit(status)" will now exit with "status"

This commit fixes py_nomainwindow_SlicerPythonCodeTest2 fixing a regression
introduced in r25083 (STYLE: Automatically enable "ignore-slicerrc" if
"testing" option is given).

Associating the test with "--testing" option was causing the application
to always exit with EXIT_SUCCESS when "exit(EXIT_FAILURE)" was called.

This commit ensures the all to slicer.app.exit() in "slicer.util.exit()"
is considered.

Revision 25099 - Directory Listing
Modified Sat May 21 00:10:14 2016 UTC (16 months, 4 weeks ago) by jcfr
STYLE: Simplifies SlicerApp tests

Revision 25087 - Directory Listing
Modified Thu May 19 07:10:54 2016 UTC (17 months ago) by jcfr
BUG: Ensure modules set with --modules-to-ignore are not saved in settings

This commit updates the modules panel adding "modulesToAlwaysIgnoreChanged"
signal emitted only with a list of modules excluding the one passed
as argument to "--modules-to-ignore" command line arguments.

Also adds "SlicerOptionModulesToIgnoreTest" and teaches "SlicerAppTesting.run()"
to understand the "shell" parameter

Revision 25085 - Directory Listing
Modified Thu May 19 07:10:51 2016 UTC (17 months ago) by jcfr
ENH: Add command line option "--modules-to-ignore"

Revision 25083 - Directory Listing
Modified Thu May 19 07:10:48 2016 UTC (17 months ago) by jcfr
STYLE: Automatically enable "ignore-slicerrc" if "testing" option is given

This simplifies writing of tests.

Revision 25082 - Directory Listing
Modified Thu May 19 07:10:46 2016 UTC (17 months ago) by jcfr
ENH: Add "--keep-temporary-settings" option

When specified with "disable-settings", it prevents the temporary settings
from being cleared. This is useful when writing test checking effect
of settings values.

Revision 25078 - Directory Listing
Modified Wed May 18 23:35:58 2016 UTC (17 months ago) by jcfr
BUG: Ensure "--disable-settings" clear all temporary settings

Revision 25077 - Directory Listing
Modified Wed May 18 23:35:56 2016 UTC (17 months ago) by jcfr
STYLE: Refactor MeasureStartupTimes introducing SlicerAppTesting module

This commit adds reusable methods "run", "runSlicer" and "runSlicerAndExit"
along side with "timecall" decorator.

Revision 25076 - Directory Listing
Modified Wed May 18 23:35:55 2016 UTC (17 months ago) by jcfr
ENH: Add convenience script to measure the application startup time

For example, on Ubuntu 15.10, 64GB/M.2 PCIe NVMe SSD/Quad Core 3.80GHz.

For a release build, Startup times are the following:

//------------------------
Slicer --no-splash --exit-after-startup
8.641 seconds

Slicer --no-splash --exit-after-startup --disable-builtin-cli-modules
5.663 seconds

Slicer --no-splash --exit-after-startup --disable-builtin-loadable-modules
5.691 seconds

Slicer --no-splash --exit-after-startup --disable-builtin-scripted-loadable-modules
7.107 seconds

Slicer --no-splash --exit-after-startup --disable-builtin-cli-modules --disable-builtin-scripted-loadable-modules
4.017 seconds

Slicer --no-splash --exit-after-startup --disable-modules
1.885 seconds

Slicer --no-splash --exit-after-startup --disable-python
5.727 seconds

Slicer --no-splash --exit-after-startup --disable-python --disable-builtin-cli-modules
3.106 seconds

Slicer --no-splash --exit-after-startup --disable-python --disable-builtin-loadable-modules
3.750 seconds

Slicer --no-splash --exit-after-startup --disable-python --disable-builtin-scripted-loadable-modules
6.139 seconds

Slicer --no-splash --exit-after-startup --disable-python --disable-builtin-cli-modules --disable-builtin-scripted-loadable-modules
3.131 seconds

Slicer --no-splash --exit-after-startup --disable-python --disable-modules
0.838 seconds
//------------------------

Revision 25008 - Directory Listing
Modified Wed Apr 13 16:39:57 2016 UTC (18 months ago) by lassoan
BUG: Fixed subject hierarchy node naming tests

Revision 24958 - Directory Listing
Modified Fri Mar 4 18:50:25 2016 UTC (19 months, 2 weeks ago) by lassoan
ENH: Added 3D Table view to layouts

3D Table view consists of a 3D view and a table with a vertical divider.

Revision 24955 - Directory Listing
Modified Thu Mar 3 06:16:24 2016 UTC (19 months, 2 weeks ago) by jcfr
ENH: Improve --additional-module-paths to support extension build directory

This commit teaches Slicer to check if any given "additional-module-path"
is the build or install directory of an extension.

Revision 24953 - Directory Listing
Modified Fri Feb 26 15:26:44 2016 UTC (19 months, 3 weeks ago) by lassoan
ENH: Remove test execution delay when building RUN_TESTS target manually

When RUN_TESTS target was built in VIsual Studio manually then the py_nomainwindow_MRMLCreateNodeByClassWithSetReferenceCountToOne tests crashed (as expected) and an error popup was displayed to the user. The test execution stopped until the user acknowledged the popup (and also a Windows Error Report was generated). This caused unnecessary delays in the test execution and false positive error reports.

Solved the issue by forcing CTest to disable error popups for this particular test when building RUN_TESTS manually. CTest disables error reporting for all tests when run from the command-line.

Revision 24902 - Directory Listing
Modified Thu Jan 28 04:21:57 2016 UTC (20 months, 3 weeks ago) by jcfr
BUG: Fix registration addressing regression in vtkITKTransformConverter.

Fixes #4139

This commit allows BRAINSFit registration to complete by addressing
a regression introduced in r24875 (BUG: Fix transform tests by not
using dynamic_cast in vtkITKTransformConverter)

It basically ensure the comparison of transform name includes
all derived type associated with itk::MatrixOffsetTransformBase

The python code allowing to reproduce the issue is reported below
and has been integrated into a self-test named "BRAINSFitRigidRegistrationCrashIssue4139"

8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---
import SampleData
from SampleData import SampleDataLogic
sampleDatalogic = SampleDataLogic()

fixed = sampleDatalogic.downloadMRBrainTumor1()
moving = sampleDatalogic.downloadMRBrainTumor2()

outputTransform = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(outputTransform)

outputVolume = slicer.vtkMRMLScalarVolumeNode()
slicer.mrmlScene.AddNode(outputVolume)

parameters = {
'fixedVolume' : fixed,
'movingVolume' : moving,
'linearTransform' : outputTransform,
'outputVolume' : outputVolume,
'useRigid' : True
}
cmdLineNode = slicer.cli.runSync(slicer.modules.brainsfit, parameters=parameters)
8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---

Reported-by: Christian Herz <christian.herz@mevis.fraunhofer.de>
Suggested-by: Hans Johnson <hans-johnson@uiowa.edu>

Revision 24900 - Directory Listing
Modified Tue Jan 26 05:30:37 2016 UTC (20 months, 3 weeks ago) by jcfr
STYLE: Replace manually created qMessageBox by slicer.util method calls.

From: Christian Herz <christian.herz@mevis.fraunhofer.de>

Revision 24865 - Directory Listing
Modified Tue Jan 12 17:38:36 2016 UTC (21 months ago) by pinter
BUG: Fixed SH node creation if there are multiple series node for the same series UID

In some cases there might be multiple subject hierarchy nodes for the same DICOM series, for example if a series contains instances that load to different node types that cannot be simply added under one series folder node. This can happen if for one type the node corresponds to the series, but in the other to the instances, like segmentation nodes vs markup nodes under a folder node.

Fixed SubjectHierarchyGenericSelfTest that failed due to empty scene object in scene model


Revision 24857 - Directory Listing
Modified Fri Jan 8 19:15:25 2016 UTC (21 months, 1 week ago) by johan.andruejol
STYLE: CLIEvent testing

This is a test that shows how Slicer handles CLI events.
Note that this only reflects how the application works now.

Revision 24856 - Directory Listing
Modified Fri Jan 8 19:15:23 2016 UTC (21 months, 1 week ago) by johan.andruejol
COMP: Ensure CLI tests pass independently of Slicer_BUILD_CLI

This commit updates the tests introduced in r24834
 (BUG: Fix CLI running issues and add tests to prevent future regression).
by using "CLI4Test" instead of "ThresholdScalarVolume".

This ensures that the tests "TwoCLIsInARowTest" and "TwoCLIsInParallelTest"
always work if Slicer_BUILD_CLI_SUPPORT is ON and Slicer_BUILD_CLI is OFF.

Revision 24834 - Directory Listing
Modified Wed Jan 6 22:29:27 2016 UTC (21 months, 1 week ago) by jcfr
BUG: Fix CLI running issues and add tests to prevent future regression.

Before, the CLI module logic would add the observer before running the CLI
and remove it once the CLI is modified. This proved to be error prone, for
example if two CLIs are ran at the same time. One CLI would finish and
remove the observation, preventing the other one from ever finishing.
Instead, we propose to always listen to the event. This make the code
simpler and more robust.

Thanks to Alexis and Dzenan for their help creating a simple test case.

Reported-by: Dzenan Zukic <dzenan.zukic@kitware.com>
Co-authored-by: Alexis Girault <alexis.girault@kitware.com>
Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Johan Andruejol <johan.andruejol@kitware.com>

Revision 24830 - Directory Listing
Modified Wed Dec 23 22:41:25 2015 UTC (21 months, 3 weeks ago) by lassoan
ENH: Avoid long wait for MRMLCreateNodeByClassWithoutSetReferenceCount test timeout on Windows

Revision 24823 - Directory Listing
Modified Wed Dec 23 19:21:13 2015 UTC (21 months, 3 weeks ago) by lassoan
BUG: Fixed clip model node name in Slicer4Minute test

Revision 24801 - Directory Listing
Modified Tue Dec 1 20:06:37 2015 UTC (22 months, 2 weeks ago) by jcfr
STYLE: Remove VTKv5 support

As discussed during the developer hangout of 2015-03-31, this commit
removes support for VTKv5.

Most of the h/cxx files have been updated automatically using the
script "slicer_remove_vtk5_support.py" [1]. See below.

The remaining of h/cxx, python and CMake files have been updated
manually.


slicer_remove_vtk5_support.py:
cd ~/Project/Slicer
~/Download/slicer_remove_vtk5_support.py $(ack -l VTK_MAJOR_VERSION)

[1] https://gist.github.com/jcfr/91d2f5d07c2a36320e48

Revision 24798 - Directory Listing
Modified Tue Dec 1 18:51:08 2015 UTC (22 months, 2 weeks ago) by pinter
ENH: Added CLI support for Subject hierarchy #1

1. Moved vtkMRMLSubjectHierarchyNode and constants to MRML core. Moved transform related functions to SH logic from the node
2. Added reference argument support for Volume (image) and Model (geometry) nodes when outputs of a CLI module

Revision 24795 - Directory Listing
Modified Tue Dec 1 13:32:25 2015 UTC (22 months, 2 weeks ago) by pinter
ENH: Added DICOMUtils convenience function library

Revision 24783 - Directory Listing
Modified Mon Nov 30 19:46:18 2015 UTC (22 months, 2 weeks ago) by lassoan
ENH: Added support for Tables

* New module added: Tables. Create create/view/edit/delete tables, freeze column/row header, lock to read-only (vtkMRMLTableNode).
* Tables can be shown in the view layout (new layout added: Four-up table, more can be added as needed)
* Load/save csv, tsv, txt files as table nodes
* Copy-paste to/from Excel
* SubjectHierarchy plugin (show/hide, edit, clone tables)
* Use tables as input/output for CLI modules (PET Standard Uptake Value Computation module is updated to use tables; there was no need to change the Slicer Execution Model, the Table data type was already usable)
* Reusable widget added for viewing/editing tables in C++ and Python modules


Revision 24776 - Directory Listing
Modified Thu Nov 26 20:49:35 2015 UTC (22 months, 3 weeks ago) by pinter
BUG: Fixed SubjectHierarchyCorePluginsSelfTest

Test broke after rev24770 that fixed a bug in SH clone node plugin. The test was asserting the opposite of what it was supposed to. Access of postfix made possible from python so that no hard-coded strings need to be used.

Revision 24767 - Directory Listing
Modified Sat Nov 21 05:39:29 2015 UTC (22 months, 4 weeks ago) by jcfr
BUG: Fix regression in SubjectHierarchyCorePluginsSelfTest

This commit fixes a typo introduced in r24759 (STYLE: Update python
tests to use more specific asserts.):

  File "<string>", line 1, in <module>
  File "/path/to/Slicer-build/lib/Slicer-4.5/qt-scripted-modules/SubjectHierarchyCorePluginsSelfTest.py", line 186
    self.assertEqual( slicer.mrmlScene.GetNumberOfNodesByClass('vtkMRMLMarkupsFiducialStorageNode'), 2 )
       ^
SyntaxError: invalid syntax

Revision 24759 - Directory Listing
Modified Fri Nov 20 03:56:01 2015 UTC (22 months, 4 weeks ago) by jcfr
STYLE: Update python tests to use more specific asserts.

Using the more specific assert functions usually gives more useful
error messages.

Suggested-by: Csaba Pinter <csaba.pinter@queensu.ca>
Suggested-by: Max Smolens <max.smolens@kitware.com>

Revision 24758 - Directory Listing
Modified Fri Nov 20 03:55:52 2015 UTC (22 months, 4 weeks ago) by jcfr
STYLE: Update python scripts to use "is None" instead of "== None"

Rational copied from https://www.python.org/dev/peps/pep-0290/#testing-for-none

// -----------------
 Since there is only one None object, equality can be tested with identity. Identity tests are slightly faster than equality tests. Also, some object types may overload comparison, so equality testing may be much slower.

Pattern:

if v == None  -->  if v is None:
if v != None  -->  if v is not None:
// -----------------

Reviewed-by: Csaba Pinter <csaba.pinter@queensu.ca>
Reviewed-by: Max Smolens <max.smolens@kitware.com>

Revision 24652 - Directory Listing
Modified Wed Oct 21 02:02:28 2015 UTC (23 months, 4 weeks ago) by jcfr
BUG: ExtensionsWizard: Fix CERTIFICATE_VERIFY_FAILED publishing error

This commit fixes SSL a regression introduced when updating the
version of python in r24526 (ENH: Upgrade to Python 2.7.10) because
of python/cpython@ae5b953 (pep 476: verify certificates by default (#22417))

The error was first reported in [1] and happened when contributing
an extension using the steps report below.

[1] http://slicer-devel.65872.n3.nabble.com/Problem-with-the-ExtensionWizard-td4035337.html

This commit fixes the issue by setting the SSL_CERT_FILE as suggested in
PEP-0476. See https://www.python.org/dev/peps/pep-0476/

Step to reproduce the problem:

// ----------------
$ bin/slicerExtensionWizard --create Slicer-MyTestExtension --addModule cli:MyTestCLI  ~
copy template
'/home/jcfr/Projects/Slicer/Utilities/Templates/Extensions/Default' to
'/home/jcfr/Slicer-MyTestExtension', replacing 'TemplateKey' -> 'Slicer-
MyTestExtension'
[...]
created module 'MyTestCLI'

$ bin/slicerExtensionWizard --publish ~/Slicer-MyTestExtension/
Creating initial commit containing the following files:
  MyTestCLI/Testing/Cxx/CMakeLists.txt
[...]
Continue y,n? y
creating github repository
Username for 'https://github.com': jcfr
Password for 'https://jcfr@github.com':
failed to publish extension: [SSL: CERTIFICATE_VERIFY_FAILED] certificate
verify failed (_ssl.c:590)
// ----------------

Reported-by: Jean-Baptiste Vimort <jvimort@umich.edu>

Revision 24622 - Directory Listing
Modified Thu Oct 8 17:15:57 2015 UTC (2 years ago) by jcfr
STYLE: Update python scripts to not import from __main__

This commit simplifies the scripts removing extra `from __main__`
statements and improve the integration with Python IDE ensuring python
package like "slicer" can simply be imported.

The `from __main__` statement most likely became obsolete since
r24155 (ENH: Fixes #3549. Import scripted module as python module).

Remarks:

A global replace of "from __main__ import" into "import" as been done
except in:
 * EditOptions: "from __main__ getNodes" changed into "from slicer.util import getNodes"
 * slicer/module[dm|logic|mrml|widget]/__init__.py where it makes sense to keep it.

Revision 24586 - Directory Listing
Modified Wed Sep 30 14:21:47 2015 UTC (2 years ago) by fedorov
ENH: Update DMCTK to use version DCMTK-3.6.1_20150924

The important improvements provided by the new version of DCMTK
is the support for new API that in particular greatly simplify creation of and
interaction with DICOM Segmentation image objects.

More specifically, it introduces the dcmiod, dcmfg and dcmseg classes
helpful in creating multiframe DICOM objects, such as segmentation and
parametric map objects.

Considering that standard and private dictionaries can now be  embedded
in DCMTK library, this commit partially reverts r24473 (ENH: Add support
for DCMTK private dictionary). The test DCMTKPrivateDictTest.py was updated to
not expect DCMDICTPATH environment variable that is no longer needed and is not
initialized.

List of DCMTK changes:

$ git shortlog 3366181..DCMTK-3.6.1_20150924 --no-merges

Andreas Thiel (1):
      Updated man pages for new development snapshot.

Jan Schlamelcher (86):
      Some workarounds for VC6 compiler peculiarity.
      Introduced OFunique_ptr as a fallback if std::unique_ptr is not available.
      Make use of  unique pointer (free memory if C-MOVE/C-FIND is canceled).
      Fixed dll build on windows.
      Correction of inconsistent previous commit.
      Fixed DcmSCPPool test case failing on older systems.
      Enabled shutdown functionality of DcmSCPPool.
      Fixed building with mingw-w64.
      Fixed most of the warnings in dcmjpeg.
      Fixed potential bug in dcmjpeg 12 and 16 bit variants.
      Marked SCPPool-Test (dcmnet_scp_pool) as exhaustive.
      Fixed most of the warnings in dcmdata.
      Fixed a mistake in CHANGES.361.
      Minor fixes in dcmdata.
      Added support for some C++11 types, literals and traits.
      Added documentation for the new macro "DOXYGEN".
      Fixed most of the warnings in ofstd and oflog.
      Added support for some additional C++11 traits.
      Introduced the new explicit boolean type OFExplicitBool.
      Fixed possibly wrong overload resolution in DSRCodedEntryValue.
      Minor fixes (whitespace and line ending errors).
      Modified DcmQuantColorHashTable to perform lazy initialization.
      Introduced OFoptional, implementing optional types.
      Renamed DoxygenLayout.xml to comply with filename conventions.
      Minor fixes and workarounds for Microsoft's compilers.
      Fixed ofstd_tatof error on older MSVC versions.
      Fixed DCMTK-Exports for custom module setups.
      Fixed and suppressed some warnings.
      Added 'DCMTK_USE_CXX11_STL' and 'DCMTK_CXX11_FLAGS'.
      Updated manpages.
      Updated DCMTK_ABI_VERSION for new development snapshot.
      Clarified an ambiguous configure message.
      Removed misleading comment in dcmjpeg.
      Fixed a wrong type-alias for OFintegral_constant.
      Introduced C++11-like alignment support.
      Fixed an alignment problem in OFoptional.
      Fixed building 32 bit targets with mingw-w64.
      Refined definition of numeric types and traits.
      Fixed a problem with Microsoft Safe CRT in oflog.
      Fixed a bug in dcmdata.
      Introduced DcmOutputBufferStream::filled() method.
      Fixed a problem in storescp.
      Modified some of OFoptional's comparison operators.
      Introduced OFtuple implementing generic tuples.
      Introduced move emulation for pre C++11 compilers.
      Small fixes for a previous commit about OFtuple.
      Several fixes and additions for yesterday's commits.
      Reintroduced bugfix-comment in dcmjpeg.
      Fixed autoconf install regarding ofstd variadic.
      Introduced OFnumeric_limits.
      Several fixes regarding OFnumeric_limits.
      Fixed possible arith.h generation problem on MinGW.
      Introduced basic support for assisted cross compiling.
      Fixed some problems regarding DCMTK's C++11 support.
      Added support for trusted client certificates.
      Adjusted DCMNET's default socket buffer length.
      Introduced cross compiling support for Android.
      Fixed a const correctness problem within DCMTLS.
      Introduced check-exhaustive targets to Autoconf.
      Corrections regarding recent commits.
      Modified CMake minimum version as required.
      Revised cleanup of temporary unit test files.
      Updated Autoconf dependencies.
      Updated man pages for new development snapshot.
      Updated DCMTK_ABI_VERSION for new development snapshot.
      Fixed a CMake problem with paths containing spaces.
      Moved some utility functions inside OFStandard.
      Modified fallback implementation of OFtuple.
      Added additional configuration methods for DCMTLS.
      Updated Makefile dependencies.
      Updated DCMTK_ABI_VERSION for new development snapshot.
      Moved CHANGES.361 to /docs.
      Updated Doxygen configuration files.
      Updated man pages.
      Updated default compiler flags.
      Refactored handling of some <cmath> functions.
      Fixed problems with previous commit.
      Fixed cross compiling via MinGW and Wine.
      Fixed building on FreeBSD.
      Fixed building on FreeBSD with C++11 enabled.
      Fixed inconsistent defines in CMake's osconfig.h.
      Fixed a problem in DcmAttributeFilter's unit test.
      Fixed building via GCC 4.2 on OpenBSD.
      Updated man pages for new development snapshot.
      Updated DCMTK_ABI_VERSION for new development snapshot.
      Updated CHANGES.361 for new development snapshot.

Joerg Riesmeier (511):
      Added support for CP-1236 to data dictionary.
      Added support for CP-1236 to checkAndUpdateVR() method.
      Added support for Supplement 154 to the data dictionary.
      Added support for new SOP Class UIDs from Supplement 154.
      Added support for directory record type "SURFACE SCAN".
      Added new SOP Class UID from Supplement 162.
      Added missing assignment of member variable.
      Added full support for the new Comprehensive 3D SR IOD.
      Fixed various issues in syntax usage output.
      Minor fixes in comments, e.g. typos.
      Minor fixes in comments. Also made some input parameters "const".
      Use non-throwing new and delete operator.
      Fixed two possible memory leaks.
      Added comment to variable that is currently unused.
      Fixed issue with odd-length pixel data.
      Added missing sub-directory to "make install" target.
      Added some debug output to lookForXfer() method.
      Added some debug output to read() method.
      Added new print options for SOP class output.
      Added new command line options for print output.
      Fixed bug in checkSOPClassUID() method.
      Added note on support for shared libraries.
      Added support for CP-1246 and CP-1249 to data dictionary.
      Fixed some tag key constants of recently retired attributes.
      Fixed issue with unnecessary call to clearNodeCursorStack().
      Added missing support for the new print options.
      Enhanced output to trace logger.
      Fixed inconsistencies introduced with last commit.
      Various fixes to comments. Removed trailing spaces.
      Added support for recently approved Correction Items.
      Enhanced documentation of complete flag methods.
      Added support for Supplement 157 to data dictionary.
      Added SOP Class UIDs from Supplement 157.
      Minor fixes to comments on VOI-related methods.
      Fixed bug in getTimeZoneFromString() method.
      Fixed issue with misplaced log output.
      Replaced "OFString::length() == 0" by "OFString::empty()".
      Replaced "OFString::length() != 0" by "!OFString::empty()".
      Replaced "OFString::length() > 0" by "!OFString::empty()".
      Added support for new VR "Other Double String" (OD)
      Added private tags for AGFA IMPACS 6.5.x Solution.
      Fixed wrong VR for private AGFA IMPAX tag.
      Updated version number of snapshot compilers.
      Added comment on inappropriate use of EC_IllegalCall.
      Fixed various oddities and inconsistencies:
      Replaced tabulator by space characters.
      Fixed various oddities and inconsistencies.
      Really call shouldStopAfterCurrentSOPInstance():
      Fixed further documentation issues.
      Removed trailing space characters.
      Fixed various typos.
      Added releaseAssociation() and abortAssociation()
      Fixed various typos and other Doxygen issues.
      Enable WITH_THREADS for thread-related classes.
      Added new condition constants.
      Fixed various typos.
      Use optional fields in sendSTOREResponse().
      Reimplemented sendSTOREResponse() method.
      Modified log output in loadAssociationCfgFile().
      Fixed issues with optional message fields.
      Removed unused fields from sendACTIONResponse().
      Added file missing for last commit :(
      Added progress notification to DcmSCP.
      Removed trailing spaces.
      Added global helper function createDirectory().
      Fixed some minor Doxygen issues.
      Added new class DcmStorageSCP.
      Added new command line tool "dcmrecv".
      Added comments to unused exit codes.
      Rebuilt Makefile dependencies.
      Updated man pages.
      Function createDirectory() also works on Windows:
      Updated CMake version.
      Fixed various typos.
      Deprecated closeAssociation() method.
      Added support for Supplement 163 to data dictionary.
      Added meta header to stored DICOM files.
      Fixed various typos in comments.
      Pass existing dataset to handleSTORERequest().
      Fixed various inconsistencies in comments.
      Do not copy received dataset in memory.
      Removed class name from derived method calls.
      Removed "&" from constant integer parameters.
      Fixed wrong log message in handleMOVERequest().
      Fixed various typos in comments.
      Restructured implementation of handleSTORERequest().
      Introduced dataset storage mode.
      Fixed various typos in comments.
      Receive C-STORE request dataset directly to file.
      Added new dataset storage mode.
      dded new storage mode options.
      Updated copyright dates (where appropriate).
      Added support for generating a Doxygen tag file.
      Fixed wrong Doxygen reference to a method.
      Minor fixes, e.g. added Doxygen markup.
      Fixed issue with CP-246 files and private tags.
      Slightly changed output of print() method.
      Added new print flag for showing invalid codes.
      Added new option for printing invalid codes.
      Added missing references to closed DCMTK features.
      Fixed typos.
      Added support for <InlineBinary> XML element.
      Clarified use of writeXML() flags.
      Fixed typo copied from Supplement 163.
      Output a warning message if the VR is unknown.
      Output currently processed line of input file.
      Removed superfluous footnote symbol "(*)".
      Fixed various coding style issues.
      Added trace log message on VR replacement.
      Added two new global flags for VR generation.
      Made use of new global flags for VR generation:
      Updated our email address for bug reports.
      Updated to autoconf 2.69.
      Added definition of DCMTK_PACKAGE_URL.
      Added Doxygen tag file to .gitignore.
      Added *.patch files to .gitignore.
      Also updated autoconf support files.
      Updated automake script to version 1.14.
      Fixed typos.
      Fixed various typos.
      Fixed various typos in comments.
      Added method to determine SpecificCharacterSet.
      Added 'charset' parameter to checkStringValue().
      Added new variant of checkElementValue().
      Avoid unnecessary copies of sequence elements.
      Enhanced implementation of checkCode() method.
      Report warning on unsupported character set.
      Use helper function findAndGetSequence().
      Updated comment on current character set issue.
      Fixed memory leak in log4cplus code.
      Minor fixes in comments.
      Minor changes to comments.
      Updated Doxygen configuration files.
      Removed outdated custom CSS file.
      Updated URL of DCMTK's home page.
      Fixed timeout issue in handleAssociation().
      Fixed source code formatting and various comments.
      Fixed wrong content type of XML element in DTD.
      Do not output group length in Native DICOM Model.
      Fixed outdated comment on 1st PN component group.
      Removed redundant API comment.
      Added support for CP-1268 to data dictionary.
      Added support for Supplement 168 to data dictionary.
      Added support for new UID from Supplement 168.
      Never output NULL bytes to markup string/stream.
      Adapted test cases for markup conversion.
      Iterate more efficiently over sequence items.
      Use helper method for deleting data elements.
      Added comments on missing features.
      Fixed small typos in comments.
      Added support for Real World Value Mapping objects.
      Added comment on getFrameList() method.
      Moved checkCurrentValue() to "protected" section.
      Slightly enhanced comments.
      Check return value of write() methods.
      Added support for Referenced Segment Number.
      Updated CMake version.
      Fixed small issue reported by CMake 2.8.12.
      Added Corneal Topography Map Storage SOP Class.
      Fixed bug that could cause a crash.
      Fixed doubled output of XML start tag for VR=OD.
      Added comment on wrong color model for icon images.
      Fixed issue with color icon images.
      Removed trailing white spaces from man pages files.
      Fixed build issue with shared libraries (Win32).
      Avoid CMake warning on non-installable files.
      Added missing break statements to switch cases.
      Removed redundant and outdated Word document.
      Added global flag for disabling the VR checker.
      Added new option for disabling the VR checker.
      Fixed minor Doxygen-related issue in documentation.
      Fixed name of PN component in Native DICOM Model.
      Fixed minor Doxygen-related issue in documentation.
      Fixed issue with test "ofstd_markup_6" (Win32).
      Fixed various typos in man pages.
      Fixed output of AT values in Native DICOM Model.
      Do not check valueLoaded() for Native DICOM Model.
      Completed support for <InlineBinary> XML element.
      Second try to fix the issue with "ofstd_markup_6".
      Fixed typos, comments and coding style.
      Replaced deprecated DcmSCU::closeAssociation().
      Removed check on number of command line arguments.
      Cleaned up source code in various aspects.
      Again, fixed comments to be consistent with code.
      Fixed comments and documented default values.
      Added support for recently approved CPs.
      Added support for Supplement 165 to data dictionary.
      Added support for new UIDs from Supplement 165.
      Fixed wrong/missing comment on method parameter.
      Fixed various minor documentation issues.
      Added missing module dcmrt to include directories.
      Removed comment on UID_HangingProtocolStorage.
      Added support for approved but still missing CPs.
      Added comments on some ACR/NEMA attributes.
      Fixed timeout issue in DIMSE_moveUser().
      Fixed typos in comments.
      Moved ACR/NEMA data dictionary to a separate file.
      Fixed issue with wrong check on stream compression.
      Fixed wrong VR for some retired command fields.
      Consistently use upper case letters for DICOM tags.
      Added new test cases for testing helper functions.
      Fixed typo and added comment.
      Added OFFilename versions to some helper functions.
      Added new helper function for renaming files.
      Added function for appending filename extension.
      Added wide character support to this tool.
      Added new helper function for copying files.
      Changed file mode bits back from "0755" to "0644".
      Fixed typo in comment.
      Added new command line option --create-backup.
      Avoid passing invalid values to rename().
      Avoid passing NULL to OFString, which is deprecated.
      Added support for wide chars to DICOMDIR code.
      Fixed issue when compiled with wide char support.
      Added new condition constant and fixed typo.
      Fixed issue with missing terminating NULL byte.
      Always use OFFilename() instead of "" as a default.
      Use printError() instead of OFLOG_FATAL().
      Fixed further issues with wide char support.
      Allow empty file-set ID in DICOMDIR (type 2).
      Fixed some comments.
      Fixed wrong tag in CodingSchemeIdentificationSequence.
      Made installation of tag file optional.
      Added another addContentItem() method.
      Replaced tabs by spaces and fixed indention.
      Fixed various issues in Doxygen comments.
      Fixed various minor issues in new helper class.
      Rebuilt Makefile dependencies.
      Added missing data elements to BD profiles.
      Added check for Shared Functional Groups Sequence.
      DIMSE_createFilestream() now uses an OFFilename.
      Fixed various typo.
      Pass OFString to DIMSE_createFilestream().
      Added support for CP-1090 to the data dictionary.
      Fixed issue with automatically generated classes.
      Removed superfluous quotations marks.
      Fixed small typos in comments.
      Added readPatientData() and readStudyData().
      Updated outdated comments on "log stream".
      Made sure that header file is parsed by Doxygen.
      Made sure that "Files" section is available.
      Added further header files to Doxygen documentation.
      Added support for recently approved CPs.
      Fixed some issues with wide character support.
      Added test for OFStandard::appendFilenameExtension().
      Fixed issue with untyped NULL reported by MSVC++.
      Fixed various typos in comments.
      Enhanced removeRootDirFromPathname() function.
      Enhanced createDirectory() function.
      Use non-throwing new and delete operator.
      Fixed typo in comment.
      Output to debug logger if memory allocation fails.
      Simplified creation of temporary DICOMDIR file.
      Optionally disable isFilenameValid() check.
      Added support for new UIDs from Supplement 124.
      Added support for Supplement 124 to data dictionary.
      Removed superfluous member initialization.
      Fixed typo in comments.
      Added support for determining the FrameTime.
      Access the (total) number of frames in an image.
      Fixed inconsistent parameter type.
      Added explicit type casts to avoid warnings.
      Fixed inconsistent parameter type.
      Updated data dictionary for DICOM 2013 edition.
      Fixed typos in comments.
      Added further error handling options.
      Fixed typos in comments.
      Fixed typos, added missing documentation, etc.
      Various minor fixes for development version.
      Fixed typos in comments.
      Made sure that the move originator is cleared.
      Fixed issue with text alignment in PatternLayout.
      Fixed some Doxygen related issues (and a typo).
      Consistently use "presInfo" for variables/parameters.
      Added support for Supplement 159 to data dictionary.
      Added support for new UID from Supplement 159.
      Added support for new SR IOD from Supplement 159.
      Added DcmSCP::abortAssociation() method.
      Fixed typo and updated copyright date.
      Removed meaningless layout file setting.
      Renamed Doxygen's layout file again.
      Made sure that header file is parsed by Doxygen.
      Group condition constants in Doxygen output.
      Avoid full directory path in Doxygen footer.
      Replaced CMake variable in Doxygen config file.
      Removed outdated comment on DICOM 2008 standard.
      Added missing empty line.
      Fixed typos and other minor issues.
      Updated reference to DICOM standard edition.
      Updated DCMTK's copyright date.
      Added support for CP-1125 to SR implementation.
      Fixed incomplete #include comment.
      Added support for recently approved CPs.
      Updated comment based on CP-1335.
      Added support for new Colon CAD SR constraints.
      Fixed various typos and minor Doxygen issues.
      Updated data dictionary for DICOM 2014a edition.
      Removed year component from version field.
      Minor fixes to file's comment header.
      Updated copyright date and other minor changes.
      Implemented copy constructors and added clone().
      Added explaining comment on new copy constructor.
      Removed outdated CMake exclude pattern.
      Excluded "*.md5" files from installation.
      Made sure that all top-level nodes are deleted.
      Added method counting the number of nodes.
      Added two new convenience functions.
      Fixed issue with tests run in different order.
      Fixed various Doxygen-related issues.
      Introduced new class DSRDocumentSubTree.
      Implemented copy constructors for tree classes.
      Added getPreviousNode() and getChildNode().
      Added further checking methods to cursor class.
      Added gotoFirst() and gotoLast() methods.
      Minor fixes on "const" declaration of pointers.
      Added cloneSubTree() method to tree classes.
      Changed return type of addContentItem(node*).
      Reimplemented various getXXX() methods.
      Cleaned up handling of "unknown" relationships.
      Restructured classes for nodes and trees.
      Fixed a bug in convertNewlineCharacters().
      Added insertSubTree() method to subtree class.
      Added checking of IOD-specific constraints.
      Fixed two memory leaks in recently added code.
      Clarified use of template identification.
      Removed DLL specifier from template classes.
      Slightly enhanced layout of Doxygen documentation.
      Added public method to change SR document type.
      Fixed wrong term in Doxygen documentation.
      Added removeSubTree() method to subtree class.
      Added extractSubTree() method to tree classes.
      Enhanced support for by-reference relationships.
      Further enhanced by-reference relationships.
      Insert a subtree into an empty document tree.
      Added dcmIsImageStorageSOPClassUID() function.
      Added check on valid "IMAGE" SOP Classes.
      Added support for optional JPEG fill byte.
      Removed misleading comment from checkStringValue().
      Fixed typos in comments and other minor issues.
      Added support for new value representation "UR".
      Updated data dictionary for DICOM 2014b edition.
      Added functions to enable/disable post-1993 VRs.
      Enhanced rewriting rules in DcmVR::getValidEVR().
      Use new VR "UR" for Pixel Data Provider URL.
      Fixed typo in method name.
      RLE images should not use multiple fragments.
      Added missing documentation for --propose-deflated.
      Attribute (0040,4005) has not been retired.
      Fixed wrong term "Device Driving Level".
      Updated "dcmrt" classes based on DICOM 2014b.
      Added "data correction" options to findscu.
      Fixed issue when scaling certain images.
      Removed unneeded header include.
      Fixed typo in comment.
      Fixed wrong validation of PN, LO and SH values.
      Added check for requirements clarified by CP-1401.
      Updated data dictionary for DICOM 2014c edition.
      Added support for new UIDs from DICOM 2014c.
      Fixed typo in comment.
      Added new temporarily generates files.
      Use "try and catch" block around new[].
      Fixed error handling in detachValueField().
      Fixed error handling in changeValue().
      Added new test case for VR=FD.
      Changed attribute used for the "FD" test.
      Added support for new value representation "UC".
      Added support for recently approved CPs.
      Added Mapping Resource UID from CP-1417.
      Removed outdated name suffix from EXS_xxx constant.
      Added missing standard include for assert().
      Fixed another CMake 3.1.x quotation issue.
      Updated latest tested CMake version.
      Fixed documentation of default TCP buffer length.
      Updated data dictionary for DICOM 2015a edition.
      Fixed typos in comments and other minor issues.
      Updated Makefile dependencies again.
      Updated outdated API documentation.
      Output message to logger on wrong pixel data class.
      Enhanced use of DSRCodingSchemeIdentificationList.
      Added support for recently approved CPs.
      Added support for Supplement 173 to dictionary.
      Added support for new UIDs from Supplement 173.
      Added support for recently approved CP-1425.
      Fixed test after after implementing CP-1425.
      Added further test cases for VR checker.
      Added read flag to all readXXX() methods.
      Optionally accept invalid content item values.
      Distinguish b/w invalid content items and values.
      Enhanced output to debug logger.
      Fixed wrong position counter in tree node.
      Added regression test for DSRTree::getPosition().
      Added method for counting number of child nodes.
      Fixed issue with VR checker for PN values.
      Fixed warning C4800 reported by Visual Studio.
      Updated data dictionary for DICOM 2015b edition.
      Ignore empty value for XML element 'charset'.
      Added support for optional Mapping Resource UID.
      Pass OFList parameter by-reference not by-value.
      Fixed issue with interpolation algorithm.
      Added hasTemplateIdentification() method.
      Replace the document tree of an SR document.
      Added initial support for SR templates.
      Added helpers for setting a value from dataset.
      Set observation date/time from dataset.
      Moved various methods to protected section.
      Added helpers for setting a value from element.
      Set observation date/time from element.
      Avoid using "check" parameter of SR code class.
      Introduced new error code "Unknow VR".
      Fixed source code and/or comment formatting.
      Do not check invalid UID values for IMAGE node.
      Added support for long code values (CP-1031).
      New class for "Basic Coded Entry Attributes".
      Fixed bug in time normalization code.
      Added missing empty() method to OFMap.
      Added new option for print() method.
      Added new comparison method to DSRCodedEntryValue.
      Made getAndRemoveRootNode() public.
      Fixed issue with addNode() in basic tree class.
      Added new and enhanced existing swap() function.
      Check whether a template is extensible.
      Added initial support for Supplement 186.
      Added initial support for Supplement 180.
      Made constructor and destructor "protected".
      Removed explicit name of base class from call.
      Added mechanism for remembering node positions.
      Added base class for context groups.
      Added initial version of DCM code definitions.
      Added first specific Templates and Context Groups.
      Updated "DCM" codes for DICOM 2015c edition.
      Updated data dictionary for DICOM 2015c edition.
      Fixed issue with wrong quotation marks.
      Added static initialization function (MT-safe).
      Fixed issue in OFStandard::combineDirAndFilename().
      Enhanced check on empty dataset.
      Improved documentation of disableXXXCheck().
      Consistently use "file-set" and "file format".
      Allow for disabling check on "DICOM file format".
      Renamed ANNOUNCE file (removed version suffix).
      Enhanced documentation of createNewSOPInstance().
      Added conversion operator to context group class.
      Added support for CID 42 (Numeric Value Qualifier).
      Added function that initializes all context groups.
      Updated copyright date.
      Fixed wrong documentation of return value.
      Removed superfluous OFStringStream_ends statement.
      Fixed wrong exit code on invalid input file.
      Added support for further Context Groups.
      Fixed various typos in comments.
      Enhanced handling of empty Measured Value Sequence.
      Added check for CID 42 to NUM values.
      Added support for Context Group CID 29.
      Added general information on coding scheme "DCM".
      Added easier method to set a composite reference.
      Fixed issue reported by Clang 3.5 on OpenBSD.
      Introduced condition constant EC_NotYetImplemented.
      Do not set empty concept name codes.
      Added missing DCMTK_DCMDATA_EXPORT macro.
      Added new helper method gotoEntryFromNodeList().
      Added method to look up a context group entry
      Added new mode for adding nodes to the tree.
      Fixed typos in comment.
      Added comment on reserved error codes (for "cmr").
      Fixed wrong comment.
      Introduced new flag to customize the print output.
      Added new command line options to dsrdump.
      Added specific logger for submodule "dcmsr/cmr".
      Added parameter "pos" to getStringValueFromDataset.
      Added static method setEnhancedEncodingMode().
      Clarified use of invalid coded entries.
      Added support for Context Group CID 244.
      Made sure that IOD constraint checker is used.
      Added "Extensible SR" to known document types.
      Added enhanced versions of CID 29, 244 and 4031.
      Added cleanup() function to context group classes.
      Fixed typo and other minor issues in comments.
      Added name prefix to class ContentMappingResource.
      Fixed copyright header in module "dcmsr".
      Added new optional parameter "vm" to readSequence.
      Added methods to read/write to/from sequence items.
      Fixed inconsistencies regarding the use of OFMap.
      Updated Makefile dependencies.
      Added enhanced versions of CID 10013 and 10033.
      Added initial version of SRT and UCUM codes.
      Introduced type for list of CID 7445 values.
      Updated Makefile dependencies.
      Added initial version of TID 1600 (Image Library).
      Slightly changed conversion operator.
      Extracted general information from template.
      Avoid seperator if time component is empty.
      Added support for annotating content items.
      Added support for Context Group CID 100 and 7021.
      Added support for clearing tree node annotations.
      Made sure that tree node annotations are copied.
      Made sure that "dicom.dic" is loaded for tests.
      Fixed various issues in test case.
      Fixed "cardinality" for SQ elements in comments.
      Added comment that "Big Endian" is retired.
      Removed version suffix "3" from dictionary entries.
      Check logger for debug output of template tree.
      Introduced global definitions for certain tags.
      Added CREDITS file.
      Added "YXLON" to the new CREDITS file.
      Added support for recently approved CPs.
      Added support for Supplement 156 to dictionary.
      Added support for new UIDs from Supplement 156.
      Check for recently approved multi-frame images.
      Updated currently supported compiler versions.
      Fixed various minor issues in module descriptions.
      Fixed order of modules in main HTML file.
      Added three new DCMTK modules to README.

Marco Eichelberg (5):
      Introduced OFStandard::dropPrivileges().
      Tools now use OFStandard::dropPrivileges().
      Fixed minor bug in DICOM upper layer FSM.
      Always use current dicom.dic for dcmdata unit tests.
      Removed unsupported wwwapps and perl scripts from module dcmwlm.

Michael Onken (84):
      Added (optional) originating C-MOVE AE title and message ID to C-STORE message.
      Make DcmStorageSCU make use of new MoveOriginator feature.
      Added optional status detail when sending C-MOVE response.
      Make sure memcpy does not copy to NULL destination. Thanks to Francesco Gigante     for the report.
      Added option to discard illegal characters when converting between     DICOM character sets.
      Add "Discard illegal character" support to dcmconv and classes like DcmItem.
      Make sure SCU and SCP request/response data structures are initially zeroed.
      Fixed typo (coersion -> coercion) in DIMSE status constant.
      Added missing kudos.
      Fixed too small buffer for UID in Q/R server.
      Fixed issues where JPEG marker map was not cleared if more than one JPEG     was converted using the same plugin instance.
      Fixed possible doubled destruction of association.
      Make sure oflog also compiles if threads are disabled.
      Always write meta header when receiving files. Removed Winsock comment.
      Added missing CHANGES entry.
      Warning to re-create index.dat after 20130705:
      Create DcmFileFormat from DcmDataset w/o copying.
      Do not copy DcmDataset during C-GET receive.
      Worklist SCP support for Responsible Person/Role.
      Replaced tabs with spaces.
      Support explicit item length denoting too many bytes.
      Corrected misleading transfer syntax error message.
      Fixed Comments.
      Described movescu storage SCP timeout problem.
      Make sure CMAKE_BUILD_TYPE has a default value.
      Fixed doubled tag output in XML output of VR OF.
      Avoid second OpenSSL initialization in constructor.
      Documentation for CMAKE_BUILD_TYPE default value.
      Fixed typo.
      Fixed CHANGES entries.
      Fixed some inconsistencies in documentation.
      Make sure to handle setuid() return code properly.
      Add libjpeg dependency for libtiff and minor changes.
      Fixed shared library build under Unix (configure).
      Enhanced DCMTK CMake exports for external projects.
      Capitalized all CMake key words for consistency.
      Ensure CMake v2.6 still writes DCMTKConfig.cmake.
      DCMTK.cmake and DCMTKTargets.cmake documentation.
      Added helpers to copy common modules between items.
      Fixed Makefile.dep for new files from last comit.
      Switched windows line endings to unix line endings.
      Added further module helpers and fixed small issues.
      Fixed comments and error message.
      Updated module helpers to latest DICOM 2013 draft.
      Fixed wrong ifdef syntax.
      Add connection timeout setting to SCU class.
      Fixed possible memory leak.
      Specific error if no presentation context proposed.
      Reverted false retirement status of some SOP Classes.
      Fix last commit by including implementation file.
      New compare() function for dcmdata object values.
      Make sure dcmdata tests compile with autoconf.
      Make new compare() method more reliable.
      Fixed conversion of color to palette color mode.
      Documented DCMTK's C++ cast macros.
      Fixed installation and added CHANGES file.
      Disable built-in dictionary for CMake Unix builds.
      Make sure presentation contexts do not interfer.
      Fixed iterator type.
      Introduced new modules dcmiod, dcmfg and dcmseg.
      Removed accidentially checked in test files.
      Removed more accidentially checked in test files.
      Fixed iterator dereference.
      Fixed iterator constness.
      Fixed possible DICOM VR problems.
      Removed unused method.
      Fixed mostly constness for some compilers.
      Fixed various doxygen formatting issues.
      Fixed compilers errors (mostly STL-specific).
      Removed unused link libraries.
      Made copyright header consistent in new modules.
      Build flags for internal and external dictionary.
      Updated dictionary build and code documentation.
      Added shared library export maro to IODModule.
      Added more files to be ignored by git.
      Added mising "check-exhaustive" targets.
      Replaced tab characters with spaces.
      Use static_cast instead of dynamic_cast.
      Renamed dictionary configuration build options.
      Simplified builtin dictionary infrastructure.
      Fixed typo in CMake script that can cause warnings.
      Fixed typo and made documentation more consistent.
      Fixed another typo.
      Enable private tags in builtin dictionary on CMake.

Nikolas Goldhammer (1):
      Replaced deprecated CMake expressions.

Uli Schlachter (13):
      Fixed wrong definition of Value Representation Person Name (PN)
      Removed unused local variable which shadowed a variable with the same name.
      Use ".NOTPARALLEL:" to make parallel builds (e.g. -j4) possible.
      Update rootconf for changes which were done directly to generated files.
      Fixed various issues found via cppcheck.
      Use DcmTagKey's output operator where possible.
      Don't include intrin.h on Visual Studio 2005 because of build errors.
      Fixed bug in OFString::copy() and improved unit tests.
      Fixed compiler warnings in ConvertIntegerToString with unsigned integers.
      Worked around compiler warnings on 32bit systems for too large shifts.
      Fixed crash if less than four transfer syntaxes are enabled.
      Silence some more compiler warnings about implicit casts.
      Don't set the defines for thread local storage support incorrectly.

Revision 24577 - Directory Listing
Modified Wed Sep 23 17:09:10 2015 UTC (2 years ago) by pinter
BUG: Fixed SubjectHierarchyCorePluginsSelfTest

It failed due to a recent change in the clone node plugin. The scenario when adding a data node to the scene triggered creation of display and/or storage nodes was not handled.
Also implemented restoring original DICOM directory in SH generic self test for convenience.

Revision 24571 - Directory Listing
Modified Tue Sep 22 15:31:31 2015 UTC (2 years ago) by msmolens
BUG: Fix libpng warnings in console when loading images with Qt 4.8.7

This commit eliminates the following libpng warning seen when loading certain
PNG images using libpng 1.6.x, which is included in Qt 4.8.7:

    libpng warning: iCCP: known incorrect sRGB profile

To fix the images I ran them through ImageMagick, which removes the incorrect
profiles, as suggested in [1]:

    convert image.png image.png

libpng 1.6.17 describes the warning in png.c line 2308:

    /* These profiles are known to have bad data that may cause
     * problems if they are used, therefore attempt to
     * discourage their use, skip the 'have_md5' warning below,
     * which is made irrelevant by this error.
     */

[1] http://stackoverflow.com/questions/22745076/libpng-warning-iccp-known-incorrect-srgb-profile

From: Max Smolens <max.smolens@kitware.com>

Revision 24563 - Directory Listing
Modified Fri Sep 18 14:53:08 2015 UTC (2 years, 1 month ago) by msmolens
BUG: Fix py_nomainwindow_DCMTKPrivateDictTest on Windows

Test py_nomainwindow_DCMTKPrivateDictTest fails on Windows because of a line
ending issue. Although the test passed on a local build after r24557 [1], the
test still fails on factory-south-win7.kitware.

This commit changes the test to use Python's universal newlines [2] when parsing
dcmdump's output.

[1] http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24557
[2] https://docs.python.org/2/glossary.html#term-universal-newlines

From: Max Smolens <max.smolens@kitware.com>

Revision 24527 - Directory Listing
Modified Wed Sep 9 17:58:55 2015 UTC (2 years, 1 month ago) by pieper
STYLE: fix typo in variable name and add some extra documentation

Revision 24521 - Directory Listing
Modified Tue Sep 8 20:49:49 2015 UTC (2 years, 1 month ago) by jcfr
ENH: Add test for DCMTK private dictionary. See issue #4013

Philips phantom DWI dataset is included. The test runs dcmdump command,
and looks for the description of tag (2001,1003), which should be
DiffusionBFactor, and can only be recognized when private dictionary
support is enabled in DCMTK.

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Tested-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Andrey Fedorov <fedorov@bwh.harvard.edu>

Revision 24458 - Directory Listing
Modified Tue Jul 21 14:48:42 2015 UTC (2 years, 2 months ago) by pinter
STYLE: Removed unnecessary developer mode setting from self tests

Revision 24444 - Directory Listing
Modified Fri Jul 17 05:00:57 2015 UTC (2 years, 3 months ago) by jcfr
BUG: Fix memory leaks in qSlicerAppMainWindow

This commit fixes the error(s) reported below by valgrind memcheck tool.

Valgrind was used on Ubuntu 14.04 against a Debug build of Slicer. It was
exected doing the following:
 (1) Start a terminal with the appropriate environment: ./Slicer --gnome-terminal
 (2) Start Slicer using valgrind: valgrind --log-file=2015-07-16-Slicer-memcheck.txt --tool=memcheck --leak-check=yes ./bin/SlicerApp-real --disable-python --disable-cli-modules
 (3) Exit Slicer and inspect valgrind log file

Valgrind error:

==29339== 5,172 (40 direct, 5,132 indirect) bytes in 1 blocks are definitely lost in loss record 2,404 of 2,448
==29339==    at 0x4C2B0E0: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==29339==    by 0x4E57C53: qSlicerAppMainWindowPrivate::setupUi(QMainWindow*) (qSlicerAppMainWindow.cxx:334)
==29339==    by 0x4E56C59: qSlicerAppMainWindowPrivate::init() (qSlicerAppMainWindow.cxx:122)
==29339==    by 0x4E5A98D: qSlicerAppMainWindow::qSlicerAppMainWindow(QWidget*) (qSlicerAppMainWindow.cxx:676)
==29339==    by 0x406553: (anonymous namespace)::SlicerAppMain(int, char**) (Main.cxx:184)
==29339==    by 0x406D30: main (Main.cxx:254)

Revision 24424 - Directory Listing
Modified Wed Jul 15 18:23:42 2015 UTC (2 years, 3 months ago) by jcfr
STYLE: Facilitate release process updating wiki URL with Nightly namespace

This commit updates the templates to use wiki documentation url
mentioning the Nightly version. This will facilitate maintenance avoiding
to explicitly update the file after each release.

More specifically, thanks to the previous commit (ENH: Update wiki URLs
in module panel to reference correct documentation.), the module panel has
been instrumented to update the module description so that documentation
URLs are updated at runtime to point to the correct version of the wiki
documentation.

Note also that a new FAQ section entitled "Documentation Writing" has
been added to the Developer FAQ [1]. At the time of this commit, it reference
the following question:

  How to reference module or extension documentation hosted on the Slicer wiki ?

[1] http://wiki.slicer.org/slicerWiki/index.php?title=Documentation/Nightly/Developers/FAQ#Developer_FAQ:_Writing_Documentation

Revision 24397 - Directory Listing
Modified Tue Jul 7 17:54:49 2015 UTC (2 years, 3 months ago) by naucoin
BUG: only time out extra storable message during testing

The pop up window that gives the user feedback about how
not to lose new storable data after creating a scene view
was timing out before some testers could finish reading
and understanding the information. Added a boolean property
to the capture tool bar, popupsTimeOut, that the main
window can set to true when the enable testing attribute
has been turned on. Verified that the test
AddStorableDataAfterSceneViewTest
still passes and doesn't hang.

Issue #3956

Revision 24395 - Directory Listing
Modified Tue Jul 7 17:54:42 2015 UTC (2 years, 3 months ago) by naucoin
BUG: update file list members, scene vars, update test

Update the MRB save/restore test to use the slicer util delayDisplay method,
as well as not counting file paths that point to the deleted bundle
expansion directory.
In scene view nodes make sure to also reset the file list
Restore the url and root direcotry after saving a scene to the data bundle
directory so that absolute paths can be calculatediproperly

Issue #3956

Revision 24394 - Directory Listing
Modified Tue Jul 7 17:54:36 2015 UTC (2 years, 3 months ago) by naucoin
BUG: Add a test that checks file paths after MRML and MRB save/load

Add a test that checks the paths in the scene with saving to mrml (have to force
a write of a sample data node since the saveScene call only writes out the MRML file,
no storage nodes are triggered to write) and MRB and reloading and saving to MRB.
Remove skipping the master scene view as paths of storage nodes there do need to be updated.
TBD: fix the paths after saving the MRB a second time (they get reset to the deleted bundle directory from the first MRB save).

Issue #3956

Revision 24390 - Directory Listing
Modified Tue Jul 7 17:54:03 2015 UTC (2 years, 3 months ago) by naucoin
ENH: stress test saving and restoring MRBs, util methods added

Add a test to save and restore MRBs in a loop, fixing the bug note in the
save restore test as well.
Clean up the testing of saving and loading MRBs by exposing the core io
manager loadScene method to Python, and adding a saveScene one. This will
simplify testing since it uses detects that it needs to use the scene writer
which will use the application logic save to MRB bundle directory + zip calls,
so from python you won't need to make the two calls with attendant managing of
temporary directories. Added a note to the application logic header file
pointing to saveScene for general use.

Issue #3956

Revision 24375 - Directory Listing
Modified Tue Jul 7 17:52:58 2015 UTC (2 years, 3 months ago) by naucoin
BUG: update test with more correct visibility toggles

Digging into the missing fiducials data I realised that on MRB
load and then scene view restore the individual fiducial visibility
will not get saved/restored in scene views since that information is
saved in the file on disk, only the list level visibility is saved.
Updated the test to only test list level fiducial visibility.

TBD: find a backward compatible way to move the per markup visibility
into the markups display node. This behaviour is confusing since
from a freshly started Slicer in which you create new scene views, the
per markup visibility toggling does work (node copies are in memory),
it will just cease to work once the scene is saved to disk and then
re-opened.

Issue #3956

Revision 24370 - Directory Listing
Modified Tue Jul 7 17:52:40 2015 UTC (2 years, 3 months ago) by naucoin
BUG: adding a test to show MRB and scene view bug

Set up a scene with a volume and a fiducial list.
Save scene views.
Save to MRB.
Close scene, reload MRB, restore scene view, save to MRB.
Reload the MRB and make sure that the volume and fiducial
list are as expected - when this bug is not fixed, the
fiducial list size will be zero at this point.

Issue #3956

Revision 24310 - Directory Listing
Modified Wed Jun 17 15:43:57 2015 UTC (2 years, 4 months ago) by jcfr
BUG: VTKObservationMixin: Fix removeObservers method and add unittests

Revision 24293 - Directory Listing
Modified Thu Jun 4 21:28:22 2015 UTC (2 years, 4 months ago) by pinter
ENH: Added labelmap node support to subject hierarchy

Subject hierarchy knew about the single vtkMRMLScalarVolumeNode class, but now that the vtkMRMLLabelMapVolumeNode has been introduced, a separate subject hierarchy plugin was created for labelmaps. This way it is cleaner that one role plugin assigns one icon and the same set of functionality to its owned nodes.

Fixed issue in sitkUtils: it created a scalar volume node regardless whether a labelmap was already created

Removed temporary contour references from model slice displayable manager (segmentations has its own displayable manager)

Added concept of virtual subject hierarchy branches, which is a branch for which its parent is solely reaponsible, i.e. the child nodes do not correspond to actual MRML nodes, but to items contained in the parent node to enable per-item handling from subject hierarchy (e.g. segments in segmentations and fiducials in markups)

Create and expose cloneSubjectHierarchyNode method in qSlicerSubjectHierarchyCloneNodePlugin to enable easy cloning of any node (clone SH node, data node, display and storage nodes)

Revision 24291 - Directory Listing
Modified Thu Jun 4 20:12:02 2015 UTC (2 years, 4 months ago) by lassoan
ENH: Use vtkMRMLLabelMapVolumeNode class for labelmap volumes

Before vtkMRMLScalarVolumeNode was used for both scalar and label map
volumes and the LabelMap custom MRML node attribute was used for
distinguishing between them (0=scalar; 1=label map volume).
This made conversion between labelmap/scalar volumes very easy but made
it difficult to customize behavior, display, processing of segmentation
information.

Now a new vtkMRMLLabelMapVolumeNode class is used for storing segmentation
information (still using vtkMRMLScalarVolume used as base class for backward
compatibility; but in the future the base class may be changed to reflect
that segmentation can be represented in various ways, not just as volumes).

Notes:

A new "segmentation" node has been developed that is based on vtkMRMLLabelMapVolumeNode,
which can store segmentation information in various ways (not just labelmaps but planar
contours, closed surfaces, etc). To allow using of this new segmentation node,
first the vtkMRMLLabelMapVolumeNode has to be integrated into the Slicer core.

When reading a scene that was saved with an old version of Slicer, label maps are stored
in vtkMRMLScalarVolumeNode with label map attribute set to 1. Added a check for this case
and handle it by converting the vtkMRMLScalarVolumeNode to a vtkMRMLLabelMapVolumeNode during import.


Revision 24263 - Directory Listing
Modified Tue May 19 16:19:05 2015 UTC (2 years, 5 months ago) by lassoan
ENH: Made disclaimer popup configurable

Disclaimer popup is shown by default at the first startup of the application. The disclaimer text has to be configurable when custom applications are built on the Slicer platform.

Revision 24251 - Directory Listing
Modified Wed May 13 15:27:31 2015 UTC (2 years, 5 months ago) by naucoin
BUG: update fiducial layout test to check RAS

The former version of this test was set to always pass
since there was still a > 1 pixel difference in starting
and ending fiducial display coordinates. Brainstorming
on the slicer dev hangout brought up the possibility
that since the fiducial RAS position was still correct,
the layout switching might have included some FOV adjustments
to fit the volume to the slice widget. This change will
go on to check the fiducial RAS position against the
volume RAS position if the display positions don't match.

Update the layout switching test to:
- fail on the dashboard if it fails
- show all output for debugging
- check both display coordinates and RAS coordinates
- only fail if both are out of tolerance
- remove the redundant delayDisplay methods and use the slicer.util
version with a shorter time out to speed up the test run time

Issue #1914

Revision 24248 - Directory Listing
Modified Wed May 13 07:36:40 2015 UTC (2 years, 5 months ago) by jcfr
ENH: Add self test DTINotReproducibleIssue3977. See issue #3977

This test has been added to check that successive
run of the "DWI to DTI estimation" CLI module returns the same output.

Problem has been documented in issue #3977. Commit r24240 fixes the problem
by updating vtkTeemEstimateDiffusionTensor class.

Revision 24162 - Directory Listing
Modified Thu Apr 9 02:12:42 2015 UTC (2 years, 6 months ago) by jcfr
STYLE: Remove unused forward declarations from qSlicerAppMainWindow

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 24159 - Directory Listing
Modified Sun Apr 5 17:35:41 2015 UTC (2 years, 6 months ago) by lassoan
ENH: Added logging of Python console user input

If the user type anything into the Python console then it is logged at debug level.
It makes debugging/troubleshooting easier.

Revision 24155 - Directory Listing
Modified Sat Apr 4 00:42:28 2015 UTC (2 years, 6 months ago) by jcfr
ENH: Fixes #3549. Import scripted module as python module

This will allow each scripted module to defined top-level variables that
will not clobber each other.

For example, if we consider these two modules:

8<----8<----8<----8<----8<----8<----8<----8<----
File: ModuleA.py

FOO = 1

class ModuleA(ScriptedLoadableModule):
  def __init__(self, parent):
    ModuleA.__init__(self, parent)
    [...]
  def doSomething(self):
    if FOO == 1:
      [...]
    else:
      [...]
8<----8<----8<----8<----8<----8<----8<----8<----

8<----8<----8<----8<----8<----8<----8<----8<----
File: ModuleB.py

FOO = 2

class ModuleB(ScriptedLoadableModule):
  def __init__(self, parent):
    ModuleB.__init__(self, parent)
    [...]
  def doSomething(self):
    if FOO == 1:
      [...]
    else:
      [...]
8<----8<----8<----8<----8<----8<----8<----8<----

Assuming ModuleA, and then ModuleB are imported. Before this commit,
both scripts were executed in the __main__ scope and FOO variable would
have the value associated with the last imported module.

After this commit, both module will see their own copy of the FOO
variable with the expected value.

It also avoid the hack when we explicitly save/set/restore
both "__name__" and "__file__" variable.

Changes to "DICOMScalarVolumePlugin" fixes the test failing test
"py_RSNAVisTutorial" and "py_SubjectHierarchyGenericSelfTest". It basically
fixes the following error by ensuring all object are imported:

//--------------
test_SubjectHierarchyGenericSelfTest_FullTest1 (SubjectHierarchyGenericSelfTest.SubjectHierarchyGenericSelfTestTest) ... Traceback (most recent call last):
  File "/path/to/Slicer-build/lib/Slicer-4.4/qt-scripted-modules/DICOMLib/DICOMWidgets.py", line 615, in getLoadablesFromFileLists
    loadablesByPlugin[plugin] = plugin.examineForImport(fileLists)
  File "/path/to/Slicer-build/lib/Slicer-4.4/qt-scripted-modules/DICOMScalarVolumePlugin.py", line 47, in examineForImport
    loadablesForFiles = self.examineFiles(files)
  File "/path/to/Slicer-build/lib/Slicer-4.4/qt-scripted-modules/DICOMScalarVolumePlugin.py", line 71, in examineFiles
    loadable = DICOMLib.DICOMLoadable()
NameError: global name 'DICOMLib' is not defined
//--------------

Revision 24154 - Directory Listing
Modified Sat Apr 4 00:42:23 2015 UTC (2 years, 6 months ago) by jcfr
ENH: Add test illustrating issue #3549 related to scripted module import

The test is currently passing but comment in the script explain which
behavior is really expected.

In a nutshell, scripted module shouldn't be executed in the global scope
but should instead be imported as module.

Revision 24088 - Directory Listing
Modified Mon Mar 23 18:58:25 2015 UTC (2 years, 6 months ago) by jcfr
STYLE: Remove commented code from qSlicerAppMainWindow

Revision 24086 - Directory Listing
Modified Tue Mar 17 23:20:20 2015 UTC (2 years, 7 months ago) by jcfr
STYLE: Set "desc. file" property in slicerMacroBuildAppLibrary macro

This commit moves the setting of the description file used by the
packaging code into the application CMakeLists.txt

Revision 24085 - Directory Listing
Modified Tue Mar 17 23:20:18 2015 UTC (2 years, 7 months ago) by jcfr
STYLE: Set "desc. summary" property in slicerMacroBuildAppLibrary macro

This commit moves the setting of the description summary used by the
packaging code into the application CMakeLists.txt

Revision 24082 - Directory Listing
Modified Tue Mar 17 23:20:13 2015 UTC (2 years, 7 months ago) by jcfr
STYLE: Move and rename "Slicer3.png" to "Slicer-ModulePanelLogo.png"

Since the image is used to illustrate the module panel area in the main
windows, the file is move into the Resources application folder and is
renamed accordingly.

Revision 24081 - Directory Listing
Modified Tue Mar 17 23:20:10 2015 UTC (2 years, 7 months ago) by jcfr
STYLE: Rename SlicerApp icon files to match application name "Slicer"

Revision 24080 - Directory Listing
Modified Tue Mar 17 23:20:07 2015 UTC (2 years, 7 months ago) by jcfr
STYLE: Remove unused Slicer png files from top-level Resources folder

This files were initially added in r20128 (add extra icon sizes and a
.ico file for convenience), then they have been added to the qSlicer.qrc
file in r20348 (BUG: 0002094. Move 3DSlicer icons into appropriate subdirectories.)

Since the resources are not referenced anywhere and the corresponding
file have been moved into the SliceApp application resource directory (r14748),
this commit removes them.

Revision 24062 - Directory Listing
Modified Fri Mar 13 14:26:48 2015 UTC (2 years, 7 months ago) by jcfr
STYLE: Display module loading stats only once

Since (1) following r24059 (ENH: Write all info to the log file as
formatted log messages), module stats are displayed using qDebug() and
(2) following r24052 , module stats are displayed if verboseModuleDiscovery is
enabled, this commit revert r24052 and ensure stats are displayed once.

Revision 24056 - Directory Listing
Modified Wed Mar 11 03:48:00 2015 UTC (2 years, 7 months ago) by jcfr
BUG: Fix slicer_nomainwindow_DisableModulesCommandLineOptionsTest

Fix failure introduced by r24050 (ENH: Display module loading stats only
if verbose module discovery is set.)

Revision 24055 - Directory Listing
Modified Wed Mar 11 03:47:57 2015 UTC (2 years, 7 months ago) by jcfr
STYLE: Remove commented / unused code from Main.cxx

Revision 24053 - Directory Listing
Modified Tue Mar 10 21:30:42 2015 UTC (2 years, 7 months ago) by jcfr
STYLE: Fix help message layout removing logging of application name

This commit removes the debug message added in r24004 (ENH: Allow
application name to be defined by argv0)

Prior to this commit, the name of the application was displayed
between the launcher help message and the application one:

8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---
[...]
  --xterm                                      Start xterm
  --gdb                                        Start gdb
applicationName:  "Slicer"
  --, --ignore-rest                             Ignores the rest of the labeled arguments following this flag. (default: false)
  -h, --help                                    Display available command line arguments
[...]
8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---

Revision 24050 - Directory Listing
Modified Tue Mar 10 21:30:25 2015 UTC (2 years, 7 months ago) by jcfr
ENH: Display module loading stats only if verbose module discovery is set.

Revision 24040 - Directory Listing
Modified Tue Mar 10 02:46:17 2015 UTC (2 years, 7 months ago) by jcfr
BUG: Remove obsolete NeurosurgicalPlanningTutorial QtTesting based test

QtTesting XML tests are hard to maintain.  Considering tutorial tests are
now all written in python as SelfTest, this commit removes the last QtTesting
tests.

For example, in the case of the NeurosurgicalPlanningTutorial test, the
play back is failing because the tree indices first recorded are now
invalid. Most likely because the associated widget has been updated.
Considering that (1) the XML is hard to manually update and debug and
(2) is is difficult to re-record only a section of the test starting from
the expected state, it would usually require the developer to re-record
the full test. This is time consuming and sub-optimal. With better
instrumentation or by using the QtTesting python based test (instead of
the XML), it may be worth reconsidering.

Also remove DiffusionTensorImagingTutorial related files (the associated
test has been disabled in r22388)

Revision 24039 - Directory Listing
Modified Tue Mar 10 02:30:03 2015 UTC (2 years, 7 months ago) by lassoan
ENH: Added vtkInfoMacro

Added in a new vtkAddon library, which contains Slicer's VTK add-ons that eventually could be moved to VTK proper.

Resolves https://github.com/Slicer/Slicer/pull/205

Revision 24024 - Directory Listing
Modified Thu Mar 5 22:41:18 2015 UTC (2 years, 7 months ago) by jcfr
ENH: Add slicerMacroBuildAppLibrary and slicerMacroBuildApplication

Facilitate maintenance introducing two new marcos allowing to more easily
create application executable and library.

Revision 24023 - Directory Listing
Modified Thu Mar 5 16:24:14 2015 UTC (2 years, 7 months ago) by lassoan
BUG: Fixed Slicer settings and paths issues

The issue was that on Windows \ is used instead of / in paths.

Revision 24011 - Directory Listing
Modified Tue Mar 3 22:34:45 2015 UTC (2 years, 7 months ago) by jcfr
STYLE: Associate application test driver with correct folder

This commit fixes a typo first introduced in r23961 (ENH: Improve build
targets organization in IDE that support folders).

Revision 24004 - Directory Listing
Modified Mon Mar 2 15:04:58 2015 UTC (2 years, 7 months ago) by pieper
ENH: Allow application name to be defined by argv0

The qCoreApplication::applicationName controls the discovery
of QSettings files and some other parts of the internal
machinery of the application.  When making a custom version of
slicer, we want to keep the settings independent of the
original slicer, so that, for example, they can have different
module paths related to the extensions that are bundled.

See:

http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/CustomSlicerGenerator

Revision 23978 - Directory Listing
Modified Sat Feb 21 16:02:53 2015 UTC (2 years, 7 months ago) by lassoan
BUG: Fixed VisualStudio launcher option for VS10 and later

CMAKE_BUILD_TOOL (http://www.cmake.org/cmake/help/v3.0/variable/CMAKE_BUILD_TOOL.html, http://www.cmake.org/cmake/help/v3.0/variable/CMAKE_MAKE_PROGRAM.html#variable:CMAKE_MAKE_PROGRAM) points to IDE (msdev, VS9 an earlier) or build tool (msbuild, VS10 or later). The --VisualStudio option should launch the IDE, so the correct CMake variable to use is CMAKE_VS_DEVENV_COMMAND (http://www.cmake.org/cmake/help/v3.0/variable/CMAKE_VS_DEVENV_COMMAND.html#variable:CMAKE_VS_DEVENV_COMMAND).

Revision 23961 - Directory Listing
Modified Thu Feb 5 00:11:16 2015 UTC (2 years, 8 months ago) by jcfr
ENH: Improve build targets organization in IDE that support folders

This commit set the FOLDER property on all targets to group them
into meaningful "units". This will make development easier ensuring
it is possible to quickly re-build and open the source files associated
with the targets of either a given module, the core libraries or even
the Slicer application.

Currently the grouping is:
* App-SlicerApp
* CMakePredefinedTargets
* Core-Base
* Core-Libs
 * FreeSurfer
 * ITKFactoryRegistration
 * [...]
* Module-<NameOfModule>
* [...]

If for some reason, the folder organization needs to be disabled. Slicer
could be configured with Slicer_USE_FOLDERS set to OFF.

Projects updated in this commit:
* CTK
* SlicerExecutionModel
* OtsuThresholdImageFilter

Notes:

 (1) some of the targets (EMSegment, BRAINSTools, MultiVolume, ...)
are still associated to the root and not yet categorized.

 (2) ideally few more  macros/functions should be introduced: one to
easily configure subject hierarchy plugin, and one to easily configure
tests associated with a CLI.


CTK changes:

// -------------
commit commontk/CTK@ac1370e
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed Feb 4 14:47:09 2015 -0500

    Add FOLDER parameter to ctkMacroBuildQtPlugin

    If specified, the target(s) associated with designer, icon engine and
    style plugins will be added into the specified folder when the project is
    configured for an IDE supporting it.

    For more details, see http://www.cmake.org/cmake/help/v2.8.9/cmake.html#prop_tgt:FOLDER
// -------------


SlicerExecutionModel changes:

// -------------
commit Slicer/SlicerExecutionModel@0b780eb
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed Feb 4 18:06:25 2015 -0500

    ENH: SEMMacroBuildCLI - Add possibility to associate FOLDER with CLI targets

    In project building a lot of modules (i.e Slicer), whenever possible, it
    is better to keep the huge list of targets organized. To help with this,
    CMake allows to set a FOLDER target property.

    See http://www.cmake.org/cmake/help/v2.8.3/cmake.html#prop_tgt:FOLDER

    This commit extends the SEMMacroBuildCLI API to accept an optional FOLDER
    parameter. If not set, the folder name will default to:

      <SlicerExecutionModel_DEFAULT_CLI_TARGETS_FOLDER_PREFIX><MODULE_NAME>

    By default the prefix is set to an empty string and the folder will be
    named after the module name.

    There are two ways to specify a default prefix value:

     (1) Set the variable SlicerExecutionModel_DEFAULT_CLI_TARGETS_FOLDER_PREFIX
    in the current scope before calling 'SEMMacroBuildCLI'

     (2) Configure the SlicerExecutionModel project with the option
    SlicerExecutionModel_DEFAULT_CLI_TARGETS_FOLDER_PREFIX

    Note that:
     - FOLDER support has been introduced in CMake >= 2.8.3
    and
     - it can optionally be enabled in a project by setting the global
    property named USE_FOLDERS.

    See http://www.cmake.org/cmake/help/v2.8.3/cmake.html#prop_global:USE_FOLDERS

    Finally, to associate CLI test expected to be in the same "FOLDER",
    a variable named <MODULE_NAME>_TARGETS_FOLDER is conveniently set in the
    current scope each time the macro SEMMacroBuildCLI is called.

commit Slicer/SlicerExecutionModel@e84d231
Author: Matt McCormick <matt.mccormick@kitware.com>
Date:   Thu Aug 7 11:09:39 2014 -0400

    BUG: Fix ModuleDescriptionParser test data dir.

    Fixes Parser1Test{1,2}.

    Simplify by consolidation of variables.
// -------------


OtsuThresholdImageFilter changes:

// -------------
commit :Slicer/Slicer-OtsuThresholdImageFilter@5efe412
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed Feb 4 18:08:28 2015 -0500

    Associate folder with test targets.
    [...]
// -------------

Revision 23935 - Directory Listing
Modified Sat Jan 31 03:14:07 2015 UTC (2 years, 8 months ago) by jcfr
STYLE: Display icon path associated with the launcher

Revision 23893 - Directory Listing
Modified Tue Jan 20 15:48:59 2015 UTC (2 years, 8 months ago) by lassoan
COMP: Fixed Windows build error

ConvertWindowsCommandLineToUnixArguments has been removed from kwsys therefore command-line string parsing is now uses CommandLineToArgvW.

Revision 23824 - Directory Listing
Modified Wed Dec 10 19:33:06 2014 UTC (2 years, 10 months ago) by pinter
BUG: Fix subject hierarchy node creation bug and automatic tests

Bug reported in this thread
http://slicer-users.65878.n3.nabble.com/DICOM-RT-Export-td4028406.html
fixed, now subject hierarchy nodes are also created before the user visits the SH module (only if auto-generate is turned on, or if loaded from DICOM).

Revision 23812 - Directory Listing
Modified Tue Dec 2 19:06:17 2014 UTC (2 years, 10 months ago) by pinter
COMP: Fixed linux build warnings

Also fix Subject Hierarchy failing python self tests.

Fixes #3910

Revision 23810 - Directory Listing
Modified Tue Dec 2 00:09:44 2014 UTC (2 years, 10 months ago) by pinter
ENH: Add new DICOM export feature and scalar volume plugin

DICOM export dialog and tag editor widget are new widgets for DICOM export of all kinds of data in the new DICOMLib directory of the Scripted module folder. The existing DICOM plugin mechanism is used, but extended with an export function. Although the existing DICOMLoadable python object still works, C++ containers have been added to ensure C++ support of DICOM import/export. DICOMDataExchange.py was split into DICOMExportScalarVolume.py and DICOMExportScene.py.
See all details, including design considerations and usage information here:
http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DICOMExport

Closes #3163

Revision 23794 - Directory Listing
Modified Wed Nov 19 22:45:33 2014 UTC (2 years, 10 months ago) by pinter
ENH: Add generic folder plugin to subject hierarchy

The new plugin allows the user to create arbitrary folders, instead of the fixed hierarchy of levels. Also now patient and subject nodes are strictly separated.

Fixes #3898

Revision 23785 - Directory Listing
Modified Sun Nov 16 20:23:58 2014 UTC (2 years, 11 months ago) by lassoan
STYLE: Fixed typo in Error report dialog

Revision 23773 - Directory Listing
Modified Sun Nov 2 15:07:38 2014 UTC (2 years, 11 months ago) by jcfr
ENH: Update Documentation to 4.4

Revision 23764 - Directory Listing
Modified Wed Oct 29 21:49:14 2014 UTC (2 years, 11 months ago) by naucoin
BUG: get the screenshot type without making a widget

From JC: avoid creation an instance of the widget to get the
value of the enum

Issue #3879

Revision 23763 - Directory Listing
Modified Wed Oct 29 21:49:07 2014 UTC (2 years, 11 months ago) by naucoin
BUG: fix crash when editing scripted screen shots

Fixed the default screen shot type to use the defined full layout
integer.
Added checks to avoid crashes for scripts that are in extensions.

The default screen shot type was set to -1 in the python scripts
and templates, but in the Qt widget, the screen shot type was
only defined from 0-4. Trying to open the scripted screen shot
node in the Qt widget would cause a crash since the -1 type was
cast to the enumerated WidgetType in qMRMLScreenShotDialog
resulting in an invalid number and a null widget.

Issue #3879

Revision 23708 - Directory Listing
Modified Thu Sep 18 22:15:05 2014 UTC (3 years, 1 month ago) by jcfr
STYLE: Fix comment in SlicerApp/CMakeLists.txt

Revision 23643 - Directory Listing
Modified Wed Sep 3 15:08:39 2014 UTC (3 years, 1 month ago) by jcfr
ENH: Moved error log copying to separate error reporting dialog

Error reporting dialog accessible from menu: Help / Report a bug

From: Andras Lasso <lasso@queensu.ca>

Revision 23623 - Directory Listing
Modified Tue Aug 26 23:56:34 2014 UTC (3 years, 1 month ago) by jcfr
ENH: Remove slice annotations popup startup dialog.

Following discussing on the mailing list [1], the
additional startup dialog (originally introduced
by r23612) is rather confusing and is removed by this
commit.

[1] http://slicer-devel.65872.n3.nabble.com/Slice-annotations-comments-tp4032290p4032333.html

From: Alireza Mehrtash <mehrtash@bwh.harvard.edu>

Revision 23617 - Directory Listing
Modified Sun Aug 24 17:33:11 2014 UTC (3 years, 1 month ago) by fedorov
ENH: remove annotations popup notification


Revision 23612 - Directory Listing
Modified Fri Aug 22 20:26:28 2014 UTC (3 years, 1 month ago) by pieper
ENH: Add Slice Annotations to DataProbe module

This commit enhance the DataProbe module providing an
easy way to show/hide/customize corner annotations, ruler and color bar in the
Slice viewers.

Associated setting are saved in the general settings common to
all version of Slicer installed on the workstation.

The implementation of slice view annotations in DataProbe is a part of QIICR Project [1] includes the following features:

* Corner text annotations including basic DICOM annotations.
* Interactive Color scalar bar widget for background and foreground volumes.
* Scaling ruler

[1] QIICR Slicer infrastructure projects

ENH: Add method vtkMRMLSliceLogic::GetForegroundWindowLevelAndRange

STYLE: Remove dead code

ENH: Added the following enhancements and fixes

* Added color scalar bar actors to color bar widget instead of adding it
directly to renderer. The user can move the color bar now.
* The height of color bar is now sensitive to the top right annotations.
When top right is deactive the height would be almost 100%
* Replaced the hard-coded UI with Qt Designer UI file.
* Fixed the vtk warning:
                   vtkTextActor::SetInput was passed an uninitialized
		   string
* Fixed issues with user settings
* An option added to have persistent background layer dicom annotation.
* Restore default values for all of the default settings was added.

ENH: Modified the logic to use dicom tag cache and the following fixes:

* Added dialog box for notifying slicer users about the new slice
 annotation feature
* Made Color Scalar bar off in default mode
* Code refactored in creating lines for ruler and other minor bugs fixed

From: Alireza Mehrtash <mehrtash@bwh.harvard.edu>

Revision 23527 - Directory Listing
Modified Thu Jul 31 20:53:12 2014 UTC (3 years, 2 months ago) by pinter
BUG: Fix update issues in subject hierarchy when module active

Subject hierarchy tree was not properly updated when reparenting programatically or importing/restoring scene when module was active. This has been fixed and some unnecessary code removed.
More testing added to SubjectHierarchyGenericSelfTest.

Revision 23506 - Directory Listing
Modified Tue Jul 29 23:59:34 2014 UTC (3 years, 2 months ago) by jcfr
ENH: Added developer mode and base classes for scripted modules

* Added "Enable developer mode" option in the application settings
(Developer section, next to Enable QtTesting)

* Added base classes for scripted module, widget, logic, and test: they
make scripted modules simpler and shorter and also more functions and
helper methods can be added in the future without changing each scripted
module
** Module handles selftest registration
** Widget handles reload&test (shown on GUI only in developer mode)
** Logic and Test contains delayDisplay utility function

* As an example, updated ScriptedLoadableModuleTemplate and SurfaceToolbox to use the new base classes

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 23505 - Directory Listing
Modified Tue Jul 29 23:43:49 2014 UTC (3 years, 2 months ago) by pinter
BUG: Fixed SubjectHierarchyGenericSelfTest
Fixes #3754

Additional minor fixes in handling potential nodes in the subject hierarchy tree (removed unavailable context menu items)
Removed potential subject hierarchy node list and related classes (model, proxy model, designer plugin)

Revision 23385 - Directory Listing
Modified Thu Jun 26 22:08:51 2014 UTC (3 years, 3 months ago) by inorton
BUG: set main app shortcut context to allow unambiguous QActions handlers in child widgets

Revision 23358 - Directory Listing
Modified Sun Jun 22 15:44:02 2014 UTC (3 years, 3 months ago) by jcfr
COMP: Fix "RCC No resources warning" by removing empty resource files.

Revision 23323 - Directory Listing
Modified Mon Jun 9 22:35:07 2014 UTC (3 years, 4 months ago) by mwoehlke
COMP: Don't specify themed icons in .ui file

Remove specification of themed icons from qSlicerAppMainWindow.ui, as
this requires Qt 4.8 (and apparently uic gets really grumpy about
attributes it doesn't recognize, rather than just ignoring them). For
now, we set them in qSlicerAppMainWindow.cxx instead.

See also r23322.

Revision 23322 - Directory Listing
Modified Mon Jun 9 19:18:24 2014 UTC (3 years, 4 months ago) by mwoehlke
ENH: Clean up icon usage

Create new "XSmall" icon size for 16x16 icons, enabling us to provide
separate 16x16 (e.g. menu) and 22x22 (e.g. tool bar) icon sizes. Replace
ugly undo/redo icons with icons from the (public domain) Tango[1] theme.
Replace home icon with its Tango version for better consistency. Create
a script to generate qSlicerBaseQTGUI.qrc, as manually adding as many as
five entries per new icon is unnecessarily awkward. Arrange to use
themed icons when possible.

(1: http://tango.freedesktop.org/Tango_Icon_Library)

Revision 23305 - Directory Listing
Modified Wed Jun 4 18:42:43 2014 UTC (3 years, 4 months ago) by jcfr
ENH: Add Multi-sampling option

This commits leverage the functionality already added in CTK [1] by
adding "Views" settings panel allowing to enable/disable
anti-aliasing.

[1] https://github.com/commontk/CTK/commit/b39d95edd9be0965a85bcd9fbc12bb64edb9041a

From: Eric Larson <larson.eric.d@gmail.com>

Revision 23303 - Directory Listing
Modified Tue Jun 3 21:20:56 2014 UTC (3 years, 4 months ago) by mwoehlke
BUG: Don't nuke external settings changes

Update CTK to include recently added ctkSettingsDialog::reloadSettings
method. Use this to force a reload of settings prior to showing the
settings dialog. This is required in order for the dialog to show
changes that have been made externally (e.g. by installing extensions)
and, more importantly, to avoid overwriting the same when closing (even
canceling!) the dialog.

Issue #3658

Revision 23256 - Directory Listing
Modified Wed May 28 22:04:19 2014 UTC (3 years, 4 months ago) by jcfr
BUG: Update CTK - Fix "No such slot" warning and optimize ctkVTKConnection

* Fixes #3361: Fix "No such slot" warning and optimize ctkVTKConnection

* Fixes #3719: py_SubjectHierarchyGenericSelfTest passes but it output warning about slot disconnection

* Improve performance of ctkVTKConnection creation/removal

* Add Qt5 support to CTK

* Thanks to Eric Larson. ctkAbstractView now provides a method allowing to
set multisampling.

* Since ctkErrorLogModel has been moved from CTKCore to CTKWidget (because
QStandardItemModel belongs to QtGUI), similarly the error log model has
been moved from qSlicerCoreApplication to qSlicerApplication.

Details:

$ git shortlog daaf705c..6f2c55809 --no-merges
Eric Larson (1):
      Added static method to set multisampling.

Jean-Christophe Fillion-Robin (18):
      Fix compilation of tests against VTK6
      Fix qDebug operator to handle case when VTKObject is null
      Improve documentation of setStrictTypeCheck() method
      Remove unused signal "isBroke()"
      Refactor ctkVTKConnectionTest1 for easier maintenance and readability
      Update ctkVTKConnectionTest1 to use ctkCallback
      Update ctkVTKConnectionTest1 to allow each test case to be run independently
      Split disconnect function
      Allow ctkVTKConnection pimpl to be subclassed
      Add method to return VTK object associated with ctkVTKConnection
      Add ctkVTKConnectionTestObjectDelete
      Fix ctkVTKConnectionTestObjectDelete
      Improve performance disabling "deletion" observation
      Fix ctkVTKConnectionTest1 removing connection time ratio test
      ENH: Pass Qt CMake variable using "mark_as_superbuild"
      Fixes configuration when enabling PythonQt wrapping
      Remove extra CMake debug statement introduced by commit 47b34216
      Update CTKWidget PythonQt decorator to fix build error following Qt5 transition

Julien Finet (1):
      Add support for Qt5

Matthew Woehlke (1):
      Allow compiling/installing generated Python files

Sascha Zelzer (8):
      First set of build system patches for Qt5 support.
      This commit enables Qt5 support for the CTK Core library, issue #277.
      Use Qt5 CMake 2.8.12 features.
      Qt5 compatibility for almost all libraries.
      Do not assume a specific Qt5 install structure.
      Make more libs and apps compatible with Qt5.
      Use Qt5 compatible qRestAPI version.
      Fix Qt5 dependencies in case only CTK_BUILD_ALL is enabled.

Revision 23255 - Directory Listing
Modified Wed May 28 17:59:07 2014 UTC (3 years, 4 months ago) by jcfr
BUG: Update SubjectHierarchyGenericSelfTestTest to support VTK6. Fixes #3720

In both VTK 5 and 6 cases, the pipeline is connected and the
explicit call to "Update()" is not required.

Revision 23244 - Directory Listing
Modified Tue May 27 21:45:06 2014 UTC (3 years, 4 months ago) by jcfr
BUG: Fixed subject hierarchy core plugins self test

Which failed due to renaming of GetAssociatedDataNode to GetAssociatedNode in
vtkMRMLSubjectHierarchyNode. It has been renamed, because by making
vtkMRMLHierarchyNode::GetAssociatedNode virtual, it became possible to override
it in subject hierarchy so that it can handle nested associations.

From: Csaba Pinter <csaba.pinter@queensu.ca>

Revision 23241 - Directory Listing
Modified Tue May 27 21:44:51 2014 UTC (3 years, 4 months ago) by jcfr
ENH: Subject hierarchy python tests moved to SlicerApp

As the subject hierarchy tests cover multiple modules, they have been moved
from the SubjectHierarchy folder to Applications/SlicerApp/Testing/Python;
Occasional SlicerRT strings removed/replaced in subject hierarchy code
(mostly include dir comments)

From: Csaba Pinter <csaba.pinter@queensu.ca>

Revision 23165 - Directory Listing
Modified Tue May 13 17:42:40 2014 UTC (3 years, 5 months ago) by mwoehlke
STYLE: Remove non-existing qrc reference

Remove odd relative path reference to a .qrc file in a ".designer"
directory, that is not part of the repository and likely does not exist
on most machines.

Revision 23077 - Directory Listing
Modified Fri Apr 11 04:10:41 2014 UTC (3 years, 6 months ago) by jcfr
ENH: Remove ITKv3 support

As discussed on the mailing list [1] and reported on the Roadmap [2],
this commit removes all conditional code that was allowing Slicer4 to be
compiled against ITKv3.

Code that was building only against ITKv3 has also been removed. This
includes DicomToNrrdConverter CLI module
and SlicerITKv3N4MRIBiasFieldCorrectionImageFilter class.

[1] http://slicer-devel.65872.n3.nabble.com/Removal-of-ITKv3-support-tt4031364.html

[2] http://wiki.slicer.org/slicerWiki/index.php/Roadmap#Deprecation_.2F_API_Changes

Revision 23058 - Directory Listing
Modified Tue Apr 8 17:41:15 2014 UTC (3 years, 6 months ago) by jcfr
ENH: Associate a component with install rules

Revision 23037 - Directory Listing
Modified Tue Apr 1 23:13:50 2014 UTC (3 years, 6 months ago) by mwoehlke
BUG: Fix creation of launcher configuration

Remove hack to delete the launcher configuration as part of the build.
The launcher CMake helpers should now be producing correct dependency
information such that the hack is unnecessary, and the dependencies for
the hack were not set up correctly, causing ninja builds to fail to
recreate the configuration on alternating runs (which would prevent
slicer from running).

Revision 23036 - Directory Listing
Modified Tue Apr 1 23:13:49 2014 UTC (3 years, 6 months ago) by mwoehlke
BUG: Fix/improve launcher path setup

Take advantage of recent changes in the CTK AppLauncher to use the list
form of setting up additional environment path lists. Particularly, we
now declare as path lists those environment variables that are (i.e.
QT_PLUGIN_PATH, PYTHONPATH) so that we no longer lose the user's paths
that have been set in these.

Revision 23030 - Directory Listing
Modified Tue Apr 1 07:51:04 2014 UTC (3 years, 6 months ago) by jcfr
ENH: Update windows launcher with Slicer icon.

Thanks to the convenience executable "CTKResEdit" allowing to update
resources of any executables or libraries, on windows, the CTK application
launcher is updated with the Slicer icon.

Fixes #1136

Revision 23021 - Directory Listing
Modified Wed Mar 26 17:45:15 2014 UTC (3 years, 6 months ago) by hjohnson
STYLE: Remove end of line spaces

Spaces at the end of lines can cause noise in patch sets
when editors or git gobbles them up during other relatively
minor changes to files.

Removing end of line changes makes long term maintenance easier as
well.

When reviewing git histories or patch sets, the "--ignore-space-change"
option can be useful in filtering out changes due only to spacing.

i.e.
git diff HEAD~2 --ignore-space-change

Revision 22870 - Directory Listing
Modified Tue Feb 11 16:51:38 2014 UTC (3 years, 8 months ago) by jcfr
COMP: Adding support for Apple's Retina display for fonts

Enable improved rendering of fonts on Apple's retina displays by
adding a custom bundle plist file with the following additional
elements:

<key>NSPrincipalClass</key>
<string>NSApplication</string>
<key>NSHighResolutionCapable</key>
<string>True</string>

The remainder of the input plist file is based on the current in file
from CMake.

For reference: https://blog.qt.digia.com/blog/2013/04/25/retina-display-support-for-mac-os-ios-and-x11/

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Bradley Lowekamp <blowekamp@mail.nih.gov>

Revision 22851 - Directory Listing
Modified Mon Jan 27 14:29:54 2014 UTC (3 years, 8 months ago) by jcfr
ENH: slicer.util - Add convenience method "modulePath(moduleName)"

Revision 22850 - Directory Listing
Modified Fri Jan 24 09:03:31 2014 UTC (3 years, 8 months ago) by jcfr
BUG: Fix "Reload and Test" function

While commit r22839 re-factored the code associated with "Reload" function,
it also made the "Reload and Test" function fails.

This commit fixes the issue by setting the "<moduleName>" key into
the global dictionary of the reloaded module so that it can be
referenced in the "onReloadAndTest()" function.

Note that the overall approach to reload modules could be revisited to
leverage either the "rollback importer" method or a more sophisticated one
like the "python-reloader" [2][3]

Thanks to "Csaba Pinter <csaba.pinter@queensu.ca>" for reporting the issue.

[1] http://pyunit.sourceforge.net/notes/reloading.html
[2] http://www.indelible.org/ink/python-reloading/
[3] https://github.com/jparise/python-reloader

Revision 22839 - Directory Listing
Modified Sun Jan 19 07:59:22 2014 UTC (3 years, 8 months ago) by jcfr
ENH: Factor out scripted module reload function into 'slicer.util'

At least two versions of the code were used to reload a scripted module
were existing. This commit add the most recent version into
the function 'slicer.util.reloadScriptedModule' and update the
Slicer modules to use it.

Note that since not all module implements the 'cleanup' function,
an additional test has been added to check if the method is available.

Revision 22793 - Directory Listing
Modified Fri Jan 3 19:05:19 2014 UTC (3 years, 9 months ago) by pieper
COMP: handle case where TCL is disabled but EM is set to ON.

If you have first configured with TCL on, then EMSegment is on
by default too.  But turning off TCL does not turn off EMSegment,
so the linker was failing to find the EMSegment logic library.

This patch is consistent with the rest of the logic in the
CMakeLists, but longer term EMSegment should be explicitly
disabled if it doesn't have the right prerequisites.

Revision 22763 - Directory Listing
Modified Wed Dec 4 22:26:21 2013 UTC (3 years, 10 months ago) by jcfr
ENH: Consolidate qSlicerAppMainWindow

qSlicerAppMainWindowCore brings confusion to the code. It is now merged
with qSlicerAppMainWindow.
The custom macro is replaced by the automatic signal/slot connection of Qt
i.e. on_<SENDER_NAME>_<SENDER_SIGNAL>())
The objects had to be renamed to support the feature.

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Julien Finet <julien.finet@kitware.com>

Revision 22759 - Directory Listing
Modified Tue Dec 3 23:03:32 2013 UTC (3 years, 10 months ago) by jcfr
COMP: Remove unnecessary includes in vtkMRMLAbstractLogic header

This has the side effect of having a faster compilation

External module OpenIGTLinkIF and MultiVolumeExplorer have already been
updated according to change in vtkMRMLAbstractLogic header.
See #3493 / r22712  and  #3494 / r22693

On the other hand, no test build have been done for the extension. Issue
will be resolved on case by case following the dashboard results.

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Julien <julien.finet@kitware.com>

Revision 22742 - Directory Listing
Modified Tue Nov 26 22:25:00 2013 UTC (3 years, 10 months ago) by naucoin
ENH: update RSNA Vis tutorial for 2013

Ported changes from 4.3.1:
Rename to more generic test name as updating the tutorial for RSNA 2013
Use new data sets from Sonia.
Add screen shot GUI elements and flags and method, capture screen shots at tutorial steps.
Added the volume rendering in part 1.
Tweaked all parts to match up to tutorial.

Updated test to work with new DICOM widget on the trunk.

Issue #3507



Revision 22741 - Directory Listing
Modified Tue Nov 26 16:34:28 2013 UTC (3 years, 10 months ago) by naucoin
ENH: Updating RSNA Quant tutorial for 2013

Rename to more generic test name so it's not tied to a year.
Use new data sets from Sonia
Add screen shot GUI elements and flags and method, capture screen shots at tutorial steps.
Tweaked all parts to match up to tutorial (first part was already tested
in the Vis tutorial, swapped it out for the Ruler)
Updated CMakeLists.txt so that this commit is independent of the Vis tutorial commit.

Issue #3507

Revision 22689 - Directory Listing
Modified Thu Nov 7 16:54:34 2013 UTC (3 years, 11 months ago) by pieper
ENH: dicom header viewer added to DICOMLib using ctkDICOMObjectListWidget

ENH: update DICOM module for Table View

New interface to support better searching and header display.

Now plugins are selectable to avoid wasting time on unneeded plugins.

Plugins are now evaluated on-demand, to simplify the workflow.

http://www.commontk.org/index.php/CTK-Hackfest-May-2013#DICOM_Database_and_Networking

https://github.com/commontk/CTK/pull/361

ENH: update to latest CTK for header widget

Also fix lingering rebase issue (stray variable).

BUG: Give header popup independent geometry setting

Also fix incorrect end of line character

ENH: examine button diabled until needed

STYLE: remove tabs in code

Revision 22676 - Directory Listing
Modified Sun Nov 3 23:07:48 2013 UTC (3 years, 11 months ago) by jcfr
STYLE: Avoid confusion renaming SceneView API: "Nodes" into "StoredScene"

The following renaming have been done:
 - ivar Nodes -> StoredScene
 - method "UpdateSnapshotScene" -> "UpdateStoredScene"
 - method "GetNodes" -> "GetStoredScene"

Also remove the unused parameter from "UpdateStoredScene"

Revision 22659 - Directory Listing
Modified Wed Oct 30 20:25:31 2013 UTC (3 years, 11 months ago) by naucoin
BUG: update link to LiverData.mrb

Fixed the scene file to show the model hierarchies and uploaded
a new mrb file to midas at 
http://slicer.kitware.com/midas3/download?items=117033

Issue #3469



Revision 22657 - Directory Listing
Modified Wed Oct 30 16:59:30 2013 UTC (3 years, 11 months ago) by jcfr
COMP: Fix MacOSX build issue when building against Qt 4.7.4. Fixes #3471

Since "QSysInfo::MV_10_8" has been first introduced in Qt 4.8.3,
exclude the fix for issue #3460 introduced in commit r22641.

Revision 22641 - Directory Listing
Modified Fri Oct 25 21:52:07 2013 UTC (3 years, 11 months ago) by jcfr
BUG: Attempt to fix font issue related to webkit performance on MacOSX 10.9

Associated message in the system log:
CoreText performance note: Client called CTFontCreateWithName() using name "Lucida Grande" and got font with PostScript name "LucidaGrande". For best performance, only use PostScript names when calling this API.

See https://bugreports.qt-project.org/browse/QTBUG-32789 and
http://successfulsoftware.net/2013/10/23/fixing-qt-4-for-mac-os-x-10-9-mavericks/

Fixes #3460

Revision 22587 - Directory Listing
Modified Thu Oct 3 20:29:15 2013 UTC (4 years ago) by naucoin
BUG: adding a test to show layout switch bug

Fiducial display positions aren't updated correctly
on linux according to bug 1914. This test illustrates this in a
non failing test way so that cross platform behaviour can be
determined.

Issue #1914


Revision 22570 - Directory Listing
Modified Thu Oct 3 02:34:11 2013 UTC (4 years ago) by jcfr
BUG: Prevent leaks when factory methods are used from python

There is currently no automatic/clean mechanism to release the object
created by factory methods.

The only "hack" that exists for now is to decrease the reference
count manually in your code:

For more details, see [1], [2], [3] and [4]

[1] http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/MemoryManagement
[2] http://massmail.spl.harvard.edu/public-archives/slicer-devel/2011/007513.html
[3] http://www.vtk.org/Bug/view.php?id=12139
[4] http://www.vtk.org/pipermail/vtk-developers/2011-April/009757.html

Revision 22531 - Directory Listing
Modified Tue Oct 1 00:16:35 2013 UTC (4 years ago) by fedorov
ENH: adding 3x3 layout

see issue 2384


Revision 22426 - Directory Listing
Modified Wed Sep 11 22:18:00 2013 UTC (4 years, 1 month ago) by jcfr
BUG: Add close button to "About dialog". Fixes #3172

Revision 22407 - Directory Listing
Modified Wed Sep 4 10:48:34 2013 UTC (4 years, 1 month ago) by jcfr
ENH: Update Documentation to 4.3

Revision 22397 - Directory Listing
Modified Tue Sep 3 22:24:08 2013 UTC (4 years, 1 month ago) by jcfr
BUG: Fixes py_NeurosurgicalPlanningTutorial test

Beside of memory leak and error related to the glyphing pipeline (captured
by issue #3349).
The script can be successfully replayed within Slicer or if executed
using CTest with a Slicer build without leak detection.

// ---------------------------
Errors:

565: ERROR: In /home/jchris/Projects/Slicer-AHM-Superbuild-Release/VTK/Filtering/vtkDemandDrivenPipeline.cxx, line 727
565: vtkStreamingDemandDrivenPipeline (0x957b600): Input port 0 of algorithm vtkExtractSelectedPolyDataIds(0x957b370) has 0 connections but is not optional.
565:
565:
565: ERROR: In /home/jchris/Projects/Slicer-AHM/Libs/vtkTeem/vtkDiffusionTensorGlyph.cxx, line 222
565: vtkDiffusionTensorGlyph (0xcd1db10): No data to glyph!
// ---------------------------

// ---------------------------
Leaks:

565: vtkDebugLeaks has detected LEAKS!
565: Class "vtkSynchronizedTemplatesCutter3D" has 21 instances still around.
565: Class "vtkTransformPolyDataFilter" has 21 instances still around.
565: Class "vtkInformationVector" has 441 instances still around.
565: Class "vtkMatrix4x4" has 42 instances still around.
565: Class "vtkCoordinate" has 42 instances still around.
565: Class "vtkPlane" has 21 instances still around.
565: Class "vtkInformation" has 525 instances still around.
565: Class "vtkSynchronizedTemplates3D" has 21 instances still around.
565: Class "vtkActor2D" has 21 instances still around.
565: Class "vtkRectilinearSynchronizedTemplates" has 21 instances still around.
565: Class "vtkDoubleArray" has 105 instances still around.
565: Class "vtkAlgorithmOutput" has 21 instances still around.
565: Class "vtkInformationIntegerValue" has 378 instances still around.
565: Class "vtkOpenGLPolyDataMapper2D" has 21 instances still around.
565: Class "vtkGridSynchronizedTemplates3D" has 21 instances still around.
565: Class "vtkCutter" has 21 instances still around.
565: Class "vtkInformationExecutivePortVectorValue" has 21 instances still around.
565: Class "vtkContourValues" has 105 instances still around.
565: Class "vtkTransform" has 21 instances still around.
565: Class "vtkStreamingDemandDrivenPipeline" has 42 instances still around.
565: Class "vtkTimerLog" has 21 instances still around.
565: Class "vtkInformationExecutivePortValue" has 21 instances still around.

// ---------------------------

Fixes #2808

Co-authored-by: Jean-Christophe Fillion-Robin <JChris.FillionR@kitware.com>

From: Chrystel Juan <chrystel.juan@kitware.com>

Revision 22388 - Directory Listing
Modified Tue Sep 3 04:04:53 2013 UTC (4 years, 1 month ago) by jcfr
BUG: Remove DTI tutorial until pipeline for glyphing is fixed.

See r22363 [1], issue #3323 [2] and issue #2808 [3]

[1] http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22363
[2] http://www.na-mic.org/Bug/view.php?id=3323
[2] http://www.na-mic.org/Bug/view.php?id=2808

Co-authored-by: Chrystel Juan <chrystel.juan@kitware.com>

Revision 22386 - Directory Listing
Modified Tue Sep 3 03:10:31 2013 UTC (4 years, 1 month ago) by jcfr
ENH: Associate icon with the new Slice view layouts

This is a follow-up of previous commit r22385

See #2384

From: Andrey Fedorov <fedorov@bwh.harvard.edu>

Revision 22385 - Directory Listing
Modified Mon Sep 2 21:57:29 2013 UTC (4 years, 1 month ago) by jcfr
ENH: Adding three new layouts

Slice view only configurations added: 4x3, 4x2, 5x2.

See #2384

From: Andrey Fedorov <fedorov@bwh.harvard.edu>

Revision 22377 - Directory Listing
Modified Sat Aug 31 05:25:08 2013 UTC (4 years, 1 month ago) by jcfr
ENH: In Recently loaded menu, rename "Clear Menu" into "Clear History"

See #1669

Revision 22373 - Directory Listing
Modified Fri Aug 30 22:33:45 2013 UTC (4 years, 1 month ago) by jcfr
BUG: Apply "ShowToolButtonText" settings to mainwindows on restart

While the slot qSlicerSettingsStylesPanel::onShowToolButtonTextToggled()
is properly called when the settings is registered at startup, it failed
to disable/enable the toolButton property because the mainwindow is not
instantiated.

This commit ensure this is the case in the main windows readSettings()
function.

Fixes #2164

Revision 22367 - Directory Listing
Modified Fri Aug 30 04:18:52 2013 UTC (4 years, 1 month ago) by jcfr
ENH: Add python interpreter to the "Dialog" toolbar

Revision 22345 - Directory Listing
Modified Wed Aug 28 03:48:39 2013 UTC (4 years, 1 month ago) by jcfr
BUG: Hide initialization info when running Slicer as python interpreter.

Add method "qSlicerCoreCommandOptions::verbos" currently returning false
only  if slicer runs a python script directly passed as a command line
argument.

Later on, the system could be extended so that all initialization
information are hidden by default. They would be displayed
only if --verbose is explicitly passed.

Fixes #3285

Revision 22307 - Directory Listing
Modified Thu Aug 22 04:47:58 2013 UTC (4 years, 1 month ago) by jcfr
BUG: Ensure ErrorLog/PythonConsole menu entry bring dialog to foreground

This commit partly revert commit r19500 making sure the errorLog and
pythonconsole menu entry are non-checkable. It means that if one of the
dialog is already shown but in the background, selecting the menu entry
will bring the dialog to the foreground instead of hiding it.

Also simplify who the errorLog button interact with its associated
ErrorLog dialog by simply associated the corresponding QAction.

Note also that the QAction icon is the one that is now
highlighted/unhighlighted based on the addition of new
warning/error/cricial messages. The icon is now updated both
in the bottom right corner (Error log button) and in the menu entries.

See issue #1349

Revision 22305 - Directory Listing
Modified Wed Aug 21 20:15:20 2013 UTC (4 years, 1 month ago) by jcfr
STYLE: Simplify error log widget eventFilter

Instead of creating a specific event filter class "qSlicerErrorLogWidgetEventFilter",
re-use the already installed eventFilter associated with the main window.
See "qSlicerAppMainWindow::eventFilter"

See issue #1349

Co-authored-by: Julien Finet <julien.finet@kitware.com>

Revision 22304 - Directory Listing
Modified Tue Aug 20 23:27:13 2013 UTC (4 years, 1 month ago) by jcfr
BUG: Add error log button to mainwindow

Each time a Warning/Error/Fatal message is logged, the tool button
associated with the error icon is highlighted.

If the user either

 (1) click on the button

or

 (2) focus on the error log widget in case it was already visible, the
 icon associated with the tool button is "un-highlighted".

Fixes #1349
Fixes #2537

Revision 22295 - Directory Listing
Modified Mon Aug 19 15:35:16 2013 UTC (4 years, 2 months ago) by jcfr
BUG: Associate "--cmd" with installed launcher on windows

To start a console with the Slicer environement, from an installed tree,
instead of doing:

  .\Slicer.exe --launch "C:/Windows/System32/cmd.exe" /c start cmd

user will be able to simply do:

  .\Slicer.exe --cmd

Fixes #2917

Revision 22261 - Directory Listing
Modified Tue Aug 6 16:39:56 2013 UTC (4 years, 2 months ago) by jcfr
BUG: Name SampleData internal widget for easy referencing by QtTesting

See #2808

Revision 22240 - Directory Listing
Modified Fri Jul 26 20:58:44 2013 UTC (4 years, 2 months ago) by johan.andruejol
BUG: Ensure qSlicerStyle is used when using SlicerApp-Real

When the launcher isn't used, for example when using SlicerApp-Real
directly, the plugin library cannot be found before the qSlicerApplication
is created. (QT_PLUGIN_PATH isn't set).

However once the application is started, the current location of the
executable is automaticaly added to the application library paths by Qt.

See Qt-doc: http://qt-project.org/doc/qt-4.7/qcoreapplication.html#id-a4ff2599-e40c-4218-82e7-14e570ebf822
"The directory of the application executable (NOT the working directory) is always added (...)"

Since this also corresponds to the location that needs to be set for the
plugins, the styles are automaticaly discovered.

See also the discussion:
http://massmail.spl.harvard.edu/public-archives/slicer-devel/2013/013320.html

Fixes #3252

Revision 22235 - Directory Listing
Modified Thu Jul 25 20:33:00 2013 UTC (4 years, 2 months ago) by johan.andruejol
ENH: Custom style for slicer

Allow the slicer to use custom styles. This rests on the Qt style plugin
framework. The style plugins must be compiled with the same Qt as slicer,
in the same mode (debug, release...) and in shared library mode.
To facilitate the creation of new plugins, a cmake macro was added to
slicer cmake directory.
Every slicer style must inherits from qSlicerStyle. They are not detected
by the application otherwise.

The new styles can be set like modules. A setting page is added for them
where user can specify the directory containing his plugin. The additionnal
paths and the style key are added as settings. This means that the next
time slicer's session is opened, the application will automatically load
the custom style if it still exists.
Adding or removing paths necessit the application to be restarted. This
comes from the fact that the QStyleFactory is only updated upon its
creation which only happens when starting the application.
Changing the style however doesn't need to restart the application.
At this occasion, a Slicer dark style was added to the list of available
styles.

On the implementation side, the designer plugin export definition was
shortened and includes the "DESIGNER" term so it is different than the
style export macro.

Finaly, adding a fix to the slice controller widget label style so
it can work with the new dark style.

Revision 22209 - Directory Listing
Modified Thu Jul 18 13:22:56 2013 UTC (4 years, 3 months ago) by finetjul
BUG: "Add data" shortcut is CTRL+O or CTRL+A, and not "CTRL+O + CTRL+A"

Closes #1819

Revision 22208 - Directory Listing
Modified Wed Jul 17 23:44:48 2013 UTC (4 years, 3 months ago) by finetjul
ENH: Cleanup shortcuts(actions) dialog

Closes #1819

Revision 22202 - Directory Listing
Modified Tue Jul 16 19:54:42 2013 UTC (4 years, 3 months ago) by millerjv
BUG: #2739: Add configuration of two slice viewers

Added layout with just two slice viewers arranged side by side

Revision 22184 - Directory Listing
Modified Sat Jul 13 08:30:18 2013 UTC (4 years, 3 months ago) by jcfr
BUG: Fix TranslatorPlayer tests to account for ctkSpinBox renaming

Commit r22128 updated CTK to propagate renaming of ctkSpinBox
into ctkDoubleSpinBox, this commit also fixes the test that were
using ctkSpinBox.

Revision 22175 - Directory Listing
Modified Sat Jul 13 04:17:13 2013 UTC (4 years, 3 months ago) by jcfr
ENH: Add toolbar for the Extensions Manager and Error log

Fixes #3151

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Chrystel Juan <chrystel.juan@kitware.com>

Revision 22139 - Directory Listing
Modified Thu Jul 4 22:20:40 2013 UTC (4 years, 3 months ago) by finetjul
ENH: Disable scrolling everywhere there is an active scrollarea

Don't do it only for comboboxes.
Closes #1820, #1462

Revision 22080 - Directory Listing
Modified Wed Jun 5 20:42:50 2013 UTC (4 years, 4 months ago) by pieper
BUG: try to fix test failures on some platforms

This test was failing on the windows factory machines but not
on non-windows.  Possibly this is due to the window size or another related
variable causing the painting to happen outside the visible
region of the MR in the slice view.  This change makes sure the clicks
occur near the center of the slice view so as to avoid the
boundary case.

Revision 22075 - Directory Listing
Modified Tue Jun 4 19:31:29 2013 UTC (4 years, 4 months ago) by johan.andruejol
BUG: Fix MRMLScene import and export

In the selection node, the unit didn't add a
NodeReferenceMRMLAttributeNames for each of its reference role. These
attributes are used when saving the mrml scene to describe what the
reference role is used for. Most notably, this can be used when importing
a scene.
However, since there wasn't any defined for the selection node, a saved
scene would look like this:
 ... selected="false" ="vtkMRMLUnitNodeApplicationLength" "vtkMRMLUnitNodeApplicationTime" activeVolumeID="NULL" ...
Which is an invalid format for the scene.

Adding a NodeReferenceMRMLAttributeNames is usually done in the class
constructor. In our case, we assume that we don't know what kind of unit
quantity can be added. Thus we don't know the ReferenceRoles we will need
at constructor time. So we add theses roles in the SetUnitNodeID().
The roles names are based on the quantity, and aren't actually used
anywhere.

To make sure this works, a test opening Slicer, saving a scene and loading
it again is added.

See Issue #3145

Revision 22023 - Directory Listing
Modified Fri May 17 22:05:19 2013 UTC (4 years, 5 months ago) by jcfr
BUG: Ensure library can be loaded from different place using @rpath

Before this commit, attempt have been made (r18311, r18325, r18581) to
install both built-in CLI and extension CLI executable in a folder
located at some depth of the main Slicer executable. This was needed
because all libraries were referenced based on the location of the main
Slicer executable using "@executable_path". This was working *only* in the
case of built-in CLI but wasn't scaling very well for the extension CLI
executable. Indeed, being able to both differentiate the different
installed extension and keeping the depth to 1 level wasn't easily
feasible:

  /path/to/Slicer.app/Contents/MacOS/Slicer
  /path/to/Slicer.app/Contents/cli-modules/MyCLI
  /path/to/Slicer.app/Contents/Extensions-21855/SkullStripper/cli-modules/MyCLI

A solution could have been to install extensions directly in "Slicer.app"
folder and update the cli install sub dir to get something like:

  /path/to/Slicer.app/Extensions-21855/SkullStripper/MyCLI

While possible, it would have remain a special case to maintain.

Instead, by using "@rpath", CLI modules can now be installed in the Slicer
standard location "Slicer_CLIMODULES_LIB_DIR" instead of "Slicer_CLIMODULES_SUBDIR".
This commit remove the special case which never worked (issue #3051)

Waiting the topic "tweak-bundleutilities-for-rpath" is fully matured and
integrated in CMake, use custom version of BundleUtilities and GetPrerequisites.
See http://cmake.org/gitweb?p=stage/cmake.git;a=shortlog;h=refs/heads/tweak-bundleutilities-for-rpath

Since our custom version of the CMake modules now consider "~/usr/.*/lib",
the implementation of "gp_resolved_file_type_override" has been removed.

Remove the hack specific to LibArchive (introduced by commit r19615), since
the library is fixed up using the default library matching pattern, it
will be installed in the expected location.

SlicerExecutionModel has also been updated to link the CLI executable
and library with "-rpath" so that they can resolve the location of Slicer
libraries.

Revision 22003 - Directory Listing
Modified Thu May 16 04:41:10 2013 UTC (4 years, 5 months ago) by jcfr
COMP: Fix DiffusionTensorImagingTutorial

The XML file has been updated to account for the changes
added by previous updated related to introduction of
ctkSpinBox (r21902) and Editor layout re-organization.

Revision 21980 - Directory Listing
Modified Sat May 11 17:09:13 2013 UTC (4 years, 5 months ago) by hjohnson
ENH: Add MGH test suite for reading/writing.

Revision 21967 - Directory Listing
Modified Tue May 7 12:51:51 2013 UTC (4 years, 5 months ago) by pieper
BUG: disable the ChangeTracker test when the module is not available

ChangeTracker is now an extension, so it won't typically be
available when tests are being run.

Revision 21948 - Directory Listing
Modified Fri Apr 26 22:17:12 2013 UTC (4 years, 5 months ago) by jcfr
COMP: Fix config error introduced in r21943 by using PYTHON_LIBRARY_PATH

See issue #1180 - http://www.na-mic.org/Bug/view.php?id=1180

Revision 21943 - Directory Listing
Modified Fri Apr 26 21:19:08 2013 UTC (4 years, 5 months ago) by jcfr
BUG: Fix startup crash due to improper dynamic linking of python dll

This problem affect the a windows build tree of Slicer.

On windows, as explained in [1], system path are searched before path
appended to PATH variable.

[1] Title: Search Path Used by Windows to Locate a DLL
    Link:  http://msdn.microsoft.com/en-us/library/7d83bc18(v=vs.90).aspx

Following the introduction of CMake'ified python (r21863), python 2.7.3 is
now used. Since developer also have a similar version installed on their
system, this is causing Slicer to crash due to binary incompatibility
between the patched version build by Slicer (r21848) and the one
installed on the system.

While this commit address the immediate issue specific to python, the same
problem would occur with VTK, Qt, ITK or any other Slicer external projects
is already installed in the system. The solution implemented by this commit
will have to be revisited.

See http://www.na-mic.org/Bug/view.php?id=1180
Fixes #1180

Revision 21870 - Directory Listing
Modified Fri Apr 5 17:48:44 2013 UTC (4 years, 6 months ago) by pieper
BUG: fix paths for DICOM executable searches

Since the helper executables are not in the slicer bin directory
for a local build of slicer, be sure to also check in the DCMTK-build
bin directory to find the actual executable.

Revision 21865 - Directory Listing
Modified Fri Apr 5 03:20:20 2013 UTC (4 years, 6 months ago) by jcfr
COMP: Do not include or use i18n macros if Slicer_BUILD_I18N_SUPPORT is OFF

Commit r21856 disabled internationalization support by default and
it introduced the option Slicer_BUILD_I18N_SUPPORT allowing to enable it.

This commit takes care of excluding the associated CMake macro and its
invocation if the option is disabled.

Revision 21844 - Directory Listing
Modified Wed Mar 27 22:35:14 2013 UTC (4 years, 6 months ago) by nicky
ENH: Add JRC2013 visualization tutorial test script

Revision 21798 - Directory Listing
Modified Tue Mar 12 11:20:21 2013 UTC (4 years, 7 months ago) by jcfr
STYLE: Fix typo and remove "Qt" from message associated with slicerMacroBuildQtModule

Revision 21797 - Directory Listing
Modified Tue Mar 12 11:20:19 2013 UTC (4 years, 7 months ago) by jcfr
ENH: Add python unitTest testing slicer.util.{saveNode, saveScene} methods

Revision 21795 - Directory Listing
Modified Tue Mar 12 11:20:14 2013 UTC (4 years, 7 months ago) by jcfr
ENH: Clean code and add command line option "--temporary-path"

Remove unused headers

Remove tempDirectory initially added with r11985,
qSlicerCoreApplication::temporaryPath  (added with r15424) should be used
instead.

Calling slicer with both --testing and --temporary-path options returns
the directory associated with testing.

$ ./Slicer --temporary-path
/tmp/Slicer

$ ./Slicer --testing --temporary-path
/tmp/Slicer-tmp

Revision 21781 - Directory Listing
Modified Thu Feb 28 00:14:41 2013 UTC (4 years, 7 months ago) by pieper
ENH: Added one-up quantitative layout
Closes #2969

Revision 21720 - Directory Listing
Modified Sat Feb 16 02:38:18 2013 UTC (4 years, 8 months ago) by jcfr
STYLE: Fix indent

Revision 21716 - Directory Listing
Modified Fri Feb 15 23:57:22 2013 UTC (4 years, 8 months ago) by fedorov
ENH: Add ChangeTracker dependency

ChangeTracker is being mmigrated into extension


Revision 21704 - Directory Listing
Modified Thu Feb 14 22:05:23 2013 UTC (4 years, 8 months ago) by jcfr
STYLE: For consistency, change CMake macro from "SIMPLE_TEST" to "simple_test"

Use of lower case CMake function/macro when including underscore has been
first introduced with r17191.

See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=17191

Revision 21671 - Directory Listing
Modified Fri Feb 8 16:11:34 2013 UTC (4 years, 8 months ago) by jcfr
COMP: On MacOSX, force bundling of ITKv3 IOReview library to ensure proper loading of extension

Thanks to Csaba Pinter for testing that the patch worked as expected.

See http://slicer-devel.65872.n3.nabble.com/ITK-lib-missing-from-Mac-Slicer-package-needed-for-Plastimatch-tt4027274.html

Revision 21668 - Directory Listing
Modified Thu Feb 7 16:13:07 2013 UTC (4 years, 8 months ago) by pieper
BUG: fix the self-test registration for tractography tests

Revision 21652 - Directory Listing
Modified Wed Jan 30 22:00:44 2013 UTC (4 years, 8 months ago) by jcfr
COMP: Ensure itkFactoryRegistration code is included when building against ITKv4

See http://www.na-mic.org/Bug/view.php?id=2900

Fixes #2900

Revision 21632 - Directory Listing
Modified Wed Jan 23 22:58:14 2013 UTC (4 years, 8 months ago) by jcfr
STYLE: For consistency, rename "*[Ee]xtensionManager*" methods into "*[Ee]xtensionsManager*"

Note the extra "s" added to the word "Extension".

Revision 21618 - Directory Listing
Modified Fri Jan 18 22:21:47 2013 UTC (4 years, 9 months ago) by jcfr
ENH: Associated icon with copy, cut and paste action

Icons are licensed under Creative Commons License (CC-BY-SA 3.0)
See http://creativecommons.org/licenses/by-sa/3.0/

They have respectivaly been downloaded from:
 http://openiconlibrary.sourceforge.net/gallery2/?./Icons/actions/edit-copy-6.png
 http://openiconlibrary.sourceforge.net/gallery2/?./Icons/actions/edit-cut-6.png
 http://openiconlibrary.sourceforge.net/gallery2/?./Icons/actions/edit-paste-6.png

Before being uploaded on "openiconlibrary", the icons originally have
been obtained from http://www.oxygen-icons.org/

Revision 21617 - Directory Listing
Modified Fri Jan 18 21:38:57 2013 UTC (4 years, 9 months ago) by jcfr
BUG: Update QtTesting XML files to reference the appropriate module widget

This is a follow-up on commit r21613 where the xml files haven't been
updated as expected.

See #2247

Revision 21592 - Directory Listing
Modified Fri Jan 11 21:29:52 2013 UTC (4 years, 9 months ago) by jcfr
COMP: Add ITKFactoryRegistration library centralizing ITK IO factory registration

This commit will ensure that ITK IO factory are properly registered on all
supported platforms.

When ITKv4 is build shared, the library holding the factory registration code
are build statically. As a consequence, when CLI module are loaded as library
the factory are registered multiple times. Around 800 factories where registered
and this was leading to poor performance when loading images.

This commit enable the building of a shared library named ITKFactoryRegistration
that should be linked against to ensure loading of the factory. This approach
can succeed thanks to the help of the ITK variable ITK_NO_IO_FACTORY_REGISTER_MANAGER.

This variable allow to disable the automatic registration of factory in selected part
of the code.

The following two cases are handled:
 - Registration of the factories within the Slicer executable.
 - Registration of the factories within CLI executable.

Fixes #2813

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 21579 - Directory Listing
Modified Thu Jan 10 17:51:01 2013 UTC (4 years, 9 months ago) by finetjul
ENH: Add Scene Performance test

It measures time spent by some scene actions such as loading, closing,
restoring, relayouting a scene or modifying/adding nodes.
Issue #2642

Example of performance on a MacBookPro laptop (2.4GHz):
AddData (BrainAtlas2012.mrb) took 44865 msecs
CloseScene () took 28706 msecs
AddData (BrainAtlas2012.mrb) took 44579 msecs
ModifyNode (vtkMRMLScalarVolumeNode1) took 4 msecs
ModifyNode (vtkMRMLScalarVolumeNode2) took 35 msecs
ModifyNode (vtkMRMLScalarVolumeNode3) took 20 msecs
ModifyNode (vtkMRMLModelHierarchyNode2) took 14 msecs
ModifyNode (vtkMRMLModelNode4) took 0 msecs
ModifyNode (vtkMRMLModelDisplayNode5) took 14 msecs
ModifyNode (vtkMRMLModelHierarchyNode3) took 13 msecs
ModifyNode (vtkMRMLModelStorageNode1) took 4 msecs
ModifyNode (vtkMRMLModelHierarchyNode301) took 18 msecs
ModifyNode (vtkMRMLModelDisplayNode304) took 23 msecs
ModifyNode (vtkMRMLModelHierarchyNode51) took 19 msecs
AddNode (vtkMRMLModelNode302) took 46 msecs

Revision 21573 - Directory Listing
Modified Wed Jan 9 23:39:20 2013 UTC (4 years, 9 months ago) by demian
ENH: Added W/L controls for fiber bundles (mantis ID: 0002789)

Revision 21570 - Directory Listing
Modified Tue Jan 8 22:42:50 2013 UTC (4 years, 9 months ago) by demian
ENH: Added a test class for the tractography display test_tractography_display

Revision 21559 - Directory Listing
Modified Wed Jan 2 17:50:29 2013 UTC (4 years, 9 months ago) by sankhesh
BUG: Load translations before instantiating the GUI

Moved loadTranslations() and loadLanguage() methods from qSlicerApplicationHelper
to qSlicerCoreApplication. This enables loading them before instantiating the
main Slicer GUI.
Many thanks to zengwenye <iamzengwenye@163.com> for submitting the patch.
Fixes issue 2836

Revision 21496 - Directory Listing
Modified Fri Dec 7 21:47:35 2012 UTC (4 years, 10 months ago) by naucoin
STYLE: update links to pubdb for brain and knee atlas

Revision 21495 - Directory Listing
Modified Fri Dec 7 19:56:27 2012 UTC (4 years, 10 months ago) by naucoin
BUG: remove unintended check ins

Revision 21494 - Directory Listing
Modified Fri Dec 7 19:53:01 2012 UTC (4 years, 10 months ago) by naucoin
BUG: fix fiducial display in light box mode.

Use the renderer from the light box proxy manager if it's defined
When in light box mode, switch to using 2d point handles for fiducials.
Avoid seed widget and representation having different renderers on creation.
Unify light box index calculation.
Fix the annotations showing up in the 0th light box when the annotation
should be in the -1th. 
Take into account volume spacing, calculate the distance between the fiducial
and the slice at this light box index using distance from the fiducial point and the slice plane.
Reset the glyph type when changing in and out of lightbox mode.

Issue #1690


Revision 21482 - Directory Listing
Modified Fri Dec 7 00:23:59 2012 UTC (4 years, 10 months ago) by jcfr
ENH: Support per user per revision extensions settings

There is now a clear distinction between:
 - userSettings -> i.e. ~/.config/NA-MIC/Slicer.ini
 - revisionUserSettings -> i.e. ~/.config/NA-MIC/Slicer-<revision>.ini

The following slicer settings are now revision specific:
 - Extensions/ManagerEnabled
 - Extensions/ServerUrl
 - Extensions/InstallPath
 - Modules/AdditonalPath
 - Modules/IgnoreModules

Additionally, the launcher version has also been updated to be able to
consider settings associated with a user, application and revision. This is
captured by the new parameter APPLICATION_REVISION, ORGANIZATION_DOMAIN,
ORGANIZATION_NAME and USER_ADDITIONAL_SETTINGS_FILEBASENAME passed to the CMake
function "ctkAppLauncherConfigure".

qSlicerCoreApplication API has also been extended and now includes methods
like:
  - QSettings* userSettings()  [settings() method is deprecated and kept for backward compatibility]
  - QSettings* revisionUserSettings()
  - QString launcherRevisionUserSettingsFilePath()
  - QString slicerUserSettingsFilePath()
  - QString slicerRevisionUserSettingsFilePath()

In addition to the settings, the extensions install path is also revision
specific, it means that it's now possible to have multiple version of slicer
running with different set of extensions.

Fixes #2791, #2143, #2720, #2533


Since the version of the launcher is updated, launcher will return EXIT_FAILURE
also when no application is been set in the launcher settings.

Fixes #2767

Revision 21364 - Directory Listing
Modified Wed Nov 14 15:32:07 2012 UTC (4 years, 11 months ago) by pieper
ENH: for easier testing, avoid re-download of prostate mrb

Revision 21363 - Directory Listing
Modified Wed Nov 14 15:20:24 2012 UTC (4 years, 11 months ago) by pieper
ENH: clean up the prostate demo test to make it faster and more verbose

To help with debugging the crash on exit issue #2512

Revision 21361 - Directory Listing
Modified Wed Nov 14 15:20:15 2012 UTC (4 years, 11 months ago) by pieper
BUG: Clean up implementation of RSNA2012ProstateDemo

Make this a proper self test module for easier testing.

Work on progress for a fix to #2512

Revision 21351 - Directory Listing
Modified Tue Nov 13 23:23:42 2012 UTC (4 years, 11 months ago) by pieper
ENH: speed up atlas tests by minimizing delay while printing status

Revision 21350 - Directory Listing
Modified Tue Nov 13 23:16:52 2012 UTC (4 years, 11 months ago) by pieper
BUG: use updated name for download of brain atlas

fix for failing tests related to brain atlas in bug #2513

Revision 21346 - Directory Listing
Modified Tue Nov 13 01:10:31 2012 UTC (4 years, 11 months ago) by naucoin
BUG: New brain atlas mrb (uploaded to Nightly dir), cleaned up storage nodes.
STYLE: give feedback about how many model hierarchies and scene views there are to test.

Still to do: clean up the mrml file of extraneous view and camera nodes.

Issue #2513



Revision 21326 - Directory Listing
Modified Wed Nov 7 22:52:30 2012 UTC (4 years, 11 months ago) by millerjv
ENH: added date axis and boxplot

dcommit failed a pre-commit hook and unstaged a series of commits.
recommitting as a single commit

    ENH: support for dates on X-axis

    First attempt at supporting date axes.

    jqPlot date support is designed for continuous dates like in
    tracking stocks.  It allows for "gaps" in the dates, which are
    interpolated across for line plots and remain as gaps in bar plots.
    However, this scheme does not really align with our use case.

    Therefore, Slicer internally uses categorical axes when told
    to display dates.

    The logic for varyBarColor was modified so the default is off
    and it is only turned on when a lookup table is assigned to a series.

    A few method names in the private implementation were modified
    to make them consistent with new methods added.

    Slicer passes dates in the DoubleArrayNode, which stores things as
    floats.  Thus, dates must be represented as seconds since
    January 1, 1970. Fractional seconds are allowed.  Internally, these
    timestamps are converted to javascript timestamps which are in
    milliseconds.

    Date formating is currently fixed and limited to YYYY-MM-DD style.

    ENH: added boxplot

    Adapted a boxplot renderer from Joshua Bronson. https://bitbucket.org/jab/jqplot/changeset/f0f8eaa7e09e

    Added support for outliers and caching the y-axis bounds

    First version of jqplot that we are tarballing ourselves with modifications/additions from the
    main jqplot repository. Currently using a repository on github (millerjv)
    and will move to Slicer Community.  Slicer Community repository is being used for tarballs.

    Major rewrite of the qMRMLChartWidget to refactor the chart generation into separate
    routines for each chart type.

Revision 21318 - Directory Listing
Modified Mon Nov 5 23:11:23 2012 UTC (4 years, 11 months ago) by pieper
BUG: ensure that the temp directory is unique

Avoid possible name clashes with other tests.

Revision 21314 - Directory Listing
Modified Mon Nov 5 13:25:22 2012 UTC (4 years, 11 months ago) by fedorov
STYLE: fix notification message


Revision 21313 - Directory Listing
Modified Mon Nov 5 03:02:29 2012 UTC (4 years, 11 months ago) by fedorov
ENH: self-test to reproduce crash in issue 2512


Revision 21311 - Directory Listing
Modified Fri Nov 2 19:01:08 2012 UTC (4 years, 11 months ago) by millerjv
ENH: reset the orientation at the beginning of test

If test is run multiple times, this makes the runs more
consistent.

Revision 21302 - Directory Listing
Modified Fri Nov 2 15:19:15 2012 UTC (4 years, 11 months ago) by jcfr
STYLE: Fix indent in CMakeLists.txt

Revision 21300 - Directory Listing
Modified Thu Nov 1 12:57:35 2012 UTC (4 years, 11 months ago) by millerjv
BUG: modifying test to output measures to help trackdown test failing on a dashboard machine

Revision 21296 - Directory Listing
Modified Wed Oct 31 20:20:33 2012 UTC (4 years, 11 months ago) by millerjv
BUG: reduced tolerance for test. restructured to percentage not absolute

Revision 21294 - Directory Listing
Modified Wed Oct 31 12:58:40 2012 UTC (4 years, 11 months ago) by pieper
STYLE: avoid DeprecationWarning messages from vtk wrapping

When passing a float to a vtk method that expects int, a
DeprecationWarning is issued, but it does not provide any
diagnositic information about the method or class that caused
the issue. To get the information, you need to issue the following
python commands before the warning is triggered:

 import warnings
 warnings.simplefilter('error')

This generates a stack trace that can be used to find the issue.

Revision 21286 - Directory Listing
Modified Tue Oct 30 18:41:33 2012 UTC (4 years, 11 months ago) by naucoin
BUG: issue #2513 updated mrb from Marianna: fixed label map, scene view camera angles/slice visib

Revision 21262 - Directory Listing
Modified Sat Oct 27 01:10:37 2012 UTC (4 years, 11 months ago) by naucoin
BUG: issue #2513 point to new mrb file with proper model hierarchy, scene views. Added checking that there is a display node associated with model hierarchies as manually added ones may not have them.

Revision 21244 - Directory Listing
Modified Thu Oct 25 19:58:13 2012 UTC (4 years, 11 months ago) by millerjv
BUG: new test to baseline for bug #1926

Test case for the interaction between the ViewControllers module, linking, slice
interpolation, and the selection of background, foreground, and label images.
When entering the ViewControllers module, extra View Controllers are created and
configured.  If linking is on, then foreground, backgroud, and label selection
can be propagated to the other views incorrectly. If the node selectors are
bocked from emitting signals, then the viewers maintain their proper volumes.
However the slice interpolation widget is then not managed properly.

This test baselines that entering the ViewControllers module does not modify
which volumes are being displayed in the Slice Views.

A future checkin will test whether the interpolation buttons are accessible.

Revision 21234 - Directory Listing
Modified Tue Oct 23 23:35:11 2012 UTC (4 years, 11 months ago) by naucoin
BUG: issue #2513 uploaded a new version of the brain atlas mrb with proper color id and the missing scene view pngs

Revision 21231 - Directory Listing
Modified Tue Oct 23 19:30:18 2012 UTC (4 years, 11 months ago) by naucoin
BUG: issue #2515 to show the changes in the model hierarchies need to use the delay display call to allow rendering

Revision 21230 - Directory Listing
Modified Tue Oct 23 19:11:08 2012 UTC (4 years, 11 months ago) by naucoin
BUG: issue # 2515 use new version of the mrb with scene view snapshots

Revision 21210 - Directory Listing
Modified Thu Oct 18 19:09:59 2012 UTC (5 years ago) by jcfr
ENH: Using "--settings-path" output text an all platform

See http://www.na-mic.org/Bug/view.php?id=2376

Fixes #2376

Revision 21203 - Directory Listing
Modified Wed Oct 17 16:21:58 2012 UTC (5 years ago) by jcfr
ENH: Move initialization function from Main.cxx to qSlicerApplicationHelper

The idea is to promote re-use of the initialization function and avoid
code duplication.

Revision 21202 - Directory Listing
Modified Tue Oct 16 23:12:20 2012 UTC (5 years ago) by sankhesh
ENH: 2592 Renamed TractographyFiducialSeedingModule

Renamed the module directory as well as all references to the module

Revision 21195 - Directory Listing
Modified Tue Oct 16 12:27:52 2012 UTC (5 years ago) by pieper
BUG: include & in the list of valid characters for PercentEncode

Also update the test to be more helpful in diagnosing.

Revision 21185 - Directory Listing
Modified Mon Oct 15 15:27:08 2012 UTC (5 years ago) by fedorov
ENH: the test is simplified: the crash happens trying to quit Slicer after initializing the node selectors in the first step of the wizard (see issue #2590)


Revision 21184 - Directory Listing
Modified Mon Oct 15 13:33:39 2012 UTC (5 years ago) by pieper
BUG: fix for #2605 - special characters in data bundle filenames

Since data bundles must sometimes make filenames on-the-fly
based on the node names, add a step to ensure filenames
do not contain special characters (like colon or slash).

Revision 21178 - Directory Listing
Modified Sun Oct 14 16:46:52 2012 UTC (5 years ago) by pieper
ENH: re-enable all atlas tests for the general testing case

Revision 21177 - Directory Listing
Modified Sun Oct 14 16:46:49 2012 UTC (5 years ago) by pieper
BUG: avoid calling non-test method during unittest

The python unittest framework considers any test* method to be
a test and calls it with no arguments.  By renaming the helper
method to be perform_ rather than test_ we let the test
succeed.

Revision 21156 - Directory Listing
Modified Thu Oct 11 11:49:56 2012 UTC (5 years ago) by pieper
BUG: fix name of logic class in RSNA Quant test

Revision 21155 - Directory Listing
Modified Thu Oct 11 03:25:05 2012 UTC (5 years ago) by fedorov
ENH: adding test to reproduce the issue described in bug report #2590; confirmed on Mac Snow Leopard the test replicates the issue


Revision 21154 - Directory Listing
Modified Wed Oct 10 21:09:39 2012 UTC (5 years ago) by pieper
ENH: Finish RSNA quantitative tutorial (issue #2517)

Revision 21149 - Directory Listing
Modified Tue Oct 9 21:12:21 2012 UTC (5 years ago) by millerjv
ENH: new test for SliceLinkLogic

Tests Compare View for data selection, lightbox configuration, reseting
field of view, panning, zooming, slice offset, and changing orientation.

Revision 21137 - Directory Listing
Modified Tue Oct 9 05:04:33 2012 UTC (5 years ago) by finetjul
STYLE: Volume logic CreateLabelVolume should not add node to scene

Only CreateAndAddLabelVolume() can add a node to the scene.
Closes #2626

Revision 21126 - Directory Listing
Modified Sat Oct 6 22:11:50 2012 UTC (5 years ago) by pieper
ENH: #2517 - tests for 2 or 3 parts

Add test for basic 4 minute tutorial and for the ChangeTracker.
PETCT is TBD.

Note that ChangeTracker test triggers assert on closing scene.
Bug report to be filed.

Revision 21124 - Directory Listing
Modified Sat Oct 6 19:51:49 2012 UTC (5 years ago) by pieper
BUG: Fix leak in liver and lung tests

don't use GetNodesByClass (vtkCollection) api to access scene

Revision 21121 - Directory Listing
Modified Fri Oct 5 21:13:49 2012 UTC (5 years ago) by pieper
BUG: provide option to wait for index completion

Since dicom indexer uses QFuture threading, it may return before
the database is ready.

Requires:

https://github.com/commontk/CTK/commit/868c4dbb552dbbc076a3ae7aa135e17be5dbfba2

Revision 21120 - Directory Listing
Modified Fri Oct 5 21:13:47 2012 UTC (5 years ago) by pieper
BUG: better managment of startup conditions for dicom database

In particular for self testing on systems where dicom module
has not previously been run.

Revision 21119 - Directory Listing
Modified Fri Oct 5 21:13:44 2012 UTC (5 years ago) by pieper
BUG: free the indexer instance so that indexing threads will finish

The indexer uses the QFuture mechanism, so the operation may not have
completed when the call returns and the next step begins.

Revision 21118 - Directory Listing
Modified Fri Oct 5 20:12:42 2012 UTC (5 years ago) by pieper
BUG: handle case where no dicom database exists for RSNA dicom test

Handles the case of a fresh install where the dicom module
has never been run before.

Revision 21096 - Directory Listing
Modified Wed Oct 3 15:16:16 2012 UTC (5 years ago) by pieper
ENH: implement test for RSNA Course 1 (#2516)

This test covers all the operations as closely as possible.
Note that some of the camera views do not match the ones used
in the slides, but are fairly close and exercise the underlying
view functionality.

Revision 21091 - Directory Listing
Modified Tue Oct 2 19:12:16 2012 UTC (5 years ago) by sankhesh
BUG: 2494. Fixed tutorial tests to work with latest Slicer HEAD

Renaming VTKSliceView to SliceView
Renaming "Tractography Fiducial Seeding Module" to "Tractography
Interactive Seeding Module"
CurrentNodeChanged issues

Revision 21076 - Directory Listing
Modified Fri Sep 28 22:45:58 2012 UTC (5 years ago) by naucoin
BUG: separate out the abdomen and knee tests to make tracking errors easier

Revision 21068 - Directory Listing
Modified Thu Sep 27 14:20:57 2012 UTC (5 years ago) by millerjv
ENH: Added charting SelfTest

Cycles through a few charting modes.

Currently a Smoke Test

Revision 21067 - Directory Listing
Modified Thu Sep 27 13:32:18 2012 UTC (5 years ago) by millerjv
ENH: added SelfTest for the Slicer4Minute Tutorial (Tutorial 0)

Currently only testing Part 2 of the Tutorial.

Test is currently only a Smoke Test.

Revision 21058 - Directory Listing
Modified Wed Sep 26 19:05:37 2012 UTC (5 years ago) by jcfr
BUG: Ensure that dependency of explicit modules are also instantiated

Note that the module settings panel does NOT yet allow to differentiate
between module that have been ignored, failed to load or not specified in
the explicit list.

See #2251 / http://www.na-mic.org/Bug/view.php?id=2251

Revision 21045 - Directory Listing
Modified Tue Sep 25 22:20:23 2012 UTC (5 years ago) by jcfr
ENH: Factor code allowing to setup factory manager into library SlicerBaseQTApp

See http://www.na-mic.org/Bug/view.php?id=2251

Partial fix for #2251

Revision 21040 - Directory Listing
Modified Tue Sep 25 22:20:12 2012 UTC (5 years ago) by jcfr
COMP: Remove unused / extra translation files

Revision 21020 - Directory Listing
Modified Thu Sep 20 16:02:25 2012 UTC (5 years ago) by naucoin
BUG: issue 2514 point to new version of the mrb with valid scene view thumbnails

Revision 20990 - Directory Listing
Modified Fri Sep 14 22:58:55 2012 UTC (5 years, 1 month ago) by naucoin
ENH: add auto testing of the model heirarchies for the atlases

Revision 20982 - Directory Listing
Modified Wed Sep 12 22:14:09 2012 UTC (5 years, 1 month ago) by naucoin
ENH: RSNA demo testing, iterate over scene views and restore them

Revision 20975 - Directory Listing
Modified Wed Sep 12 16:50:44 2012 UTC (5 years, 1 month ago) by pieper
STYLE: fix comment in cmake file and add link

Revision 20969 - Directory Listing
Modified Tue Sep 11 16:28:48 2012 UTC (5 years, 1 month ago) by pieper
ENH: better testing script

Revision 20968 - Directory Listing
Modified Tue Sep 11 12:53:29 2012 UTC (5 years, 1 month ago) by pieper
ENH: make sure labels are always visible for test

Taking into account the size of the slice viewer ensures the
test data won't be clipped.

Revision 20965 - Directory Listing
Modified Mon Sep 10 22:42:44 2012 UTC (5 years, 1 month ago) by pieper
ENH: add new self test covering issue 2428

Currently fails due display ID issue.

Revision 20957 - Directory Listing
Modified Fri Sep 7 22:09:03 2012 UTC (5 years, 1 month ago) by pieper
ENH: Add additional self tests related to atlases

Currently these test for download and load of the atlases, but
do not confirm that they function or display correctly.

Revision 20953 - Directory Listing
Modified Fri Sep 7 16:33:02 2012 UTC (5 years, 1 month ago) by naucoin
BUG: issue 2030 unifty how screen shots are taken, using the ctk::grabVTKWidget and passing QImages to the scene writer. Fixes white background screen shots in saving mrml and mrb

Revision 20939 - Directory Listing
Modified Thu Sep 6 17:57:15 2012 UTC (5 years, 1 month ago) by pieper
BUG: ignore slicerrc file when running basic tests

Since slicerrc may refer to user-specific data it can cause
false-positive failed tests.

Revision 20936 - Directory Listing
Modified Thu Sep 6 14:40:40 2012 UTC (5 years, 1 month ago) by pieper
BUG: be sure to call superclass with correct arguments

Need to pass the methodName parameter to the test case if you
are going to provide an __init__ method with arguments.

Revision 20935 - Directory Listing
Modified Thu Sep 6 14:24:41 2012 UTC (5 years, 1 month ago) by pieper
BUG: call the superclass __init__ so it will run in ctest

Avoids this error:

http://slicer.cdash.org/testDetails.php?test=2874114&build=38429

Revision 20931 - Directory Listing
Modified Wed Sep 5 20:10:33 2012 UTC (5 years, 1 month ago) by pieper
ENH: Add scene view restore to MRB test

Revision 20904 - Directory Listing
Modified Fri Aug 31 16:15:55 2012 UTC (5 years, 1 month ago) by pieper
ENH: add a test to confirm that slice displays restore from MRB files

Related to bug #2120

Revision 20900 - Directory Listing
Modified Fri Aug 31 16:15:46 2012 UTC (5 years, 1 month ago) by pieper
ENH: improved testing of mrb saving

Revision 20890 - Directory Listing
Modified Wed Aug 29 13:26:50 2012 UTC (5 years, 1 month ago) by pieper
COMP: copy fiber bundle test script to build tree

This way it will be included in the runtime TestCases.

Revision 20888 - Directory Listing
Modified Tue Aug 28 18:54:09 2012 UTC (5 years, 1 month ago) by pieper
ENH: add a new (failing) test for bug 2438

The clicked signal generates a crash as described in the
bug report.

This test required exposing more widget API to python.

Revision 20876 - Directory Listing
Modified Mon Aug 27 20:03:49 2012 UTC (5 years, 1 month ago) by pieper
ENH: add new test for bug 2049

This test is run as part of ctest, but can also be invoked at runtime
via the SelfTests module.

Revision 20828 - Directory Listing
Modified Wed Aug 22 19:55:12 2012 UTC (5 years, 1 month ago) by christopher.mullins
ENH: Adds Cut, Copy, and Paste into Edit menu

See http://na-mic.org/Mantis/view.php?id=1670

Fixes #1670

Revision 20818 - Directory Listing
Modified Wed Aug 22 14:35:41 2012 UTC (5 years, 1 month ago) by pieper
ENH: improve MRB test with valid output and qt import

The test fails on image compare, which is correct because the images
do not match and the reload is not successful.  But the test is
taking place without letting the GUI update, which may explain the
incorrect layout.  Next update to test should include app.processEvents
to allow layout to fix.

Revision 20805 - Directory Listing
Modified Tue Aug 21 15:34:01 2012 UTC (5 years, 1 month ago) by Michael.jeulinl
ENH: Make the file type support mode more flexible

Remove the IOFileType enum and use instead a QString.

Revision 20789 - Directory Listing
Modified Mon Aug 20 14:45:54 2012 UTC (5 years, 1 month ago) by finetjul
STYLE: Update http links to 4.1 documentation

Revision 20788 - Directory Listing
Modified Mon Aug 20 13:36:18 2012 UTC (5 years, 1 month ago) by pieper
BUG: add missing import of vtk to test

Avoid test failures like this one:

http://slicer.cdash.org/testDetails.php?test=2720535&build=34629

Revision 20779 - Directory Listing
Modified Thu Aug 16 21:41:20 2012 UTC (5 years, 2 months ago) by pieper
ENH Merge branch '2385-mrb-testing'

Adds a test for scene building, saving, restoring.  Includes sceneviews
and tractography.  Currently test fails for various reasons as described
in the bug report.

* 2385-mrb-testing:
  ENH: improved documentation for MRB test
  BUG: fix mrb and add image testing
  BUG: fix crash due to incorrect order of arguments to Zip
  ENH: finish scene and mrb save and restore steps
  ENH: better testing
  ENH: add testing skeleton for MRB

Revision 20687 - Directory Listing
Modified Wed Jul 25 07:42:19 2012 UTC (5 years, 2 months ago) by jcfr
COMP: Add missing include required when building without default option

Revision 20685 - Directory Listing
Modified Wed Jul 25 07:27:52 2012 UTC (5 years, 2 months ago) by christopher.mullins
ENH: Adds 'Recently Loaded' File menu entry

This commit result from a collaborative work between Christopher Mullins
and Jean-Christophe Fillion-Robin.

See http://na-mic.org/Mantis/view.php?id=1669

Fixes #1669

Revision 20665 - Directory Listing
Modified Tue Jul 24 07:39:53 2012 UTC (5 years, 2 months ago) by jcfr
COMP: Fix unused variable warnings

Revision 20609 - Directory Listing
Modified Thu Jul 12 21:47:53 2012 UTC (5 years, 3 months ago) by jcfr
COMP: Fix build error including the appropriate PythonQt header

Thanks for Hans for reporting the issue.

Revision 20590 - Directory Listing
Modified Fri Jul 6 22:47:39 2012 UTC (5 years, 3 months ago) by jcfr
BUG: ensure Module Panel is visible when user click on icon in the toolbar

See http://www.na-mic.org/Bug/view.php?id=2314
Fixes #2314

Revision 20588 - Directory Listing
Modified Fri Jul 6 22:20:46 2012 UTC (5 years, 3 months ago) by jcfr
COMP: Remove unused variable from qSlicerAppMainWindowCore.cxx

Revision 20585 - Directory Listing
Modified Fri Jul 6 06:25:53 2012 UTC (5 years, 3 months ago) by jcfr
ENH: Associate icon with python interactor and set window title

See http://www.na-mic.org/Bug/view.php?id=2305

Fixes #2305

Revision 20547 - Directory Listing
Modified Mon Jul 2 21:47:43 2012 UTC (5 years, 3 months ago) by christopher.mullins
ENH: Remove home module from module toolbar.

Additionally, in Application settings, label "Home" has been renamed into
"Default startup module".

See http://na-mic.org/Mantis/view.php?id=2180

Fixes #2180

Revision 20514 - Directory Listing
Modified Thu Jun 28 20:40:21 2012 UTC (5 years, 3 months ago) by benjamin.long
ENH: Internationalized Slicer

Added Internationalization setting panel to enable/disable this behavior.
Added language combo box into general setting panel if enabled.
Added function to load language when we start the application.

Revision 20505 - Directory Listing
Modified Wed Jun 27 23:05:24 2012 UTC (5 years, 3 months ago) by jcfr
COMP: Add option Slicer_BUILD_DICOM_SUPPORT

See http://na-mic.org/Mantis/view.php?id=2271

Fixes #2271

Revision 20504 - Directory Listing
Modified Wed Jun 27 21:50:53 2012 UTC (5 years, 3 months ago) by benjamin.long
BUG: Fix bad command in the DiffusionTensorImagingTutorial

Revision 20503 - Directory Listing
Modified Wed Jun 27 21:50:51 2012 UTC (5 years, 3 months ago) by benjamin.long
BUG: Fix both qtTesting tutorials

Revision 20497 - Directory Listing
Modified Wed Jun 27 17:28:45 2012 UTC (5 years, 3 months ago) by benjamin.long
ENH: QtTesting updated to the last version and updated tutorials.

- Added modal/unmodal behavior to the player dialog.
- Added severals unit tests, and fix associated class.

See http://paraview.org/gitweb?p=QtTesting.git;a=summary to have all
the modifications.
Close #2264, #1983

Revision 20407 - Directory Listing
Modified Tue Jun 19 18:25:12 2012 UTC (5 years, 4 months ago) by millerjv
ENH: Added layout with 3 slice views and 3 chart views.

Revision 20379 - Directory Listing
Modified Sat Jun 16 21:05:05 2012 UTC (5 years, 4 months ago) by finetjul
COMP: Fix unused variable warnings

Revision 20367 - Directory Listing
Modified Thu Jun 14 21:02:40 2012 UTC (5 years, 4 months ago) by benjamin.long
STYLE: Fix bad indent in SlicerApp/Testing/Python/CMakeLists.txt

Revision 20366 - Directory Listing
Modified Thu Jun 14 20:11:59 2012 UTC (5 years, 4 months ago) by benjamin.long
STYLE: Moved slicerappdatapaths.py.in into SlicerApp/Testing/Python

Revision 20360 - Directory Listing
Modified Thu Jun 14 16:15:20 2012 UTC (5 years, 4 months ago) by finetjul
ENH: Redesign ModifiedSinceRead

ModifiedSinceRead can no longer be set externally, it's the nodes themselves that computes it based on the last time the data was stored and on the modifications.
ModifiedSinceRead is no longer a vtkMRMLNode property but a vtkMRMLStorableNode property.
The storage nodes have been cleaned-up (factorized) in the process.
At exit time, the scene is checked to see if it has been modified or if its storable nodes have been modified since read/write.

Some other changes:
Removed vtkMRMLModelNode::GetDefaultWriteFileExtension() it is a duplicate from vtkMRMLModelStorageNdoe::GetDefaultWriteFileExtension()
Removed vtkMRMLColorNode::AddColorName() as it is not used and increase code complexity
Removed vtkMRMLAnnotation*StorageNode::WriteData(vtkMRMLNode* refNode) as it was doing the same than vtkMRMLAnnotationStorageNode::WriteData(vtkMRMLNode* refNode)

Remaining issues:
The check on the modified scene is not perfect and can be fine tuned.
The loading of annotations are marking the nodes as ModifiedSinceRead but it shouldn't.
The loading of a vtkMRMLVolumePropertyNode from within a scene load incorrectly marks the node as ModifiedSinceRead


Revision 20354 - Directory Listing
Modified Wed Jun 13 22:26:08 2012 UTC (5 years, 4 months ago) by benjamin.long
BUG: Move ApplicationSlicerAppData.py into Base/Python/slicer/slicerappdatapaths.py

Close #2194

Revision 20353 - Directory Listing
Modified Wed Jun 13 20:35:56 2012 UTC (5 years, 4 months ago) by naucoin
COMP: remove unused var d

Revision 20349 - Directory Listing
Modified Mon Jun 11 19:30:29 2012 UTC (5 years, 4 months ago) by benjamin.long
BUG: Disable qttesting test if slicer dependencies are not enabled

Test using CLI module needs Slicer_BUILD_CLI enabled
Test using "SampleData" and "Editor" module needs Slicer_USE_PYTHONQT

Close #2169

Revision 20348 - Directory Listing
Modified Mon Jun 11 19:07:49 2012 UTC (5 years, 4 months ago) by Michael.jeulinl
BUG: 0002094. Move 3DSlicer icons into appropriate subdirectories.

Revision 20347 - Directory Listing
Modified Mon Jun 11 16:47:24 2012 UTC (5 years, 4 months ago) by benjamin.long
BUG: Fix function to Disabled native menu bar if Slicer use QtTesting.

Revision 20334 - Directory Listing
Modified Fri Jun 8 05:23:27 2012 UTC (5 years, 4 months ago) by finetjul
ENH: Cosmetics and update for the file menu

Closes #1740

Revision 20333 - Directory Listing
Modified Fri Jun 8 04:51:13 2012 UTC (5 years, 4 months ago) by finetjul
ENH: Add option to save scene as Data Bundle in Save Data dialog

+ minor bugs due to previous commits
Closes #2097

Revision 20320 - Directory Listing
Modified Mon Jun 4 20:19:27 2012 UTC (5 years, 4 months ago) by benjamin.long
BUG: Updated NeurosurgicalPlanningTutorial to avoid issue with the editor

This tutorial is still failing for memory leak see issue #2162

Revision 20319 - Directory Listing
Modified Mon Jun 4 18:33:58 2012 UTC (5 years, 4 months ago) by benjamin.long
BUG: Fix macro slicer_add_python_test

Now, "SLICER_ARGS" variable accepts multiple values.

Revision 20318 - Directory Listing
Modified Mon Jun 4 15:41:35 2012 UTC (5 years, 4 months ago) by benjamin.long
STYLE: Renamed tutorials tests and associated python files

Closed issue #2159

Revision 20316 - Directory Listing
Modified Sun Jun 3 19:52:13 2012 UTC (5 years, 4 months ago) by Michael.jeulinl
COMP: Main application name is now an advanced CMake option

Ensures that an icns icon file always exists when configuring slicer on MacOSX platform.

Revision 20312 - Directory Listing
Modified Fri Jun 1 21:09:02 2012 UTC (5 years, 4 months ago) by jcfr
STYLE: Improve readability by re-organizing CMake code in SlicerApp/Testing/Python/CMakeLists.txt

Revision 20311 - Directory Listing
Modified Fri Jun 1 21:08:59 2012 UTC (5 years, 4 months ago) by jcfr
COMP: Properly specify parameter associated with tutorial tests

Revision 20292 - Directory Listing
Modified Wed May 30 18:45:10 2012 UTC (5 years, 4 months ago) by benjamin.long
ENH: Added first 2 tests using Qttesting framework

- Added new Sample Datas, used by QtTesting framework tests
- Named all buttons in SampleData module, and added function to download
files from Midas

Revision 20282 - Directory Listing
Modified Tue May 29 06:14:01 2012 UTC (5 years, 4 months ago) by jcfr
BUG: Associate version information with MacOSX bundle.

While r19946 fixed the problem, r19957 removed the fix previously introduced.

This commit re-applies the changes.

See http://www.na-mic.org/Bug/view.php?id=1940

Closes #1940

Revision 20272 - Directory Listing
Modified Mon May 28 21:52:09 2012 UTC (5 years, 4 months ago) by jcfr
BUG: Fix extension bundling and simplify mechanism used to specify the main application

1) In Applications/SlicerApp/CMakeLists.txt:

  Improve comment explaining what should be considered when adding an other
application into Applications folder.

  Given the fact Slicer_APPLICATION_NAME is used locally, minimize confusion
by renaming variable renaming it into SlicerApp_APPLICATION_NAME.

  In case the application being configured is the *Main* application,
explicitly compare "PROJECT_NAME" with "Slicer_MAIN_PROJECT".


2) Rename variable Slicer_APPLICATION_NAME used to identified the main
application into Slicer_MAIN_PROJECT_APPLICATION_NAME. This will
minimize confusion and help maintaining the code.

3) Let's note that the mechanism used to fixup application should probably
be extended to account for other application build in the Applications folder.

4) In top-level CMakeLists, move code specific to main application description
into its own section.

5) Configure variable "Slicer_MAIN_PROJECT" and "Slicer_MAIN_PROJECT_APPLICATION_NAME"
into SlicerConfig so that "SlicerExtensionCPackBundleFixup" could successfully
refer to Slicer_MAIN_PROJECT_APPLICATION_NAME. This closes #2130

See http://www.na-mic.org/Bug/view.php?id=2130

Revision 20271 - Directory Listing
Modified Mon May 28 21:52:06 2012 UTC (5 years, 4 months ago) by jcfr
STYLE: Remove extra comment amd name variable consistently

Revision 20161 - Directory Listing
Modified Sun May 27 01:52:27 2012 UTC (5 years, 4 months ago) by jcfr
COMP: Fix unused variable warning in qSlicerAppMainWindow

Revision 20155 - Directory Listing
Modified Fri May 25 20:25:45 2012 UTC (5 years, 4 months ago) by Michael.jeulinl
ENH: Provide a mechanism to build several applications

Configure the applications and packaging with
two variables to configure the build:
- Slicer_MAIN_PROJECT # main project
- ${Slicer_MAIN_PROJECT}_APPLICATION_NAME # application name

Make the packaging given the main application name.

Revision 20134 - Directory Listing
Modified Mon May 21 19:30:22 2012 UTC (5 years, 4 months ago) by finetjul
BUG: Fix unit tests following Cameras module move to be a loadable module

Revision 20120 - Directory Listing
Modified Sun May 20 04:33:11 2012 UTC (5 years, 5 months ago) by finetjul
ENH: Open Extension Manager dialog from Extensions settings panel

Issue #1870

Revision 20118 - Directory Listing
Modified Sat May 19 06:34:26 2012 UTC (5 years, 5 months ago) by finetjul
STYLE: Rename settings panel titles, and Favorite Modules toolbar

Issue #1870

Revision 20113 - Directory Listing
Modified Fri May 18 14:36:47 2012 UTC (5 years, 5 months ago) by Michael.jeulinl
ENH: Alias application image resources for SlicerApp.

Make resources access more generic.

Revision 20100 - Directory Listing
Modified Thu May 17 02:36:02 2012 UTC (5 years, 5 months ago) by Michael.jeulinl
ENH: Alias application image resources for SlicerApp.

Decouple the application from the corp.
Make the management of the resources more flexible.

Revision 20098 - Directory Listing
Modified Wed May 16 22:26:19 2012 UTC (5 years, 5 months ago) by benjamin.long
ENH: Save the current module when we start to record a QtTesting macro.

Custom settings :
Current module and current panel are now automatically recorded.

See commit associated in CTK :
https://github.com/commontk/CTK/commit/16bc2f2becaab31969889c1addcfda8f1839fb18

Revision 20059 - Directory Listing
Modified Wed May 9 23:04:22 2012 UTC (5 years, 5 months ago) by benjamin.long
ENH: Added new recording behavior to QtTesting

See CTK commit :
https://github.com/commontk/CTK/commit/d4ee01baca5b91b2cbc3c071f5c05a5da1b08974
For more details.

Revision 20035 - Directory Listing
Modified Tue May 8 18:06:24 2012 UTC (5 years, 5 months ago) by benjamin.long
BUG: QtTesting - Fix the extension .xml when selecting a file to record.

Revision 20013 - Directory Listing
Modified Fri May 4 15:50:00 2012 UTC (5 years, 5 months ago) by pieper
BUG: avoid colons in filenames for windows

Explicitly specify the date format for the temp file
since ISODate includes a colon and that is not valid
on windows.

Revision 20012 - Directory Listing
Modified Fri May 4 15:49:58 2012 UTC (5 years, 5 months ago) by pieper
BUG: correctly detect/add .mrb file extension

Revision 20007 - Directory Listing
Modified Fri May 4 00:06:39 2012 UTC (5 years, 5 months ago) by pieper
ENH: implement Save to MRB functionality

Creates a temp directory for saving and then zips
into the file selected by the user.

Revision 20006 - Directory Listing
Modified Fri May 4 00:06:37 2012 UTC (5 years, 5 months ago) by pieper
ENH: adapt Slicer Data Bundle menu

Only offer save to directory and MRB in file menu

Load is now handled via qSlicerIO

Revision 20002 - Directory Listing
Modified Fri May 4 00:06:28 2012 UTC (5 years, 5 months ago) by pieper
ENH: re-enable and rename data bundle menu items

These are not yet hooked up

Revision 19976 - Directory Listing
Modified Wed May 2 13:49:07 2012 UTC (5 years, 5 months ago) by jcfr
COMP: Remove empty directory. Using git-svn option --rmdir would avoid this commit.

Revision 19975 - Directory Listing
Modified Wed May 2 01:04:45 2012 UTC (5 years, 5 months ago) by finetjul
ENH: Add option in settings to enable QtTesting. Off by default

Revision 19973 - Directory Listing
Modified Tue May 1 23:30:04 2012 UTC (5 years, 5 months ago) by benjamin.long
BUG: Fix qtTesting tests when slicer use qtTesting.

Bug fix in CTK, commit:
8b399aea484ef6fca0eef26b7f59f0d00f6a7b05

Revision 19959 - Directory Listing
Modified Mon Apr 30 23:11:21 2012 UTC (5 years, 5 months ago) by benjamin.long
ENH: Add Qt Testing support

Expose signals/slots on some widget APIs for qttesting recording/replay

Revision 19958 - Directory Listing
Modified Mon Apr 30 21:40:57 2012 UTC (5 years, 5 months ago) by Michael.jeulinl
ENH: Rename Slicer application classes

- Use to make distinction between inner and outer files.
- Make it more generic to be able to derive SlicerApp.
- Decouple resource usage between core and application.

Revision 19957 - Directory Listing
Modified Mon Apr 30 21:40:43 2012 UTC (5 years, 5 months ago) by Michael.jeulinl
ENH: Generalize naming associated with SlicerQt application

Revision 19946 - Directory Listing
Modified Thu Apr 26 14:30:29 2012 UTC (5 years, 5 months ago) by jcfr
BUG: Associate version information with MacOSX bundle. Fixes #1940

See:
  https://developer.apple.com/library/mac/#documentation/General/Reference/InfoPlistKeyReference/Articles/CoreFoundationKeys.html
  http://www.na-mic.org/Bug/view.php?id=1940
  http://www.cmake.org/cmake/help/cmake-2-8-docs.html#prop_tgt:MACOSX_BUNDLE_INFO_PLIST

Revision 19922 - Directory Listing
Modified Sat Apr 21 00:07:37 2012 UTC (5 years, 5 months ago) by jcfr
COMP: Prevent confusion by removing unused Testing code

Revision 19921 - Directory Listing
Modified Sat Apr 21 00:07:22 2012 UTC (5 years, 5 months ago) by jcfr
COMP: Ensure that Slicer can compile with Python support disabled

Fix typo and add #ifdef were it was missing.

Revision 19869 - Directory Listing
Modified Wed Apr 11 15:29:59 2012 UTC (5 years, 6 months ago) by jcfr
BUG: Fix  py_nomainwindow_SlicerSceneObserverTest by importing 'vtk' module

Revision 19852 - Directory Listing
Modified Wed Apr 11 10:56:33 2012 UTC (5 years, 6 months ago) by jcfr
BUG: Ensure generic Python module tests pass when build as extension

After commit r19844 that ensure that python unittest will fail if it applies,
a problem associated with generic python module tests has been discovered.

The following error message was displayed:

   AttributeError: 'module' object has no attribute 'scriptedloadableextensiontemplate'


This was explained by the fact the path where the module was located
wasn't considered by the module factory manager.

To address that problem, a new command line option named

  --additional-module-paths

has been added.


The given list of path will added to the factory module manager.

Revision 19848 - Directory Listing
Modified Wed Apr 11 10:56:25 2012 UTC (5 years, 6 months ago) by jcfr
BUG: Ensure that failing python unit tests are reported as failing test

* This regression was introduced following r19581 [1]

* To prevent this issue from occurring again, a regression test
is also added.

[1] http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=19581

Revision 19829 - Directory Listing
Modified Mon Apr 9 09:29:01 2012 UTC (5 years, 6 months ago) by jcfr
BUG: Ensure Launcher withou IO Console support is installed when it applies.

Revision 19825 - Directory Listing
Modified Mon Apr 9 00:23:35 2012 UTC (5 years, 6 months ago) by jcfr
ENH: Ensure that console IO is enabled when Slicer is started from build tree

* Version 0.1.5 rc1 of the launcher is now used.

* The launcher has some new command line options:
   --launcher-version             Show launcher version information
   --launcher-dump-environment    Launcher will print environment variables to be set, then exit
   --launcher-additional-settings Additional settings file to consider

* It also now detects if Qt special command line option are passed
and make sure to pass them to the application to launch.
See http://doc.qt.nokia.com/latest/qapplication.html#QApplication

* On platform that support it, an additional launcher executable is
available. The additional launcher will have the suffix "W" appended
to its name and doesn't have console IO support. This second launcher
is considered when packaging Slicer. Indeed, having the console attached
to the launcher when starting Slicer from an install tree is not wanted.

Revision 19823 - Directory Listing
Modified Sun Apr 8 07:14:57 2012 UTC (5 years, 6 months ago) by jcfr
COMP: Exclude tests relying on console output when Slicer_BUILD_WIN32_CONSOLE is ON

This should prevent the following tests from failing when option
Slicer_BUILD_WIN32_CONSOLE is OFF:

   qSlicerApplicationTpyclTest1

   slicer_nomainwindow_DisableModulesCommandLineOptionsTest

   MRMLCreateNodeByClassWithoutSetReferenceCount (if VTK_DEBUG_LEAKS also ON)


Also introduced the convenient variable Slicer_HAS_CONSOLE_IO_SUPPORT

Revision 19822 - Directory Listing
Modified Sun Apr 8 07:14:55 2012 UTC (5 years, 6 months ago) by jcfr
COMP: Move build option specific to SlicerQT into associated CMakeLists.txt

Revision 19809 - Directory Listing
Modified Sat Apr 7 08:41:27 2012 UTC (5 years, 6 months ago) by jcfr
ENH: Add python module 'saferef' allowing to create weak reference to method/function.

* This module is the equivalent of built-in module 'weakref'. The difference
is that 'saferef' safely create weak reference to any function,
including bound methods whereas the 'weakref' module deals "only"
with objects [1].

[1] http://docs.python.org/library/weakref.html

* This module has been imported from "django" code base at revision 17875
See https://code.djangoproject.com/browser/django/trunk/django/dispatch/saferef.py?rev=17875

* The license associated is BSD. Since the code has been originally imported
from PyDispatcher and modified by django, both the license of (a) PyDispatched
and (b) Django are included at the top of the file.

 a) https://code.djangoproject.com/browser/django/trunk/django/dispatch/license.txt?rev=17875

 b) https://code.djangoproject.com/browser/django/trunk/LICENSE?rev=17875

* The associated unittest has also been added. Currently living in
"Base/Python/tests" and added within "Application/SlicerQT/Testing/Python/CMakeLists.txt",
this may change. The macro "SLICER_ADD_PYTHON_UNITTEST" has also been
adapted to understand absolute path.

* Currently, the test itself isn't installed, this may also change in
the future.

Revision 19806 - Directory Listing
Modified Sat Apr 7 01:12:16 2012 UTC (5 years, 6 months ago) by jcfr
ENH: Add settings allowing to enable Extension Manager

* Edit -> Application Settings -> Extensions Settings -> "Enable extensions manager"

Revision 19779 - Directory Listing
Modified Tue Apr 3 14:30:06 2012 UTC (5 years, 6 months ago) by jcfr
COMP: Ensure test MRMLCreateNodeByClassWithoutSetReferenceCount passes on Windows

* Given the fact the message "vtkDebugLeaks has detected LEAKS!" is not
reported by ctest on windows, we were not using a "fail expression" that
was matched on all operating system.

* Note that the extra "?" is not a mistake, it's here to match the following
expression:
  "instance still around"
  "instances still around"

* This could be explain looking at the source code of vtkDebugLeaks.cxx,
indeed if the leaks are printed on a dashboard running on windows, the message
"vtkDebugLeaks has detected LEAKS!" won't be printed.

This corresponds to the case DASHBOARD_TEST_FROM_CTEST is set and
macro _WIN32 is defined.

See http://vtk.org/gitweb?p=VTK.git;a=blob;f=Common/vtkDebugLeaks.cxx;h=9632ec89b20b0663b98194d0be85d5ba70551c3f;hb=HEAD#l359

Revision 19778 - Directory Listing
Modified Tue Apr 3 12:20:00 2012 UTC (5 years, 6 months ago) by jcfr
COMP: Make sure test MRMLCreateNodeByClassWithoutSetReferenceCount is excluded when required

Since within SuperBuild.cmake, the variable "Slicer_USE_VTK_DEBUG_LEAKS" is used
to set and pass the variable VTK_DEBUG_LEAKS, VTK_DEBUG_LEAKS should be
used to exclude the test.

Revision 19772 - Directory Listing
Modified Mon Apr 2 06:30:17 2012 UTC (5 years, 6 months ago) by jcfr
ENH: Illustrate how vtkMRMLNode::CreateNodeByClass and SetReferenceCount should be used from python

This is a addendum to the mail [1] previously send on the list.

The reference count shouldn't be decreased using the naive approach where
it is set to one. Indeed, internally, the reference count could be any
number greater than one. It doesn't have to be 2.

Considering this last remark, using the following approach is *REQUIRED*,
otherwise it will lead to a CRASH of the application.

 n = slicer.mrmlScene.CreateNodeByClass('vtkMRMLViewNode')
 slicer.mrmlScene.addNode(n)
 n.SetReferenceCount(n.GetReferenceCount() - 1)

Even better, this specific example can be simplified using the following
syntax, this is the *RECOMMENDED* approach, it will prevent bug, memory
leaks and crashes:

  n = slicer.mrmlScene.addNode(slicer.vtkMRMLViewNode())

And if the name of the node is generated at runtime, this could be done:

  n = eval('slicer.mrmlScene.AddNode(slicer.%s())' % 'vtkMRMLViewNode')


[1] http://massmail.spl.harvard.edu/public-archives/slicer-devel/2011/007513.html

Revision 19771 - Directory Listing
Modified Mon Apr 2 06:30:15 2012 UTC (5 years, 6 months ago) by jcfr
BUG: Use new spelling for --disable-*-modules command line option.

* This is a regression introduced following commit r17177
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=17177

* Added a regression test named "slicer_nomainwindow_DisableModulesCommandLineOptionsTest"
that could help to catch the problem if it occurs again. It also check
that the command line option works as expected.

Revision 19770 - Directory Listing
Modified Mon Apr 2 06:30:13 2012 UTC (5 years, 6 months ago) by jcfr
ENH: Add test showing that using --python-code with Exception works as expected.

Revision 19769 - Directory Listing
Modified Mon Apr 2 06:30:11 2012 UTC (5 years, 6 months ago) by jcfr
COMP: Prevent confusion by removing unneeded command line option passed to "slicer_add_python_unittest"

* The option '--testing' is already passed by default. Indeed, the macro
being name "...add_..._test" it means the flags will be added automatically.

Revision 19768 - Directory Listing
Modified Mon Apr 2 06:30:10 2012 UTC (5 years, 6 months ago) by jcfr
STYLE: Prevent confusion by re-organizing code in SlicerQT/Testing/Python/CMakeLists.txt

* When test are added it's important to read the comment surrounding
existing tests to ensure it make sens to add it in a given section.

* As an example, let's consider "SlicerSceneObserverTest", this test was
previously added under the section "Check if 'slicer.testing.runUnitTest()'
works as expected", this didn't make sens.

The associated CMake code has been moved under a new section entitled
"Application tests"

Revision 19767 - Directory Listing
Modified Mon Apr 2 06:30:07 2012 UTC (5 years, 6 months ago) by jcfr
ENH: Update python tests to use new "exit" mechanism

* To indicate an error, regular python Exception can be used.

* For more details refer to r19581.
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=19581

Revision 19706 - Directory Listing
Modified Mon Mar 26 04:20:49 2012 UTC (5 years, 6 months ago) by jcfr
BUG: Only code passed using '-c' is executed in "shebang" mode.

* Restore the original behavior associated with '--python-code', if this
option is used, all modules will be loaded and Slicer won't exit.

* Code passed using the option '-c' is executed similarly to what's done
with the regular python interpreter. See http://docs.python.org/tutorial/interpreter.html

* Main.cxx has been simplified, function "initializePython" has been
removed and corresponding code has been moved into qSlicerCoreCommandOption.
Commit 19377 make it possible because the "parseArgument" has been moved into
the "init" method of qSlicerCoreApplication pimpl.

Revision 19691 - Directory Listing
Modified Fri Mar 23 23:16:14 2012 UTC (5 years, 6 months ago) by finetjul
ENH: restore change to enum from string of ModifiedEvent for vtk 5.10 compatibility

This reverts commit r19679 which was reverting r19670.

Revision 19684 - Directory Listing
Modified Thu Mar 22 08:13:30 2012 UTC (5 years, 6 months ago) by jcfr
COMP: Allow extension to include testing macros.

* Split CMake/TestingMacros.h into MRML/Core/{vtkMRMLCoreTestingMacros, vtkMRMLDebugLeaksMacro}

* MRML/Core being a directory already included, when building extension
the header providing the testing macro will be found.

* Also split the macro allowing to consider leaks as error into "vtkMRMLDebugLeaksMacro.h"

Revision 19679 - Directory Listing
Modified Wed Mar 21 22:14:16 2012 UTC (5 years, 6 months ago) by pieper
BUG: revert change to enum from string of ModifiedEvent for vtk 5.10 compatibility

Revision 19670 - Directory Listing
Modified Wed Mar 21 08:42:53 2012 UTC (5 years, 6 months ago) by jcfr
COMP: Improve robustness of the code by using vtk.vtkCommand.ModifiedEvent instead of string "ModifiedEvent"

* Assuming the code is tested, doing so will allow to enforce
valid event are used by avoiding misspelled  error associated to event
specified as string.

Revision 19662 - Directory Listing
Modified Tue Mar 20 08:15:28 2012 UTC (5 years, 7 months ago) by jcfr
COMP: Minimize confusion and improve readability by consistently using ".toLatin1()"

* There were occurrences of:
   .toLatin1().data()
   .toStdString().c_str()
   .toAscii().data()

these ones have been replaced with the shorter and equivalent form ".toLatin1()"

* The function qPrintable() is also used to print a QString within a std stream.

Revision 19661 - Directory Listing
Modified Tue Mar 20 06:18:53 2012 UTC (5 years, 7 months ago) by jcfr
STYLE: Fix name inconsistency associated with target SlicerQT.

* Library and test executable names start with the same prefix.

* See #1615

Revision 19655 - Directory Listing
Modified Mon Mar 19 07:02:07 2012 UTC (5 years, 7 months ago) by jcfr
COMP: Avoid confusion by defining SIMPLE_TEST macro only once.

* Consistently set the variable KIT within the Testing/Cxx/CMakeLists.txt of
each library.

* Fix name inconsistency. See #1615

Revision 19634 - Directory Listing
Modified Sat Mar 17 14:28:47 2012 UTC (5 years, 7 months ago) by finetjul
BUG: Restore Module Panel menu action

r19503 removed the custom QAction of the module panel, but didn't use instead the dock toggle view action.

Revision 19596 - Directory Listing
Modified Wed Mar 14 01:59:18 2012 UTC (5 years, 7 months ago) by finetjul
ENH: Add cmd.exe as command line argument for launcher

It opens a new window with the Slicer environment

Revision 19585 - Directory Listing
Modified Tue Mar 13 17:51:12 2012 UTC (5 years, 7 months ago) by jcfr
ENH: Exit Slicer after code specified using '-c' or '--python-code' is executed.

* This is done toward having Slicer behaving like the python interpreter.

* Note that more or work is required to consolidate the command line API
and write the corresponding documentation.

* The use case motivating that change is the possibility to execute the
script 'get-pip.py'.
See https://github.com/pypa/pip/blob/develop/pip/req.py#L222

Revision 19582 - Directory Listing
Modified Tue Mar 13 14:19:03 2012 UTC (5 years, 7 months ago) by jcfr
ENH: Slicer can be used as python interpreter with minimum overhead.

* Introduced property "runPythonAndExit" indicating that Slicer should
exit after execution of a given python script.

* This applied to python scripts executed using the following syntax:
   ./Slicer <scriptname>

* Ideally, it should be possible to lazily load slicer modules.

Revision 19518 - Directory Listing
Modified Tue Mar 6 15:59:57 2012 UTC (5 years, 7 months ago) by finetjul
BUG: Exit current module before closing Slicer

Exiting the current module in the module panel destructor is not enough.
It happens too late, ideally it should happen before the layout manager
is destructed but also before the current layout is saved into settings as
exiting a module can "revert" the current layout.

qSlicerModuleSelectorToolBar::actionSelected was crashing when the QAction
was 0.

Closes #1787

Revision 19513 - Directory Listing
Modified Mon Mar 5 21:26:59 2012 UTC (5 years, 7 months ago) by finetjul
BUG: Fix crash in qSlicerMainWindowTest1

In the test, there is no python console instantiated.

Revision 19503 - Directory Listing
Modified Sat Mar 3 21:05:21 2012 UTC (5 years, 7 months ago) by finetjul
STYLE: Use QToolBar::toggleViewAction() instead of custom actions

QToolBar already comes with QAction to show/hide. Use it instead of doing it manually.

Revision 19500 - Directory Listing
Modified Sat Mar 3 08:17:47 2012 UTC (5 years, 7 months ago) by finetjul
ENH: Make Python console and error log widget visibility "checkable"

Closes #1745

Revision 19499 - Directory Listing
Modified Sat Mar 3 08:17:44 2012 UTC (5 years, 7 months ago) by finetjul
ENH: Rename and reorganize toolbars

Issue #1745

Revision 19496 - Directory Listing
Modified Fri Mar 2 16:47:15 2012 UTC (5 years, 7 months ago) by naucoin
BUG: fixing bug 1761, for safety don't allow the user to select a non empty directory for the data bundle

Revision 19471 - Directory Listing
Modified Wed Feb 29 21:26:00 2012 UTC (5 years, 7 months ago) by naucoin
BUG: fixing bug 1761, passing the correct directory to create a data bundle, and confirming the user wishes to save there if there are files already present (they get deleted to create a clean archive).

Revision 19468 - Directory Listing
Modified Wed Feb 29 21:01:36 2012 UTC (5 years, 7 months ago) by finetjul
ENH: Add Modules/PreferExecutableCLI setting

In order to limit memory consumption, when Slicer has the choice,
it can load executable CLI instead of loadable CLI.
The setting can be set into the Appication Settings Modules panel.
Closes #1762

Revision 19463 - Directory Listing
Modified Wed Feb 29 00:09:58 2012 UTC (5 years, 7 months ago) by jcfr
STYLE: Help string associated with loadable and scripted module will match slicer version.

* This has been done by relying on Slicer_VERSION_MAJOR and Slicer_VERSION_MINOR
within the loadable module and using 'slicer.app.majorVersion' and 'slicer.app.minorVersion'
within the scripted module.

* Ideally, we could define a small meta langage including special string
like: '<WIKIURL>" "<VERSION>" "<MODULENAME>", "<CONTRIBUTOR1>", ... that could
be used. the module manager would take of the substituation so that
the correct is rendered.

Revision 19457 - Directory Listing
Modified Tue Feb 28 13:23:00 2012 UTC (5 years, 7 months ago) by pieper
BUG: turn off slicer data bundle until save behavior is stable

Revision 19436 - Directory Listing
Modified Mon Feb 27 09:50:20 2012 UTC (5 years, 7 months ago) by jcfr
BUG: Read settings to ensure the ExtensionsManager menu entry is visible if it applies

* This was omitted and should have been integrated to commit r19434

Revision 19434 - Directory Listing
Modified Mon Feb 27 08:16:57 2012 UTC (5 years, 7 months ago) by jcfr
ENH: Integrate qSlicerExtensionsManagerDialog to the main window "View" menu

* Associate an icon to the "ExtensionManager" action appearing in the "View" menu

* Waiting we update the code of "slicer.kitware.com" server, and also time
to test the feature on all platform, the menu entry allowing to
show the extension manager is hidden.

It can be enabled by editing the Slicer settings and adding an
entry named "ManagerEnabled" to the "Extensions" group.

For example:

[Extensions]
...
ManagerEnabled=1
...

Using the following command could be useful to find out where the settings
are located on a given platform.

 ./Slicer --settings-path

or

 .\Slicer.exe --settings-path  [Will display the path only if Slicer is built with Slicer_BUILD_WIN32_CONSOLE:ON]

Revision 19433 - Directory Listing
Modified Mon Feb 27 08:16:55 2012 UTC (5 years, 7 months ago) by jcfr
ENH: Remove "legacy" extension wizard

* The "ExtensionManager" menu item is also hidden

Revision 19426 - Directory Listing
Modified Mon Feb 27 08:16:32 2012 UTC (5 years, 7 months ago) by jcfr
STYLE: Improve code readability by removing unused headers in qSlicerMainWindow

Revision 19387 - Directory Listing
Modified Sat Feb 25 19:34:42 2012 UTC (5 years, 7 months ago) by finetjul
ENH: Control Favorites Modules in toolbar using settings

Revision 19377 - Directory Listing
Modified Fri Feb 24 22:36:20 2012 UTC (5 years, 7 months ago) by finetjul
ENH: Add --testing launcher argument

By being in testing mode, it uses different settings than user settings.

Revision 19372 - Directory Listing
Modified Fri Feb 24 18:54:50 2012 UTC (5 years, 7 months ago) by finetjul
BUG: Fix failing test qSlicerModuleFactoryManagerTest1

Before being loaded, modules must be instantiated first

Revision 19357 - Directory Listing
Modified Thu Feb 23 22:18:48 2012 UTC (5 years, 7 months ago) by finetjul
ENH: Module factory manager handles more use cases.

Support failed to load modules (in red)
Unload modules in the reverse order they were loaded.
No duplicated module (if registered when factory manager was set, and
initialized after that).

Revision 19341 - Directory Listing
Modified Wed Feb 22 20:51:59 2012 UTC (5 years, 7 months ago) by wjp@bwh.harvard.edu
ENH: finishing up misc icons for file menu

Revision 19336 - Directory Listing
Modified Wed Feb 22 19:23:53 2012 UTC (5 years, 7 months ago) by finetjul
STYLE: Align center of Copyright cells

Nudge the layout.

Revision 19334 - Directory Listing
Modified Wed Feb 22 18:13:00 2012 UTC (5 years, 7 months ago) by finetjul
ENH: Register factories and scan directories only once.

Only module names (QString) can be used as method/slot parameters. No module
pointer directly.

Move module registration/instantiation/loading in a unique factory manager class.
qSlicerModuleManager is a placeholder for module specific actions with the scene
and the application: "Edit properties...", setCurrentModule, ...

Add modulesToIgnore property to prevent modules from being loaded for
performance (and clarity) reasons.

Revision 19331 - Directory Listing
Modified Wed Feb 22 16:38:21 2012 UTC (5 years, 7 months ago) by joe.snyder
ENH: Update Slicer 'About' dialog links

Added the correct Html code to make the "NIHRoadmap" a working link.
Corrected the library links to not include spaces as part of the
link.
Add an HTML table to the SlicerLinksTextBrowser to eliminate the need for
manually spacing the links.

Revision 19317 - Directory Listing
Modified Tue Feb 21 03:56:00 2012 UTC (5 years, 7 months ago) by wjp@bwh.harvard.edu
ENH: Modifying Slicer's load/save toolbar as per Ron's request

Revision 19315 - Directory Listing
Modified Mon Feb 20 16:26:16 2012 UTC (5 years, 7 months ago) by fedorov
ENH: adding icon for Four up quantitative layout, and changing the setup files
to use it.


Revision 19314 - Directory Listing
Modified Mon Feb 20 16:09:10 2012 UTC (5 years, 7 months ago) by fedorov
ENH: adding Two-over-Two slice viewers layout. Layouts that do not have 3d
viewer are particularly useful for conventional radiology applications.


Revision 19290 - Directory Listing
Modified Tue Feb 14 21:38:09 2012 UTC (5 years, 8 months ago) by joe.snyder
STYLE: Improve layout of 'About dialog'

Change the image used in the 'About' dialog from the splash screen to the vertical logo.
Remove the button from the bottom of the dialog box.
Change the layout of the box from a verical layout (QVBoxLayout) to a horizonal one (QHBoxLayout).

Change the QTextEdit box used in the dialog to a QTextBrowser which lets HTML links be clickable.

Change the qSlicerAboutDialog.cxx to have have the QText browser change the size of the font for
more impotant text and to change the order to put the thanks text above the copyright messages.

Change the qSlicerCoreApplication pair to include a new function called 'thanks' which returns
the thanks text in the About dialog, this was created to separate this text from the copyrights
text.  Also change the 'copyrights' text to be in HTML with the links taking you to each of
the used libraries main page.

Revision 19229 - Directory Listing
Modified Mon Feb 6 23:20:38 2012 UTC (5 years, 8 months ago) by finetjul
BUG: Fix width of module panel

The dock widget could resize to a size smaller than the "minimumSizeHint"
of the module representations. Because the modules are contained by a
 scrollarea, the size hints don't work properly, they must be reimplemented.
Note that the sizing of a dockwidget or a scrollarea is controlled by the
observed widget (QDockWidget::widget() or QScrollArea::widget()). There
is no impact to change teh size policy of the dockwidget or scrollarea
directly.

Closes #1681

Revision 19130 - Directory Listing
Modified Tue Jan 24 16:03:44 2012 UTC (5 years, 8 months ago) by pieper
ENH: give the layout frame of the CentralWidget a unique name so modules can easily locate it

Revision 19114 - Directory Listing
Modified Fri Jan 20 21:02:42 2012 UTC (5 years, 8 months ago) by finetjul
STYLE: Rename "About SlicerQT" into "About 3D Slicer"

Revision 19102 - Directory Listing
Modified Thu Jan 19 00:03:15 2012 UTC (5 years, 9 months ago) by pieper
ENH: add a failing test showing that having an observer on the scene can cause a problem for the tear-down logic of slicer

Revision 19087 - Directory Listing
Modified Sun Jan 15 19:05:29 2012 UTC (5 years, 9 months ago) by millerjv
ENH: Initial ChartView checkin for charts that can be packed in layouts

Contains ChartView, ChartWidget, ChartControllerWidget, ChartViewNode, ChartNode.

Two temporary layouts defined to hold charts, name "*Quantitative"

Data to plot is held in DoubleArrayNodes and added to ChartNodes

Uses jqPlot to plot within a QWebView.

ChartControllerWidget is a place-holder.

Plots can only be generated programmatically. See Libs/MRML/Widgets/Testing/qMRMLChartViewTest.py for an example.

Todo: property specifications
Todo: rework javascript code to be more modular.
Todo: fix packing issues with QWebView in a larger layout.
Todo: remove or implement proper ChartViewDisplayableManager and ChartViewInteractorStyle.

Revision 19063 - Directory Listing
Modified Wed Jan 11 22:05:45 2012 UTC (5 years, 9 months ago) by jcfr
COMP: Remove unused include

Revision 19040 - Directory Listing
Modified Sun Jan 8 04:34:35 2012 UTC (5 years, 9 months ago) by jcfr
COMP: Move Core modules from "Base/QtCoreModules" into "Modules/Core"

* All Slicer modules are now all located in the Modules subdirectory

Revision 19006 - Directory Listing
Modified Sat Dec 31 22:47:09 2011 UTC (5 years, 9 months ago) by finetjul
ENH: ctkConfirmExitDialog is obsolete, ctkMessageBox is the new version

Move the disclaimer dialog in the main window.

Revision 19003 - Directory Listing
Modified Fri Dec 30 18:33:44 2011 UTC (5 years, 9 months ago) by Michael.jeulinl
ENH: Allow Drag & Drop to add data from the explorer.

Authorize the drag&drop action within qSlicerMainWindow and qSlicerDataDialog.

Revision 18970 - Directory Listing
Modified Thu Dec 22 23:09:35 2011 UTC (5 years, 9 months ago) by finetjul
BUG: Fix main window toolbar buttons style to support Qt::ToolButtonTextUnderIcon

The tool button style is controlled in the Advanced Settings General panel.

From Qt 4.6.3 doc:
QToolBar::toolButtonStyle - "Note that if you add a QToolButton with the addWidget() method, it will not get this button style"

The following behavior does not seem  to work:
QToolButton::toolButtonStyle - QToolButton automatically connects this slot to the relevant signal in the QMainWindow in which is resides.

Revision 18955 - Directory Listing
Modified Mon Dec 19 22:42:31 2011 UTC (5 years, 10 months ago) by finetjul
BUG: Don't instantiate widgets if Slicer is run in no-mainwindow mode

Revision 18937 - Directory Listing
Modified Thu Dec 15 08:31:42 2011 UTC (5 years, 10 months ago) by jcfr
COMP: SlicerQT/CMakeLists.txt - Use variable to avoid repeating splash image path

Revision 18935 - Directory Listing
Modified Thu Dec 15 07:47:45 2011 UTC (5 years, 10 months ago) by jcfr
ENH: Remove empty dir

Revision 18932 - Directory Listing
Modified Thu Dec 15 07:45:27 2011 UTC (5 years, 10 months ago) by jcfr
ENH: Hide PythonInteractor menu item if Slicer_USE_PYTHONQT is OFF

Revision 18931 - Directory Listing
Modified Thu Dec 15 07:45:25 2011 UTC (5 years, 10 months ago) by jcfr
ENH: Add Slicer_BUILD_EXTENSIONMANAGER_SUPPORT option

* If disabled:
 - extension manager won't be integrated
 - external project qCDashAPI and LibArchive won't be checkedout

Revision 18930 - Directory Listing
Modified Thu Dec 15 07:45:21 2011 UTC (5 years, 10 months ago) by jcfr
COMP: Remove unused directory - Applications/GUI

The corresponding source code is still available in Slicer3 repository.

Revision 18929 - Directory Listing
Modified Thu Dec 15 07:45:18 2011 UTC (5 years, 10 months ago) by jcfr
COMP: Add Slicer_BUILD_CLI_SUPPORT

* When disabled, neither the CLI factories or the CLI modules will be built.

Revision 18920 - Directory Listing
Modified Wed Dec 14 15:56:59 2011 UTC (5 years, 10 months ago) by jcfr
COMP: Update signature of test entry function to be "(int, char*[])"

* This should address the following linking issue:

unresolved external symbol "int __cdecl qSlicerApplicationTpyclEMSegmentIntegrationTest(int,char * * const)" (?qSlicerApplicationTpyclEMSegmentIntegrationTest@@YAHHQAPAD@Z)

See http://slicer.cdash.org/viewBuildError.php?buildid=6120

Signed-off-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 18917 - Directory Listing
Modified Tue Dec 13 23:51:22 2011 UTC (5 years, 10 months ago) by jcfr
ENH: Add test checking integration of EMSegmentInterface with qSlicerApplication

Revision 18910 - Directory Listing
Modified Mon Dec 12 20:45:56 2011 UTC (5 years, 10 months ago) by jcfr
STYLE: Change SLICER_ADD_PYTHON_(UNIT)TEST CMake macros to lowercase

Revision 18896 - Directory Listing
Modified Sat Dec 10 01:08:08 2011 UTC (5 years, 10 months ago) by finetjul
STYLE: Decrease confusion by renaming slicer home TCL variable

The TCL variable confusively looks a lot like the environment variable
SLICER_HOME, it is renamed to give a more propert name.

Revision 18878 - Directory Listing
Modified Thu Dec 8 06:08:35 2011 UTC (5 years, 10 months ago) by finetjul
ENH: Add generic way to handle batch node insertion/removal in vtkMRMLScene

vtkMRMLScene has now a notion of state. If the scene is loading a mrml scene file, its state is ImportState( ::BatchProcessState

The previous scene behavior has been kept (pseudo backward compatible), the scene still fires the same (renamed) events for each Close, Import and Restore calls.
Events have been renamed:
 SceneAboutToBeClosedEvent -> StartCloseEvent
 SceneClosedEvent -> EndCloseEvent
 SceneAboutToBeImportedEvent -> StartImportEvent
 SceneImportedEvent -> EndImportEvent
 SceneAboutToBeRestoredEvent -> StartRestoreEvent
 SceneRestoredEvent -> EndRestoreEvent

New events are added:
 - StartBatchProcessEvent: notably (but not only) fired when StartCloseEvent, StartImportEvent, and StartRestoredEvent are fired
 - EndBatchProcessEvent: notably (but not only) fired when EndCloseEvent, EndImportEvent, and EndRestoredEvent are fired
 - ProgressBatchProcessEvent, ProgressCloseEvent, ProgressImportEvent, ProgressRestoreEvent: not yet fired
 - StartSaveEvent: fired when the scene starts to be saved
 - EndSaveEvent: fired when the scene finished to be saved

StartState(vtkMRMLScene::StateType) and EndState(vtkMRMLScene::StateType) control the scene state. Nested states are supported, but each state events are fired only once (e.g. two successive call to StartState(BatchProcessState) fire StartBatchProcessEvent only once).
Internally, the methods Clear(), Connect(), Import() and Commit() set the scene states.
In addition, the state can be set externally by any node (e.g. vtkMRMLSceneViewNode) or logic (e.g. vtkMRMLColorLogic)

Preliminary work has been started to fire progress events, but it hasn't been completed (needs to be implemented in AddNode(), RemoveNode(), Import() and Close()).

Revision 18876 - Directory Listing
Modified Thu Dec 8 01:42:11 2011 UTC (5 years, 10 months ago) by finetjul
COMP: MRMLWidgets doesn't exist, qMRMLWidgets does

The confusion comes from qMRMLWidgets is in MRML/Widgets
A better fix could be to change qMRMLWidgets into MRMLWidgets

However, the new name MRMLWidgets could be misleading, as it reminds of
VTK Widgets.
This is maybe why Qt/KWWidgets libraries are usually named GUI and not
widgets.

Revision 18871 - Directory Listing
Modified Tue Dec 6 21:37:46 2011 UTC (5 years, 10 months ago) by jcfr
COMP: Remove empty dirs

Revision 18870 - Directory Listing
Modified Tue Dec 6 20:53:52 2011 UTC (5 years, 10 months ago) by jcfr
BUG: Fix qSlicerModuleFactoryManagerTest1

* Use Cameras instead of Transforms module since this later one
is now a loadable module.

Revision 18866 - Directory Listing
Modified Tue Dec 6 20:53:14 2011 UTC (5 years, 10 months ago) by jcfr
COMP: Move all MRML libraries into Libs/MRML sub-directory

* Also rename MRML library into MRMLCore library

Revision 18864 - Directory Listing
Modified Tue Dec 6 20:49:19 2011 UTC (5 years, 10 months ago) by jcfr
COMP: Source code of all modules is now located in Modules sub-directory

Revision 18819 - Directory Listing
Modified Tue Dec 6 00:09:42 2011 UTC (5 years, 10 months ago) by jcfr
COMP: Move qSlicerExport.h.in into CMake sub-directory

Revision 18797 - Directory Listing
Modified Fri Dec 2 13:30:44 2011 UTC (5 years, 10 months ago) by jcfr
COMP: Add advanced option to disable/enable the building of ChangeTrackerPy, EMSegment and SkullStripper

Revision 18794 - Directory Listing
Modified Fri Dec 2 01:36:09 2011 UTC (5 years, 10 months ago) by finetjul
STYLE: vtkMRMLScene doesn't inherit from vtkCollection but vtkObject

The nodes are contained in vtkCollection* vtkMRMLScene::Nodes

Revision 18786 - Directory Listing
Modified Thu Dec 1 02:14:19 2011 UTC (5 years, 10 months ago) by jcfr
COMP: Integrate SkullStripper extension as an external project

Revision 18777 - Directory Listing
Modified Sat Nov 26 17:14:00 2011 UTC (5 years, 10 months ago) by pieper
ENH: remove the disclaimer about missing functionality

Revision 18776 - Directory Listing
Modified Sat Nov 26 13:07:48 2011 UTC (5 years, 10 months ago) by pieper
BUG: fix documentation style that was breaking the build

Revision 18775 - Directory Listing
Modified Sat Nov 26 01:12:12 2011 UTC (5 years, 10 months ago) by naucoin
STYLE: use xml paragraph breaks

Revision 18774 - Directory Listing
Modified Sat Nov 26 01:05:52 2011 UTC (5 years, 10 months ago) by naucoin
STYLE: use xml style paragraph marks

Revision 18773 - Directory Listing
Modified Sat Nov 26 00:59:45 2011 UTC (5 years, 10 months ago) by naucoin
STYLE: longer tool tips, html in description

Revision 18771 - Directory Listing
Modified Fri Nov 25 23:22:46 2011 UTC (5 years, 10 months ago) by demian
ENH: Improved Diffusion Documentation

Revision 18769 - Directory Listing
Modified Fri Nov 25 22:30:39 2011 UTC (5 years, 10 months ago) by jcfr
COMP: qSlicerApplicationTpyclTest1 - PythonQt doesn't have to be explicitly initialized

See https://github.com/Slicer/Slicer/commit/72231b6e9880b3ad1ffc93d415e937bcaf192ed6

Revision 18763 - Directory Listing
Modified Fri Nov 25 14:43:45 2011 UTC (5 years, 10 months ago) by finetjul
COMP: updatePythonOsEnviron is not public anymore

Revision 18762 - Directory Listing
Modified Thu Nov 24 22:22:24 2011 UTC (5 years, 10 months ago) by jcfr
ENH: Initialization of python context done within qSlicerCoreApplication

Revision 18758 - Directory Listing
Modified Thu Nov 24 12:21:11 2011 UTC (5 years, 10 months ago) by hjohnson
COMP: ComputeSUVBodyWeight with ITKv3.

This tool depends on features of ITKv3
that only exists in GDCM version 1.0. In addition
it used the long deprecated OrientedImage construct.

Revision 18752 - Directory Listing
Modified Wed Nov 23 22:42:55 2011 UTC (5 years, 10 months ago) by millerjv
ENH: updated documentation-url

Revision 18751 - Directory Listing
Modified Wed Nov 23 21:24:22 2011 UTC (5 years, 10 months ago) by fedorov
ENH: change default value per Ron's request


Revision 18742 - Directory Listing
Modified Wed Nov 23 09:04:47 2011 UTC (5 years, 10 months ago) by finetjul
ENH: Remove Undo/Redo menu from the toolbar

The option has been removed, its menu should also be removed

Revision 18735 - Directory Listing
Modified Tue Nov 22 23:20:51 2011 UTC (5 years, 10 months ago) by naucoin
STYLE: update comment to reflect output format

Revision 18733 - Directory Listing
Modified Tue Nov 22 23:05:23 2011 UTC (5 years, 10 months ago) by naucoin
STYLE: module doc on wiki needs same name as source dir

Revision 18731 - Directory Listing
Modified Tue Nov 22 22:34:54 2011 UTC (5 years, 10 months ago) by naucoin
BUG: take out RSNA specific module

Revision 18730 - Directory Listing
Modified Tue Nov 22 22:34:03 2011 UTC (5 years, 10 months ago) by naucoin
BUG: update this module with the required computations/changes for RSNA 2011: read dicom volume for header info instead of a .dat file, generate output strings, read the proper colour table to get the label names

Revision 18722 - Directory Listing
Modified Tue Nov 22 02:21:27 2011 UTC (5 years, 10 months ago) by naucoin
BUG: quick and dirty port of ComputeSUVBodyWeight to use Slicer3's PETCTFusion Logic to get data from dicom header, still work to be done before Nov 27

Revision 18712 - Directory Listing
Modified Mon Nov 21 02:37:22 2011 UTC (5 years, 10 months ago) by fedorov
ENH: update acks


Revision 18707 - Directory Listing
Modified Fri Nov 18 01:33:16 2011 UTC (5 years, 11 months ago) by jcfr
ENH: ctkLogger has been deprecated - Use q{Debug, Critical, Warning}() instead

Revision 18705 - Directory Listing
Modified Thu Nov 17 20:12:45 2011 UTC (5 years, 11 months ago) by hjohnson
ENH: Explicitly state which tools should be built with Slicer.

Revision 18697 - Directory Listing
Modified Wed Nov 16 22:54:53 2011 UTC (5 years, 11 months ago) by jcfr
COMP: Main.cxx - Move slicerQtMain into anonymous namespace

Revision 18686 - Directory Listing
Modified Mon Nov 14 20:24:33 2011 UTC (5 years, 11 months ago) by pohl
STYLE: Ron wanted to have Command Line listed under specialized module catgegory

Revision 18679 - Directory Listing
Modified Sat Nov 12 02:12:59 2011 UTC (5 years, 11 months ago) by finetjul
COMP: Typo in slicerQtMain function name

Revision 18677 - Directory Listing
Modified Fri Nov 11 23:27:29 2011 UTC (5 years, 11 months ago) by finetjul
ENH: Add option to build Slicer with no console on Windows

Add Slicer_BUILD_WIN32_CONSOLE at superbuild and build level

Revision 18645 - Directory Listing
Modified Wed Nov 9 08:43:43 2011 UTC (5 years, 11 months ago) by jcfr
ENH: Add mechanism to select a module using the layout manager

* When module will be managed by the layoutManager, this should be
revisited.

Revision 18632 - Directory Listing
Modified Tue Nov 8 18:55:12 2011 UTC (5 years, 11 months ago) by finetjul
COMP: ResampleVolume2 requires DiffusionApplications to be configured first

ResampleVolume2 requires DiffusionFilter_SOURCE_DIR to be set before
 the project is configured.
DiffusionFilter_SOURCE_DIR is initialized in DiffusionApplications.
Remove DiffusionApplications from the LEGACY.

Revision 18619 - Directory Listing
Modified Sat Nov 5 22:41:47 2011 UTC (5 years, 11 months ago) by hjohnson
STYLE: Addressing module menu ordering request

Hans,

I would like to reorganize the module listings for registration. I am
proposing to highlight brainsfit and resample image and tuck everything
else under a listing called specialized. I did this reorganization on
the wiki pages already. If you concur, please do.

While you are at it, would you mind also moving Legacy and Utilities to
the bottom of the module listing in Slicer. I did it already on the
wiki.

Thanks
Ron

Revision 18540 - Directory Listing
Modified Mon Oct 31 12:44:01 2011 UTC (5 years, 11 months ago) by millerjv
BUG: making sure default state of toolbar is set.

Revision 18537 - Directory Listing
Modified Sun Oct 30 22:07:39 2011 UTC (5 years, 11 months ago) by jcfr
COMP: BRAINSTools expects LAUNCH_EXE to be defined

* This is to ensure that platform not having RPath (or similar mechanism)
 could successfully load the dependent libraries of a test executable.

Revision 18533 - Directory Listing
Modified Sat Oct 29 23:02:24 2011 UTC (5 years, 11 months ago) by jcfr
ENH: Move "Application Settings" under "Edit" menu

Revision 18522 - Directory Listing
Modified Fri Oct 28 04:27:25 2011 UTC (5 years, 11 months ago) by jcfr
COMP: BRAINSTools - disable GTract on all platform

* Waiting the install rules of GTract modules are fixed, let's disable them.

Revision 18517 - Directory Listing
Modified Fri Oct 28 01:51:26 2011 UTC (5 years, 11 months ago) by jcfr
COMP: Explicitly disable BRAINSTools GTRACT on windows

* This is temporary waiting we solve some link/compile error

Revision 18513 - Directory Listing
Modified Thu Oct 27 23:48:07 2011 UTC (5 years, 11 months ago) by jcfr
COMP: Make sure ITK_VERSION_MAJOR is added to the cache so that BRAINSTools compiles as expected.

* BRAINSTools expects the variable to be in the cache. Having the variable
defined but not cached won't affect the set() command.
See https://github.com/BRAINSia/BRAINSStandAlone/blob/master/Common.cmake#L12

Revision 18504 - Directory Listing
Modified Thu Oct 27 19:27:32 2011 UTC (5 years, 11 months ago) by millerjv
ENH: Removing colors module from the module toolbar.

Revision 18475 - Directory Listing
Modified Wed Oct 26 07:56:34 2011 UTC (5 years, 11 months ago) by jcfr
COMP: Update BRAINSTools Git tab

* Include the latest changes pushed on jcfr fork / topic clean-buildsystem

Revision 18473 - Directory Listing
Modified Wed Oct 26 02:21:12 2011 UTC (5 years, 11 months ago) by jcfr
STYLE: Rename SlicerBRAINSTools into BRAINSTools

* The project is named "BRAINSTools"

Revision 18448 - Directory Listing
Modified Tue Oct 25 02:28:13 2011 UTC (5 years, 11 months ago) by millerjv
ENH: new toolbar to control viewers.

Currently just presents a control for managing the crosshair.

Revision 18447 - Directory Listing
Modified Tue Oct 25 02:27:42 2011 UTC (5 years, 11 months ago) by millerjv
ENH: Crosshair toolbar (checkpoint)

If ViewersToolBar just using .ui file. To be replaced with a proper
subclass of ToolBar.

Revision 18435 - Directory Listing
Modified Mon Oct 24 14:18:47 2011 UTC (5 years, 11 months ago) by finetjul
ENH: Split qMRMLAbstractLogic::ProcessMRMLEvents into qMRMLAbstractLogic::ProcessMRMLSceneEvents and qMRMLAbstractLogic::ProcessMRMLNodesEvents

In order to reduce the confusion inside qMRMLAbstractLogic::ProcessMRMLEvents, we separate the processing of the scene events from the nodes events.
Add qMRMLAbstractDisplayableManager::ProcessWidgetsEvents to process graphical user interactions (typically via vtk widgets).

Revision 18430 - Directory Listing
Modified Mon Oct 24 07:23:52 2011 UTC (5 years, 11 months ago) by jcfr
COMP: Include BRAINSTools dependency

* Similarly to what's done with EMSegment and ChangeTrackerPy, the source
code is checked out using an External project. Then, the corresponding
source directory is added as a "regular" Slicer directory.

Revision 18429 - Directory Listing
Modified Mon Oct 24 07:23:46 2011 UTC (5 years, 11 months ago) by jcfr
COMP: CLI/CMakeLists.txt - Include directory containing custom itkTestMain.h only if ITKv4 is used.

Revision 18421 - Directory Listing
Modified Fri Oct 21 23:15:30 2011 UTC (5 years, 11 months ago) by fedorov
BUG: fix label/description


Revision 18385 - Directory Listing
Modified Thu Oct 20 16:54:27 2011 UTC (6 years ago) by naucoin
STYLE: taking out the image

Revision 18384 - Directory Listing
Modified Thu Oct 20 16:34:14 2011 UTC (6 years ago) by naucoin
STYLE: trying an image link

Revision 18383 - Directory Listing
Modified Thu Oct 20 16:11:13 2011 UTC (6 years ago) by naucoin
STYLE: fix xml formatting

Revision 18382 - Directory Listing
Modified Thu Oct 20 16:10:03 2011 UTC (6 years ago) by naucoin
STYLE: try using CDATA to escape html formatting in the description. Doesn't look good in the --xml output, but renders okay in the GUI panel

Revision 18380 - Directory Listing
Modified Thu Oct 20 15:36:49 2011 UTC (6 years ago) by naucoin
STYLE: updating documentation for Slicer4 wiki page auto generataion

Revision 18379 - Directory Listing
Modified Thu Oct 20 14:11:29 2011 UTC (6 years ago) by fedorov
ENH: add documentation tidbits from the wiki to the xml descriptions


Revision 18287 - Directory Listing
Modified Thu Oct 6 16:19:45 2011 UTC (6 years ago) by lorensen
COMP: ITKv4 missing include

In ITKv4, ResaampleImageFilter no longer include
itkBSplineInterpolateImageFunction.
This change is compatible with ITK 3.x.



Revision 18276 - Directory Listing
Modified Tue Oct 4 19:36:25 2011 UTC (6 years ago) by jcfr
STYLE: Clean empty white spaces, update debug statements, re-order includes

Revision 18275 - Directory Listing
Modified Tue Oct 4 19:03:27 2011 UTC (6 years ago) by jcfr
COMP: Remove empty directories

Revision 18261 - Directory Listing
Modified Mon Oct 3 14:05:07 2011 UTC (6 years ago) by demian
ENH: Moving the Non-Local Means denoising algorithm for DWI images to the legacy folder

Revision 18260 - Directory Listing
Modified Sun Oct 2 18:06:21 2011 UTC (6 years ago) by alexy
BUG: fixed logic in qSlicerMainWindow::onLayoutActionTriggered()

Revision 18254 - Directory Listing
Modified Sat Oct 1 06:05:09 2011 UTC (6 years ago) by finetjul
COMP: No need of MRML in the Seeding module

Revision 18229 - Directory Listing
Modified Thu Sep 29 07:24:00 2011 UTC (6 years ago) by jcfr
ENH: Wrapped Qt libraries can now be loaded as regular python module

Revision 18165 - Directory Listing
Modified Thu Sep 22 14:30:08 2011 UTC (6 years ago) by millerjv
ENH: added dynamic compare view layouts

Modified the XML based view layout system to allow layouts to be modified.

Compare layouts are now defined programatically based on parameters in the
MRMLLayoutNode. There is a method in MRMLLayoutLogic to update the XML
descriptions for the compare view layouts.

Added menus to the layout controls (layout menu and layout toolbar) for
selecting between a variety of compare view layouts.

Added a new Compare Grid mode.

Revision 18157 - Directory Listing
Modified Wed Sep 21 19:50:42 2011 UTC (6 years ago) by jcfr
STYLE: Remove year from Kitware copyright

Revision 18156 - Directory Listing
Modified Wed Sep 21 19:49:48 2011 UTC (6 years ago) by jcfr
COMP: Remove empty Testing directory

Revision 18153 - Directory Listing
Modified Wed Sep 21 19:49:34 2011 UTC (6 years ago) by jcfr
COMP: Add macro vtkMRMLNodeNewMacro

Revision 18151 - Directory Listing
Modified Wed Sep 21 19:49:10 2011 UTC (6 years ago) by jcfr
ENH: Add qSlicerApplicationTpyclTest1

Revision 18142 - Directory Listing
Modified Wed Sep 21 19:48:51 2011 UTC (6 years ago) by jcfr
COMP: {cli, qt-scripted, qt-loadable}-modules built/installed under "share/Slicer-X.Y" directory

* ColorFiles and ParameterSets are directly available under "share/Slicer-X.Y"

* qSlicerCoreApplication set environment variable SLICER_SHARE_DIR to
have the value of "Sliscer_SHARE_DIR"

* Python and TCL scripts references resources using SLICER_SHARE_DIR environment variable

Revision 18130 - Directory Listing
Modified Tue Sep 20 21:05:47 2011 UTC (6 years ago) by finetjul
BUG: Fix crash in Execution Model Tour.

A step of 0 for an int parameter is not allowed and make crash the slider.

Revision 18128 - Directory Listing
Modified Tue Sep 20 18:55:26 2011 UTC (6 years ago) by finetjul
COMP: Fix unused variable compilation warnings

Revision 18126 - Directory Listing
Modified Tue Sep 20 17:59:34 2011 UTC (6 years ago) by finetjul
COMP: Fix unused variable compilation warnings

Revision 18111 - Directory Listing
Modified Mon Sep 19 16:44:13 2011 UTC (6 years, 1 month ago) by finetjul
STYLE: Set application logic to MouseModeToolBar

No need for global variable access here.
This improves code maintainability and robustness. 

Revision 18108 - Directory Listing
Modified Mon Sep 19 16:39:43 2011 UTC (6 years, 1 month ago) by finetjul
STYLE: vtkSlicerApplicationLogic derives from vtkMRMLApplicationLogic

There is only the need of 1 application logic.
All the modules (in MRML or Slicer) have a pointer to a unique application logic.
Rename qSlicerCoreApplication::appLogic() into qSlicerCoreApplication::applicationLogic()

Revision 18101 - Directory Listing
Modified Sat Sep 17 14:17:16 2011 UTC (6 years, 1 month ago) by alexy
BUG_FIXED: 1430: removed Undo/Redo from the Edit menu

Revision 18090 - Directory Listing
Modified Fri Sep 16 17:12:20 2011 UTC (6 years, 1 month ago) by inorton
ENH: change StoppingValue stepsize per #1426

Revision 18078 - Directory Listing
Modified Fri Sep 16 05:03:34 2011 UTC (6 years, 1 month ago) by finetjul
STYLE: Merge "Help" and "Feedbacks" menus

Update links to documentation.

Revision 18073 - Directory Listing
Modified Fri Sep 16 02:59:35 2011 UTC (6 years, 1 month ago) by finetjul
STYLE: Grey spacer, white splitter, no lightbox border in 1x1

Issue #1337

Revision 18071 - Directory Listing
Modified Fri Sep 16 01:05:23 2011 UTC (6 years, 1 month ago) by finetjul
ENH: Dump current vtk object into the EventBroker module

Revision 18067 - Directory Listing
Modified Thu Sep 15 21:23:56 2011 UTC (6 years, 1 month ago) by pieper
ENH: bring over new DicomToNrrd code from slicer3

Revision 18057 - Directory Listing
Modified Wed Sep 14 23:49:04 2011 UTC (6 years, 1 month ago) by finetjul
ENH: Central widget is grey, lighter grey for inactive lightbox borders and white for active ones

Issue #1337

Revision 18047 - Directory Listing
Modified Wed Sep 14 16:58:23 2011 UTC (6 years, 1 month ago) by jcfr
STYLE: Fix indent

Revision 18036 - Directory Listing
Modified Tue Sep 13 05:20:39 2011 UTC (6 years, 1 month ago) by finetjul
STYLE: Relink the dialogs to use CTRL + digit shortcuts

CTRL + 1: About
CTRL + 2: Settings
CTRL + 3: Python
CTRL + 4: Extension Manager
CTRL + 5: Side panel
CTRL + 6: Maximize view (not supported yet)
CTRL + 0: Error log

Revision 18031 - Directory Listing
Modified Mon Sep 12 23:25:33 2011 UTC (6 years, 1 month ago) by naucoin
ENH: add the screen capture and scene view buttons to a tool bar and add that to the main window

Revision 18030 - Directory Listing
Modified Mon Sep 12 22:07:20 2011 UTC (6 years, 1 month ago) by pieper
ENH: remove ThreeDViews and SlicesControllerToolbar

These two collapsable frames at the bottom of the module panel
were slated for removal as part of the cosmetic overhaul leading
up to the RSNA release.  J2 moved all of the slice-related functionality
into the slice controllers and 3d functionality into the 3d controller
so there was no longer a need for these.

Nicole is working on moving the SceneView buttons to the main 
toolbar.

Also removed here are the slice magnifier and the thumbnail
view of the 3D view.  We (Ron and Steve) determined that these were 
not serving their original intention and were taking up space
that would be better served by the DataProbe information.
In the future we envision the ability to create a slice magnifier
view using the layout manager.



Revision 18007 - Directory Listing
Modified Fri Sep 9 23:53:44 2011 UTC (6 years, 1 month ago) by pieper
ENH: initial checkin of Data Probe module to replace corner annotations

Track mouse location and update widget in main window to show
layer pixel information.  Relies on access to slice logic and slice
node information available from the slice widgets.  Slice widgets
are tracked via the layout manager.



Revision 18000 - Directory Listing
Modified Thu Sep 8 17:46:03 2011 UTC (6 years, 1 month ago) by hjohnson
COMP:  ITK_TYPENAME was only needed in MSVS6. Now that MSVS is c++ compliant, it is not needed.

Revision 17978 - Directory Listing
Modified Tue Sep 6 06:52:37 2011 UTC (6 years, 1 month ago) by jcfr
COMP: Force launcher settings to be reconfigured (fixes #1303)

Revision 17976 - Directory Listing
Modified Tue Sep 6 06:52:26 2011 UTC (6 years, 1 month ago) by jcfr
COMP: Option Slicer_BUILD_{CLI, LOADABLEMODULES, SCRIPTEDMODULES} shouldn't disable the functionality itself

* Enabling/Disabling these options will/will not build the modules existing
in the Slicer source tree but the code allowing to load such module will
be compiled.

Revision 17972 - Directory Listing
Modified Tue Sep 6 04:11:43 2011 UTC (6 years, 1 month ago) by jcfr
BUG: Main.cxx - "Loading module" message should be of type qDebug

Revision 17971 - Directory Listing
Modified Tue Sep 6 04:11:36 2011 UTC (6 years, 1 month ago) by jcfr
STYLE: Main.cxx - Remove unused code

Revision 17965 - Directory Listing
Modified Mon Sep 5 21:21:46 2011 UTC (6 years, 1 month ago) by jcfr
STYLE: Main.cxx - Display number of registered/loaded modules

Revision 17964 - Directory Listing
Modified Mon Sep 5 21:21:43 2011 UTC (6 years, 1 month ago) by jcfr
ENH: Update CTK Tag to include improvment related to module factories

Revision 17958 - Directory Listing
Modified Mon Sep 5 16:03:24 2011 UTC (6 years, 1 month ago) by jcfr
STYLE: Main.cxx - Start debug message with upper case

Revision 17937 - Directory Listing
Modified Sun Sep 4 23:32:40 2011 UTC (6 years, 1 month ago) by jcfr
ENH: Module are now referenced with this module name having "regular case".

* Module name is not systematically lower cased

* Module within python are still referenced using lower case module name:
   slicer.modules.add
   slicer.modules.transforms

* See https://github.com/commontk/CTK/commit/b3ddaf8123f95e0627930ae09485806aebf07e33

Revision 17928 - Directory Listing
Modified Fri Sep 2 22:43:27 2011 UTC (6 years, 1 month ago) by naucoin
ENH: scale back to just saving the scene to a directory, but leave the Zip method available for use

Revision 17927 - Directory Listing
Modified Fri Sep 2 21:36:50 2011 UTC (6 years, 1 month ago) by naucoin
ENH: first steps at creating the Slicer Data Bundle: save the scene into a dir (creating new storage nodes if necessary) and archive it using LibArchive. With the current version of libarchive can only use .tar.gz, but have #defines in place to use .zip when the version is bumped. TODO: unzip!

Revision 17915 - Directory Listing
Modified Thu Sep 1 15:03:24 2011 UTC (6 years, 1 month ago) by finetjul
STYLE: Normalize SIGNAL/SLOT connections

Fixed with Qt/util/normalize
More info on: http://marcmutz.wordpress.com/effective-qt/prefer-to-use-normalised-signalslot-signatures/

Revision 17888 - Directory Listing
Modified Tue Aug 30 14:14:06 2011 UTC (6 years, 1 month ago) by demian
ENH: JointLMMSE for DWI data: Fixed the use of the ITK writer on the source, now it can be used as a shared module

Revision 17867 - Directory Listing
Modified Sun Aug 28 06:31:22 2011 UTC (6 years, 1 month ago) by finetjul
ENH: Allow multiple file selection in the Volumes dialog.

Revision 17856 - Directory Listing
Modified Fri Aug 26 21:26:44 2011 UTC (6 years, 1 month ago) by jcfr
COMP: Rename Slicer_INSTALL_PLUGINS_BIN_DIR CMake variable into Slicer_INSTALL_CLIMODULES_BIN_DIR

Revision 17855 - Directory Listing
Modified Fri Aug 26 21:26:37 2011 UTC (6 years, 1 month ago) by jcfr
COMP: Rename CMake variables Slicer_(INSTALL_)PLUGINS_SHARE_DIR into Slicer_(INSTALL_)CLIMODULES_SHARE_DIR

Revision 17853 - Directory Listing
Modified Fri Aug 26 21:26:29 2011 UTC (6 years, 1 month ago) by jcfr
COMP: Rename Slicer_PLUGINS_BIN_DIR CMake variable into Slicer_CLIMODULES_BIN_DIR

Revision 17818 - Directory Listing
Modified Wed Aug 24 12:38:52 2011 UTC (6 years, 1 month ago) by hjohnson
ENH: Moved Legacy items to a separate menu item.

Now all legacy applications are grouped
under the same menu heading in Slicer.
Perhaps someday these can be put into an
extension.

Revision 17817 - Directory Listing
Modified Wed Aug 24 12:38:46 2011 UTC (6 years, 1 month ago) by hjohnson
STYLE:  Removed BORLAND, MSVS6 conditional code.

Revision 17816 - Directory Listing
Modified Wed Aug 24 12:38:18 2011 UTC (6 years, 1 month ago) by hjohnson
STYLE:  Configuring to use ITK style conventions

Formatting to ITK style compliance so that it is
easier to review code and make merging between
ITKv4 and BRAINSTools easier to understand.

This patch set includes no substanative changes,
only formatting changes.

Revision 17805 - Directory Listing
Modified Tue Aug 23 15:35:49 2011 UTC (6 years, 1 month ago) by hjohnson
ENH: ITKv4 Compiler warning exposed useless code

A compiler warning exposed a class constructor that was
completely useless (even in ITKv3). The code paradigm
seemed to have been propogated to every subsequent
transform class, but it was never used, and was
inconsistently implemented.

After removing, both Slicer4/ITKv3, Slicer4/ITKv4, BRAINS/ITKv3,
and BRAINS/ITKv4 built and passed tests, thus providing more
evidence that this API really had no use.

This patch set removes the useless API from the local
Slicer transforms, thus allowing both ITKv3 and ITKv4
to build from the same source tree.

Revision 17796 - Directory Listing
Modified Mon Aug 22 19:36:09 2011 UTC (6 years, 1 month ago) by millerjv
ENH: integrated the icons for the three over three and four over four layouts

Revision 17793 - Directory Listing
Modified Mon Aug 22 17:31:58 2011 UTC (6 years, 1 month ago) by millerjv
COMP: include file referenced was incorrect

Revision 17789 - Directory Listing
Modified Mon Aug 22 15:53:49 2011 UTC (6 years, 1 month ago) by finetjul
COMP: Remove unused variable warnings in qSlicerMainWindow and qSlicerVolumeRenderingSettingsPanel

Revision 17785 - Directory Listing
Modified Mon Aug 22 01:25:51 2011 UTC (6 years, 1 month ago) by hjohnson
COMP: Remove manual source copy of BRAINSTools

The manualy copied version of BRAINSTools was difficult
to maintain in Slicer because it was a copy of the main
development tree.  This caused several problems because it
was difficult to maintain a consistent version
due to merge conflicts that were constatnly arising.

A subsequent patch will add BRAINSTools as an
External_Project that pulls from a git tree that can
be more easily merged and maintained.

Revision 17784 - Directory Listing
Modified Mon Aug 22 01:25:29 2011 UTC (6 years, 1 month ago) by hjohnson
ENH: Transform classes compatible with ITKv[34]

Refactored the transform classes so that they were
compatible with both ITKv3, and ITKv4 simultaneously.

Revision 17783 - Directory Listing
Modified Mon Aug 22 01:25:24 2011 UTC (6 years, 1 month ago) by hjohnson
ENH:  ITKv4 with ITKv3 BSpline compatibility.

This patch allows building of Slicer and using the
historical ITKv3 definition of BSplineDeformableTransform.
We will be able to take advantage of the ITKv4 BSplineTransform
increamentally as each tools is converted on a needed basis.

There were some missing include headers that were
implicitly included in ITKv3, but need to be explicitly included in
ITKv4.

Revision 17779 - Directory Listing
Modified Sun Aug 21 20:22:06 2011 UTC (6 years, 1 month ago) by hjohnson
COMP: Removed unnecessary code

The code was causing compiler warning
and it was never used.

Revision 17774 - Directory Listing
Modified Sat Aug 20 19:43:27 2011 UTC (6 years, 2 months ago) by finetjul
ENH: Move Settings dialog in qSlicerApplication

Doing so allows modules to register new settings panels as the settings dialog doesn't depend on the optional main window anymore.

Revision 17765 - Directory Listing
Modified Fri Aug 19 19:51:55 2011 UTC (6 years, 2 months ago) by finetjul
COMP: Temporarily disable RobustStatisticsSegmenter until it compiles again.

Revision 17758 - Directory Listing
Modified Fri Aug 19 16:59:39 2011 UTC (6 years, 2 months ago) by naucoin
ENH: add a label map seeding test, using data from the mrml test data dir. Had to change the signature of main in Seeding.cxx as using const wouldn't let the test compile on my machine

Revision 17754 - Directory Listing
Modified Fri Aug 19 01:12:45 2011 UTC (6 years, 2 months ago) by hjohnson
COMP:  Removing compiler warning about nested '/*'

Revision 17740 - Directory Listing
Modified Wed Aug 17 19:16:22 2011 UTC (6 years, 2 months ago) by kedar_p
STYLE: Edits and file additions to rename 'SFLSRobustStat3DTest' as 'RobustStatSegmenter' which is more representative. This will be the 'module-name' used to call the algorithm from the Editor (GUI) extension (to be added soon).

Revision 17715 - Directory Listing
Modified Fri Aug 12 15:26:23 2011 UTC (6 years, 2 months ago) by alexy
ENH: replaced vtkDiffusionTensorMathematicsSimple with vtkDiffusionTensorMathematics

Revision 17709 - Directory Listing
Modified Thu Aug 11 23:30:28 2011 UTC (6 years, 2 months ago) by fedorov
BUG_FIXED: output to cout: Slicer CLI interprets output to cerr as error that
shows up in error log, this is confusing


Revision 17706 - Directory Listing
Modified Wed Aug 10 22:36:10 2011 UTC (6 years, 2 months ago) by finetjul
STYLE: Move toolbar visibility menu actions in the View menu entry

Revision 17700 - Directory Listing
Modified Wed Aug 10 17:39:19 2011 UTC (6 years, 2 months ago) by naucoin
ENH: move legacy registration algorithms to the Legacy submenu of the Registration category, bug 1328

Revision 17682 - Directory Listing
Modified Sun Aug 7 04:04:25 2011 UTC (6 years, 2 months ago) by finetjul
BUG: Don't use std::ends when using std::ostringstream

When Qt tries to read the string, it then get confused and can't convert back to integer if needed:
std::ostringstream stream;
stream << 1 << ends;
QString myString = QString::fromStdString(stream.str());
std::cout << myString.toInt() << std::endl;
console output:
0

Revision 17674 - Directory Listing
Modified Fri Aug 5 05:27:07 2011 UTC (6 years, 2 months ago) by finetjul
BUG: jointLMMSE is not suitable for being a Shared Object module

By enforcing NrrdImageIO, it prevents the ImageWriter to use MRMLIDImageIO to write the image into a shared memory with Slicer.

Revision 17659 - Directory Listing
Modified Mon Aug 1 21:37:48 2011 UTC (6 years, 2 months ago) by jcfr
STYLE: Application/SlicerQT/CMakeLists.txt - Fix typo

Revision 17598 - Directory Listing
Modified Fri Jul 29 04:24:34 2011 UTC (6 years, 2 months ago) by finetjul
COMP: Typo in includes of N4ITKBiasFieldCorrection

Fix for operating systems that enforce casing of file paths.

Revision 17595 - Directory Listing
Modified Fri Jul 29 01:06:27 2011 UTC (6 years, 2 months ago) by hjohnson
ENH:  N4 base classes are now part of ITKv4

This patch set changes the file names so that the
local ITKv3 versions do not hide the ITKv4 versions of
the files that have numerous bug fixes and documentation
enhancements.

Revision 17594 - Directory Listing
Modified Fri Jul 29 01:06:24 2011 UTC (6 years, 2 months ago) by hjohnson
ENH: Improved N4 error checking.

Revision 17592 - Directory Listing
Modified Fri Jul 29 01:06:20 2011 UTC (6 years, 2 months ago) by hjohnson
COMP: Made compilation compatible with ITKv4

Use of Rigid3DTransform in Slicer was not
following the intended use of the class, and
it was possible that the use was not safe.

In many cases the intended behavior (and
more correct use) is to use the base class
to gain access to the polymorphic
member functions.

This patch implements the proposed changes
outlined by Luis Ibanez on the ITKv4
developer mailing list:

http://www.itk.org/mailman/private/insight-developers/2011-January/016720.html

Revision 17591 - Directory Listing
Modified Fri Jul 29 01:06:17 2011 UTC (6 years, 2 months ago) by hjohnson
ENH:  Added ExtractImageFilter Strategy

ITKv4 requires that the ExtractImageFilter
define the collapse strategy to be used.

Revision 17590 - Directory Listing
Modified Fri Jul 29 01:06:13 2011 UTC (6 years, 2 months ago) by hjohnson
COMP: Missing include for FloatingPointExceptions

Revision 17573 - Directory Listing
Modified Tue Jul 26 16:56:42 2011 UTC (6 years, 2 months ago) by finetjul
COMP: Remove unnecessary header inclusions from implementation files (part 2)


Revision 17572 - Directory Listing
Modified Tue Jul 26 15:59:30 2011 UTC (6 years, 2 months ago) by finetjul
STYLE: Remove unnecessary header inclusions from implementation files (part1)

Revision 17557 - Directory Listing
Modified Thu Jul 21 17:01:20 2011 UTC (6 years, 2 months ago) by lorensen
ENH: ITKv4 now checks for compatible image information.

ITKv4 image filters, by default, now check that image filter inputs
occupy the same physical space This can be oridden for filters that
do not have this requirement. The baseline needed updating to
accommodate the ITKv4 changes.



Revision 17533 - Directory Listing
Modified Wed Jul 20 19:43:42 2011 UTC (6 years, 3 months ago) by alexy
ENH: fixed module names

Revision 17508 - Directory Listing
Modified Mon Jul 18 20:17:13 2011 UTC (6 years, 3 months ago) by taylor
COMP: Move baseline data of all CLIs into a respective dedicated "Data/Baseline" subdirectory

* As a first step toward the modularization of Slicer, the data files (in that case Baseline) 
have been moved at the module level.


Revision 17506 - Directory Listing
Modified Mon Jul 18 15:29:40 2011 UTC (6 years, 3 months ago) by haehn
COMP: Added FIND_PACKAGE calls to be able to compile the BRAINSTools.


Revision 17503 - Directory Listing
Modified Sat Jul 16 19:26:19 2011 UTC (6 years, 3 months ago) by lorensen
ENH: ITKv4 has renamed .txx to .hxx

Removed the include of .txx which was not used anyway. Now in ITKv4,
.txx files are renamed to .hxx.



Revision 17502 - Directory Listing
Modified Sat Jul 16 15:01:53 2011 UTC (6 years, 3 months ago) by lorensen
ENH: ITKv4 has renamed .txx to .hxx

Removed the include of .txx which was not used anyway. Now in ITKv4,
.txx files are renamed to .hxx.



Revision 17464 - Directory Listing
Modified Tue Jul 12 05:42:32 2011 UTC (6 years, 3 months ago) by finetjul
COMP: Keep strict necessary includes in header files

This fasten compilation

Revision 17459 - Directory Listing
Modified Mon Jul 11 23:41:00 2011 UTC (6 years, 3 months ago) by jcfr
STYLE: CLI/CMakeLists - Add comment

Revision 17404 - Directory Listing
Modified Sat Jul 9 01:55:20 2011 UTC (6 years, 3 months ago) by jcfr
ENH: Add '--disable-python' command line argument

* Passing this argument is equivalent to build Slicer with Slicer_USE_PYTHONQT:OFF

Revision 17396 - Directory Listing
Modified Fri Jul 8 21:05:32 2011 UTC (6 years, 3 months ago) by finetjul
ENH: vtkMRMLDisplayNode::GetImageData now returns only the end of the pipeline

It doesn't return the image up-to-date.
Use vtkMRMLDisplayNode::GetUpToDateImageData() instead.
vtkMRMLVolumeDisplayNode::GetInput() is removed, use GetInputImageData() instead.

Revision 17394 - Directory Listing
Modified Fri Jul 8 16:00:44 2011 UTC (6 years, 3 months ago) by jcfr
COMP: Exclude ScriptedModule related class given the value of Slicer_BUILD_QTSCRIPTEDMODULES

Revision 17384 - Directory Listing
Modified Fri Jul 8 09:42:53 2011 UTC (6 years, 3 months ago) by jcfr
ENH: Move baseline data of "Cast" CLI into a dedicated "Data/Baseline" subdirectory

Revision 17376 - Directory Listing
Modified Thu Jul 7 17:23:04 2011 UTC (6 years, 3 months ago) by jcfr
COMP: RegisterImagesModule refers to CommandLineSharedLibraryWrapper.cxx using Slicer_CLI_SHARED_LIBRARY_WRAPPER_CXX

* This fix the last hardcoded reference of CommandLineSharedLibraryWrapper.cxx
that was omitted in commit r17370

Revision 17375 - Directory Listing
Modified Thu Jul 7 17:23:02 2011 UTC (6 years, 3 months ago) by jcfr
COMP: Test named 'itkTestMainExtendedScalarTest' associated with ResampleDTI should not reference "Add" baseline

 Waiting the problem is fixed, a warning will be reported.

 Indeed, the baseline associated with each command line module has been moved within
the Data/Baseline subdirectory of each module. For that reason, ResampleDTI shouldn;t
reference the baseline 'AddTest_DOUBLE.mha' as input data.

Revision 17374 - Directory Listing
Modified Thu Jul 7 17:22:59 2011 UTC (6 years, 3 months ago) by jcfr
ENH: Move baseline data of "Add" CLI into a dedicated "Data/Baseline" subdirectory

Revision 17372 - Directory Listing
Modified Thu Jul 7 15:53:25 2011 UTC (6 years, 3 months ago) by lorensen
BUG: Missing include after CLI reorganization

Need to add Applications/CLI to include path to find itkTestMain.h.



Revision 17370 - Directory Listing
Modified Thu Jul 7 04:52:12 2011 UTC (6 years, 3 months ago) by jcfr
COMP: DiffeomorphicDemonsRegistration and REgisterImagesmodule refers CommandLineSharedLibraryWrapper.cxx using Slicer_CLI_SHARED_LIBRARY_WRAPPER_CXX

Revision 17347 - Directory Listing
Modified Wed Jul 6 20:42:40 2011 UTC (6 years, 3 months ago) by jcfr
ENH: Move CLI module sources and tests to a dedicated folder

* This is a first step toward the modularization of Slicer

* The different steps are described below:

# Make cli module directory
cd Applications/CLI
ls -1 *.xml | cut -d'.' -f1 | xargs mkdir

# Open each future CMakeLists.txt using gedit
for i in `ls -1 *.xml | cut -d'.' -f1`; do `gedit $i/CMakeLists.txt&` ; done

# Manual operation: Copy CMake code from Applications/CLI/CMakeLists.txt to each CMakeLists.txt

# Make cli Tesing module directory
for i in `ls -1 *.xml | cut -d'.' -f1`; do mkdir $i/Testing ; done

# Open each future Testing/CMakeLists.txt using gedit
for i in `ls -1 *.xml | cut -d'.' -f1`; do `gedit $i/Testing/CMakeLists.txt&` ; done

# Manual operation: Copy CMake code from Applications/CLI/CMakeLists.txt to each CMakeLists.txt

# Get the list of modules that should be add in Applications/CLI/CMakeLists.txt using add_subdirectory()
ls -1 *.xml | cut -d'.' -f1

# Move *.{xml, cxx} files into their respective directory
for i in `ls -1 *.xml | cut -d'.' -f1`; do mv $i.{xml,cxx} $i; done

ENH: Add Slicer_BaseCLI_INCLUDE_DIRS to SlicerConfig

* Note that ideally the file provided by SlicerBaseCLI should be added
to SlicerExecutationModel.

COMP: Remove find_package and include_dir from CLI/CMakeLists.txt

* Each module should include its required dependencies

Revision 17344 - Directory Listing
Modified Tue Jul 5 23:35:29 2011 UTC (6 years, 3 months ago) by jcfr
COMP: Speed up compilation of CLI Tests by linking to loadable module instead of recompiling when possible.

* Thanks to Casey Goodlett for its contribution

Revision 17339 - Directory Listing
Modified Tue Jul 5 22:54:20 2011 UTC (6 years, 3 months ago) by jcfr
COMP: Applications/CLI/Testing/CMakeLists.txt - Remove extra code

* include_regular_expression("^.*$") is not required. The default value is
alreadt set to "^.*$". See http://www.cmake.org/cmake/help/cmake-2-8-docs.html#command:include_regular_expression

Revision 17291 - Directory Listing
Modified Fri Jul 1 14:09:05 2011 UTC (6 years, 3 months ago) by jcfr
STYLE: Remove extra comment

Revision 17287 - Directory Listing
Modified Fri Jul 1 04:15:51 2011 UTC (6 years, 3 months ago) by jcfr
ENH: SlicerExecutionModel is now an external project

* A single find_package(SlicerExecutionModule) can be used.

* Calling find_package(SlicerExecutionModule ...) will systematically define the
ModuleDescriptionParser_DIR, GenerateCLP_DIR and TCLAP_DIR

* Assuming ModuleDescriptionParser_DIR, GenerateCLP_DIR or TCLAP_DIR are defined,
the corresponding find_package() call are still valid.

* Call of the form find_package(SlicerExecutionModule REQUIRED GenerateCLP) or
find_package(SlicerExecutionModule REQUIRED ModuleDescriptionParser) are valid and
will:
  - include the target of the specified components
  - set SlicerExecutionModel_INCLUDE_DIRS, SlicerExecutionModel_LIBRARIES appropriately.

* Known issue: SlicerExecutionModel_LIBRARY_DIRS is not defined. Since the
list of library SlicerExecutionModel_LIBRARIES is defined and the associated
CMake target imported. If CMake 2.6 or above is used, this shouldn't be a problem.

Revision 17274 - Directory Listing
Modified Wed Jun 29 20:53:30 2011 UTC (6 years, 3 months ago) by haehn
STYLE: Annotations: First batch of renaming the module to Annotations.

- to rename the module from "Annotation" to "Annotations", the following first steps were performed:
  - move folder QTModules/Annotation to QTModules/Annotations
  - updated QTModules/CMakeLists.txt to point to the new folder
  - inside the Annotations module, all libraries follow the new naming conventions. This includes:
   -- qSlicerAnnotationsModuleWidgets
   -- qSlicerAnnotationsModuleWidgetsPythonQt
   -- qSlicerAnnotationsModuleWidgetsPlugin
   -- vtkSlicerAnnotationsModuleMRML
   -- vtkSlicerAnnotationsModuleMRMLPython
   -- vtkSlicerAnnotationsModuleMRMLPythonD
   -- AnnotationsCxxTests   
   -- qSlicerAnnotationsModule
  - the following modules were updated to link against the new targets:
   -- VolumeRendering
   -- CropVolume
   -- TractographyFiducialSeeding
  - all references to the Annotations module in Base/ were updated (including comments)
  
- IMPORTANT: before re-building Slicer4, please delete the following files to remove old Annotation libraries
  - bin/*Anno*
  - qt-loadable-modules/*Anno*
  - QTModules/Annotation/
  - bin/Python/slicer/modulemrml/*Anno*
  


Revision 17264 - Directory Listing
Modified Tue Jun 28 07:48:42 2011 UTC (6 years, 3 months ago) by jcfr
BUG: DicomToNrrdConverterTest - Following suggestion of Mark S, Scully , added --useBMatrixGradientDirections DicomToNrrdConverterTest.

* The problem is fixed on Linux.

Revision 17263 - Directory Listing
Modified Tue Jun 28 07:48:40 2011 UTC (6 years, 3 months ago) by jcfr
COMP: Rename some tests to avoid name duplication.

Revision 17244 - Directory Listing
Modified Sun Jun 26 23:43:20 2011 UTC (6 years, 3 months ago) by demian
BUG: #0001160 Diffusion tensor mathematics: Corrected spelling and calculation of middle eigenvalue

Revision 17208 - Directory Listing
Modified Thu Jun 23 19:18:09 2011 UTC (6 years, 3 months ago) by jcfr
STYLE: Rename Doc/copyright/copyright.txt into COPYRIGHT.txt

Revision 17191 - Directory Listing
Modified Thu Jun 23 01:39:37 2011 UTC (6 years, 3 months ago) by jcfr
STYLE: Move CMake commands to match new conventions

The next step in removing end-of-lines is to run through all the
CMakeLists.txt files and clean them up.

This also changes all the key words to lower
case. The primary reason for changing key words is that all documentation for
CMakeLists.txt now shows the key words as lower case. Even the printed
“Mastering CMake v5” uses lower case. I’ve come across this several
times in my class where students stumble over the fact that the
documentation about Cmake does not match the implementation in ITK.

I have a script (a wrapper around a vim macro) written that can make
these substituions reliably (Tested on the BRAINS tree, the Slicer3
tree, and the ITK tree without causing any errors).  More complete
documentation can be found in
ITK/Utilities/Maintenance/HowToCreateTheCMakeCaseConversion.txt

Revision 17177 - Directory Listing
Modified Wed Jun 22 16:55:15 2011 UTC (6 years, 3 months ago) by jcfr
STYLE: Change arguments "--disable-*-module" into "--disable-*-modules"

* Since all modules are expected to be disabled, it make sens to use
the plural form.

Revision 17176 - Directory Listing
Modified Wed Jun 22 16:55:11 2011 UTC (6 years, 3 months ago) by jcfr
ENH: Add --disable-scripted-loadable-module option

* It's now possible to either disable the loadable modules or the scripted
loadable modules.

Revision 17147 - Directory Listing
Modified Mon Jun 20 03:59:45 2011 UTC (6 years, 4 months ago) by finetjul
COMP: Don't include python console settings when pythonqt is turned off

Revision 17132 - Directory Listing
Modified Sat Jun 18 23:47:24 2011 UTC (6 years, 4 months ago) by jcfr
COMP: Enable CTKAppLauncher on mac (#1211)

This reverts commit r17002 and fix issue #1211

See http://na-mic.org/Mantis/view.php?id=1211

Revision 17129 - Directory Listing
Modified Sat Jun 18 23:47:18 2011 UTC (6 years, 4 months ago) by jcfr
ENH: CMake - Use "LIST(REMOVE_ITEM ..)" instead of deprecated "REMOVE(...)"

Revision 17128 - Directory Listing
Modified Sat Jun 18 23:47:11 2011 UTC (6 years, 4 months ago) by jcfr
ENH: SIMPLE_TEST macro now considers ${ARGN}

* ARGN: holds the list of argument past the last expected argument

Revision 17127 - Directory Listing
Modified Sat Jun 18 23:47:01 2011 UTC (6 years, 4 months ago) by jcfr
STYLE: Use "IF(BUILD_TESTING) .. ENDIF()" format consistently

Revision 17120 - Directory Listing
Modified Sat Jun 18 21:11:11 2011 UTC (6 years, 4 months ago) by lorensen
BUG: Floating point divide by zero

Added divisor 0 blockers to prevent floating point divide by
zero. Suspect something else may be wrong.



Revision 17119 - Directory Listing
Modified Sat Jun 18 13:58:00 2011 UTC (6 years, 4 months ago) by jcfr
ENH: Slicer_Base_INCLUDE_DIRS now contains only directory from Slicer/Base

Revision 17118 - Directory Listing
Modified Sat Jun 18 13:57:57 2011 UTC (6 years, 4 months ago) by jcfr
COMP: Use <PROJECT_NAME>_INCLUDE_DIRS variable whenever possible

* Update vtkITKConfig and vtkTeemConfig to expose the new variable.

* Simplify Libs/CMakeLists.txt

Revision 17091 - Directory Listing
Modified Fri Jun 17 23:44:55 2011 UTC (6 years, 4 months ago) by finetjul
ENH: Add revision number in qSlicerAboutDialog help.

Revision 17086 - Directory Listing
Modified Fri Jun 17 17:12:40 2011 UTC (6 years, 4 months ago) by lorensen
COMP: Disable FP excpetions for NRRD

The vtkNRRDReader/Writer purposely have divide by zero code. Since the
itk test driver enables floating point exceptions, this patch disables
floating point exception checking for those tests that use
vtkNRRDReader and/or Writer.



Revision 17084 - Directory Listing
Modified Fri Jun 17 13:45:51 2011 UTC (6 years, 4 months ago) by lorensen
COMP: ITKv4 API change.

The API for ThreadedGenerateData has been changed in ITKv4.
Prior to ITKv4 it was:
void ThreadedGenerateData( const OutputImageRegionType &,
                           int) ;
In ITKv4 it is:
void ThreadedGenerateData( const OutputImageRegionType &,
                           ThreadIdType) ;




Revision 17083 - Directory Listing
Modified Fri Jun 17 13:39:18 2011 UTC (6 years, 4 months ago) by lorensen
COMP: ITKv4 API change.

The API for ThreadedGenerateData has been changed in ITKv4.
Prior to ITKv4 it was:
void ThreadedGenerateData( const OutputImageRegionType &,
                           int) ;
In ITKv4 it is:
void ThreadedGenerateData( const OutputImageRegionType &,
                           ThreadIdType) ;




Revision 17082 - Directory Listing
Modified Fri Jun 17 13:22:19 2011 UTC (6 years, 4 months ago) by lorensen
COMP: ITKv4 API change.

The API for ThreadedGenerateData has been changed in ITKv4.
Prior to ITKv4 it was:
void ThreadedGenerateData( const OutputImageRegionType &,
                           int) ;
In ITKv4 it is:
void ThreadedGenerateData( const OutputImageRegionType &,
                           ThreadIdType) ;



Revision 17051 - Directory Listing
Modified Fri Jun 17 05:59:37 2011 UTC (6 years, 4 months ago) by finetjul
BUG: qMRMLEventLoggerWidget was deleted when it went out of scope

Revision 17047 - Directory Listing
Modified Thu Jun 16 19:08:30 2011 UTC (6 years, 4 months ago) by demian
BUG: Corrected bug in tensor estimation using masks

Revision 17009 - Directory Listing
Modified Tue Jun 14 14:49:52 2011 UTC (6 years, 4 months ago) by finetjul
BUG: Hangs if closeAllWindows() is called in closeEvent()

Revision 17002 - Directory Listing
Modified Mon Jun 13 09:19:05 2011 UTC (6 years, 4 months ago) by jcfr
COMP: Disable CTKAppLauncher on mac

Revision 16991 - Directory Listing
Modified Sun Jun 12 22:19:30 2011 UTC (6 years, 4 months ago) by finetjul
ENH: Closing the mainwindow shall close all the windows

If there is no window to start with, then it's the last closed window that exit the application.

Revision 16988 - Directory Listing
Modified Sun Jun 12 22:16:14 2011 UTC (6 years, 4 months ago) by jcfr
COMP: Rename macro Slicer_INSTALL_* into Slicer_* to be consistent with the values used to configure them.

* In vtkSlicerConfigure.h, the macro were improperly names.

#define Slicer_INSTALL_QtPlugins_DIR "@Slicer_QtPlugins_DIR@"

instead of

#define Slicer_QtPlugins_DIR "@Slicer_QtPlugins_DIR@"

Revision 16947 - Directory Listing
Modified Sat Jun 11 22:04:48 2011 UTC (6 years, 4 months ago) by jcfr
ENH: If it applies, propose to restart Slicer when settings dialog is closed.

Revision 16931 - Directory Listing
Modified Sat Jun 11 04:31:47 2011 UTC (6 years, 4 months ago) by finetjul
ENH: Initialy show the splashscreen with a message

Revision 16917 - Directory Listing
Modified Fri Jun 10 15:57:12 2011 UTC (6 years, 4 months ago) by finetjul
ENH: Cleanup splash screen messages

Revision 16916 - Directory Listing
Modified Fri Jun 10 15:10:46 2011 UTC (6 years, 4 months ago) by finetjul
BUG: At startup display the correct module to be loaded in the splashscreen

Revision 16915 - Directory Listing
Modified Fri Jun 10 14:55:17 2011 UTC (6 years, 4 months ago) by finetjul
ENH: Closes all the top level windows on exit.

Revision 16909 - Directory Listing
Modified Fri Jun 10 00:04:11 2011 UTC (6 years, 4 months ago) by jcfr
BUG: Call updatePythonOsEnviron() after python is initialized.

Before that change, python was initialized within qSlicerCoreApplication
as a side effect of calling executeScript().

Ideally, the python manager should be fixed to prevent calling its
methods if pythonqt hasn't been explicitly initialized.

If possible, an other approach could be to proceed to all required initialization
within its constructor.

Revision 16877 - Directory Listing
Modified Wed Jun 8 15:44:22 2011 UTC (6 years, 4 months ago) by jcfr
BUG: DiffusionWeightedMasking - Fix memory leaks

Revision 16876 - Directory Listing
Modified Wed Jun 8 15:31:02 2011 UTC (6 years, 4 months ago) by jcfr
BUG: Fix RegisterImagesMultiResTest

 * Use add_test(NAME ... COMMAND ..) signature
 * Refer to the test executable using a generator expression

Revision 16875 - Directory Listing
Modified Wed Jun 8 14:41:02 2011 UTC (6 years, 4 months ago) by jcfr
BUG: Fix SparseFieldLevelSetContourTest

* Rename entry point from SparseFieldLevelSetContour1Test to SparseFieldLevelSetContourTest

Revision 16874 - Directory Listing
Modified Wed Jun 8 14:37:28 2011 UTC (6 years, 4 months ago) by jcfr
BUG: Fix MergeModelsTestCompare

* Simplify run_MergeModelsTest
* Use generator expression in add_test() call. the generator expression
will be expanded to match the location of the associated target.

Revision 16868 - Directory Listing
Modified Wed Jun 8 11:40:04 2011 UTC (6 years, 4 months ago) by jcfr
ENH: Change environment variable Slicer_HOME to SLICER_HOME

On windows, environment variable names are case insensitive, when using
either QProcessEnvironement() or os.putenv(), both Qt and python
will set the variable using uppercase(name).

To properly work with python and Qt, the environment variable Slicer_HOME
has been changed into SLICER_HOME. That way the name used to set the variable
will allow to retrieve the environment variable value across all platforms
and using either Qt, python or Tcl.

Revision 16867 - Directory Listing
Modified Wed Jun 8 10:59:16 2011 UTC (6 years, 4 months ago) by jcfr
ENH: Quit if Slicer QMainWindow is closed

Note that if Slicer is started with "--no-main-window"
and "--show-python-interactor", closing the python interactor will also
quit the application.

Revision 16847 - Directory Listing
Modified Wed Jun 8 00:18:54 2011 UTC (6 years, 4 months ago) by jcfr
COMP: Print an error if Application/GUI is included and INCR_{TCL,TK}_LIBRARY not defined

Revision 16844 - Directory Listing
Modified Tue Jun 7 22:47:06 2011 UTC (6 years, 4 months ago) by jcfr
ENH: Add more explicit message when enabling launcher additional option

The following format is considered:

 Enabling Slicer launcher option: --<LONG_ARG>

Revision 16831 - Directory Listing
Modified Tue Jun 7 17:28:48 2011 UTC (6 years, 4 months ago) by finetjul
ENH: Add "--VisualStudio" launcher option to open Visual Studio

Revision 16803 - Directory Listing
Modified Sat Jun 4 06:56:02 2011 UTC (6 years, 4 months ago) by jcfr
ENH: Add "--gnome-terminal", "--xterm", "--ddd" and "--gdb" arguments to launcher if it applies.

Revision 16802 - Directory Listing
Modified Sat Jun 4 06:55:55 2011 UTC (6 years, 4 months ago) by jcfr
ENH: CTKAppLauncher - Add terminal command line option to the NO_SPLASH list

Command line option like "--help", "--version", ... shouldn't
display a splash screen.

Revision 16801 - Directory Listing
Modified Sat Jun 4 06:55:48 2011 UTC (6 years, 4 months ago) by jcfr
ENH: Add "--designer" argument to launcher if Qt designer is available

Revision 16798 - Directory Listing
Modified Sat Jun 4 06:55:32 2011 UTC (6 years, 4 months ago) by jcfr
STYLE: Remove commented code, remove extra empty lines and fix indent

Revision 16777 - Directory Listing
Modified Sat Jun 4 06:48:05 2011 UTC (6 years, 4 months ago) by jcfr
ENH: On Apple set SlicerQT's OUTPUT_NAME to be Slicer.app

Also re-enable the AppLauncher in the build tree but don't install it in the install tree (for now).

Revision 16771 - Directory Listing
Modified Sat Jun 4 06:47:35 2011 UTC (6 years, 4 months ago) by jcfr
ENH: Refactor Install rule variables to only be used in install commands.

Added a second set of variables named Slicer_<blah>_DIR which contain the appropriate directory prefixes such as bin lib share. These variables can be used reference file in the build or install trees such as the input/output of a configure command. Slicer_INSTALL_<blah> should only be used for install commands as on the Mac these variables will be prefixed with Slicer.app\Contents which we likely do not want in the root of the build tree.

Revision 16712 - Directory Listing
Modified Tue May 31 22:35:41 2011 UTC (6 years, 4 months ago) by jcfr
ENH: Delegates the instantiation of qSlicerCoreCommandOptions / qSlicerCommandOptions to their qSlicerApplication pimpl equivalent

Revision 16710 - Directory Listing
Modified Tue May 31 22:35:35 2011 UTC (6 years, 4 months ago) by jcfr
ENH: Factorized qSlicer{Core}Application initialization steps

 - Removed methods qSlicer{Core}Application::initialize
 - Removed methods qSlicerCoreApplication::isInitialized
 - Added method qSlicerCoreApplication::parseArguments(bool& exitWhenDone)
 - Move initialization code specific to MRMLScene into qSlicerCoreApplication::setMRMLScene
 - Remove call to initialize in qSlicer tests
 - Split code from Main.cxx into smaller local functions:
     * initializePython
     * initializePythonConsole
     * registerLoadableModuleFactory
     * registerCLIModuleFactory
     * showMRMLEventLoggerWidget

Revision 16709 - Directory Listing
Modified Tue May 31 22:35:31 2011 UTC (6 years, 4 months ago) by jcfr
ENH: qSlicerCLI{Loadable, Executable}Factory do not rely directly on qSlicerApplication

The method "setTempDirectory()" has been added. If no temp directory is set,
 QDir::tempPath() will be used.

Revision 16701 - Directory Listing
Modified Mon May 30 20:48:00 2011 UTC (6 years, 4 months ago) by jcfr
STYLE: SlicerUnitTestTest - Fix indent and add doc string

Revision 16700 - Directory Listing
Modified Mon May 30 20:47:58 2011 UTC (6 years, 4 months ago) by jcfr
COMP: Add SlicerMacroPythonTesting file

It contains the following helper macros:
  SLICER_ADD_PYTHON_TEST
  SLICER_ADD_PYTHON_UNITTEST

Revision 16698 - Directory Listing
Modified Mon May 30 20:47:55 2011 UTC (6 years, 4 months ago) by jcfr
BUG: Fix macro SLICER_ADD_PYTHON_TEST - SCRIPT_ARGS is a multivalue arg

Revision 16697 - Directory Listing
Modified Mon May 30 20:47:53 2011 UTC (6 years, 4 months ago) by jcfr
ENH: Add unittest support to slicer.testing

Revision 16696 - Directory Listing
Modified Mon May 30 20:47:51 2011 UTC (6 years, 4 months ago) by jcfr
ENH: SLICER_ADD_PYTHON_TEST macro - Ignore Slicer resource file when using --python-script command line argument

Revision 16695 - Directory Listing
Modified Mon May 30 20:47:48 2011 UTC (6 years, 4 months ago) by jcfr
ENH: Add test checking if "--python-code" command line argument works properly

Revision 16684 - Directory Listing
Modified Fri May 27 21:24:11 2011 UTC (6 years, 4 months ago) by jcfr
ENH: Python - Add slicer testing module

The testing module allows to enable testing and exit slicer with the
appropriate exit code. The function exitSuccess() and exitFailture()
allow to set the exit code.

Added application attribute named "AA_EnableTesting". This attribute can
be set from python using 'slicer.testing.setEnabled()'

Revision 16680 - Directory Listing
Modified Fri May 27 21:24:03 2011 UTC (6 years, 4 months ago) by jcfr
STYLE: Fix indent and remove extra comment

Revision 16679 - Directory Listing
Modified Fri May 27 21:24:01 2011 UTC (6 years, 4 months ago) by jcfr
ENH: Show disclaimer dialog after Qt event loop is started

The dialog will be shown after the command line arguments are processed.

This will allow to both:
 - check if testing mode is enabled before showing the popup.
 - and ensure that calling  QCoreApplication::exit() within handleCommandLineArguments
works as expected.

Revision 16677 - Directory Listing
Modified Fri May 27 21:23:58 2011 UTC (6 years, 4 months ago) by jcfr
COMP: Rename LAUNCH_EXE into Slicer_LAUNCH_COMMAND

Revision 16676 - Directory Listing
Modified Fri May 27 21:23:44 2011 UTC (6 years, 4 months ago) by jcfr
COMP: Rename Slicer_EXECUTABLE into Slicer_LAUNCHER_EXECUTABLE

Revision 16675 - Directory Listing
Modified Fri May 27 20:23:52 2011 UTC (6 years, 4 months ago) by finetjul
ENH: The default size hint of qMRMLThreeDViewsControllerWidget is too big

for the Slicer application. We don't want to listen to its size hint then.

Revision 16674 - Directory Listing
Modified Fri May 27 19:57:22 2011 UTC (6 years, 4 months ago) by haehn
ENH: Added BSplineToDeformationField from the Slicer3 trunk as a CLI.



Revision 16657 - Directory Listing
Modified Wed May 25 17:09:05 2011 UTC (6 years, 4 months ago) by jcfr
ENH: Do not use ctkErrorLogStatusMessageHandler

Application status message won't be logged.

Revision 16651 - Directory Listing
Modified Tue May 24 20:46:46 2011 UTC (6 years, 4 months ago) by pieper
COMP: don't build shared ibrary version of tensor scalar estimation since it uses the nrrd reader and does not understand the shared memory pointer access

Revision 16602 - Directory Listing
Modified Wed May 18 01:27:52 2011 UTC (6 years, 5 months ago) by jcfr
STYLE: Fix spell check - "instantiate" instead of "instanciate"

Revision 16596 - Directory Listing
Modified Tue May 17 19:46:18 2011 UTC (6 years, 5 months ago) by demian
ENH: Refactoring diffusion tensor estimation

Revision 16594 - Directory Listing
Modified Tue May 17 18:22:26 2011 UTC (6 years, 5 months ago) by zach.mullen
BUG: Copy parallel-safe midas.cmake into BRAINSTools.

Revision 16592 - Directory Listing
Modified Tue May 17 17:11:08 2011 UTC (6 years, 5 months ago) by jcfr
COMP: SparseFieldLevelSetContour - Fix spellcheck and append Lib prefix to exports macro

Indeed, to work properly the exports macro should match the name of
the associated project. In the present case, the library SparseFieldLevelSetContourLib
and not the executable SparseFieldLevelSetContour is being built.

Using the proper should get rid of the "inconsistent dll linkage" errors.

Revision 16591 - Directory Listing
Modified Tue May 17 16:59:23 2011 UTC (6 years, 5 months ago) by jcfr
COMP: SparseFieldLevelSetContour - Fix link error by exporting symbol

Revision 16590 - Directory Listing
Modified Tue May 17 16:59:21 2011 UTC (6 years, 5 months ago) by jcfr
COMP: Rename SparseFieldLevelSetContour1Test into SparseFieldLevelSetContourTest

Revision 16587 - Directory Listing
Modified Tue May 17 06:41:15 2011 UTC (6 years, 5 months ago) by jcfr
COMP: OrientImageTest - Use valid directory to reference testing data

Revision 16586 - Directory Listing
Modified Tue May 17 06:41:07 2011 UTC (6 years, 5 months ago) by jcfr
COMP: Add_test now uses the generator expression $<TARGET_FILE:...>

Revision 16585 - Directory Listing
Modified Tue May 17 06:40:55 2011 UTC (6 years, 5 months ago) by jcfr
COMP: Replace '${Slicer_BINARY_DIR}/Slicer3' with ${Slicer_EXECUTABLE}

Revision 16582 - Directory Listing
Modified Tue May 17 06:40:39 2011 UTC (6 years, 5 months ago) by jcfr
STYLE: Remove extra comments and unused code

Revision 16581 - Directory Listing
Modified Tue May 17 06:40:30 2011 UTC (6 years, 5 months ago) by jcfr
STYLE: Change 'Slicer3' into 'Slicer' in comments and description text

Revision 16580 - Directory Listing
Modified Tue May 17 06:40:21 2011 UTC (6 years, 5 months ago) by jcfr
COMP: Remove called to "find_package(Slicer3)" in Modules CMakeLists.txt

Revision 16566 - Directory Listing
Modified Mon May 16 19:39:34 2011 UTC (6 years, 5 months ago) by mscully
BUG: Corrected B-Value threshold.

Revision 16565 - Directory Listing
Modified Mon May 16 19:09:38 2011 UTC (6 years, 5 months ago) by mscully
ENH: Added full DicomToNrrdConverter testing suite that pulls data from midas.

Revision 16527 - Directory Listing
Modified Wed May 11 18:21:18 2011 UTC (6 years, 5 months ago) by pieper
COMP: fix for issue reported by haiyeong@gmail.com where grayscalemodelmaker was built as shared library module even though the code requires it to be an executable

Revision 16523 - Directory Listing
Modified Tue May 10 22:40:48 2011 UTC (6 years, 5 months ago) by pieper
STYLE: add warning when a missing module name is encountered (avoid crash)

Revision 16504 - Directory Listing
Modified Sat May 7 00:32:40 2011 UTC (6 years, 5 months ago) by dpace
ENH: Add slice magnifier widget.

- Adds magnififier on bottom left hand side of UI, which toggles to navigation view when the mouse is not over a slice view.

This is a combination of 8 commits.
ENH: Add CTKVTKMagnifyWidget to ThreeDViewsControllerWidget

- QStackedWidget contains the navigation widget and the magnify widget, and toggles between them via slot

ENH: Zoom in on 2D slice views via connection to the magnify widget

BUG: Incorrect widget name in .ui versus in code

ENH: Update qMRMLThreeDViewsControllerWidget.ui now that ctkCursorPixmapWidget has plugin

ENH: qMRMLThreeDViewsControllerWidget initializes to navigation display mode

ENH: Fix qMRMLThreeDViewsControllerWidget widget sizing, stretching and colors

STYLE: Update to reflect changes in CTK naming scheme

ENH: Connect magnify widget within code for ThreeDViewsControllerWidget.

Revision 16493 - Directory Listing
Modified Fri May 6 20:21:18 2011 UTC (6 years, 5 months ago) by lorensen
ENH: ITKv4 include file regressions.

Although #include "vxl/vcl/vcl_complex.h" worked it was never intended to be used. According to Brad King,

"AFAIK we never intended that style of inclusion.  Just plain

 #include "vcl_complex.h"

should have always worked if one included ${ITK_USE_FILE} in CMake code
as documented.

We can't possibly anticipate every possible way that a header used to
be include-able just because of the way the directory structure happened
to be arranged.  One could have done

 #include "../Common/itkMacro.h"

before and it would have worked.  Now it won't."



Revision 16490 - Directory Listing
Modified Fri May 6 19:40:24 2011 UTC (6 years, 5 months ago) by jcfr
ENH: Slicer Base libraries, ModuleMRML and ModuleLogic targets are exported

Both global list Slicer_Libs_LIBRARIES and Slicer_Base_LIBRARIES have
been removed. It means libraries are expected to specify explicitly
their dependencies.

Variable Slicer_CORE_LIBRARY and Slicer_GUI_LIBRARY have been introduced.
They should be used each time it's required to link against qSlicerBaseQTCore
or qSlicerBaseQTGUI.

The variable MRML_LIBRARIES has been introduced, it should be used each
time a module is expected to link against the trhee libraries
 MRML, MRMLLogic and MRMLDisplayableManager. The rational behind this variable
is too anticipate a future possible relocation of MRML related libraries
outside of Slicer.

Waiting we setup a way to export the include directory associated with
all libraries so that they can be available to extension using SlicerConfig.
tThese diretories are still automatically appended to the global variables:
Slicer_Libs_INCLUDE_DIRS, Slicer_Base_INCLUDE_DIRS, Slicer_ModuleMRML_INCLUDE_DIRS
and Slicer_ModuleLogic_INCLUDE_DIRS

Revision 16427 - Directory Listing
Modified Mon May 2 23:45:43 2011 UTC (6 years, 5 months ago) by hjohnson
ENH:  ITKv4 compatibility issues, and syncronized with Slicer3.

Revision 16413 - Directory Listing
Modified Fri Apr 29 16:11:00 2011 UTC (6 years, 5 months ago) by alexy
BUG_FIXED: revert accidental commit

Revision 16412 - Directory Listing
Modified Fri Apr 29 16:09:48 2011 UTC (6 years, 5 months ago) by alexy
ENH: Volume rendering fixes

Revision 16368 - Directory Listing
Modified Tue Apr 26 08:29:33 2011 UTC (6 years, 5 months ago) by jcfr
STYLE: Rename SlicerCTKAppLauncherSettings into SlicerBlockCTKAppLauncherSettings

Revision 16366 - Directory Listing
Modified Tue Apr 26 08:29:28 2011 UTC (6 years, 5 months ago) by jcfr
COMP: Update CMake policy requirements

Revision 16360 - Directory Listing
Modified Tue Apr 26 08:29:01 2011 UTC (6 years, 5 months ago) by jcfr
STYLE: Fix indent, add comment in CMakeLists.txt and Slicer Build macros

Revision 16356 - Directory Listing
Modified Tue Apr 26 08:28:50 2011 UTC (6 years, 5 months ago) by jcfr
COMP: Move Slicer.icns into Application/SlicerQT/Resources

Revision 16353 - Directory Listing
Modified Tue Apr 26 08:28:44 2011 UTC (6 years, 5 months ago) by jcfr
COMP: Remove occurences of Slicer_USE_QT variable

Revision 16320 - Directory Listing
Modified Mon Apr 25 22:06:03 2011 UTC (6 years, 5 months ago) by finetjul
ENH: Remove qSlicerModulePanel dependency over qSlicerApplication

Now we explicitly have to set the module manager to the module panels.

Revision 16293 - Directory Listing
Modified Wed Apr 20 21:51:57 2011 UTC (6 years, 6 months ago) by jcfr
COMP: Command line module 'CLIModule4Test' moved into Base/QTCLI/Testing

Revision 16287 - Directory Listing
Modified Wed Apr 20 21:51:46 2011 UTC (6 years, 6 months ago) by jcfr
ENH: Add qSlicerCoreApplication::AA_DisablePython

If set, python related code won't be executed.

This attribute could be used:
 - when writing test that doesn't rely on python
 - for debug purpose

Revision 16283 - Directory Listing
Modified Wed Apr 20 18:20:03 2011 UTC (6 years, 6 months ago) by pieper
ENH: merge in module from Lauren

Revision 16274 - Directory Listing
Modified Mon Apr 18 21:22:10 2011 UTC (6 years, 6 months ago) by finetjul
COMP: WIN32 in ADD_EXECUTABLE makes the application console-less but expects WinMain() instead of main()

We don't have any WinMain() definition, only a main() definition, don't use WIN32 in ADD_EXECUTABLE then.

Revision 16257 - Directory Listing
Modified Thu Apr 14 12:25:16 2011 UTC (6 years, 6 months ago) by partyd
ENH: Set bundle location to . for now. If one day Slicer wishes to ship it's bundle in a directory then we would define that with Slicer_BUNDLE_LOCATION

Revision 16238 - Directory Listing
Modified Thu Apr 7 15:26:44 2011 UTC (6 years, 6 months ago) by finetjul
BUG: Remove warnings when quitting slicer when a volume was loaded

Quitting slicer destruct vtkMRMLColorLogic which removes the color nodes
 from the scene. The result is that any loaded volume with a lut can't
be normally displayed.
We make sure here to not display the volumes when Slicer is quitting.

Revision 16218 - Directory Listing
Modified Tue Apr 5 19:05:51 2011 UTC (6 years, 6 months ago) by lorensen
ENH: ITKv4 API change

itkAnalyeImageIO is deprecated in ITKv4. It is no longer, by default,
registered. An explicit call ObjectFactoryBase::RegisterFactory(
itk::AnalyzeImageIOFactory::New() ) is needed.



Revision 16210 - Directory Listing
Modified Mon Apr 4 17:37:05 2011 UTC (6 years, 6 months ago) by lorensen
ENH: ITKv4 include file regressions.

Although #include "vxl/vcl/vcl_complex.h" worked it was never intended to be used. According to Brad King,

"AFAIK we never intended that style of inclusion.  Just plain

 #include "vcl_complex.h"

should have always worked if one included ${ITK_USE_FILE} in CMake code
as documented.

We can't possibly anticipate every possible way that a header used to
be include-able just because of the way the directory structure happened
to be arranged.  One could have done

 #include "../Common/itkMacro.h"

before and it would have worked.  Now it won't."



Revision 16209 - Directory Listing
Modified Mon Apr 4 17:33:53 2011 UTC (6 years, 6 months ago) by lorensen
ENH: ITKv4 include file regressions.

Although #include "vxl/vcl/vcl_complex.h" worked it was never intended to be used. According to Brad King,

"AFAIK we never intended that style of inclusion.  Just plain

 #include "vcl_complex.h"

should have always worked if one included ${ITK_USE_FILE} in CMake code
as documented.

We can't possibly anticipate every possible way that a header used to
be include-able just because of the way the directory structure happened
to be arranged.  One could have done

 #include "../Common/itkMacro.h"

before and it would have worked.  Now it won't."



Revision 16206 - Directory Listing
Modified Mon Apr 4 17:29:46 2011 UTC (6 years, 6 months ago) by lorensen
ENH: Need local copy of itkTestMain.h after modularization

After the ITKv4 modularization change over, itkTestMain.h is no longer
used in ITK. A new testing mechanism is introduced in ITKv4. To
expedite the transition of Slicer4 to modular ITK, We copy the old
itkTestMain.h into the CLI directory. Eventually, it may be
appropriate to use the new ITKv4 test framework.




Revision 16202 - Directory Listing
Modified Mon Apr 4 16:27:28 2011 UTC (6 years, 6 months ago) by lorensen
ENH: Need local copy of itkTestMain.h after modularization

After the ITKv4 modularization change over, itkTestMain.h is no longer
used in ITK. A new testing mechanism is introduced in ITKv4. To
expedite the transition of Slicer4 to modular ITK, we copy the old
itkTestMain.h into the CLI directory. Eventually, it may be
appropriate to use the new ITKv4 test framework.



Revision 16192 - Directory Listing
Modified Sun Apr 3 16:14:49 2011 UTC (6 years, 6 months ago) by finetjul
STYLE: Remove unnecessary functions to qMRMLLayoutManager

qMRMLLayoutManager::switchToXXX() are not used anymore, setLayout(int)
is preferred as it is more extandable.

Revision 16174 - Directory Listing
Modified Sat Apr 2 05:53:58 2011 UTC (6 years, 6 months ago) by jcfr
STYLE: BrainsCommonLib - Remove doc group "Apply Field" and "Create Field"

Revision 16166 - Directory Listing
Modified Fri Apr 1 22:22:57 2011 UTC (6 years, 6 months ago) by jcfr
ENH: Update qSlicerMainWindowTest1 to instantiate ctkPythonConsole

Revision 16165 - Directory Listing
Modified Fri Apr 1 22:22:55 2011 UTC (6 years, 6 months ago) by jcfr
STYLE: Remove extra comment from Main.cxx

Revision 16164 - Directory Listing
Modified Fri Apr 1 18:59:14 2011 UTC (6 years, 6 months ago) by jcfr
BUG: Re-enable screenshot button previously disable after commit 15602

Revision 16163 - Directory Listing
Modified Fri Apr 1 18:55:14 2011 UTC (6 years, 6 months ago) by finetjul
ENH: Add a MRML scene to the test

-> memory leak at exit

Revision 16160 - Directory Listing
Modified Fri Apr 1 13:09:05 2011 UTC (6 years, 6 months ago) by finetjul
BUG: Fixup qSlicerAboutDialogTest1, qSlicerApplicationTest1 and qSlicerCoreApplicationTest1

Revision 16157 - Directory Listing
Modified Fri Apr 1 03:33:05 2011 UTC (6 years, 6 months ago) by finetjul
ENH: Add tests for qSlicerAboutDialog, qSlicerMainWindowCore and qSlicerMainWindow

Revision 16137 - Directory Listing
Modified Thu Mar 31 14:43:15 2011 UTC (6 years, 6 months ago) by finetjul
STYLE: Rename "Save Scene" into "Save" in the File Menu.

Revision 16129 - Directory Listing
Modified Tue Mar 29 20:52:20 2011 UTC (6 years, 6 months ago) by finetjul
BUG: GrayscaleModelMaker was not working as a shared lib

Similar to r15634, we can't check if a file exists using fopen if the
module is run as a shared dll because the volume file name is a memory
address and not a file path.

Revision 16124 - Directory Listing
Modified Tue Mar 29 18:12:20 2011 UTC (6 years, 6 months ago) by mscully
BUG: Sylvain's DicomToNrrdConverter scaleFactor fix

Revision 16119 - Directory Listing
Modified Mon Mar 28 22:13:50 2011 UTC (6 years, 6 months ago) by jcfr
ENH: Integrate ctkErrorLogModel

ctkErrorLogModel is instantiated and owned by qSlicerCoreApplication

qSlicerCoreApplication::errorLogModel() or qSlicerApplication::errorLogModel()
allows to retrieve the associated instance.

At startup time, messages are both catched by ctkErrorLogModel and printed in the terminal,
it's only when slicer is sure that application is stated with a UI that
output are "completely" redirected into the ctkErrorLogModel.

Using the command line option "--disable-message-handlers", all messages
will be printed into the terminal.

Within the UI, the menu "Window->Error Log" allows to pop-up the associated
widget.

Output associated:
 - with Qt, std::cout, fprintf, ITK and VTK are all handled.

 - with log4Qt are NOT yet handled

Case when command line option of the form 'display...AndExit' are passed is taking care off

Revision 16103 - Directory Listing
Modified Fri Mar 25 19:00:15 2011 UTC (6 years, 6 months ago) by millerjv
ENH: more files that I forgot to check in a few minutes ago

Revision 16100 - Directory Listing
Modified Thu Mar 24 22:41:52 2011 UTC (6 years, 6 months ago) by millerjv
ENH: initial widescreen compare view

Revision 16093 - Directory Listing
Modified Wed Mar 23 18:07:27 2011 UTC (6 years, 6 months ago) by hjohnson
COMP:  Increased tolerance to allow test to pass.

Revision 16092 - Directory Listing
Modified Wed Mar 23 17:45:02 2011 UTC (6 years, 6 months ago) by hjohnson
ENH:  Merged Slicer3 and Slicer4 versions of the BRAINSTools.

Revision 16089 - Directory Listing
Modified Wed Mar 23 13:16:02 2011 UTC (6 years, 6 months ago) by demian
ENH: Adding CLI for tractography labelmap seeding

Revision 16062 - Directory Listing
Modified Mon Mar 14 22:36:38 2011 UTC (6 years, 7 months ago) by naucoin
ENH: Link up the three d views controller widget with the scene views module so that the expanded scene view dialogue pops up. STYLE: continue renaming so that use scene view instead of screen shot. BUG: fix a memory leak by deleting node after adding it to the scene

Revision 16026 - Directory Listing
Modified Fri Mar 4 17:28:00 2011 UTC (6 years, 7 months ago) by pieper
BUG: merge fix from slicer3

------------------------------------------------------------------------
r16154 | pieper | 2011-03-04 07:51:32 -0500 (Fri, 04 Mar 2011) | 1 line

BUG: fix failing test: duplicate entries were being added to the bValues table and the calculation of the max bValue caused and array subscript error



Revision 16025 - Directory Listing
Modified Thu Mar 3 15:57:05 2011 UTC (6 years, 7 months ago) by finetjul
ENH: Add new layouts (conventional widescreen, triple 3D, tabbed 3D)

Multiple 3d views are not correctly supported yet.

Revision 16023 - Directory Listing
Modified Tue Mar 1 23:11:08 2011 UTC (6 years, 7 months ago) by finetjul
ENH: Synchronize the layout icon with the real layout

When a layout was set programatically (loading a scene, restoring a scene
view), the icon of the current layout was not up to date.
Store the layout index into the layout QAction data.

Revision 16010 - Directory Listing
Modified Thu Feb 24 06:50:31 2011 UTC (6 years, 7 months ago) by finetjul
ENH: Share registered items between factories

In order for the factories not to register items already registered
(e.g., try to register loadable CLI and if can't find it, try to register
executable CLI but not both), they need to share the list (hashmap) of
items already registered.

Revision 16008 - Directory Listing
Modified Thu Feb 24 04:29:23 2011 UTC (6 years, 7 months ago) by jcfr
COMP: DiffusionTensorEstimation CLI module is now built as an executable only

Revision 16000 - Directory Listing
Modified Wed Feb 23 20:54:18 2011 UTC (6 years, 7 months ago) by lorensen
COMP: Comparing files with floating point numbers is bad.

The test SparseFieldLevelSetContour1Test was failing because it used a
cmake-supplied compare_files program. Since the results of this test
is a polydata file with floaing point coordinates, it is unlikely
that a simple byte-byte comparision is justified.




Revision 15989 - Directory Listing
Modified Sat Feb 19 18:29:02 2011 UTC (6 years, 7 months ago) by lorensen
COMP: ITKv4 modularization changes.

In anticipation of ITKv4 modularization, all references in
CMakeLists.txt to ITK libraries have been replaced with
${ITK_LIBRARIES}. This change is fully backward compatible with ITKv3.

ITKv4 will change the directory structure of the ITK code base
resulting in many, smaller groups of files. The library names will
change accordingly.

The cmake variable ${ITK_LIBRARIES} has always been available for use
in CMakeLists.txt files, but it was seldolm used. Developers should
start using ${ITK_LIBRARIES} rather than individual library names such
as ITKIO, ITKCommon and ITKStatistics.



Revision 15987 - Directory Listing
Modified Sat Feb 19 18:20:04 2011 UTC (6 years, 7 months ago) by lorensen
COMP: ITKv4 changes to RealTimeClock API.

Revision 15986 - Directory Listing
Modified Sat Feb 19 18:18:15 2011 UTC (6 years, 7 months ago) by lorensen
COMP: ITKv4 changes to RealTimeClock API.

Revision 15970 - Directory Listing
Modified Thu Feb 17 20:07:39 2011 UTC (6 years, 8 months ago) by lorensen
BUG: Set default threads to 0 -> use max threads for processor.

Revision 15961 - Directory Listing
Modified Tue Feb 8 20:12:06 2011 UTC (6 years, 8 months ago) by lorensen
ENH: Change default number of threads to 1.

Revision 15960 - Directory Listing
Modified Tue Feb 8 20:10:47 2011 UTC (6 years, 8 months ago) by lorensen
ENH: Add to tolerance for ITKv4

Revision 15949 - Directory Listing
Modified Wed Feb 2 16:44:24 2011 UTC (6 years, 8 months ago) by naucoin
ENH: set the pad flag to true by default, expanded the description

Revision 15943 - Directory Listing
Modified Mon Jan 31 22:37:53 2011 UTC (6 years, 8 months ago) by naucoin
ENH: add the option to pad the input image so that closed surfaces can be generated from label volumes that have voxels of interest in the outer slices. Added a test.

Revision 15924 - Directory Listing
Modified Sun Jan 30 01:51:20 2011 UTC (6 years, 8 months ago) by jcfr
ENH: Application name and version are now set from SlicerQT/Main.cpp

Revision 15923 - Directory Listing
Modified Sun Jan 30 01:47:13 2011 UTC (6 years, 8 months ago) by jcfr
COMP: Remove ref to KWWidgets, Slicer_USE_PYTHON, Slicer_BUILD_MODULES, ...

KWWidgets external project has been removed

Reference to Slicer_USE_PYTHON have been removed

Reference to Slicer_BUILD_MODULES has been removed

Launcher.tcl also has been cleaned

Deprecated function from qSlicerCoreApplication have been removed

Reference to Tcl wrapping within the core component of Slicer have been
removed. note that Slicer/Libs haven't been updated. Indeed, in case other
project want to benefit from Tcl wrapping ...

Revision 15922 - Directory Listing
Modified Sat Jan 29 23:46:08 2011 UTC (6 years, 8 months ago) by jcfr
ENH: PythonConsole is now using an AutocompletePreferenceList

This list is:
  slicer, slicer.modules and qt.QPushButton

See https://github.com/commontk/CTK/commit/e94a1857438e8610bb73dbc6d100dff354895be6

Revision 15921 - Directory Listing
Modified Sat Jan 29 23:46:07 2011 UTC (6 years, 8 months ago) by jcfr
ENH: Added qSlicerSettingsPythonPanel

This panel allows to change the display settings of the python shell.

Revision 15918 - Directory Listing
Modified Sat Jan 29 23:46:01 2011 UTC (6 years, 8 months ago) by jcfr
ENH: Rename qSlicerSettingsPanel into qSlicerSettingsGeneralPanel

Revision 15917 - Directory Listing
Modified Sat Jan 29 23:45:58 2011 UTC (6 years, 8 months ago) by jcfr
ENH: Update code to account for renaming of ctkPythonShell into ctkPythonConsole

Revision 15899 - Directory Listing
Modified Wed Jan 26 15:26:45 2011 UTC (6 years, 8 months ago) by finetjul
STYLE: Cleanup code in qSlicerMainWindow for improved readability

Revision 15898 - Directory Listing
Modified Wed Jan 26 15:26:43 2011 UTC (6 years, 8 months ago) by finetjul
ENH: Restore layout at startup

If the setting to save/restore the geometry of the application is ON,
then it should also save/restore the layout of the views.
vtkMRMLLayoutNode::SlicerLayoutInitialView (value = 0) should be handled as
a conventional view.

Revision 15860 - Directory Listing
Modified Wed Jan 19 20:43:36 2011 UTC (6 years, 9 months ago) by lorensen
BUG: Problems with threaded ResampleImageFilter.

The new ResampleImageFilter creates copies of its transforms for each
thread. Usually, the SetParameter/GetParameter sequence is suffient to
create a copy of a transform. The WarpTransform3D however has no
parameters. Rather, it uses a DeformationField to define the
transform. This patch provides a mechanism to create a copy of the
transform. It follows the pattern used in itk::BSplineDeformationTransform.



Revision 15857 - Directory Listing
Modified Wed Jan 19 00:22:25 2011 UTC (6 years, 9 months ago) by dpace
ENH: PolyDataToLabelmap CLI reads .vtk models

Revision 15848 - Directory Listing
Modified Mon Jan 17 20:00:16 2011 UTC (6 years, 9 months ago) by lorensen
ENH: New baselines for ITKv4.

Revision 15845 - Directory Listing
Modified Sun Jan 16 21:28:11 2011 UTC (6 years, 9 months ago) by lorensen
BUG: Keep threads for reample at default.

Revision 15844 - Directory Listing
Modified Sun Jan 16 20:32:11 2011 UTC (6 years, 9 months ago) by lorensen
ENH: Implement pre virtual methods for ITKv4.

In ITK3, itk::Transform provided dummy implementations for some
methods that should be implemented by derived classes. These dummy
methods printed a warning "This method should be implemented in
subclasses".In ITK4, to make developers aware that they should
implement these methods for derived subclasses, these methods are pure
virtual. This means that subclasses that do not provide an
implementation for these methods will no longer compile. Slicer's
Applications/CLI/DiffusionApplications/ResampleDTI/itkWarpTransform3D
did not implement TransformVector(), TransformVnlVector() and
TransformCovariantVector(). The Slicer4 code now provides these
methods and throws an exception if they are used.


Revision 15843 - Directory Listing
Modified Sun Jan 16 18:26:27 2011 UTC (6 years, 9 months ago) by lorensen
ENH: Changed tolerance for ITKv4.

Revision 15842 - Directory Listing
Modified Sat Jan 15 17:46:03 2011 UTC (6 years, 9 months ago) by fedorov
ENH: propagate updates from itk4


Revision 15839 - Directory Listing
Modified Fri Jan 14 17:24:41 2011 UTC (6 years, 9 months ago) by mscully
BUG: Running the program with no inputs now returns an error instead of a segfault

Revision 15831 - Directory Listing
Modified Thu Jan 13 16:27:19 2011 UTC (6 years, 9 months ago) by finetjul
ENH: Show Annotation and Colors in the Fast module selector toolbar

Renamed the Color module into Colors (to be consistent with Models, Transforms, Volumes...)

Revision 15829 - Directory Listing
Modified Thu Jan 13 15:09:38 2011 UTC (6 years, 9 months ago) by partyd
ENH: Officialy require CMake 2.8.2 as many of the sub modules already do.

Revision 15820 - Directory Listing
Modified Wed Jan 12 20:54:42 2011 UTC (6 years, 9 months ago) by francois_budin
BUG: addition of dummy function for ITK4 compatibility problems

Revision 15817 - Directory Listing
Modified Wed Jan 12 20:22:32 2011 UTC (6 years, 9 months ago) by domibel
BUG: Use ITK_VERSION_MAJOR instead of ITK_VERSION (closes #1070)

Revision 15811 - Directory Listing
Modified Tue Jan 11 12:46:10 2011 UTC (6 years, 9 months ago) by jcfr
COMP: SparseFieldLevelSetContour - Fix unused variable warnings

Revision 15807 - Directory Listing
Modified Mon Jan 10 21:12:28 2011 UTC (6 years, 9 months ago) by jcfr
COMP: Fix unused variable warning

Revision 15805 - Directory Listing
Modified Sun Jan 9 21:23:41 2011 UTC (6 years, 9 months ago) by lorensen
ENH: For ITK4 (and ITK3) throw exception for unimplemented methods.

Revision 15799 - Directory Listing
Modified Sun Jan 9 10:14:24 2011 UTC (6 years, 9 months ago) by jcfr
ENH: If an extra python script is directly passed as argument, main-window is disabled

Revision 15798 - Directory Listing
Modified Sun Jan 9 10:14:22 2011 UTC (6 years, 9 months ago) by jcfr
ENH: Use qSlicerCoreCommandOptions::extraPythonScript instead of overwriting parsedArguments

Revision 15797 - Directory Listing
Modified Sun Jan 9 09:43:37 2011 UTC (6 years, 9 months ago) by jcfr
BUG: Do not set attribute 'Qt::WA_QuitOnClose' on PythonShell

Doing so allows the application to exit if no-main-window is passed
and if the python shell is closed.

Revision 15795 - Directory Listing
Modified Sun Jan 9 07:52:37 2011 UTC (6 years, 9 months ago) by jcfr
ENH: Python script directly passed as argument to slicer executable are now supported

Calling "./Slicer myscript.py" will trigger the execution of the given script

Revision 15793 - Directory Listing
Modified Sun Jan 9 07:15:57 2011 UTC (6 years, 9 months ago) by jcfr
ENH: Revert "Invoke signal qSlicerApplication::mainWindowInstantiated when required"

This reverts commit 15782

Signal 'mainWindowInstantiated' isn't needed anymore since SlicerRC file
is now loaded after the event loop is started. At that time, we are now sure
QMainWindow is instantiated

Revision 15791 - Directory Listing
Modified Sun Jan 9 07:15:48 2011 UTC (6 years, 9 months ago) by jcfr
ENH: Added command line option: --show-python-interactor

If set, the python interactor will be set visible at startup

Revision 15788 - Directory Listing
Modified Sun Jan 9 07:15:35 2011 UTC (6 years, 9 months ago) by jcfr
ENH: ctkPythonShell created in Main.cxx instead of qSlicerMainWindowCore

Revision 15787 - Directory Listing
Modified Sun Jan 9 07:15:28 2011 UTC (6 years, 9 months ago) by jcfr
ENH: CommandLine option "no-main-window" now keeps MainWindow from being instantiated

Revision 15785 - Directory Listing
Modified Sun Jan 9 07:15:23 2011 UTC (6 years, 9 months ago) by jcfr
STYLE: SlicerQT/Main.cxx - Rename variable 'enableMain' into 'enableMainWindow'

Revision 15782 - Directory Listing
Modified Sun Jan 9 01:12:38 2011 UTC (6 years, 9 months ago) by jcfr
ENH: Invoke signal qSlicerApplication::mainWindowInstantiated when required

If build with Python support, this signal is invoked when the mainwindow
is instantiated.

Within python, this could be useful, for example, to associate keyboard
shortcut with the mainwindow when appropriate.

Revision 15770 - Directory Listing
Modified Sat Jan 8 20:58:53 2011 UTC (6 years, 9 months ago) by lorensen
ENH: Skip building of BRAINSTools and DicomToNrrdConverter for ITK4.

Revision 15736 - Directory Listing
Modified Thu Jan 6 21:27:46 2011 UTC (6 years, 9 months ago) by jcfr
COMP: Fix unused variable warning

Revision 15732 - Directory Listing
Modified Thu Jan 6 20:02:26 2011 UTC (6 years, 9 months ago) by pieper
ENH: add command line option to disable display of main window

Revision 15728 - Directory Listing
Modified Thu Jan 6 17:30:24 2011 UTC (6 years, 9 months ago) by finetjul
BUG: Warning message was referencing Slicer alpha instead of beta

Revision 15721 - Directory Listing
Modified Wed Jan 5 23:15:29 2011 UTC (6 years, 9 months ago) by finetjul
ENH: Support the "Home" module, a favorite module to launch at startup

Revision 15701 - Directory Listing
Modified Tue Jan 4 20:12:54 2011 UTC (6 years, 9 months ago) by finetjul
ENH: Use vtkMRMLAbstractLogic instead of vtkSlicerLogic as a base class for

all the modules logics.
Move pure MRML functionalities from vtkSlicerColorLogic into
vtkMRMLColorLogic

Revision 15691 - Directory Listing
Modified Tue Jan 4 00:49:25 2011 UTC (6 years, 9 months ago) by finetjul
BUG: By default transform parameter with no type is linear

When a transform is in the output chanel, the node selector allow the user to create a transform node. If the type is not specify, the type is vtkMRMLTransformNode which is abstract and can't be instanciated. In that case, consider the transform node to be linear (to support old Slicer3 modules).
Affine registration transform output is linear, specify it explicitely.

Revision 15685 - Directory Listing
Modified Sun Jan 2 15:55:12 2011 UTC (6 years, 9 months ago) by hjohnson
COMP:  Making typedef change to be compliant with both ITKv4 and ITKv3.

Revision 15684 - Directory Listing
Modified Fri Dec 31 21:00:08 2010 UTC (6 years, 9 months ago) by finetjul
ENH: Use pimpl for qSlicerActionsDialog

Python wrapping has some issues with including a ui file in the header. Do
it in the implementation.

Revision 15683 - Directory Listing
Modified Wed Dec 29 23:33:46 2010 UTC (6 years, 9 months ago) by hjohnson
ENH:  Changed from the alias itk::OStringStream to the standard std::ostringstream.  This makes everything more consistent, and also prepares for ITKv4 compatibility.  ENH:  Removed Brains2MaskImage support since it was only relevant for data created at Iowa, and is not compliant with data standards enforced by Slicer4 for physical space representation.

Revision 15672 - Directory Listing
Modified Sat Dec 18 14:34:01 2010 UTC (6 years, 10 months ago) by zach.mullen
BUG: Fix typos in midas_add_test macros that were causing failing tests

Revision 15668 - Directory Listing
Modified Sat Dec 18 02:11:41 2010 UTC (6 years, 10 months ago) by finetjul
BUG: ModelMaker wasn't running as on shared module on Windows

addresses don't start like 0x on Windows.

Revision 15651 - Directory Listing
Modified Fri Dec 17 19:41:49 2010 UTC (6 years, 10 months ago) by zach.mullen
ENH: Move BRAINSTools testing data to midas.kitware.com and reference the remote data in the tests

Revision 15645 - Directory Listing
Modified Fri Dec 17 02:05:11 2010 UTC (6 years, 10 months ago) by finetjul
BUG: Make the toolbars respond to the trigger signal of menu qactions

Problem: minimize application, restore it and the module panel disappear
When the application is minimized, QDockWidget receive the HideEvent and
fire its signal visibilityChanged that got connected to the menu QAction
which fire its own signal toggled(bool).
If the QDockWidget::setVisible(bool) is connected to this toggled() signal
setVisible(false) would be called and really hide the QDockWidget (before
it wasn't really hidden, see QWidget::IsVisibleTo() for more info).
To avoid all this issue, QDockWidgets::setVisible should only respond to
the triggered(bool) signals of the menu QAction.
For consistency, apply the same logic to the QToolBars and their associated
menu QActions.

Revision 15644 - Directory Listing
Modified Fri Dec 17 00:54:11 2010 UTC (6 years, 10 months ago) by jcfr
COMP: Application/SlicerQT/CMakeLists.txt - Forwarded executable is not built anymore

The name of the executable is still SlicerQT-real so that existing
launcher can still refer to it.

Revision 15640 - Directory Listing
Modified Fri Dec 17 00:46:50 2010 UTC (6 years, 10 months ago) by jcfr
STYLE: Remove extra comments from Application/SlicerQT/CMakeLists.txt

Revision 15634 - Directory Listing
Modified Thu Dec 16 22:03:37 2010 UTC (6 years, 10 months ago) by pieper
BUG: merge bug fix from slicer3 trunk for crash when certain label options selected; also ENH: check for valid file when argument is not a slicer shared memory reference

Revision 15625 - Directory Listing
Modified Thu Dec 16 17:42:01 2010 UTC (6 years, 10 months ago) by hjohnson
ENH:  Merged recent changes contributed by Slicer4 developers into Slicer3 and BRAINS3.

Revision 15614 - Directory Listing
Modified Thu Dec 16 06:36:49 2010 UTC (6 years, 10 months ago) by finetjul
BUG: Connect toolbar visibility actions with toolbar on signal toggled

instead of triggered because triggered is only fired if it's the user that
change the checked property and not if it is done programatically.

Revision 15613 - Directory Listing
Modified Thu Dec 16 05:36:46 2010 UTC (6 years, 10 months ago) by finetjul
BUG: using settings, toolbars can be hidden, synchronize with action

Directly connect the menu actions controlling the toolbar visibility with
the toolbars themselves (done in the ui).
After reading the settings, make sure the menu actions are synchro with the
toolbar visibility
Rename ModuleSelector into ModuleSelectorToolBar

Revision 15612 - Directory Listing
Modified Thu Dec 16 05:36:43 2010 UTC (6 years, 10 months ago) by finetjul
ENH: Display the Modules in the same order than ModuleToolBarList is

Revision 15559 - Directory Listing
Modified Tue Dec 14 16:03:55 2010 UTC (6 years, 10 months ago) by finetjul
BUG: Don't use FILE to check if a file exist in a CLI

because the input file might just be a pointer on the memory and not a file

Revision 15520 - Directory Listing
Modified Fri Dec 10 22:04:40 2010 UTC (6 years, 10 months ago) by finetjul
COMP: Remove unused variable

Revision 15495 - Directory Listing
Modified Fri Dec 10 05:00:26 2010 UTC (6 years, 10 months ago) by finetjul
ENH: Add Extension management wizard to Slicer

Revision 15493 - Directory Listing
Modified Thu Dec 9 22:38:36 2010 UTC (6 years, 10 months ago) by finetjul
BUG: Use the proper way to set the application style. The way it was done before was creating a style twice. Once by default in the constructor of QApplication then once in the constructor of qSlicerApplication. The style should be set prior to instanciating the application, typically in Main.cxx. the problem was had with the previous design was that a qgtkstyle was instanciated and anytime a palette was set to the application, the base and window color role (not the text role)of the qmenu, qtoolbar and qcombobox were reset to the system color, wich resulted into invisible menus (brown background under brown text

Revision 15463 - Directory Listing
Modified Wed Dec 8 06:02:24 2010 UTC (6 years, 10 months ago) by jcfr
ENH: Switch to version 0.1.2 of CTKAppLauncher

The launcher is now configured using relatively to a Target instead of the
location of a generated executable. TARGET parameter should be specified
instead of APPLICATION_PATH

Also move the call to the macro at in the CMakeLists where the associated
target is defined.

Related changes:
 - Launcher properly configured on windows by using custom_target
and ensuring the intermediate build directory is properly passed
 - Remove suffix ADDITIONAL_ from macro signature
 - Argument given on the command line are now properly passed to the target application

Revision 15452 - Directory Listing
Modified Tue Dec 7 04:02:49 2010 UTC (6 years, 10 months ago) by finetjul
ENH: Add preliminary work for the Extension Management Wizard

Revision 15443 - Directory Listing
Modified Tue Dec 7 00:23:46 2010 UTC (6 years, 10 months ago) by jcfr
COMP: Base libraries and slicerQt application CMakeLists uses CDash labels

Revision 15442 - Directory Listing
Modified Tue Dec 7 00:23:38 2010 UTC (6 years, 10 months ago) by jcfr
COMP: ExtractSkeleton/CMakeLists - Uses CDash labels and slicerMacroBuildCLI

Simplify the code using slicerMacroBuildCLI

Revision 15441 - Directory Listing
Modified Tue Dec 7 00:23:36 2010 UTC (6 years, 10 months ago) by jcfr
COMP: DownloadSlicerTutorials/CMakeLists - Uses CDash labels and slicerMacroBuildCLI

Simplify the code using slicerMacroBuildCLI

Revision 15440 - Directory Listing
Modified Tue Dec 7 00:23:33 2010 UTC (6 years, 10 months ago) by jcfr
COMP: MRIBiasFieldCorrection/CMakeLists - Uses CDash labels and slicerMacroBuildCLI

Simplify the code using slicerMacroBuildCLI

Revision 15439 - Directory Listing
Modified Tue Dec 7 00:23:30 2010 UTC (6 years, 10 months ago) by jcfr
COMP: DiffusionApplications/CMakeLists updated to use CDash Labels and to build both CLI library and executable

Also simplify the code by using macro slicerMacroBuildCLI

Revision 15438 - Directory Listing
Modified Tue Dec 7 00:23:26 2010 UTC (6 years, 10 months ago) by jcfr
COMP: DicomToNrrdConverter/CMakeLists - Uses CDash labels

Revision 15437 - Directory Listing
Modified Tue Dec 7 00:23:23 2010 UTC (6 years, 10 months ago) by jcfr
COMP: BatchmakeApplications/CMakeLists - Uses CDash labels and slicerMacroBuildCLI

Simplify the code using slicerMacroBuildCLI

Revision 15436 - Directory Listing
Modified Tue Dec 7 00:23:19 2010 UTC (6 years, 10 months ago) by jcfr
COMP: N4ITKBiasFieldCorrection/CMakeLists - Uses CDash labels and slicerMacroBuildCLI

Simplify the code using slicerMacroBuildCLI

Revision 15435 - Directory Listing
Modified Tue Dec 7 00:23:16 2010 UTC (6 years, 10 months ago) by jcfr
COMP: Realign/CMakeLists - Uses CDash labels and slicerMacroBuildCLI

Simplify the code using slicerMacroBuildCLI

Revision 15434 - Directory Listing
Modified Tue Dec 7 00:23:13 2010 UTC (6 years, 10 months ago) by jcfr
COMP: RegisterImages*/CMakeLists - use Cdash labels

Revision 15433 - Directory Listing
Modified Tue Dec 7 00:23:10 2010 UTC (6 years, 10 months ago) by jcfr
COMP: RobustStatisticsSegmenter/CMakeLists - Uses CDash labels and slicerMacroBuildCLI

Simplify the code using slicerMacroBuildCLI

Revision 15432 - Directory Listing
Modified Tue Dec 7 00:23:07 2010 UTC (6 years, 10 months ago) by jcfr
COMP: SparseFieldLevelSetContour/CMakeLists - Uses CDash labels and slicerMacroBuildCLI

Simplify the code using slicerMacroBuildCLI

Revision 15431 - Directory Listing
Modified Tue Dec 7 00:23:05 2010 UTC (6 years, 10 months ago) by jcfr
COMP: CLI and CLI/Testing uppdated to use CDash labels

Also simplify the code by using macro slicerMacroBuildCLI

Revision 15429 - Directory Listing
Modified Tue Dec 7 00:22:57 2010 UTC (6 years, 10 months ago) by jcfr
STYLE: Remove extra IF() statement in CLI CMakeLists.txt

Revision 15425 - Directory Listing
Modified Mon Dec 6 07:52:05 2010 UTC (6 years, 10 months ago) by finetjul
COMP: Fix pythonQt compilation errors

Need to wrap PythonQt code with #ifdef Slicer_USE_PythonQt

Revision 15424 - Directory Listing
Modified Mon Dec 6 06:22:03 2010 UTC (6 years, 10 months ago) by finetjul
ENH: Add support for settings

Revision 15420 - Directory Listing
Modified Mon Dec 6 02:35:11 2010 UTC (6 years, 10 months ago) by jcfr
ENH: Added QTScripted module factory and associated classes

The QTScripted module factory is composed of:
 - the factory itself
 - concrete implementations of qSlicerLoadableModule, qSlicerAbstractModuleWidget
and vtkSlicerModuleLogic

These concrete implementations are:
- qSlicerScriptedLoadableModuleWidget
- qSlicerScriptedLoadableModule
- vtkSlicerScriptedLoadableModuleLogic

All have a method named "setPythonSource".


After setting the python script, the corresponding python implementation
will be retrieved.

Revision 15398 - Directory Listing
Modified Mon Dec 6 02:33:16 2010 UTC (6 years, 10 months ago) by jcfr
ENH: Expose qSlicerMainWindow::moduleSelector to scripted langage using Q_Invokable

Revision 15388 - Directory Listing
Modified Mon Dec 6 02:32:35 2010 UTC (6 years, 10 months ago) by jcfr
COMP: Add CMakeLists allowing to test SlicerQT using python

Revision 15385 - Directory Listing
Modified Mon Dec 6 02:32:22 2010 UTC (6 years, 10 months ago) by jcfr
COMP: Move Cpp tests from Application/SlicerQt/Testing to Cpp subdirectory

Revision 15383 - Directory Listing
Modified Mon Dec 6 02:32:11 2010 UTC (6 years, 10 months ago) by jcfr
ENH: Added command line option: --python-code and --python-script

Revision 15382 - Directory Listing
Modified Mon Dec 6 02:32:08 2010 UTC (6 years, 10 months ago) by jcfr
ENH: Enable pythonqt wrapping for Base/QTCore and Base/QTGUI libraries

Revision 15309 - Directory Listing
Modified Wed Nov 24 19:35:26 2010 UTC (6 years, 10 months ago) by mscully
BUG: Corrected minimum cmake version

Revision 15308 - Directory Listing
Modified Wed Nov 24 19:14:40 2010 UTC (6 years, 10 months ago) by mscully
ENH: Added logic to check for strange gradients in Siemens data and added a command line argument to force the calculation of the B values and directions from the B-matrix which exists in a private tag in siemens data.
BUG: Updated to correctly handle endianness differences between dicom and system.
STYLE: Cleaned up some of the code and slightly improved cross-platform compatibility.


Revision 15296 - Directory Listing
Modified Mon Nov 22 13:39:44 2010 UTC (6 years, 10 months ago) by pieper
COMP: include definitions of lookup table (removed from mrml node.h file)

Revision 15243 - Directory Listing
Modified Wed Nov 10 22:02:47 2010 UTC (6 years, 11 months ago) by jcfr
COMP: Use "generator expression" with add_test()

Doing so will avoid to use CMAKE_BUILD_TYPE and will ensure the executable
associated with the selected configuration type is used.

Revision 15237 - Directory Listing
Modified Tue Nov 9 18:50:38 2010 UTC (6 years, 11 months ago) by finetjul
ENH: Add qMRMLNavigationView a 3D render view that thumbnails any 3D render view

previously in Base/GUI/vtkSlicerViewControlGUI

Revision 15234 - Directory Listing
Modified Tue Nov 9 16:20:24 2010 UTC (6 years, 11 months ago) by finetjul
STYLE: Add comments

Revision 15215 - Directory Listing
Modified Tue Nov 2 21:34:34 2010 UTC (6 years, 11 months ago) by jcfr
ENH: Added scene shapshot feature

Revision 15214 - Directory Listing
Modified Tue Nov 2 20:46:35 2010 UTC (6 years, 11 months ago) by fedorov
ENH: add description for sharpening parameter


Revision 15213 - Directory Listing
Modified Tue Nov 2 20:43:18 2010 UTC (6 years, 11 months ago) by fedorov
BUG: merge bug fix 1037


Revision 15200 - Directory Listing
Modified Fri Oct 29 20:06:23 2010 UTC (6 years, 11 months ago) by jcfr
ENH: Added Screenshot Capture dialog

Revision 15182 - Directory Listing
Modified Thu Oct 28 05:35:19 2010 UTC (6 years, 11 months ago) by jcfr
STYLE: Do not use IMMEDIATE with CONFIGURE_FILE. Default behavior since cmake 2.2

See http://www.mail-archive.com/cmake@cmake.org/msg22231.html

Revision 15170 - Directory Listing
Modified Wed Oct 27 23:50:02 2010 UTC (6 years, 11 months ago) by jcfr
STYLE: Use BUILD_TESTING variable

Change occurrences of Slicer_BUILD_TESTING into BUILD_TESTING

Revision 15162 - Directory Listing
Modified Mon Oct 25 23:23:07 2010 UTC (6 years, 11 months ago) by jcfr
COMP: Update policy requirements for Libs, Modules, QTModules and Applications

Revision 15157 - Directory Listing
Modified Mon Oct 25 23:22:18 2010 UTC (6 years, 11 months ago) by jcfr
COMP: Enable CMake policy CMP0001 and update scripts accordingly

CMP0001 : CMAKE_BACKWARDS_COMPATIBILITY should no longer be used.

Revision 15154 - Directory Listing
Modified Mon Oct 25 23:21:38 2010 UTC (6 years, 11 months ago) by jcfr
COMP: CMake 2.8.2 is now required

Revision 15148 - Directory Listing
Modified Thu Oct 21 20:50:30 2010 UTC (6 years, 11 months ago) by jcfr
STYLE: Following commit 763148b902 in CTK, rename CTK_*_CXX macros into CTK_*_CPP

Revision 15139 - Directory Listing
Modified Tue Oct 19 23:11:24 2010 UTC (7 years ago) by fedorov
BUG: fix for bug #1002


Revision 15121 - Directory Listing
Modified Tue Oct 12 15:09:06 2010 UTC (7 years ago) by jcfr
BUG: sparsefieldlevelsetcontour - Make sure emptyIntVec pointer is initialized

Revision 15117 - Directory Listing
Modified Fri Oct 8 03:44:58 2010 UTC (7 years ago) by jcfr
COMP: Rename "$HeadURL: http://www.na-mic.org/svn/Slicer3" into "$HeadURL: http://svn.slicer.org/Slicer4"

Revision 15116 - Directory Listing
Modified Fri Oct 8 03:44:47 2010 UTC (7 years ago) by jcfr
COMP: Rename "Program:   Slicer3" into "Program:   Slicer"

Revision 15115 - Directory Listing
Modified Fri Oct 8 03:44:34 2010 UTC (7 years ago) by jcfr
COMP: Rename "$HeadURL: http://svn.slicer.org/Slicer3/trunk/" into "$HeadURL: http://svn.slicer.org/Slicer4/trunk/"

Revision 15113 - Directory Listing
Modified Fri Oct 8 03:44:00 2010 UTC (7 years ago) by jcfr
COMP: Rename project Slicer3 into Slicer

Revision 15111 - Directory Listing
Modified Fri Oct 8 03:41:55 2010 UTC (7 years ago) by jcfr
COMP: Rename Slicer3_BUILD_WIN32_CONSOLE into Slicer_BUILD_WIN32_CONSOLE

Revision 15110 - Directory Listing
Modified Fri Oct 8 03:41:48 2010 UTC (7 years ago) by jcfr
COMP: Rename Slicer3_EXE into Slicer_EXE

Revision 15108 - Directory Listing
Modified Fri Oct 8 03:41:29 2010 UTC (7 years ago) by jcfr
COMP: Rename Slicer3_{Base,Libs}* into Slicer_{Base,Libs}*

Revision 15104 - Directory Listing
Modified Fri Oct 8 03:40:31 2010 UTC (7 years ago) by jcfr
COMP: Rename comment "/* Slicer3_USE_* */" into "/* Slicer_USE_* */"

Revision 15097 - Directory Listing
Modified Fri Oct 8 03:39:47 2010 UTC (7 years ago) by jcfr
COMP: Rename Slicer3_HOME into Slicer_HOME

Revision 15095 - Directory Listing
Modified Fri Oct 8 03:38:56 2010 UTC (7 years ago) by jcfr
COMP: Rename Slicer3_BUILD_MODULES into Slicer_BUILD_MODULES

Revision 15094 - Directory Listing
Modified Fri Oct 8 03:38:50 2010 UTC (7 years ago) by jcfr
COMP: Rename Slicer3_BUILD_TESTING into Slicer_BUILD_TESTING

Revision 15093 - Directory Listing
Modified Fri Oct 8 03:38:42 2010 UTC (7 years ago) by jcfr
COMP: Rename Slicer3_INSTALL_QTLOADABLEMODULES* into Slicer_INSTALL_QTLOADABLEMODULES*

Revision 15091 - Directory Listing
Modified Fri Oct 8 03:34:10 2010 UTC (7 years ago) by jcfr
COMP: Rename Slicer3_USE_KWWIDGETS into Slicer_USE_KWWIDGETS

Revision 15090 - Directory Listing
Modified Fri Oct 8 03:33:56 2010 UTC (7 years ago) by jcfr
COMP: Rename Slicer3_USE_PYTHON into Slicer_USE_PYTHON

Revision 15089 - Directory Listing
Modified Fri Oct 8 03:33:34 2010 UTC (7 years ago) by jcfr
COMP: Rename Slicer3_USE_PYTHONQT into Slicer_USE_PYTHONQT

Revision 15088 - Directory Listing
Modified Fri Oct 8 03:33:20 2010 UTC (7 years ago) by jcfr
COMP: Rename Slicer3_USE_QT into Slicer_USE_QT

Revision 15087 - Directory Listing
Modified Fri Oct 8 03:33:07 2010 UTC (7 years ago) by jcfr
COMP: Rename Slicer3_BUILD_CLI into Slicer_BUILD_CLI

Revision 15086 - Directory Listing
Modified Fri Oct 8 03:32:57 2010 UTC (7 years ago) by jcfr
COMP: Rename Slicer3_BUILD_QTLOADABLEMODULES into Slicer_BUILD_QTLOADABLEMODULES

Revision 15083 - Directory Listing
Modified Fri Oct 8 03:32:44 2010 UTC (7 years ago) by jcfr
COMP: Rename Slicer3_USE_MIDAS into Slicer_USE_MIDAS

Revision 15082 - Directory Listing
Modified Fri Oct 8 03:32:40 2010 UTC (7 years ago) by jcfr
COMP: Rename Slicer3_USE_BatchMake into Slicer_USE_BatchMake

Revision 15071 - Directory Listing
Modified Thu Oct 7 03:29:35 2010 UTC (7 years ago) by jcfr
COMP: Rename variables Slicer3_VERSION* into Slicer_VERSION*

Revision 15070 - Directory Listing
Modified Thu Oct 7 03:29:24 2010 UTC (7 years ago) by jcfr
COMP: Rename variable Slicer3_INSTALL_* into Slicer_INSTALL_*

Revision 15069 - Directory Listing
Modified Thu Oct 7 02:41:47 2010 UTC (7 years ago) by jcfr
ENH: Splashcreen flag Qt::WindowStaysOnTopHint turned off

That should allow other application to appear above slicer splashscreen

Revision 15047 - Directory Listing
Modified Fri Oct 1 22:06:39 2010 UTC (7 years ago) by ygao
STYLE: change kernelFactor from 60 to 20

Revision 15042 - Directory Listing
Modified Thu Sep 30 16:41:04 2010 UTC (7 years ago) by ygao
PERF: for the RSS module, change the feature image type from itkImage of double, to of float, to reduce the memory consumption. tested with the tutorial data set and this change to pixel type does not affect the results. This may suggest that the extract accuracy of double is not needed.

Revision 15036 - Directory Listing
Modified Tue Sep 28 17:30:28 2010 UTC (7 years ago) by haehn
COMP: The new name of the side-by-side layout had to propagated the UI Resource.

Revision 15025 - Directory Listing
Modified Mon Sep 20 20:31:39 2010 UTC (7 years ago) by wjp@bwh.harvard.edu
ENH: adding extra label name to output csv file as per clinician's request. names and output csv are formatted for her specific needs.

Revision 15020 - Directory Listing
Modified Sat Sep 18 00:39:52 2010 UTC (7 years, 1 month ago) by fedorov
BUG: allow non-1 labels; merge fix from 3.6


Revision 15017 - Directory Listing
Modified Fri Sep 17 16:03:07 2010 UTC (7 years, 1 month ago) by hjohnson
BUG:978: Resolves Bug report:    http://www.na-mic.org/Bug/view.php?id=978

This work was performed by Joy Matsui.  Including code modifications, documentation, and testing.

Some early Siemens DTI data had some gradients coded incorrectly in the dicom header file.  This change identifies gradients that are very much outside the expected values, and allows for those values to be removed from the resulting NRRD file.

All changes made to DicomToNrrdConverter were done in sections of code that process Siemens data. These changes are compatible with the following Siemens data types: TrioTim B13, B15, and B17 and Verio B15V. Any generic variable that is altered during Siemens data processing that also applies to GE and Philips is only altered during Siemens data processing.

The changes include two new flags, smallGradientFix and smallGradientThreshold. smallGradientFix has two possible arguments, Remove and Rescale, for removing bad gradients and rescaling gradient magnitudes that are within a reasonable range. That reasonable range is determined by smallGradientThreshold, default setting is 0.2. If smallGradientFix is not set, the pipeline will automatically terminate when a gradient whose magnitude is outside the reasonable range is detected. Upon termination, the user will be instructed to set the smallGradientFix to deal with the bad gradients. If smallGradientFix is set to Remove, any gradient whose magnitude is outside the reasonable range is marked to not be included in the output NRRD file. If smallGradientFix is set to Rescale, each gradient will be scaled relative to the maximum b value of the scan.




Revision 15015 - Directory Listing
Modified Fri Sep 17 13:44:43 2010 UTC (7 years, 1 month ago) by haehn
COMP: Renamed the layout side-by-side view to match the name in vtkMRMLLayoutNode.

Revision 15003 - Directory Listing
Modified Wed Sep 15 14:31:05 2010 UTC (7 years, 1 month ago) by finetjul
STYLE: Use Qt private implementation instead of obsolete CTK implementation

Qt pimpls have the big advantage of supporting pimple derivation.
The recommended way of using them is shown below:
Header file:

class MyClassPrivate;
class MyClass
{
public:
   ...
   virtual ~MyClass();
   ...
protected:
   QScopedPointer<MyClassPrivate> d_ptr;
private:
   Q_DECLARE_PRIVATE(MyClass);
   Q_DISABLE_COPY(MyClass);
};

Implementation file (Private has no access to public:
class MyClassPrivate
{
public:
  ...
};
...
MyClass::MyClass():d_ptr(new MyClassPrivate)
{
}

Implementation file (Private has access to public):
class MyClassPrivate
{
   Q_DECLARE_PUBLIC(MyClass);
protected:
  MyClass* const q_ptr;
public:
  MyClassPrivate(MyClass&);
...
};
MyClassPrivate::MyClassPrivate(MyClass& o)
  :q_ptr(&o)
{
}
...
MyClass::MyClass():d_ptr(new MyClassPrivate(*this))
{
}

Revision 14968 - Directory Listing
Modified Wed Sep 8 18:37:23 2010 UTC (7 years, 1 month ago) by finetjul
ENH: Center disclaimer message on SlicerQt window

Revision 14967 - Directory Listing
Modified Wed Sep 8 18:05:18 2010 UTC (7 years, 1 month ago) by finetjul
ENH: Add disclaimer message popup in SlicerQt

Revision 14940 - Directory Listing
Modified Tue Sep 7 13:04:22 2010 UTC (7 years, 1 month ago) by fedorov
ENH: updated default values used for the prostate application


Revision 14888 - Directory Listing
Modified Thu Sep 2 20:01:45 2010 UTC (7 years, 1 month ago) by finetjul
ENH: Cleanup main window for SlicerQt and remove useless menu items

Revision 14875 - Directory Listing
Modified Thu Sep 2 15:40:49 2010 UTC (7 years, 1 month ago) by finetjul
BUG: Handle better slicer versions

Revision 14836 - Directory Listing
Modified Wed Sep 1 21:21:58 2010 UTC (7 years, 1 month ago) by jcfr
ENH: qSlicerLayoutManager - Add activeMRMLThreeDViewNodeChanged() signal

For now, the first created ThreeDView is considered to be the active one

Revision 14805 - Directory Listing
Modified Wed Sep 1 06:11:28 2010 UTC (7 years, 1 month ago) by finetjul
BUG: QDockWidget needs an extra margin to show the bar correctly

For more information, see http://bugreports.qt.nokia.com/browse/QTBUG-13327

Revision 14802 - Directory Listing
Modified Wed Sep 1 04:34:16 2010 UTC (7 years, 1 month ago) by finetjul
BUG: Make sure progress message text at loading is correctly displayed...

inside the splashscreen and not on the border

Revision 14787 - Directory Listing
Modified Tue Aug 31 22:54:42 2010 UTC (7 years, 1 month ago) by jcfr
STYLE: Add license header to QTCoreModules, QTCLI, QTGUI, QTCore, Applications/SlicerQT

Revision 14754 - Directory Listing
Modified Mon Aug 30 22:22:08 2010 UTC (7 years, 1 month ago) by finetjul
ENH: Hide the Undo/Redo and Layout toolbars by default

Revision 14750 - Directory Listing
Modified Mon Aug 30 20:16:53 2010 UTC (7 years, 1 month ago) by finetjul
ENH: Improve SlicerQT application icons (use 2 levels of transparency)

still not great though...

Revision 14748 - Directory Listing
Modified Mon Aug 30 19:44:07 2010 UTC (7 years, 1 month ago) by finetjul
ENH: Add system icon to SlicerQT application.

Revision 14705 - Directory Listing
Modified Sun Aug 29 00:30:03 2010 UTC (7 years, 1 month ago) by jcfr
STYLE: SlicerQT/Main.cxx - Remove extra includes

Revision 14645 - Directory Listing
Modified Thu Aug 19 18:45:14 2010 UTC (7 years, 2 months ago) by wjp@bwh.harvard.edu
BUG: fixed but in converting radioactivity units

Revision 14644 - Directory Listing
Modified Thu Aug 19 18:33:01 2010 UTC (7 years, 2 months ago) by hjohnson
STYLE:  Improved const correctness of the code.

Revision 14599 - Directory Listing
Modified Tue Aug 17 18:38:40 2010 UTC (7 years, 2 months ago) by francois_budin
BUG:if resampling DWI, does not transform 0 vector gradients anymore

Revision 14590 - Directory Listing
Modified Mon Aug 16 20:06:05 2010 UTC (7 years, 2 months ago) by jcfr
COMP: Exclude code related to ctkPythonShell in qSlicerMainWindowCore

Revision 14581 - Directory Listing
Modified Mon Aug 16 18:32:55 2010 UTC (7 years, 2 months ago) by jcfr
ENH: Added vtkMRMLScriptedDisplayableManager class

Since it's not possible to derive a VTK class in python (and for that same
reason rely on polymorphism), the vtkMRMLScriptedDisplayableManager C++
class is a "proxy" allowing to interface a DisplayableManager written in python.

A scripted DisplayableManager should expose the following methods:
   - Create
   - GetMRMLSceneEventsToObserve
   - ProcessMRMLEvents
   - RemoveMRMLObservers
   - UpdateFromMRML
   - OnInteractorStyleEvent
   - OnMRMLDisplayableNodeModifiedEvent

In addition to register vtk class names, the MRMLDisplayableManager factory
can now register scripted displayableManager represented by a path
to a python script ending with ".py".

qSlicerLayoutManager now provide method setScriptedDisplayableManagerDirectory
allowing to set from which directory the scripted displayableManager
should be "sourced" from.
Similarly, the code in qMRMLSliceWidget and qMRMLThreeDView allowing to
register the displayableManager have been factored out into a method named:
 - registerDisplayableManagers(const QString& scriptedDisplayableManagerDirectory);


Below are more details explaining how a scripted displayable manager could
be implemented:
 The constructor has one parameter named 'parent' corresponding to the associated instance of
 vtkScriptedDisplayableManager in the C++ world.

 The python methods listed above corresponds to the implementation of the virtual method
 available in vtkScriptedDisplayableManager.

 The only exception is the virtual method SetMRMLSceneInternal, the python class only needs to
 implement the method GetMRMLSceneEventsToObserve. This later one just return a list of integer
 representing the eventid to observe.

 It's also possible to access the API of the associated C++ instance using the self.Parent
 For example:
   self.Parent.RemoveInteractorStyleObservableEvent(26) # vtkCommand::MouseWheelForwardEvent

 Make also sure NOT to call the corresponding C++ method from it's python equivalent, it will
 result in an infinite loop.
 The following statement will likely lead to an unstable state:
    def Create(self): self.Parent.Create()

 If a a method isn't implemented, the following syntax should be used:
   def Create(self): pass

 NOTE
   Ideally, a DisplayableManager should deal only with MRMLNodes. Incriminated code should
 be moved either in the DisplayableManager itself, in the associated MRML Node or
 in a MRMLNode helper class.

 TODO
   While porting existing code, to overcome this problem, the following need to be done:
     - DisplayableManager abstract base class should have a reference to the current MRMLApplicationLogic
    - The MRMLApplicationLogic should contain a map of logics
    - The list of logic internally used by the qSlicerLayoutManager should be removed and
     the list from the MRMLApplicationLogic used instead.

Revision 14571 - Directory Listing
Modified Sun Aug 15 14:31:05 2010 UTC (7 years, 2 months ago) by pieper
BUG: fix test so it matches new behavior (new default file names)

Revision 14570 - Directory Listing
Modified Sat Aug 14 22:45:51 2010 UTC (7 years, 2 months ago) by pieper
COMP: use the windows version of snprintf if needed

Revision 14569 - Directory Listing
Modified Sat Aug 14 22:28:47 2010 UTC (7 years, 2 months ago) by pieper
ENH: allow format specification for per-slice dicom file names - default is %04d

Revision 14543 - Directory Listing
Modified Wed Aug 11 07:17:05 2010 UTC (7 years, 2 months ago) by jcfr
BUG: In qSlicerMainWindowCore - Make sure PythonShell is deleted

Revision 14542 - Directory Listing
Modified Wed Aug 11 07:17:01 2010 UTC (7 years, 2 months ago) by jcfr
STYLE: Reorganize header alphabetically in Application/SlicerQT/CMakeLists.txt

Revision 14541 - Directory Listing
Modified Wed Aug 11 07:16:58 2010 UTC (7 years, 2 months ago) by jcfr
BUG: In qSlicerMainWindow, use activateWindow (instead of setFocus) to give the focus to pythonShell

See http://doc.qt.nokia.com/4.6/qwidget.html#activateWindow

Revision 14521 - Directory Listing
Modified Tue Aug 10 19:11:46 2010 UTC (7 years, 2 months ago) by pieper
ENH: add client data point script handler function to support different interpreters (pythonqt, for instances)

Revision 14518 - Directory Listing
Modified Tue Aug 10 16:41:04 2010 UTC (7 years, 2 months ago) by pieper
ENH: focus on python console when it is raised - TODO: focus on the actual text widget, not just window

Revision 14515 - Directory Listing
Modified Tue Aug 10 05:14:59 2010 UTC (7 years, 2 months ago) by finetjul
STYLE: Remove vtksys code dependency in slicer home/bin directory search.

Use Qt code instead.

Revision 14514 - Directory Listing
Modified Tue Aug 10 04:22:32 2010 UTC (7 years, 2 months ago) by finetjul
BUG: Crash in Slicer3 hybrid mode as qSlicerApplication was initialized

with no arguments, without arguments, SlicerHomeDir can't be found.

Revision 14513 - Directory Listing
Modified Tue Aug 10 04:22:20 2010 UTC (7 years, 2 months ago) by finetjul
ENH: Add qSlicerIconEnginePlugin

Revision 14512 - Directory Listing
Modified Tue Aug 10 04:22:05 2010 UTC (7 years, 2 months ago) by finetjul
ENH: Add new icons to Slicer

Revision 14486 - Directory Listing
Modified Fri Aug 6 01:41:36 2010 UTC (7 years, 2 months ago) by finetjul
BUG: Some modules didn't show up in the Module Selector toolbar.

It's because they were hidden by not belonging to ModuleToolBar.
-> Don't hide module QActions when they don't belong to ModuleToolBarList

Revision 14479 - Directory Listing
Modified Thu Aug 5 18:57:58 2010 UTC (7 years, 2 months ago) by finetjul
ENH: Add FitToWindow and Slice FOV to qMRMLSliceControllerToolBar

qMRMLSliceControllerToolBar directly uses the logics to do processing on the
slice nodes.

Revision 14474 - Directory Listing
Modified Thu Aug 5 18:57:39 2010 UTC (7 years, 2 months ago) by finetjul
ENH: Connect qMRMLSlicesControllerToolBar actions to MRML nodes

Revision 14472 - Directory Listing
Modified Thu Aug 5 13:40:28 2010 UTC (7 years, 2 months ago) by wjp@bwh.harvard.edu
BUG: getting rid of dashboard warnings...

Revision 14452 - Directory Listing
Modified Tue Aug 3 20:01:38 2010 UTC (7 years, 2 months ago) by fedorov
BUG: a check was missing to allow the user to use bspline transform selector
for the output transform


Revision 14430 - Directory Listing
Modified Tue Aug 3 03:10:18 2010 UTC (7 years, 2 months ago) by finetjul
ENH: Replace qMRMLSlicesControllerWidget by qMRMLSlicesControllerToolBar

Revision 14427 - Directory Listing
Modified Mon Aug 2 20:36:09 2010 UTC (7 years, 2 months ago) by finetjul
ENH: Add tooltips to most of the application QActions

Revision 14426 - Directory Listing
Modified Mon Aug 2 20:36:05 2010 UTC (7 years, 2 months ago) by finetjul
ENH: Add Keyboard Shortcut dialog (qSlicerActionsDialog)

Revision 14421 - Directory Listing
Modified Mon Aug 2 19:03:10 2010 UTC (7 years, 2 months ago) by jcfr
ENH: Update qSlicerMainWindow - qSlicerMouseModeToolBar is now displayed.

Revision 14410 - Directory Listing
Modified Fri Jul 30 14:57:46 2010 UTC (7 years, 2 months ago) by finetjul
ENH: Force icons to be visible in menus depending on the OS.

On Gnome/Linux, the default behavior is to hide the icons in menu. Here we
force the icons to be shown.

Revision 14409 - Directory Listing
Modified Fri Jul 30 14:57:42 2010 UTC (7 years, 2 months ago) by finetjul
ENH: Connect help/feedbacks menu with opening the browser url

Revision 14403 - Directory Listing
Modified Fri Jul 30 01:21:44 2010 UTC (7 years, 2 months ago) by hjohnson
ENH:  Merged all 3 branches of this tree attempting to make a KWStyle compliant code base.

Revision 14400 - Directory Listing
Modified Thu Jul 29 23:31:04 2010 UTC (7 years, 2 months ago) by finetjul
ENH: Link toolbar menu actions with toolbar visibility in SlicerQT

Revision 14399 - Directory Listing
Modified Thu Jul 29 23:31:00 2010 UTC (7 years, 2 months ago) by finetjul
ENH: Add View ToolBar in SlicerQT (old ViewToolBar is now Layout ToolBar)

Revision 14398 - Directory Listing
Modified Thu Jul 29 23:30:56 2010 UTC (7 years, 2 months ago) by finetjul
ENH: Add Undo/Redo ToolBar in SlicerQT

Revision 14386 - Directory Listing
Modified Thu Jul 29 18:35:25 2010 UTC (7 years, 2 months ago) by pieper
COMP: explicitly use the std:: namespace to avoid compile issues on Sun (thanks to Attila Nagy for the patches)

Revision 14382 - Directory Listing
Modified Thu Jul 29 17:54:03 2010 UTC (7 years, 2 months ago) by finetjul
ENH: Add qSlicerModuleSelectorToolBar::removeModule

Revision 14381 - Directory Listing
Modified Thu Jul 29 17:53:59 2010 UTC (7 years, 2 months ago) by finetjul
ENH: Don't need a signal mapper for ModuleToolBar

Because qSlicerModuleSelectorToolBar and qSlicerMainWindow::ModuleToolBar
listen to the same QAction, if a QAction is triggered in ModuleToolBar,
qSlicerModuleSelectorToolBar will catch it and select the module
accordingly.

Revision 14380 - Directory Listing
Modified Thu Jul 29 17:53:56 2010 UTC (7 years, 2 months ago) by finetjul
BUG:Select module using qSlicerModuleSelectorToolBar instead of qSlicerModulePanel

Using qSlicerModulePanel to select a module doesn't trigger the QAction
associated with the module with result in not updating qSlicerModuleSelectorToolBar

Revision 14379 - Directory Listing
Modified Thu Jul 29 17:53:52 2010 UTC (7 years, 2 months ago) by finetjul
ENH: qSlicerAbstractModule reuse the same QAction multiple time ...

... instead of creating a new one everytime a qaction is needed

Revision 14378 - Directory Listing
Modified Thu Jul 29 17:53:48 2010 UTC (7 years, 2 months ago) by finetjul
BUG: Action Icons in menu where hidden, show them

For some reasons, the application doesn't show icons in menus (maybe
Qt::AA_DontShowIconsInMenu is set). We manually set the icons visible in
menus here.

Revision 14377 - Directory Listing
Modified Thu Jul 29 17:53:43 2010 UTC (7 years, 2 months ago) by finetjul
ENH: Split qSlicerAbstractModule in QTCore/qSlicerAbstractCoreModule,

In order to have QtGUI code in qSlicerAbstractModule, the class has to be
in Base/QTGUI, we rename qSlicerAbstractModule into
qSlicerAbstractCoreModule that only links with QtCore and we create a new
qSlicerAbstractModule in Bare/QTGUI. qSlicerAbstractModule contains an
icon (optionally reimplemented by all the modules), the allow the creation
of QAction directly from qSlicerAbstractModule and not by
qSlicerAbstractModuleWidget anymore. The problem with having createAction()
in qSlicerAbstractModuleWidget is that the module needed to create the
widget to be able to have QActions.(instanciate all the module widgets to
be able to have the module list in the toolbar which could slow down the
app, (a typical Slicer session doesn't need to instanciate all the module
widgets).

Revision 14376 - Directory Listing
Modified Thu Jul 29 17:53:22 2010 UTC (7 years, 2 months ago) by finetjul
ENH:Move toolbar generation from qSlicerMainWindowCore to qSlicerMainWindow

Revision 14374 - Directory Listing
Modified Thu Jul 29 17:53:07 2010 UTC (7 years, 2 months ago) by finetjul
ENH: Add qSlicerModuleSelectorToolBar, replaces qSlicerModuleSelectorWidget

Revision 14339 - Directory Listing
Modified Mon Jul 26 21:19:39 2010 UTC (7 years, 2 months ago) by finetjul
ENH: Connect "Close Scene" menu action with the scene clear command

Revision 14324 - Directory Listing
Modified Fri Jul 23 21:08:49 2010 UTC (7 years, 2 months ago) by hjohnson
ENH: After much work, an auto-formatting tools that is KWSTYLE compliant has been identified.  This tool was applied to the BRAINS source code to make is consistent with the ITK style, and to ensure that it is easy to read across all tools.  In addition, the code base was syncronized with the primary SVN repository.

Revision 14307 - Directory Listing
Modified Thu Jul 22 20:04:35 2010 UTC (7 years, 2 months ago) by fedorov
ENH: use reference image for resampled volume to initialize window/level and
colormap


Revision 14293 - Directory Listing
Modified Thu Jul 22 07:29:09 2010 UTC (7 years, 2 months ago) by jcfr
ENH: Added qMRMLThreeDViewsControllerWidget to qSlicerMainWindow

Revision 14290 - Directory Listing
Modified Thu Jul 22 07:28:36 2010 UTC (7 years, 2 months ago) by jcfr
ENH: Updated qSlicerMainWindow.ui - Now including qMRMLSlicesControllerWidget

Revision 14210 - Directory Listing
Modified Sun Jul 18 05:12:02 2010 UTC (7 years, 3 months ago) by fedorov
STYLE: fix typo


Revision 14209 - Directory Listing
Modified Sun Jul 18 05:08:07 2010 UTC (7 years, 3 months ago) by fedorov
BUG: allow to use CenterOfROI just to initialize


Revision 14207 - Directory Listing
Modified Fri Jul 16 23:21:59 2010 UTC (7 years, 3 months ago) by fedorov
BUG: center declaration was shadowed


Revision 14188 - Directory Listing
Modified Thu Jul 15 21:46:30 2010 UTC (7 years, 3 months ago) by jcfr
ENH: SlicerQT - Main.cxx - Added code to disable VTK global warnings

Revision 14173 - Directory Listing
Modified Thu Jul 15 12:11:34 2010 UTC (7 years, 3 months ago) by jcfr
ENH: SlicerQT - Update code in Main.cxx to use qMRMLEventLogger::setConsoleOutputEnabled

Revision 14157 - Directory Listing
Modified Thu Jul 15 12:10:20 2010 UTC (7 years, 3 months ago) by jcfr
ENH: MRMLScene - Rename SceneCloseEvent into SceneClosedEvent

The choice has been motivated to improve readability and limit confusion.

See http://massmail.spl.harvard.edu/public-archives/slicer-devel/2010/005057.html

Revision 14150 - Directory Listing
Modified Thu Jul 15 00:40:31 2010 UTC (7 years, 3 months ago) by fedorov
ENH: added CenterOfROI initializer to BRAINSFitHelper. This is simpler 
than CenterOfHead, and may be more universally applicable for non-brain 
applications. 
ENH: exposed CenterOfROI in BRAINSFitIGT


Revision 14146 - Directory Listing
Modified Tue Jul 13 23:33:00 2010 UTC (7 years, 3 months ago) by pieper
BUG: enable export uncompressed dicom and make it the default since this is the most compatible format in the real world

Revision 14144 - Directory Listing
Modified Tue Jul 13 21:55:55 2010 UTC (7 years, 3 months ago) by fedorov
ENH: added optional parameter to generate the grid showing the deformation.
When requested, warped grid is created only if the transform has bspline or roi 
bspline component. Warp grid spacing is initialized from the bspline grid 
spacing used in the bspline transform


Revision 14110 - Directory Listing
Modified Mon Jul 12 12:25:54 2010 UTC (7 years, 3 months ago) by vrnova
BUGFIX: rearranged function body so gcc will accept the code

Revision 14106 - Directory Listing
Modified Sun Jul 11 12:23:00 2010 UTC (7 years, 3 months ago) by wjp@bwh.harvard.edu
BUG: hopefully fixed the bug gcc was complaining about in declaration of two methods

Revision 14104 - Directory Listing
Modified Fri Jul 9 22:15:27 2010 UTC (7 years, 3 months ago) by jcfr
BUG: qSlicerMainWindowCorePrivate - Use if statement instead of assert when checking if a module has a widgetRepresentation

Revision 14097 - Directory Listing
Modified Fri Jul 9 21:08:41 2010 UTC (7 years, 3 months ago) by wjp@bwh.harvard.edu
BUG: stubbing out ComputeSUVBodyWeight CLI because of compilation error...

Revision 14096 - Directory Listing
Modified Fri Jul 9 17:29:16 2010 UTC (7 years, 3 months ago) by wjp@bwh.harvard.edu
ENH: cleaned up module error printouts

Revision 14094 - Directory Listing
Modified Fri Jul 9 17:03:20 2010 UTC (7 years, 3 months ago) by wjp@bwh.harvard.edu
ENH: adding draft of command line module for workflow engine suv computation pipeline

Revision 14080 - Directory Listing
Modified Thu Jul 8 15:48:52 2010 UTC (7 years, 3 months ago) by fedorov
STYLE: remove debugging output


Revision 14079 - Directory Listing
Modified Thu Jul 8 15:47:30 2010 UTC (7 years, 3 months ago) by fedorov
STYLE: remove debugging printout


Revision 14078 - Directory Listing
Modified Thu Jul 8 15:36:43 2010 UTC (7 years, 3 months ago) by fedorov
STYLE: Removed print statements


Revision 14077 - Directory Listing
Modified Thu Jul 8 15:31:55 2010 UTC (7 years, 3 months ago) by fedorov
ENH: Remove time extraction step to improve performance. This mode is not
applicable for the intended use cases.


Revision 14076 - Directory Listing
Modified Thu Jul 8 15:19:51 2010 UTC (7 years, 3 months ago) by fedorov
ENH: Initial commit of BRAINSFitIGT, a customized version of BRAINSFit to
support registration for image-guided procedures. The main differences from
BRAINSFit are:
 1) ROIBSpline mode is added, so that the bspline grid is initialized to cover
 just the bounding box of the aligned ROIs of the input images. Support for
 ROIBspline has been added to BRAINSFitHelper earlier.
 2) The user is given an option to maintain the list of all the intermediate
 transforms to facilitate debugging in the case of registration failure.
 3) Default bspline grid size is changed to 3x3x3, which may be sufficient for
 prostate registration.


Revision 14070 - Directory Listing
Modified Wed Jul 7 18:56:19 2010 UTC (7 years, 3 months ago) by fedorov
ENH: Added ROIBSpline registration mode. ROIBSpline can be specified instead
of BSpline transform. If requested, the bspline grid will be initialized just 
for the bounding box of the joined fixed binary mask and initially aligned moving 
binary mask. The resampled image will use the bspline transform restricted to
the bounding box region, with no deformation outside.

ENH: Added m_GenericTransformList to BRAINSFitHelper to maintain the list of
all the intermediate transforms. This feature will be used by a customized
BRAINSFit version to support registration (specifically, debugging of
registration) during image-guided procedures.


Revision 14068 - Directory Listing
Modified Wed Jul 7 18:17:22 2010 UTC (7 years, 3 months ago) by francois_budin
ENH:Addition of tests for ResampleVolume2

Revision 14065 - Directory Listing
Modified Wed Jul 7 17:41:40 2010 UTC (7 years, 3 months ago) by francois_budin
ENH:Reorganization to match ResampleDTI's organization

Revision 14055 - Directory Listing
Modified Tue Jul 6 01:26:33 2010 UTC (7 years, 3 months ago) by finetjul
ENH: Add "Add Volume", "Add Transform" and "Save Scene" dialogs in SlicerQt

Revision 14054 - Directory Listing
Modified Tue Jul 6 01:26:28 2010 UTC (7 years, 3 months ago) by finetjul
ENH: Add "About Slicer" dialog (only available in SlicerQt)

Revision 14029 - Directory Listing
Modified Sun Jul 4 23:41:52 2010 UTC (7 years, 3 months ago) by finetjul
ENH: Rename openXXXDialog to use a more standard name

Revision 14022 - Directory Listing
Modified Sat Jul 3 12:18:49 2010 UTC (7 years, 3 months ago) by fedorov
ENH: use compression for image IO


Revision 14021 - Directory Listing
Modified Sat Jul 3 00:58:38 2010 UTC (7 years, 3 months ago) by domibel
STYLE: fix typo

Revision 14018 - Directory Listing
Modified Fri Jul 2 19:54:22 2010 UTC (7 years, 3 months ago) by alexy
ENH: added scalars from tensor modes, added multiple labels in tractography/ROISelect

Revision 14014 - Directory Listing
Modified Fri Jul 2 13:54:56 2010 UTC (7 years, 3 months ago) by francois_budin
ENH:Addition of tests

Revision 14013 - Directory Listing
Modified Fri Jul 2 13:52:06 2010 UTC (7 years, 3 months ago) by francois_budin
ENH:Replaced bulk flag with nobulk flag. Bulk is now the default when module is started both as a command line and through the GUI

Revision 14008 - Directory Listing
Modified Thu Jul 1 20:33:32 2010 UTC (7 years, 3 months ago) by fedorov
ENH: remove duplicate functionality


Revision 14003 - Directory Listing
Modified Thu Jul 1 03:40:41 2010 UTC (7 years, 3 months ago) by jcfr
ENH: Update SlicerQt/Main.cxx and qSlicerMainWindow to use the layout manager

An additional toolbar allowing to switch between the different layout
is now visible on the top.

Revision 13969 - Directory Listing
Modified Mon Jun 28 16:09:22 2010 UTC (7 years, 3 months ago) by haehn
ENH: Removed warnings of the Annotation module

Revision 13964 - Directory Listing
Modified Mon Jun 28 11:45:15 2010 UTC (7 years, 3 months ago) by hjohnson
STYLE:  Removed outdated OrientImage from slicer tree.  As of recent ITK versions, and with Slicer requirement of CMAKE_USE_OREINTED_IMAGE=ON, the non-systematic use of OrientedImages is no longer needed.

Revision 13962 - Directory Listing
Modified Mon Jun 28 02:52:43 2010 UTC (7 years, 3 months ago) by jcfr
ENH: Move vtkSlicerSliceLogic and vtkSlicerSliceLayerLogic to MRMLLogic library

Also move the dependent classes: vtkImageLabelOutline, vtkImageNeighborhoodFilter,
vtkImageResliceMask, vtkImageSlice to MRMLLogic

Ultimately, these class should be added to the slicer/VTK git fork and eventually
ported to the offical VTK repository.

All Cxx classes and Tcl script referencing vtkSlicerSliceLogic and vtkSlicerSliceLayerLogic
have also been updated.

Tcl wrapping hints have been moved from Base/Logic/Wrapping/Tcl/hints to
Libs/MRMLLogic/Wrapping/Tcl/hints

Revision 13949 - Directory Listing
Modified Fri Jun 25 14:19:04 2010 UTC (7 years, 3 months ago) by francois_budin
ENH:Interface simplification and modification of the way to load a BSpline transform associated with a bulk transform

Revision 13946 - Directory Listing
Modified Thu Jun 24 22:31:08 2010 UTC (7 years, 3 months ago) by alexy
ENH: reworked Displayable Manager design

Revision 13945 - Directory Listing
Modified Thu Jun 24 22:15:16 2010 UTC (7 years, 3 months ago) by jcfr
ENH: Created directory structure supporting new libraries MRMLLogic and MRMLDisplayableManager

The dependency graph looks like:

              |----------<---- SlicerBaseLogic
              |
MRML ----- MRMLLogic ---- MRMLDisplayableManager
                            |
                            |-------< ----- SlicerBaseGUI
                            |
                            |-------< ----- SlicerBaseQTGUI

Revision 13917 - Directory Listing
Modified Wed Jun 23 03:18:19 2010 UTC (7 years, 3 months ago) by jcfr
COMP: DiffusionApplication - Fix #ifdef/#define preprocessor statement in localPluginUtilities.h

Revision 13913 - Directory Listing
Modified Tue Jun 22 19:47:21 2010 UTC (7 years, 3 months ago) by hjohnson
STYLE:  Updated code to be nearly KWSTYLE compliant.

Revision 13906 - Directory Listing
Modified Tue Jun 22 13:48:30 2010 UTC (7 years, 3 months ago) by hjohnson
ENH: A small reorganization to allow this to be built outside of Slicer3.  There is still a little CMake work that could be done so that it can build completely by itself.

Revision 13904 - Directory Listing
Modified Tue Jun 22 13:12:50 2010 UTC (7 years, 3 months ago) by francois_budin
BUG:Reference image had to be a DTI if the module was used in Slicer3

Revision 13901 - Directory Listing
Modified Tue Jun 22 11:46:58 2010 UTC (7 years, 3 months ago) by taox
BUG: Fixed a minor bug with .nrrd file output.

Revision 13899 - Directory Listing
Modified Tue Jun 22 11:30:15 2010 UTC (7 years, 3 months ago) by taox
BUG: bug888: wrong directory for output file when outputDirectory was not given. Also fixed problem with Siemens Mosaic format to .nrrd file.

Revision 13888 - Directory Listing
Modified Sun Jun 20 10:25:39 2010 UTC (7 years, 4 months ago) by jcfr
ENH: SlicerQT/Main.cxx - ctkLogger is now configured

Revision 13859 - Directory Listing
Modified Sat Jun 19 16:48:04 2010 UTC (7 years, 4 months ago) by alexy
ENH: models display manager: first cut

Revision 13801 - Directory Listing
Modified Tue Jun 15 18:12:21 2010 UTC (7 years, 4 months ago) by finetjul
ENH: Merge Base/QTBase with Base/QTCore

Some QtGUI dependent code was in Base/QTBase (qSlicerWidget,
qSlicerAbstractModuleWidget...) but Base/QTBase is not supposed to have
any QtGUI dependent code.
Moreover, QTBase and QTCore had no striking difference, they should be
merged.
QTBase is then moved into QtCore and QtGUI depending on the dependencies.
qSlicerAbstractModule (non gui) was depending on
qSlicerAbstractModuleWidget (gui), we created an intermediate class:
qSlicerAbstractModuleRepresentation (non gui) to remove the dependency
with GUI code. As the last class share a property with qSlicerWidget
(MRMLScene), we created a base class that contains the property.
ctkSettings is a gui class but is used in qSlicerCoreApplication, we now
handle QSettings in qSlicerCoreApplication and ctkSettings in
qSlicerApplication.

Revision 13786 - Directory Listing
Modified Mon Jun 14 15:57:49 2010 UTC (7 years, 4 months ago) by taox
BUG: keep the length of the diffusion vectors.

Revision 13783 - Directory Listing
Modified Mon Jun 14 00:33:50 2010 UTC (7 years, 4 months ago) by taox
ENH: turned on some debug output.

Revision 13779 - Directory Listing
Modified Sun Jun 13 16:42:44 2010 UTC (7 years, 4 months ago) by taox
BUG: Problem in demosaicing siemens datasets with padded blocks.

Revision 13778 - Directory Listing
Modified Sun Jun 13 14:47:20 2010 UTC (7 years, 4 months ago) by taox
BUG: using float for PET to ensure the right dynamic range -- do we need to go to double?

Revision 13769 - Directory Listing
Modified Fri Jun 11 18:04:12 2010 UTC (7 years, 4 months ago) by pieper
COMP: don't use kwwidgets macro unless kwwidgets is enabled

Revision 13752 - Directory Listing
Modified Thu Jun 10 21:07:07 2010 UTC (7 years, 4 months ago) by naucoin
ENH: expose the delete temporary files option for CLIs on the command line, and put it and the redirect module streams flag into the application settings interface. For now, using the flags on the command line will not override the registry settings

Revision 13740 - Directory Listing
Modified Thu Jun 10 17:30:34 2010 UTC (7 years, 4 months ago) by taox
ENH: takes care of PET/SPECT which has unsigned short data type.

Revision 13702 - Directory Listing
Modified Tue Jun 8 22:37:04 2010 UTC (7 years, 4 months ago) by fedorov
STYLE: remove newline in one parameter description (breaks sem2wiki
formatting)


Revision 13676 - Directory Listing
Modified Mon Jun 7 22:47:50 2010 UTC (7 years, 4 months ago) by hjohnson
ENH:  Merged changes with release 3-6 branch.

Revision 13658 - Directory Listing
Modified Sun Jun 6 04:46:05 2010 UTC (7 years, 4 months ago) by jcfr
BUG: Change signature of qSlicerModuleFactoryManagerTest1 main

To fix the following error:
error LNK2001: unresolved external symbol "int __cdecl qSlicerModuleFactoryManagerTest1(int,char * * const)

Changed from
  myTest(int argc, char ** argv)
to
  myTest(int argc, char* argv[])

Revision 13625 - Directory Listing
Modified Fri Jun 4 04:23:37 2010 UTC (7 years, 4 months ago) by jcfr
BUG: Fix test qSlicerModuleFactoryManagerTest1

Due to the fact the qSlicerModlesIO and qSlicerScalarOverlayIO are
registered within the registerItems method, qSlicerCoreApplication is
expected to be instanciated.

Also updated qSlicerCoreModuleFactory::registerItems method, now make sure
qSlicerCoreApplication is instanciated

Signed-off-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision 13624 - Directory Listing
Modified Fri Jun 4 02:47:43 2010 UTC (7 years, 4 months ago) by hjohnson
ENH:  Made labels shorter so that they render bettter in the image.

Revision 13613 - Directory Listing
Modified Thu Jun 3 18:08:00 2010 UTC (7 years, 4 months ago) by hjohnson
BUG:  BRAINSResample output image image was set to file instead of image.

Revision 13608 - Directory Listing
Modified Thu Jun 3 15:49:23 2010 UTC (7 years, 4 months ago) by hjohnson
ENH:  Improved code coverage by removing duplicate, or oudated functions taht are no longer needed.

Revision 13594 - Directory Listing
Modified Wed Jun 2 18:28:35 2010 UTC (7 years, 4 months ago) by hjohnson
ENH:  Added feature to BRAINSResample that allows grid lines to be created in the image.  ENH:  Made test cases more tolerant of slight image difference due to numerical precision.

Revision 13571 - Directory Listing
Modified Tue Jun 1 02:33:01 2010 UTC (7 years, 4 months ago) by hjohnson
ENH:  Fixed failing test cases by making separate baseline images.

Revision 13566 - Directory Listing
Modified Sun May 30 16:56:58 2010 UTC (7 years, 4 months ago) by hjohnson
ENH:
In response to numerous constructive critisms of the newly added suite of BRAINSTools, a code review was performed in order to make the applications work consistenently and with similar user interfaces.

Summary of ChangeLog:
-Instrumented xml files so that moving images are properly associated with their transforms in the Slicer3 MRML Interface.
-Made command line arguments consistent across tools for specifying images, transforms, similar parameters.
-Hid many advanced command line arguments from standard user interface when used from Slicer3
-Improved documentation of command line arguments to describe better what the intended purpose, and restrictions on use are.
-Added common set of image resample/warping options across all tools so that all tools provide common interface for choosing outputPixelType and interpolation mode
-Fixed reading and writing of transforms to use a common read/write paradigm, to be consistent across all tools, and to be compatible with Slicer3 (i.e. Write out Bspline transforms with the bulk transform given second).
-Increased code coverage by merging common functionality that existed in each tool separately into the BRAINSCommonLIb, thus removing code, and ensuring that exactly the same behavior was done across all tools.
-Worked around bug where ITK LSBFGSB optimizer does not properly return the number of iterations performed,  This improperly reported that Bspline registrations were never done when doing a Bspline registration alone.
-Improved source code documentation for commonly used functions.



Revision 13526 - Directory Listing
Modified Thu May 27 19:51:44 2010 UTC (7 years, 4 months ago) by millerjv
ENH: adding warp field output (not tested yet)

Revision 13517 - Directory Listing
Modified Thu May 27 16:26:01 2010 UTC (7 years, 4 months ago) by hjohnson
ENH:  Added proper documentation pages to headers.

Revision 13515 - Directory Listing
Modified Thu May 27 16:20:02 2010 UTC (7 years, 4 months ago) by hjohnson
ENH:  Fixed documentation to point ot proper directory.

Revision 13503 - Directory Listing
Modified Wed May 26 12:18:57 2010 UTC (7 years, 4 months ago) by hjohnson
ENH:  Reset baseline images to represent the algorithm in the new state.  Results have been validated with visual inspection as being virtually identical to the previous cases, but the recent improvements have slightly changed the behavior at the very edges of the images.

Revision 13500 - Directory Listing
Modified Wed May 26 11:58:47 2010 UTC (7 years, 4 months ago) by hjohnson
ENH:  Needed new reference data set after small algorithmic change was made.

Revision 13498 - Directory Listing
Modified Wed May 26 02:47:29 2010 UTC (7 years, 4 months ago) by hjohnson
ENH:  Many code cleanups and simplificaitons to make the maintenance much easier over time.  Added requested features.

Revision 13493 - Directory Listing
Modified Tue May 25 21:57:01 2010 UTC (7 years, 4 months ago) by jcfr
COMP: Fix Application/CLI/Java/CMakeLists.txt to work with CMake < 2.8.1

Revision 13490 - Directory Listing
Modified Tue May 25 21:13:04 2010 UTC (7 years, 4 months ago) by naucoin
BUG: make the java not found a status message for now, there's an issue finding Java_JAVAC_EXECUTABLE where JAVA_RUNTIME was succeeding

Revision 13486 - Directory Listing
Modified Tue May 25 19:36:39 2010 UTC (7 years, 4 months ago) by naucoin
BUG: when installed the extension TclSampleScriptedModule was getting errors on exit because the gui and logic were not defined.

Revision 13472 - Directory Listing
Modified Tue May 25 00:18:38 2010 UTC (7 years, 4 months ago) by jcfr
COMP: Update application/CLI/Java/CMakeLists.txt to display a warning if Javac is not installed

If Javac wasn't installed, project(JavaExamples Java ) was throwing an error

Also update the script to use the variables:
 Java_JAVA_EXECUTABLE, Java_JAVAC_EXECUTABLE and Java_JAR_EXECUTABLE

instead of the deprecated:
  JAVA_RUNTIME, JAVA_COMPILE and JAVA_ARCHIVE

Revision 13463 - Directory Listing
Modified Mon May 24 20:11:08 2010 UTC (7 years, 4 months ago) by hjohnson
COMP:  Removed unnecessary dependancy on the math library.

Revision 13461 - Directory Listing
Modified Mon May 24 18:04:41 2010 UTC (7 years, 4 months ago) by naucoin
BUG: install the merge models, make a library for it. Try exposing the java directory

Revision 13458 - Directory Listing
Modified Mon May 24 17:49:07 2010 UTC (7 years, 4 months ago) by hjohnson
ENH:  Improved the robustness of the debugging code, and removed errant debugging images that were being created.


Revision 13456 - Directory Listing
Modified Mon May 24 15:47:58 2010 UTC (7 years, 4 months ago) by demian
ENH: Regorganization of the Diffusion and Tractography related modules and improvement of their docmentation. Commited from revision 13442 Branch Slicer-3-6

Revision 13453 - Directory Listing
Modified Mon May 24 14:50:51 2010 UTC (7 years, 4 months ago) by hjohnson
COMP: Attempting to get the windows build requirements correct for snprintf function.

Revision 13433 - Directory Listing
Modified Fri May 21 01:45:06 2010 UTC (7 years, 5 months ago) by hjohnson
ENH:  Added improved documentation, simplified user interface, improved testing, and merged across all versions of the tools.

Revision 13427 - Directory Listing
Modified Thu May 20 19:11:55 2010 UTC (7 years, 5 months ago) by francois_budin
BUG: The file transform extension has to be .txt

Revision 13426 - Directory Listing
Modified Thu May 20 17:59:09 2010 UTC (7 years, 5 months ago) by rjosest
BUG: Remove Nonlinear option for tensor estimation (still experimental)

Revision 13423 - Directory Listing
Modified Thu May 20 15:32:41 2010 UTC (7 years, 5 months ago) by naucoin
COMP: init empty int vec to null

Revision 13419 - Directory Listing
Modified Thu May 20 13:30:51 2010 UTC (7 years, 5 months ago) by hayes
BUG: Fixed typo

Revision 13418 - Directory Listing
Modified Thu May 20 02:03:37 2010 UTC (7 years, 5 months ago) by rjosest
ENH: Updating documentation

Revision 13417 - Directory Listing
Modified Thu May 20 02:03:22 2010 UTC (7 years, 5 months ago) by rjosest
ENH: Updating documentation

Revision 13408 - Directory Listing
Modified Wed May 19 01:44:06 2010 UTC (7 years, 5 months ago) by hjohnson
ENH:  Simplified the user interface for BRAINSFit.

Revision 13392 - Directory Listing
Modified Mon May 17 21:00:16 2010 UTC (7 years, 5 months ago) by naucoin
BUG: fix link to docs

Revision 13389 - Directory Listing
Modified Mon May 17 19:13:39 2010 UTC (7 years, 5 months ago) by naucoin
BUG: remove control-m's in the .xml file by running dos2unix on it

Revision 13388 - Directory Listing
Modified Mon May 17 18:48:40 2010 UTC (7 years, 5 months ago) by pkarasev
COMP: custom test for sparse-field segment, modify the handler to not use bit-wise compare and instead use flag in the module


Revision 13385 - Directory Listing
Modified Mon May 17 15:51:37 2010 UTC (7 years, 5 months ago) by naucoin
BUG: fix doc link

Revision 13368 - Directory Listing
Modified Thu May 13 22:10:19 2010 UTC (7 years, 5 months ago) by hjohnson
BUG:0000842: Attempting to address bug issue where ScaleVersor3DTransforms are not readable/writable.

Revision 13356 - Directory Listing
Modified Thu May 13 19:29:23 2010 UTC (7 years, 5 months ago) by jcfr
COMP: Remove extra header qSlicerLayoutManager.h from SlicerQT/Main.cxx

Revision 13350 - Directory Listing
Modified Thu May 13 17:48:06 2010 UTC (7 years, 5 months ago) by jcfr
STYLE: In applications/SlicerQT/Main.cxx, remove unused call Q_INIT_RESOURCE

Revision 13348 - Directory Listing
Modified Thu May 13 15:52:50 2010 UTC (7 years, 5 months ago) by taox
ENH: handles slice interleaving dicom series now.

Revision 13347 - Directory Listing
Modified Thu May 13 14:35:08 2010 UTC (7 years, 5 months ago) by partyd
COMP: temporarily disable building EMSegmentBatchMakeModule until Kilian can fix it's EMSegmentCommandLine_GUIVersion dependency.

Revision 13337 - Directory Listing
Modified Wed May 12 18:56:37 2010 UTC (7 years, 5 months ago) by jcfr
ENH: Both signal signatures "currentMRMLSceneChanged" and "mrmlSceneChanged" were existing. Rename all to "mrmlSceneChanged"

Revision 13335 - Directory Listing
Modified Wed May 12 18:56:29 2010 UTC (7 years, 5 months ago) by jcfr
ENH: Added option --verbose-module-discovery to SlicerQT

qWarning and qDebug from the different module factory are now
surrounded by if(this->verbose) statement.

Revision 13315 - Directory Listing
Modified Tue May 11 16:43:17 2010 UTC (7 years, 5 months ago) by finetjul
ENH: Merge Slicer4 branch on trunk rev12438 -> rev13314

Revision 13311 - Directory Listing
Modified Tue May 11 12:57:25 2010 UTC (7 years, 5 months ago) by taox
BUG: some diffusion related public tags (0018|90xx, 0018|91xx) are already in gdcm dictionary. Adding them produces warnings -- rather than errors.

Revision 13310 - Directory Listing
Modified Tue May 11 12:32:19 2010 UTC (7 years, 5 months ago) by taox
BUG: some diffusion related public tags (0018|90xx, 0018|91xx) are already in gdcm dictionary. Adding them produces warnings -- rather than errors.

Revision 13293 - Directory Listing
Modified Sat May 8 17:07:44 2010 UTC (7 years, 5 months ago) by lassoan
COMP: Fixed BRAINSTools "warning LNK4217: locally defined symbol" warnings (BRAINS..._EXPORT extern int was specified for a few local methods)

Revision 13290 - Directory Listing
Modified Fri May 7 21:32:19 2010 UTC (7 years, 5 months ago) by hjohnson
ENH:  Changed tests to use long flags to avoid problem with running tests under windows.

Revision 13279 - Directory Listing
Modified Fri May 7 13:02:02 2010 UTC (7 years, 5 months ago) by pieper
BUG: fix missing test launching configurations

Revision 13277 - Directory Listing
Modified Fri May 7 02:33:04 2010 UTC (7 years, 5 months ago) by hjohnson
ENH:  Cleaned up to make command labels consistent.

Revision 13276 - Directory Listing
Modified Fri May 7 02:20:09 2010 UTC (7 years, 5 months ago) by hjohnson
ENH: After documentation, cleaned up some xml inconsistencies, and testing name consistencies.

Revision 13272 - Directory Listing
Modified Thu May 6 21:17:13 2010 UTC (7 years, 5 months ago) by hjohnson
ENH:0000829:  Addressing feature enhancment http://www.na-mic.org/Bug/view.php?id=829 submitted by fedorov.

Revision 13271 - Directory Listing
Modified Thu May 6 20:00:57 2010 UTC (7 years, 5 months ago) by pieper
COMP: merge testing path fix from release branch

Revision 13267 - Directory Listing
Modified Thu May 6 15:52:55 2010 UTC (7 years, 5 months ago) by pieper
COMP: fix warning

Revision 13263 - Directory Listing
Modified Thu May 6 13:57:41 2010 UTC (7 years, 5 months ago) by pieper
BUG: enable window paths for BRAINSTools to work with slicer build system; fixes testing on window

Revision 13262 - Directory Listing
Modified Thu May 6 13:49:43 2010 UTC (7 years, 5 months ago) by pieper
COMP: disable test on apple until it is understood what is being tested

Revision 13261 - Directory Listing
Modified Wed May 5 23:19:24 2010 UTC (7 years, 5 months ago) by naucoin
BUG: use the updated contour points, new baseline

Revision 13260 - Directory Listing
Modified Wed May 5 22:58:48 2010 UTC (7 years, 5 months ago) by naucoin
BUG: get the jar and .tcl files installed when using cpack, if out the SPECTRE stuff for now

Revision 13259 - Directory Listing
Modified Wed May 5 22:42:02 2010 UTC (7 years, 5 months ago) by naucoin
BUG: enable testing on windows now that have 32 bit baseline to compare against

Revision 13258 - Directory Listing
Modified Wed May 5 22:26:34 2010 UTC (7 years, 5 months ago) by naucoin
BUG: force xml poly data writer to write out 32 bit, and update the baseline test

Revision 13257 - Directory Listing
Modified Wed May 5 22:06:41 2010 UTC (7 years, 5 months ago) by naucoin
BUG: always write out .vtp files using Id type of int 32, and new int 32 baseline for comparison

Revision 13254 - Directory Listing
Modified Wed May 5 21:49:24 2010 UTC (7 years, 5 months ago) by naucoin
BUG: use the launcher on the merge model test. TODO: figure out why output of the cli is different on 32 and 64 bit machines

Revision 13252 - Directory Listing
Modified Wed May 5 20:00:46 2010 UTC (7 years, 5 months ago) by pieper
STYLE: rename modules to match wiki documentation

Revision 13247 - Directory Listing
Modified Wed May 5 18:47:56 2010 UTC (7 years, 5 months ago) by hjohnson
COMP:  Another attempt to try to build sufficient dependancies for supporting parallel builds of Slicer3.

Revision 13242 - Directory Listing
Modified Wed May 5 15:40:28 2010 UTC (7 years, 5 months ago) by naucoin
BUG: point to the mipav dir and SPECTRE jar file from Slicer3_HOME if it's defined

Revision 13241 - Directory Listing
Modified Wed May 5 15:03:52 2010 UTC (7 years, 5 months ago) by naucoin
BUG: use the launcher to run cmake so it can find the test code, added an error if the test command failed to run

Revision 13240 - Directory Listing
Modified Wed May 5 14:43:34 2010 UTC (7 years, 5 months ago) by alexy
ENH: fixed doc links

Revision 13237 - Directory Listing
Modified Wed May 5 13:17:04 2010 UTC (7 years, 5 months ago) by hjohnson
COMP:  Attempting to get parallel builds to work correctly under windows.

Revision 13235 - Directory Listing
Modified Wed May 5 02:18:59 2010 UTC (7 years, 5 months ago) by hjohnson
COMP: Removed unnecessary programs.

Revision 13233 - Directory Listing
Modified Tue May 4 21:59:39 2010 UTC (7 years, 5 months ago) by ygao
BUG remove two obsolete files and change the CMakeList accordingly

Revision 13232 - Directory Listing
Modified Tue May 4 21:58:49 2010 UTC (7 years, 5 months ago) by ygao
BUG remove two obsolete files

Revision 13231 - Directory Listing
Modified Tue May 4 21:55:26 2010 UTC (7 years, 5 months ago) by ygao
BUG remove an obsolete file which may cause preprocessing error

Revision 13229 - Directory Listing
Modified Tue May 4 21:43:54 2010 UTC (7 years, 5 months ago) by naucoin
BUG: changing it back, don't run this test with the launcher as we're using cmake to launch it

Revision 13219 - Directory Listing
Modified Tue May 4 21:22:00 2010 UTC (7 years, 5 months ago) by naucoin
BUG: point to the slicer3 exe in the binary dir, hopefully will work better on windows

Revision 13218 - Directory Listing
Modified Tue May 4 21:10:37 2010 UTC (7 years, 5 months ago) by naucoin
BUG: set up the test so ctest can find the test file and data files. TODO: move the test files into the proper dir, make a baseline to compare it to

Revision 13217 - Directory Listing
Modified Tue May 4 21:08:58 2010 UTC (7 years, 5 months ago) by pieper
COMP: avoid duplicate symbol errors on windows compiles

Revision 13209 - Directory Listing
Modified Tue May 4 17:29:40 2010 UTC (7 years, 5 months ago) by naucoin
BUG: set TestLocation to an empty string rather than a space, as it was leading to --launch \ TestBinary, and not finding the TestBinary

Revision 13204 - Directory Listing
Modified Tue May 4 13:33:04 2010 UTC (7 years, 5 months ago) by pieper
BUG: fix warning about unused variable

Revision 13202 - Directory Listing
Modified Tue May 4 12:07:36 2010 UTC (7 years, 5 months ago) by pieper
BUG: include launcher so test can be run with shared libraries (test still fails)

Revision 13200 - Directory Listing
Modified Tue May 4 04:22:55 2010 UTC (7 years, 5 months ago) by ibanez
ENH: Added potential path for the names of CLI executables, to be used when running them from Valgrind.


Revision 13199 - Directory Listing
Modified Tue May 4 04:12:36 2010 UTC (7 years, 5 months ago) by ibanez
ENH: Setting up configuration for automating the process of running Valgrind in the CLI Modules.


Revision 13180 - Directory Listing
Modified Mon May 3 20:09:01 2010 UTC (7 years, 5 months ago) by hjohnson
COMP:  Attempting to make external object properly built for Windows computers.

Revision 13178 - Directory Listing
Modified Mon May 3 20:00:10 2010 UTC (7 years, 5 months ago) by hjohnson
COMP:  Attempting ot blindly fix windows shared library issues.

Revision 13174 - Directory Listing
Modified Mon May 3 19:17:17 2010 UTC (7 years, 5 months ago) by naucoin
COMP: removing compiler warning, precedence

Revision 13173 - Directory Listing
Modified Mon May 3 19:14:02 2010 UTC (7 years, 5 months ago) by naucoin
COMP: removing compiler warnings

Revision 13172 - Directory Listing
Modified Mon May 3 19:05:51 2010 UTC (7 years, 5 months ago) by hjohnson
COMP: Fixed compilation of BRAINSDemonWarp by creating a separate library, and including the windows flags for that library.

Revision 13171 - Directory Listing
Modified Mon May 3 18:34:32 2010 UTC (7 years, 5 months ago) by naucoin
COMP: removing un/signed mismatch, unused vars

Revision 13160 - Directory Listing
Modified Sun May 2 17:22:30 2010 UTC (7 years, 5 months ago) by pkarasev
BUG: test data set update: 'virtual colonoscopy' from Ron

Revision 13159 - Directory Listing
Modified Sun May 2 17:11:08 2010 UTC (7 years, 5 months ago) by pkarasev
BUG: SFLS implementation: path init, update scheme

Revision 13156 - Directory Listing
Modified Sun May 2 00:42:19 2010 UTC (7 years, 5 months ago) by fedorov
ENH: move diff demons to Modules/ChangeTracker/CommandLineApplication
from Applications/CLI. This should be substituted with BRAINSDemonsWarp
in the future


Revision 13155 - Directory Listing
Modified Sun May 2 00:29:27 2010 UTC (7 years, 5 months ago) by sylvain
ENH: fix link to Slicer 3.6 documentation wiki. improve acknowledgments section. add tests and test data.

Revision 13154 - Directory Listing
Modified Sun May 2 00:25:44 2010 UTC (7 years, 5 months ago) by sylvain
ENH: Add png file with MIT logo and NAMIC logo side-by-side

Revision 13153 - Directory Listing
Modified Sat May 1 19:05:48 2010 UTC (7 years, 5 months ago) by fedorov
BUG: plugin was not installed


Revision 13150 - Directory Listing
Modified Sat May 1 12:38:53 2010 UTC (7 years, 5 months ago) by aylward
BUG: Does not check for existence of Slicer3_EXE.  Prohibits use outside of Slicer.


Revision 13149 - Directory Listing
Modified Fri Apr 30 22:41:01 2010 UTC (7 years, 5 months ago) by fedorov
BUG: initialize all variables in the constructor


Revision 13146 - Directory Listing
Modified Fri Apr 30 21:39:07 2010 UTC (7 years, 5 months ago) by naucoin
BUG: copy the ACPC test mrml file to the binary dir where it can be modified without triggering a source dir is locally modified warning on the dashboard

Revision 13145 - Directory Listing
Modified Fri Apr 30 21:26:34 2010 UTC (7 years, 5 months ago) by ibanez
BUG: Member variables m_Spacing and  m_Size were not initialized.


Revision 13140 - Directory Listing
Modified Fri Apr 30 20:13:05 2010 UTC (7 years, 5 months ago) by pkarasev
BUG: SFLS implementation: path init, update scheme

Revision 13138 - Directory Listing
Modified Fri Apr 30 20:10:02 2010 UTC (7 years, 5 months ago) by hjohnson
COMP:  Disable the test until they can be debugged.

Revision 13135 - Directory Listing
Modified Fri Apr 30 19:39:00 2010 UTC (7 years, 5 months ago) by hjohnson
ENH:  Added test suite for BRAINSTools.

Revision 13133 - Directory Listing
Modified Fri Apr 30 19:33:35 2010 UTC (7 years, 5 months ago) by hjohnson
ENH:  Adding in test suite of tools to svn.

Revision 13129 - Directory Listing
Modified Fri Apr 30 18:18:03 2010 UTC (7 years, 5 months ago) by ygao
ENH: added the RobustStaticsSegmenter into trunk/Application/CLI/RobustStatisticsSegmenter dirctory. it compiles and works on my machien: 64bit RHEL gcc 4.1.2

Revision 13127 - Directory Listing
Modified Fri Apr 30 17:37:26 2010 UTC (7 years, 5 months ago) by naucoin
BUG: skip the test on windows

Revision 13125 - Directory Listing
Modified Fri Apr 30 16:59:13 2010 UTC (7 years, 5 months ago) by taox
ENH: corrected staled document URL.

Revision 13124 - Directory Listing
Modified Fri Apr 30 16:52:02 2010 UTC (7 years, 5 months ago) by taox
ENH: corrected a typo.

Revision 13123 - Directory Listing
Modified Fri Apr 30 16:50:22 2010 UTC (7 years, 5 months ago) by naucoin
BUG: actually test the output of the merge models module, using a helper file

Revision 13120 - Directory Listing
Modified Fri Apr 30 16:22:59 2010 UTC (7 years, 5 months ago) by taox
ENH: help on UI pointed to the wrong link.

Revision 13118 - Directory Listing
Modified Fri Apr 30 16:05:06 2010 UTC (7 years, 5 months ago) by naucoin
BUG: disable SparseFieldLevelSetContourTest1 on windows, doesn't link

Revision 13116 - Directory Listing
Modified Fri Apr 30 15:11:15 2010 UTC (7 years, 5 months ago) by millerjv
ENH: documentation link was missing

Revision 13115 - Directory Listing
Modified Fri Apr 30 14:37:59 2010 UTC (7 years, 5 months ago) by naucoin
COMP: add in windows build command

Revision 13111 - Directory Listing
Modified Fri Apr 30 12:57:26 2010 UTC (7 years, 5 months ago) by pieper
BUG: disable tests for culled module

Revision 13110 - Directory Listing
Modified Fri Apr 30 11:48:10 2010 UTC (7 years, 5 months ago) by pieper
BUG: try fix for failing fresh/nightly build that doesn't find Slicer3 (because it hasn't been built yet)

Revision 13107 - Directory Listing
Modified Fri Apr 30 02:02:08 2010 UTC (7 years, 5 months ago) by taox
BUG: corrected URL for online Documentation.

Revision 13106 - Directory Listing
Modified Fri Apr 30 01:07:10 2010 UTC (7 years, 5 months ago) by taox
ENH: add more test for MedianImageFilter.

Revision 13105 - Directory Listing
Modified Thu Apr 29 23:24:43 2010 UTC (7 years, 5 months ago) by hjohnson
COMP: Newly added test only works from withing the Slicer3 Tree, adn this was causing external packages that depend on DicomToNrrd to fail.

Revision 13103 - Directory Listing
Modified Thu Apr 29 22:33:17 2010 UTC (7 years, 5 months ago) by naucoin
BUG: update doc link, moving tags to top

Revision 13101 - Directory Listing
Modified Thu Apr 29 22:14:48 2010 UTC (7 years, 5 months ago) by naucoin
BUG: pass in a test mrml file to the acpc test. The file does get over written when the test is run, but only the first node changes. The second node, vtkMRMLLinearTransformNode2, contains the expected output

Revision 13100 - Directory Listing
Modified Thu Apr 29 21:54:34 2010 UTC (7 years, 5 months ago) by pieper
BUG: implement decisions from the module cull meeting http://wiki.na-mic.org/Wiki/index.php/2010_Slicer36_Module_Cull

Revision 13099 - Directory Listing
Modified Thu Apr 29 21:41:24 2010 UTC (7 years, 5 months ago) by naucoin
BUG: switch to smart pointers to get rid of a memory leak

Revision 13098 - Directory Listing
Modified Thu Apr 29 21:30:37 2010 UTC (7 years, 5 months ago) by naucoin
BUG: adding another test to cover more of the MergeModels CLI

Revision 13094 - Directory Listing
Modified Thu Apr 29 21:21:26 2010 UTC (7 years, 5 months ago) by naucoin
BUG: change the test to a c++ based one and use the helper cmake class to compare the output and the baseline. TODO: get the comparison succeeding, new baseline needed?

Revision 13090 - Directory Listing
Modified Thu Apr 29 20:37:37 2010 UTC (7 years, 5 months ago) by taox
BUG: volume was in LPS space, while gradient vectors were still in RAS space.

Revision 13089 - Directory Listing
Modified Thu Apr 29 20:22:58 2010 UTC (7 years, 5 months ago) by finetjul
STYLE: Add documentation link for Gaussian Blur module.

Revision 13084 - Directory Listing
Modified Thu Apr 29 19:35:17 2010 UTC (7 years, 5 months ago) by naucoin
BUG: update help/ack

Revision 13083 - Directory Listing
Modified Thu Apr 29 19:29:40 2010 UTC (7 years, 5 months ago) by naucoin
BUG: add documentation link for 3.6

Revision 13081 - Directory Listing
Modified Thu Apr 29 19:14:53 2010 UTC (7 years, 5 months ago) by naucoin
BUG: update documentation and ack

Revision 13080 - Directory Listing
Modified Thu Apr 29 19:09:43 2010 UTC (7 years, 5 months ago) by francois_budin
BUG:Forgot to add 2 files

Revision 13079 - Directory Listing
Modified Thu Apr 29 18:55:53 2010 UTC (7 years, 5 months ago) by taox
ENH: more meaningful description.

Revision 13078 - Directory Listing
Modified Thu Apr 29 17:45:35 2010 UTC (7 years, 5 months ago) by pieper
ENH: fix category (promote from Experimental)

Revision 13073 - Directory Listing
Modified Thu Apr 29 15:58:49 2010 UTC (7 years, 5 months ago) by francois_budin
BUG:measurement frame with HField transform was not taken into account; problem with transforms when multithreading;improvement of interpolators implementation

Revision 13072 - Directory Listing
Modified Thu Apr 29 15:55:27 2010 UTC (7 years, 5 months ago) by taox
ENH: minor change on help info to reduce confusion.

Revision 13070 - Directory Listing
Modified Thu Apr 29 15:46:32 2010 UTC (7 years, 5 months ago) by taox
ENH: support NRRD. add user selection for output directory.

Revision 13069 - Directory Listing
Modified Thu Apr 29 15:45:59 2010 UTC (7 years, 5 months ago) by francois_budin
ENH:Test simplified

Revision 13065 - Directory Listing
Modified Thu Apr 29 15:03:06 2010 UTC (7 years, 5 months ago) by naucoin
BUG: adding missing ACPC test of the Realign lib.

Revision 13064 - Directory Listing
Modified Thu Apr 29 15:02:15 2010 UTC (7 years, 5 months ago) by naucoin
COMP: comparison mismatch warning

Revision 13061 - Directory Listing
Modified Thu Apr 29 14:29:41 2010 UTC (7 years, 5 months ago) by naucoin
BUG: update link, contributor

Revision 13051 - Directory Listing
Modified Thu Apr 29 11:42:24 2010 UTC (7 years, 5 months ago) by lorensen
ENH: Updated documentation for 3.6 release.

Revision 13049 - Directory Listing
Modified Thu Apr 29 02:34:09 2010 UTC (7 years, 5 months ago) by taox
ENH: documentation points to 3-6.

Revision 13046 - Directory Listing
Modified Thu Apr 29 01:46:17 2010 UTC (7 years, 5 months ago) by naucoin
BUG: adding help/ack

Revision 13045 - Directory Listing
Modified Thu Apr 29 01:44:19 2010 UTC (7 years, 5 months ago) by naucoin
BUG: adding more testing for Cast, found out that Long wasn't compiled in, so removing it as an option

Revision 13044 - Directory Listing
Modified Thu Apr 29 01:43:35 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13041 - Directory Listing
Modified Thu Apr 29 01:36:33 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13040 - Directory Listing
Modified Thu Apr 29 01:33:24 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13039 - Directory Listing
Modified Thu Apr 29 01:30:59 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13038 - Directory Listing
Modified Thu Apr 29 01:30:19 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13037 - Directory Listing
Modified Thu Apr 29 01:28:22 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13036 - Directory Listing
Modified Thu Apr 29 01:27:06 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13035 - Directory Listing
Modified Thu Apr 29 01:25:30 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13034 - Directory Listing
Modified Thu Apr 29 01:24:27 2010 UTC (7 years, 5 months ago) by naucoin
BUG: updating help/ack

Revision 13033 - Directory Listing
Modified Thu Apr 29 01:20:39 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13032 - Directory Listing
Modified Thu Apr 29 01:18:07 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13030 - Directory Listing
Modified Thu Apr 29 01:16:58 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13029 - Directory Listing
Modified Thu Apr 29 01:06:33 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13028 - Directory Listing
Modified Thu Apr 29 01:05:37 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13027 - Directory Listing
Modified Thu Apr 29 00:48:58 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13026 - Directory Listing
Modified Thu Apr 29 00:46:09 2010 UTC (7 years, 5 months ago) by naucoin
BUG: Trying to fix test. TODO: find last of memory leaks from tcl test. Can't use the regular compare since this outputs a .vtp file, and the cmake compare command doesn't work because Slicer3 doesn't work with the execute_process command as it keeps breaking the pipes

Revision 13024 - Directory Listing
Modified Thu Apr 29 00:44:50 2010 UTC (7 years, 5 months ago) by naucoin
BUG: cleaning up memory leaks, trying to fix test. TODO: find last of memory leaks from tcl test. Can't use the regular compare since this outputs a .vtp file, and the cmake compare command doesn't work because Slicer3 doesn't work with the execute_process command as it keeps breaking the pipes

Revision 13023 - Directory Listing
Modified Thu Apr 29 00:35:49 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13022 - Directory Listing
Modified Thu Apr 29 00:33:12 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13021 - Directory Listing
Modified Thu Apr 29 00:31:31 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13020 - Directory Listing
Modified Thu Apr 29 00:29:46 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13019 - Directory Listing
Modified Thu Apr 29 00:27:13 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13018 - Directory Listing
Modified Thu Apr 29 00:25:39 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13017 - Directory Listing
Modified Thu Apr 29 00:24:02 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13016 - Directory Listing
Modified Thu Apr 29 00:22:35 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13015 - Directory Listing
Modified Thu Apr 29 00:21:24 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13014 - Directory Listing
Modified Thu Apr 29 00:17:26 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13013 - Directory Listing
Modified Thu Apr 29 00:15:13 2010 UTC (7 years, 5 months ago) by millerjv
BUG: remove newlines

Revision 13004 - Directory Listing
Modified Wed Apr 28 21:49:30 2010 UTC (7 years, 5 months ago) by millerjv
ENH: preparing for release

Revision 13003 - Directory Listing
Modified Wed Apr 28 21:48:16 2010 UTC (7 years, 5 months ago) by fedorov
ENH: renamed output flag to avoid possible conflict


Revision 13001 - Directory Listing
Modified Wed Apr 28 21:11:50 2010 UTC (7 years, 5 months ago) by fedorov
BUG: fixing label, default values and category


Revision 12999 - Directory Listing
Modified Wed Apr 28 20:59:47 2010 UTC (7 years, 5 months ago) by fedorov
BUG: incorrect type


Revision 12998 - Directory Listing
Modified Wed Apr 28 20:58:38 2010 UTC (7 years, 5 months ago) by fedorov
ENH: improved documentation, rearranged parameters and fixed spline order type


Revision 12986 - Directory Listing
Modified Wed Apr 28 19:50:27 2010 UTC (7 years, 5 months ago) by millerjv
ENH: tests

Revision 12985 - Directory Listing
Modified Wed Apr 28 19:50:07 2010 UTC (7 years, 5 months ago) by millerjv
ENH: documentation

Revision 12980 - Directory Listing
Modified Wed Apr 28 19:14:09 2010 UTC (7 years, 5 months ago) by lorensen
ENH: Update doc to 3.6.

Revision 12979 - Directory Listing
Modified Wed Apr 28 19:12:17 2010 UTC (7 years, 5 months ago) by taox
ENH: Test working now.

Revision 12978 - Directory Listing
Modified Wed Apr 28 18:55:50 2010 UTC (7 years, 5 months ago) by fedorov
ENH: reorganization of the parameters; filled in help and acks; updated
testing to use the new parameter flags


Revision 12977 - Directory Listing
Modified Wed Apr 28 18:29:21 2010 UTC (7 years, 5 months ago) by millerjv
ENH: documentation for the release

Revision 12976 - Directory Listing
Modified Wed Apr 28 18:28:19 2010 UTC (7 years, 5 months ago) by millerjv
ENH: added some tests of the AffineRegistration

Revision 12974 - Directory Listing
Modified Wed Apr 28 18:12:49 2010 UTC (7 years, 5 months ago) by fedorov
ENH: adding test for N4 bias field correction


Revision 12973 - Directory Listing
Modified Wed Apr 28 17:52:22 2010 UTC (7 years, 5 months ago) by fedorov
BUG: incorrect initial value of the parameter caused wrong algorithm
initialization and overfitting


Revision 12972 - Directory Listing
Modified Wed Apr 28 17:49:07 2010 UTC (7 years, 5 months ago) by fedorov
ENH: code cleanup


Revision 12971 - Directory Listing
Modified Wed Apr 28 16:12:14 2010 UTC (7 years, 5 months ago) by fedorov
ENH: cleanup and build the module as a shared library


Revision 12967 - Directory Listing
Modified Wed Apr 28 14:47:40 2010 UTC (7 years, 5 months ago) by taox
BUG: forcing RAS on GE data was not doing correctly. Going back to LPS for all vendors.

Revision 12966 - Directory Listing
Modified Wed Apr 28 13:52:57 2010 UTC (7 years, 5 months ago) by pkarasev
BUG: scale color map, handle lack-of-input-vertices, attempt to run contour seg if vertices are given

Revision 12948 - Directory Listing
Modified Tue Apr 27 19:34:48 2010 UTC (7 years, 5 months ago) by pieper
ENH: to address bugs related to bad registration results for EMSegmenter and other project enable BRAINS tools by default

Revision 12944 - Directory Listing
Modified Tue Apr 27 00:02:07 2010 UTC (7 years, 5 months ago) by hjohnson
COMP:  Syncronized with BRAINS3 build suite so that maintenance will be easier.  STYLE:  Improved command line documentation in Slicer3.

Revision 12940 - Directory Listing
Modified Mon Apr 26 23:12:34 2010 UTC (7 years, 5 months ago) by fedorov
ENH: adding CLI wrapping N4ITK algorithm, see Insight Journal publication 640:
Tustison N, Gee J "N4ITK: Nick's N3 ITK Implementation for MRI Bias Field
Correction", http://hdl.handle.net/10380/3053


Revision 12939 - Directory Listing
Modified Mon Apr 26 20:29:07 2010 UTC (7 years, 5 months ago) by pieper
COMP: fix installers for BRAINS command line modules

Revision 12936 - Directory Listing
Modified Mon Apr 26 18:52:18 2010 UTC (7 years, 5 months ago) by pieper
COMP: fix windows build for BRAINSCommonLib library

Revision 12933 - Directory Listing
Modified Mon Apr 26 16:53:33 2010 UTC (7 years, 5 months ago) by pieper
BUG: avoid errors when trying to look at module variables that have no contents

Revision 12930 - Directory Listing
Modified Mon Apr 26 15:45:27 2010 UTC (7 years, 5 months ago) by taox
STYLE: changed xml to be 3.6 ready.

Revision 12927 - Directory Listing
Modified Mon Apr 26 14:31:14 2010 UTC (7 years, 5 months ago) by pieper
ENH: allow selective disabling of all scripted modules

Revision 12926 - Directory Listing
Modified Mon Apr 26 14:30:00 2010 UTC (7 years, 5 months ago) by taox
STYLE: fixed a few typos.

Revision 12923 - Directory Listing
Modified Mon Apr 26 11:01:53 2010 UTC (7 years, 5 months ago) by casey.goodlett
COMP: Accidently entered wrong filename for RegisterImagesMultiRes test baseline.

Revision 12922 - Directory Listing
Modified Mon Apr 26 10:58:28 2010 UTC (7 years, 5 months ago) by casey.goodlett
BUG: Used wrong commands for RegisterImageMultiRes test tolerance.

Revision 12920 - Directory Listing
Modified Mon Apr 26 03:13:11 2010 UTC (7 years, 5 months ago) by hjohnson
ENH:  First submission to include the suite of BRAINS registraiton tools to Slicer3.  All the test tree has been removed (due to the large size of the regression test data that is usually included.

Revision 12919 - Directory Listing
Modified Sun Apr 25 22:46:20 2010 UTC (7 years, 5 months ago) by casey.goodlett
BUG: Adjust tolerance for register images test.  Getting different
results for linux and windows but both seem reasonable.

Revision 12918 - Directory Listing
Modified Sun Apr 25 21:23:00 2010 UTC (7 years, 5 months ago) by casey.goodlett
BUG: Fix segfault when not using region of interest in RegisterImagesMultiRes

Revision 12917 - Directory Listing
Modified Sun Apr 25 21:22:56 2010 UTC (7 years, 5 months ago) by casey.goodlett
ENH: Use compression in output for RegisterImagesMultiRes

Revision 12916 - Directory Listing
Modified Sun Apr 25 21:22:52 2010 UTC (7 years, 5 months ago) by casey.goodlett
ENH: Add test for register images multi-res.

Revision 12915 - Directory Listing
Modified Sun Apr 25 19:52:06 2010 UTC (7 years, 5 months ago) by hjohnson
COMP: Added license.

Revision 12889 - Directory Listing
Modified Fri Apr 23 19:20:26 2010 UTC (7 years, 5 months ago) by lorensen
ENH: updated docs for 3.6

Revision 12887 - Directory Listing
Modified Fri Apr 23 19:10:21 2010 UTC (7 years, 5 months ago) by lorensen
ENH: updated docs for 3.6

Revision 12886 - Directory Listing
Modified Fri Apr 23 18:53:36 2010 UTC (7 years, 5 months ago) by lorensen
ENH: updated docs for 3.6

Revision 12870 - Directory Listing
Modified Thu Apr 22 20:28:20 2010 UTC (7 years, 5 months ago) by pieper
BUG: use INT rather than LONG for label map type

Revision 12866 - Directory Listing
Modified Thu Apr 22 06:22:47 2010 UTC (7 years, 5 months ago) by pkarasev
COMP: add test and reference data for SFLS CLI module . Remaining issue: CTest support for vtkXMLPolyData input ?



Revision 12859 - Directory Listing
Modified Wed Apr 21 20:49:29 2010 UTC (7 years, 5 months ago) by lorensen
ENH: updated docs for 3.6

Revision 12844 - Directory Listing
Modified Tue Apr 20 22:14:57 2010 UTC (7 years, 6 months ago) by naucoin
BUG: 166 if a bool parameter doesn't have a default, need to set it to false. Updated execution model tour to have a non default boolean arg

Revision 12843 - Directory Listing
Modified Tue Apr 20 22:13:36 2010 UTC (7 years, 6 months ago) by naucoin
COMP: remove warning about needing brackets for disambiguation

Revision 12841 - Directory Listing
Modified Tue Apr 20 20:29:57 2010 UTC (7 years, 6 months ago) by naucoin
BUG: show that can select multiple input files

Revision 12840 - Directory Listing
Modified Tue Apr 20 20:18:33 2010 UTC (7 years, 6 months ago) by lorensen
ENH: updated docs for 3.6

Revision 12839 - Directory Listing
Modified Tue Apr 20 20:01:39 2010 UTC (7 years, 6 months ago) by lorensen
ENH: Added executable for CheckerBoard.

Revision 12838 - Directory Listing
Modified Tue Apr 20 20:01:04 2010 UTC (7 years, 6 months ago) by lorensen
ENH: updated docs for 3.6

Revision 12833 - Directory Listing
Modified Tue Apr 20 17:30:17 2010 UTC (7 years, 6 months ago) by lorensen
ENH: Improved documentation.

Revision 12832 - Directory Listing
Modified Tue Apr 20 16:56:53 2010 UTC (7 years, 6 months ago) by lorensen
BUG: input must be signed. ENH: Better documentation.

Revision 12819 - Directory Listing
Modified Mon Apr 19 22:00:21 2010 UTC (7 years, 6 months ago) by ibanez
ENH: Added LONG and ULONG tests to the Applications/CLI/Add test.


Revision 12808 - Directory Listing
Modified Mon Apr 19 20:31:43 2010 UTC (7 years, 6 months ago) by ibanez
ENH: Adding tests for all the pixel types of the Applications/CLI/Add module.


Revision 12802 - Directory Listing
Modified Mon Apr 19 18:07:38 2010 UTC (7 years, 6 months ago) by francois_budin
BUG:Remove duplicated typedef

Revision 12797 - Directory Listing
Modified Mon Apr 19 14:34:36 2010 UTC (7 years, 6 months ago) by naucoin
COMP: compiler warning, init variable to null

Revision 12796 - Directory Listing
Modified Mon Apr 19 14:31:43 2010 UTC (7 years, 6 months ago) by naucoin
COMP: get rid of compiler warnings

Revision 12795 - Directory Listing
Modified Mon Apr 19 06:54:43 2010 UTC (7 years, 6 months ago) by pkarasev
BUG: crash with data improperly saved, port over tested code from standalone executable


Revision 12776 - Directory Listing
Modified Fri Apr 16 15:07:53 2010 UTC (7 years, 6 months ago) by casey.goodlett
BUG: Add locally modified box spatial object to resolve mantis 789.

This is to workaround using an unstable version of ITK for this one
fix.  This should be reverted when ITK is updated (to the release after 3.18)

Revision 12771 - Directory Listing
Modified Thu Apr 15 21:46:51 2010 UTC (7 years, 6 months ago) by francois_budin
BUG:Tells you that you cannot use a deformation field and a BSpline with a bulk transform at the same time

Revision 12770 - Directory Listing
Modified Thu Apr 15 21:43:55 2010 UTC (7 years, 6 months ago) by francois_budin
ENH:Addition of a bulk transform for BSpline

Revision 12764 - Directory Listing
Modified Thu Apr 15 18:54:37 2010 UTC (7 years, 6 months ago) by pieper
BUG: additional diagnostics for python startup

Revision 12761 - Directory Listing
Modified Thu Apr 15 18:25:52 2010 UTC (7 years, 6 months ago) by francois_budin
ENH:Addition of a bulk transform for BSpline

Revision 12748 - Directory Listing
Modified Wed Apr 14 15:37:08 2010 UTC (7 years, 6 months ago) by naucoin
BUG: new SPECTRE jar fixes path problem

Revision 12696 - Directory Listing
Modified Thu Apr 8 22:02:20 2010 UTC (7 years, 6 months ago) by naucoin
COMP: getting rid of uninit var, casting compiler warnings

Revision 12683 - Directory Listing
Modified Thu Apr 8 00:47:14 2010 UTC (7 years, 6 months ago) by hjohnson
COMP:  Fixed external compilation dependancy on the GenerateCLP program.

Revision 12682 - Directory Listing
Modified Wed Apr 7 21:38:41 2010 UTC (7 years, 6 months ago) by francois_budin
BUG:PPD resampling problem corrected and singular matrix exception throw added

Revision 12652 - Directory Listing
Modified Mon Apr 5 19:24:35 2010 UTC (7 years, 6 months ago) by francois_budin
BUG:--compare does not compare DTIs properly

Revision 12642 - Directory Listing
Modified Mon Apr 5 15:04:09 2010 UTC (7 years, 6 months ago) by francois_budin
ENH: Minor modifications in xml

Revision 12641 - Directory Listing
Modified Mon Apr 5 14:01:25 2010 UTC (7 years, 6 months ago) by francois_budin
ENH:help improved

Revision 12627 - Directory Listing
Modified Fri Apr 2 20:41:06 2010 UTC (7 years, 6 months ago) by finetjul
ENH: BatchMake: update doc and acknowledgment

Revision 12601 - Directory Listing
Modified Thu Apr 1 21:29:03 2010 UTC (7 years, 6 months ago) by francois_budin
ENH:Support inversion of transforms order in file or node (not h-field)

Revision 12600 - Directory Listing
Modified Thu Apr 1 21:28:22 2010 UTC (7 years, 6 months ago) by francois_budin
ENH:Support inversion of transforms order in file or node (not h-field)

Revision 12562 - Directory Listing
Modified Wed Mar 31 14:56:05 2010 UTC (7 years, 6 months ago) by fedorov
ENH: always use compression for output images

Revision 12555 - Directory Listing
Modified Tue Mar 30 21:53:31 2010 UTC (7 years, 6 months ago) by naucoin
STYLE: fixed typo

Revision 12545 - Directory Listing
Modified Tue Mar 30 15:36:00 2010 UTC (7 years, 6 months ago) by francois_budin
ENH:Add a test for ResampleDTI

Revision 12542 - Directory Listing
Modified Tue Mar 30 03:27:22 2010 UTC (7 years, 6 months ago) by francois_budin
ENH:Remove useless templated type to save memory

Revision 12541 - Directory Listing
Modified Tue Mar 30 03:24:04 2010 UTC (7 years, 6 months ago) by francois_budin
STYLE: Compiles first a library with the source code and then compiles the executable from this library

Revision 12528 - Directory Listing
Modified Mon Mar 29 17:35:50 2010 UTC (7 years, 6 months ago) by hjohnson
ENH: Changed the CMakeLists.txt files to have capitalization conforming to the new cmake recommendations.

Revision 12515 - Directory Listing
Modified Sun Mar 28 17:54:49 2010 UTC (7 years, 6 months ago) by casey.goodlett
STYLE: Update documentation pointer for Transform From Fiducials.

Revision 12514 - Directory Listing
Modified Sun Mar 28 16:13:08 2010 UTC (7 years, 6 months ago) by hjohnson
ENH: Encapsulated the SlicerExecutionModel requirements so that it is easier to develop compliant applications without the burden of building all of Slicer.

Revision 12512 - Directory Listing
Modified Sat Mar 27 20:43:05 2010 UTC (7 years, 6 months ago) by casey.goodlett
STYLE: Update  acknowledgements and logo for TransformFromFiducials.

Revision 12511 - Directory Listing
Modified Sat Mar 27 20:43:00 2010 UTC (7 years, 6 months ago) by casey.goodlett
STYLE: Update acknowledgements and logo for RegisterImages.

Revision 12510 - Directory Listing
Modified Sat Mar 27 20:42:57 2010 UTC (7 years, 6 months ago) by casey.goodlett
STYLE: Update acknowledgements and logo for RegisterImagesMultiRes

Revision 12509 - Directory Listing
Modified Sat Mar 27 20:41:12 2010 UTC (7 years, 6 months ago) by casey.goodlett
ENH: Remove testing section from UI for RegisterImages.

Revision 12508 - Directory Listing
Modified Sat Mar 27 20:09:38 2010 UTC (7 years, 6 months ago) by lorensen
COMP: Improved documentation.

Revision 12507 - Directory Listing
Modified Sat Mar 27 19:07:20 2010 UTC (7 years, 6 months ago) by ibanez
COMP: Fioxing warnings about local variable m_Index shadowing member variable fo the same name.


Revision 12495 - Directory Listing
Modified Fri Mar 26 20:30:23 2010 UTC (7 years, 6 months ago) by francois_budin
STYLE:Help and aknowledgement improved

Revision 12494 - Directory Listing
Modified Fri Mar 26 19:55:46 2010 UTC (7 years, 6 months ago) by taox
ENH: for images without vendor info, we treate them as a regular volume.

Revision 12489 - Directory Listing
Modified Fri Mar 26 18:11:23 2010 UTC (7 years, 6 months ago) by francois_budin
STYLE:ResampleVolume2 logo changed from ITK to NAMIC

Revision 12488 - Directory Listing
Modified Fri Mar 26 18:09:48 2010 UTC (7 years, 6 months ago) by francois_budin
STYLE:Help and aknowledgement improved

Revision 12473 - Directory Listing
Modified Thu Mar 25 20:45:01 2010 UTC (7 years, 6 months ago) by taox
BUG: Somehow the argument type was changes.

Revision 12452 - Directory Listing
Modified Wed Mar 24 21:41:08 2010 UTC (7 years, 6 months ago) by fedorov
ENH: use compression for output volumes


Revision 12404 - Directory Listing
Modified Fri Mar 19 19:51:11 2010 UTC (7 years, 7 months ago) by francois_budin
BUG:BSpline transform was not setting the non-rigid transform counter

Revision 12402 - Directory Listing
Modified Fri Mar 19 19:12:22 2010 UTC (7 years, 7 months ago) by francois_budin
BUG:BSpline transform was not setting the non-rigid transform counter

Revision 12391 - Directory Listing
Modified Fri Mar 19 14:40:11 2010 UTC (7 years, 7 months ago) by francois_budin
BUG:Deformation field could not be set in slicer3 GUI

Revision 12390 - Directory Listing
Modified Fri Mar 19 14:39:09 2010 UTC (7 years, 7 months ago) by francois_budin
STYLE:Deformation field parameters presentation improvements

Revision 12388 - Directory Listing
Modified Fri Mar 19 14:22:29 2010 UTC (7 years, 7 months ago) by francois_budin
BUG:Deformation field could not be set in slicer3 GUI

Revision 12383 - Directory Listing
Modified Thu Mar 18 23:54:59 2010 UTC (7 years, 7 months ago) by sylvain
ENH: add NAMIC logo in the MRIBiasFieldCorrection module

Revision 12382 - Directory Listing
Modified Thu Mar 18 22:18:46 2010 UTC (7 years, 7 months ago) by francois_budin
ENH:Supports float transform and code cleaned

Revision 12380 - Directory Listing
Modified Thu Mar 18 17:40:38 2010 UTC (7 years, 7 months ago) by francois_budin
STYLE:Split SetTransform function that was too long

Revision 12376 - Directory Listing
Modified Thu Mar 18 15:15:49 2010 UTC (7 years, 7 months ago) by francois_budin
STYLE:Split CheckDWMRI function that was too long

Revision 12375 - Directory Listing
Modified Thu Mar 18 14:45:44 2010 UTC (7 years, 7 months ago) by francois_budin
STYLE:Split main function that was too long

Revision 12373 - Directory Listing
Modified Wed Mar 17 21:12:49 2010 UTC (7 years, 7 months ago) by francois_budin
ENH:All the transforms are merged before being applied to the image

Revision 12372 - Directory Listing
Modified Wed Mar 17 21:11:30 2010 UTC (7 years, 7 months ago) by francois_budin
STYLE:comments modified

Revision 12370 - Directory Listing
Modified Wed Mar 17 13:30:40 2010 UTC (7 years, 7 months ago) by francois_budin
BUG:InterpolationType redefinition removed

Revision 12363 - Directory Listing
Modified Tue Mar 16 20:34:57 2010 UTC (7 years, 7 months ago) by francois_budin
STYLE:modification of order of operation in CheckDWMRI and addition of comments

Revision 12360 - Directory Listing
Modified Tue Mar 16 19:14:26 2010 UTC (7 years, 7 months ago) by francois_budin
BUG:gradient direction is now saved properly

Revision 12353 - Directory Listing
Modified Mon Mar 15 22:00:34 2010 UTC (7 years, 7 months ago) by francois_budin
ENH: Deformation field transfoms added/if multiple transforms, merges them before applying them/accepts float rigid and affine transforms

Revision 12317 - Directory Listing
Modified Mon Mar 8 23:05:21 2010 UTC (7 years, 7 months ago) by naucoin
BUG: remove the anatomy label file, it's obsolete, users can use the --color option on the command line, otherwise from the GUI the colour node is grabbed from the input volume's display node

Revision 12316 - Directory Listing
Modified Mon Mar 8 21:40:05 2010 UTC (7 years, 7 months ago) by aylward
COMP: Isolated unused vars


Revision 12310 - Directory Listing
Modified Fri Mar 5 18:30:50 2010 UTC (7 years, 7 months ago) by millerjv
ENH: moved crosshair creation to application logic

Revision 12296 - Directory Listing
Modified Wed Mar 3 20:52:58 2010 UTC (7 years, 7 months ago) by aylward
COMP: Commented-out the CountSamples test since it has a VERY long runtime.  Casey is on it...


Revision 12280 - Directory Listing
Modified Tue Mar 2 19:47:24 2010 UTC (7 years, 7 months ago) by casey.goodlett
ENH: Enable box ROI in RegisterImagesMultiRes.

Revision 12279 - Directory Listing
Modified Tue Mar 2 19:47:17 2010 UTC (7 years, 7 months ago) by casey.goodlett
ENH: Add support for creating a box spatial object from two points to be used for masking registration.

Revision 12278 - Directory Listing
Modified Tue Mar 2 19:47:12 2010 UTC (7 years, 7 months ago) by casey.goodlett
ENH: Add support for creating a fixed image region of interest from a slicer ROI input.

This adds a helper function in ConvertSlicerROIToRegion.h that creates an itk::ImageRegion from two points and an image base.

A test class is provided.

Revision 12277 - Directory Listing
Modified Tue Mar 2 19:44:29 2010 UTC (7 years, 7 months ago) by casey.goodlett
STYLE: Add header to source file in RegisterImagesMultiRes

Revision 12274 - Directory Listing
Modified Tue Mar 2 16:25:43 2010 UTC (7 years, 7 months ago) by casey.goodlett
BUG: Fix merge models when path to input contains a "."

Revision 12266 - Directory Listing
Modified Mon Mar 1 21:06:22 2010 UTC (7 years, 7 months ago) by aylward
BUG: compile arguments aren't additive.  So, created a compount argument that includes the moduleEntryPoint as well as the Support-2d-images option.


Revision 12265 - Directory Listing
Modified Mon Mar 1 20:59:20 2010 UTC (7 years, 7 months ago) by aylward
ENH: Added support for 2D images when SUPPORT_2D_IMAGES cmake var is set.


Revision 12262 - Directory Listing
Modified Sun Feb 28 21:57:16 2010 UTC (7 years, 7 months ago) by aylward
ENH: vtkRegisterImage...Configure.h.in include vtkSlicerConfigure.h, but it wasn't needed.   Libraries and execs linked with MRML, but only needed ITK_LIBRARIES.   These changes allow this module to be compiled outside of Slicer.


Revision 12253 - Directory Listing
Modified Fri Feb 26 15:01:52 2010 UTC (7 years, 7 months ago) by finetjul
COMP: Python Integration - remove d, unused variable

Revision 12237 - Directory Listing
Modified Thu Feb 25 21:49:27 2010 UTC (7 years, 7 months ago) by jcfr
ENH: SlicerQT - Added qCTKPythonShell to qSlicerMainWindow.

An instance of the python shell is lazy created when the user use
the shortcut CTRL-P or when he clicks on "Window->Python Interactor"

Revision 12236 - Directory Listing
Modified Thu Feb 25 21:49:23 2010 UTC (7 years, 7 months ago) by jcfr
STYLE: SlicerQT - Re-organize header includes. QT should be first, then qCTK, qVTK, qMRML, ITK, VTK, MRML, local includes and the last one the STD

Revision 12204 - Directory Listing
Modified Thu Feb 25 00:02:57 2010 UTC (7 years, 7 months ago) by naucoin
ENH: add a merge models CLI module. uses vtkAppendPolyData as posted by Daniel Haehn to the slicer users list

Revision 12154 - Directory Listing
Modified Wed Feb 17 04:25:55 2010 UTC (7 years, 8 months ago) by alexy
ENH: added eigenvalues for DTI math module

Revision 12022 - Directory Listing
Modified Fri Feb 5 20:37:09 2010 UTC (7 years, 8 months ago) by hjohnson
ENH:  Improved installation process for standalone builds.

Revision 12016 - Directory Listing
Modified Fri Feb 5 16:04:35 2010 UTC (7 years, 8 months ago) by jcfr
COMP: Fix various compilation warnings

Revision 12001 - Directory Listing
Modified Fri Feb 5 04:39:38 2010 UTC (7 years, 8 months ago) by jcfr
COMP: Fix various compilation warning

Revision 11995 - Directory Listing
Modified Fri Feb 5 03:03:24 2010 UTC (7 years, 8 months ago) by jcfr
ENH: SlicerQT - Added command line option "--disable-loadable-module"

Revision 11987 - Directory Listing
Modified Thu Feb 4 22:32:02 2010 UTC (7 years, 8 months ago) by jcfr
ENH: SlicerQT - Updated qSlicerCoreApplication and qSlicerApplication to make use of qCTKSettings and qSlicerCommandOptions classes.

The method initialize now requires the parameter passed by reference: exitWhenDone.
If exitWhenDone is set to True, the user of qSlicerCoreApplication or qSlicerApplication
is responsible to exit the application.

This parameter is set to true when the application should exit before
it starts the event loop. For example, when the parameter: --version or --help
are added to the command line, the application should execute the corresponding
function and exit.

Added method 'settings' to qSlicerCoreApplication, internally this method
will instantiate the application settings is not already done.
The setting filename is generated using the ApplicationName (ie Slicer),
the organizationName (ie NAMIC), the minor and major version.

In qSlicerCoreApplication, the method 'disableSettings' will instantiate a new setting object, this
time the setting filename is the same + a suffice (ie "-disabled").

In qSlicerCoreApplication, the method 'handlePreApplicationCommandLineArguments'
query the its associated commandOptions object to start the appropriate action.
All non-gui related logic should be added in that method. Calling 'terminate()'
allows to set the ExitWhenDone flag to true, this former one is checked
just after initalize finishes. If True, the application exit.

Application/SlicerQT/Main.cxx has been updated to consider the NoSplash option.

Revision 11978 - Directory Listing
Modified Thu Feb 4 20:12:55 2010 UTC (7 years, 8 months ago) by casey.goodlett
ENH: Reorganize RegisterImagesMultiRes parameters into required, optional, advanced.

Revision 11977 - Directory Listing
Modified Thu Feb 4 20:12:52 2010 UTC (7 years, 8 months ago) by casey.goodlett
ENH: Add metric tolerance and maximum line iterations parameters.

Revision 11976 - Directory Listing
Modified Thu Feb 4 20:12:48 2010 UTC (7 years, 8 months ago) by casey.goodlett
ENH: Add minimum step size parameter.

Revision 11975 - Directory Listing
Modified Thu Feb 4 20:12:42 2010 UTC (7 years, 8 months ago) by casey.goodlett
ENH: Add parameter to control the number of iterations in RegisterImagesMultiRes.

Revision 11962 - Directory Listing
Modified Wed Feb 3 23:45:03 2010 UTC (7 years, 8 months ago) by sylvain
ENH: add code for L1 norm bias field correction. convert image from ITK to VTK, process image and convert back to ITK

Revision 11957 - Directory Listing
Modified Wed Feb 3 20:50:08 2010 UTC (7 years, 8 months ago) by finetjul
ENH: SlicerQt - apply the StyledPanel to all the qCTKCollapsibleButtons. Make it by default in the designer.
Warning, setting StyledPanel by default in the designer (via qCTKCollapsibleButtonPlugin) doesn't mean that the widget is created by default with a frame.
If you instance the widget programatically, then you should then call: setContentsFrameShape(QFrame::StyledPanel).

Revision 11955 - Directory Listing
Modified Wed Feb 3 20:47:59 2010 UTC (7 years, 8 months ago) by sylvain
ENH: add options for alternate bias field correction methods

Revision 11954 - Directory Listing
Modified Wed Feb 3 19:48:57 2010 UTC (7 years, 8 months ago) by sylvain
ENH: use a templated function to handle arbitrary input scalar type. Add converters to and from VTK

Revision 11944 - Directory Listing
Modified Wed Feb 3 05:40:58 2010 UTC (7 years, 8 months ago) by sylvain
ENH: CLI module MRIBiasFieldCorrection. Code ported from Modules directory and cleaned

Revision 11925 - Directory Listing
Modified Tue Feb 2 16:56:49 2010 UTC (7 years, 8 months ago) by casey.goodlett
COMP: Silence compiler warning about unreferenced local variable in catch block.  Don't give a name to the caught exception as its never referenced.

Revision 11924 - Directory Listing
Modified Tue Feb 2 16:53:54 2010 UTC (7 years, 8 months ago) by aylward
BUG: Masked unused vars to eliminate warnings



Revision 11920 - Directory Listing
Modified Tue Feb 2 16:13:35 2010 UTC (7 years, 8 months ago) by casey.goodlett
COMP: Fix linking warning on windows for RegisterImagesMultiRes.  The name of EXPORT macro comes from the library name not the project name.

Revision 11917 - Directory Listing
Modified Tue Feb 2 05:15:01 2010 UTC (7 years, 8 months ago) by jcfr
ENH: SlicerQT - Updated SlicerQT/CMakeLists.txt, so that SlicerQT-forward executable will also include 'Slicer3_INSTALL_MODULES_BIN_DIR'

Indeed, since SlicerQT is linked against Modules/.../Logic, this path
has to be added.

Revision 11916 - Directory Listing
Modified Tue Feb 2 05:14:29 2010 UTC (7 years, 8 months ago) by jcfr
COMP: SlicerQT - For now, launcher 'Slicer3' (based on startkits) is also configured if Slicer3_USE_KWWidgets is OFF.

Required to be able to run SlicerQT on a windows build.
./slicer3 --launch SlicerQT

Some test also expect the launcher 'Slicer3' to be present. (for example VTKITKReader)
On windows, the launcher is mandatory to run the test.

Revision 11911 - Directory Listing
Modified Mon Feb 1 18:04:55 2010 UTC (7 years, 8 months ago) by naucoin
ENH: use the new return string type

Revision 11902 - Directory Listing
Modified Mon Feb 1 07:13:01 2010 UTC (7 years, 8 months ago) by jcfr
COMP: Fix shadowed variable in RegisterImagesMultiRes.cxx

Revision 11896 - Directory Listing
Modified Sun Jan 31 16:27:24 2010 UTC (7 years, 8 months ago) by ibanez
BUG: Fixing many memory leaks by introducing vtkSmartPointers.


Revision 11887 - Directory Listing
Modified Sat Jan 30 01:25:43 2010 UTC (7 years, 8 months ago) by millerjv
BUG: typo

Revision 11884 - Directory Listing
Modified Fri Jan 29 20:51:28 2010 UTC (7 years, 8 months ago) by naucoin
BUG: need quotes around path to java in case it has quotes in it

Revision 11881 - Directory Listing
Modified Fri Jan 29 20:33:27 2010 UTC (7 years, 8 months ago) by millerjv
ENH: Simple Return Parameters from CommandLineModules (integer, integer-vector, etc.)

Revision 11874 - Directory Listing
Modified Fri Jan 29 16:55:42 2010 UTC (7 years, 8 months ago) by naucoin
ENH: use the mipav java, use var names for the path to mipav and the spectre plugins, works on linux now if adjust the path vars

Revision 11847 - Directory Listing
Modified Thu Jan 28 22:08:39 2010 UTC (7 years, 8 months ago) by jcfr
ENH: SlicerQT - ModuleFactories are now registered with a ModuleFactoryManager

The class ModuleFactory has been removed and most of its behavior has been
transferred to ModuleFactoryManager.

The different module factories are now:
  - CoreModuleFactory
  - LoadableModuleFactory  (for QTModules)
  - CLILoadableModuleFactory
  - CLIExecutableModuleFactory
  - CLIPythonModuleFactory (not yet added ..)

The library dependencies have been updated from:

QTBase -> QTCLI ---------> QTCore -> QTGUI -> qSlicerQT -> SlicerQT
      |                      |
       -> QTCoreModules -----|

to

QTBase -> QTCore -> QTGUI -> qSlicerQT -> SlicerQT
                |                   |
                 -> QTCLI  ---------|
                |                   |
                 -> QTCoreModules --|

Method {initializeLoadable,CmdLine}ModulesPaths have been removed. Their
existing behavior has been added to:
  - qSlicerLoadableModuleFactory::modulePath
  - qSlicerCLIModuleFactoryHelper

The former is used by the CLI factories.

The moduleFactoryManager provides methods that allow to register/instantiate
module based on the factoryName. The factoryName corresponds the the name used
to register the factories using 'registerFactory' method. The preferred name
for a factory is its className.

Revision 11845 - Directory Listing
Modified Thu Jan 28 22:05:24 2010 UTC (7 years, 8 months ago) by jcfr
COMP: Added MRMLCLI to SlicerQT_FORWARD_PATH_INSTALL in SlicerQT/CMakeLists.txt

Revision 11843 - Directory Listing
Modified Thu Jan 28 22:05:16 2010 UTC (7 years, 8 months ago) by jcfr
COMP: Fix various compilation warnings (unused, ...)

Note: size_t is an unsigned int, it means there is no need to check if
it's value is negative.

Revision 11832 - Directory Listing
Modified Thu Jan 28 17:06:05 2010 UTC (7 years, 8 months ago) by millerjv
ENH: Extending CommandLineModule to support measurement tag (for plots)

Revision 11823 - Directory Listing
Modified Thu Jan 28 09:09:23 2010 UTC (7 years, 8 months ago) by jcfr
COMP: Fix various compilation warning (hidden virtual method, unused variable, ...)

Note1: Also moved vtkSlicerApplication.h up in the header include order
otherwise, when compiled with QT, it outputs that message:

#error qdatastream.h must be included before any header file that defines Status

Note2:
To fix such warning,
"base class‘base_class’should be explicitly initialized in the copy constructor"

the compy ctor and the '=' operator has been set as private member

Revision 11820 - Directory Listing
Modified Wed Jan 27 22:37:21 2010 UTC (7 years, 8 months ago) by millerjv
BUG: added wrapping to new library MRMLCLI to that things like QuickModel will work

Revision 11792 - Directory Listing
Modified Tue Jan 26 07:21:27 2010 UTC (7 years, 8 months ago) by jcfr
ENH: SlicerQT - in Main.cxx, comment out qMRMLEventLogger

Revision 11790 - Directory Listing
Modified Tue Jan 26 07:21:20 2010 UTC (7 years, 8 months ago) by jcfr
ENH: SlicerQT - Added qVTKRenderView to SlicerQt application UI

Revision 11784 - Directory Listing
Modified Tue Jan 26 07:20:55 2010 UTC (7 years, 8 months ago) by jcfr
ENH: SlicerQT - Add MRMLEventLoggerWidget to SlicerQT application

Revision 11772 - Directory Listing
Modified Sun Jan 24 17:09:58 2010 UTC (7 years, 8 months ago) by lorensen
ENH: Remove duplicate library references.

Revision 11752 - Directory Listing
Modified Fri Jan 22 21:23:48 2010 UTC (7 years, 8 months ago) by naucoin
BUG: the anatomy file should over ride the colour info from the input label volume. Updated text to make it clear that it's not a Slicer colour resource file

Revision 11724 - Directory Listing
Modified Thu Jan 21 22:28:40 2010 UTC (7 years, 8 months ago) by ibanez
COMP: Wrong fix. The static_cast should have use the type of the SizeType component, instead of the SizeType itself.


Revision 11721 - Directory Listing
Modified Thu Jan 21 21:49:52 2010 UTC (7 years, 8 months ago) by ibanez
COMP: Fixing warnings about casting and about local variables shadowing others.


Revision 11717 - Directory Listing
Modified Thu Jan 21 21:01:35 2010 UTC (7 years, 8 months ago) by casey.goodlett
COMP:  Remove use case specific modules as they can now be handled by presets.

Revision 11711 - Directory Listing
Modified Wed Jan 20 15:31:02 2010 UTC (7 years, 8 months ago) by casey.goodlett
BUG: Add error checking to transform from fiducials that checks the size of the lists is correct.

Revision 11710 - Directory Listing
Modified Wed Jan 20 15:30:58 2010 UTC (7 years, 8 months ago) by casey.goodlett
ENH: In RegisterImagesMultiRes, don't output debugging output unless in very verbose debug mode.

Revision 11708 - Directory Listing
Modified Wed Jan 20 00:39:20 2010 UTC (7 years, 9 months ago) by naucoin
BUG: VTK_INT_MAX is too high, memory alloc errors, try using 1 million instead

Revision 11707 - Directory Listing
Modified Wed Jan 20 00:00:57 2010 UTC (7 years, 9 months ago) by naucoin
BUG: deal with input label map volumes that contain values larger than 1024.

Revision 11700 - Directory Listing
Modified Tue Jan 19 19:22:42 2010 UTC (7 years, 9 months ago) by jcfr
COMP: SlicerQT - Fix shadow warnings

The shadowed variables where changed by adding an underscore:
 parent -> _parent

Note also that the signature in the header doesn't contain any underscore,
only the implementation file has it.

qCTKFlowLayout code has also been reviewed to be compliant with
current QT coding style

Revision 11699 - Directory Listing
Modified Tue Jan 19 18:00:47 2010 UTC (7 years, 9 months ago) by pieper
BUG: library to install directive so it will show up in packaged binaries (otherwise we get a missing lib error at startup)

Revision 11695 - Directory Listing
Modified Tue Jan 19 15:21:02 2010 UTC (7 years, 9 months ago) by haehn
ENH really exit slicer after evalpython command


Revision 11652 - Directory Listing
Modified Fri Jan 15 20:34:42 2010 UTC (7 years, 9 months ago) by jcfr
COMP: Fix various compilation warning

Revision 11650 - Directory Listing
Modified Fri Jan 15 18:35:02 2010 UTC (7 years, 9 months ago) by jcfr
COMP: Fix various compilation warning

Revision 11647 - Directory Listing
Modified Fri Jan 15 16:28:20 2010 UTC (7 years, 9 months ago) by jcfr
COMP: Fix various compilation warning

Revision 11634 - Directory Listing
Modified Thu Jan 14 18:43:33 2010 UTC (7 years, 9 months ago) by pieper
STYLE: remove unneeded update call

Revision 11629 - Directory Listing
Modified Thu Jan 14 17:52:28 2010 UTC (7 years, 9 months ago) by pieper
BUG: can't use backslashes in the xml field

Revision 11622 - Directory Listing
Modified Thu Jan 14 09:23:23 2010 UTC (7 years, 9 months ago) by pkarasev
ENH: updating interface of mesh segmentation module

Revision 11619 - Directory Listing
Modified Wed Jan 13 22:31:24 2010 UTC (7 years, 9 months ago) by naucoin
BUG: call vtkDebugLeaks::SetExitError(true) for when running locally

Revision 11618 - Directory Listing
Modified Wed Jan 13 22:28:19 2010 UTC (7 years, 9 months ago) by naucoin
BUG: call vtkDebugLeaks::SetExitError(true) for when running locally

Revision 11617 - Directory Listing
Modified Wed Jan 13 22:27:37 2010 UTC (7 years, 9 months ago) by naucoin
COMP: ImageLabelCombine uses only itk

Revision 11616 - Directory Listing
Modified Wed Jan 13 21:53:09 2010 UTC (7 years, 9 months ago) by naucoin
BUG: fixing major memory leaks

Revision 11614 - Directory Listing
Modified Wed Jan 13 21:43:47 2010 UTC (7 years, 9 months ago) by ibanez
BUG: Adding call to vtkDebugLeaks::SetExitError(true) in order to force the test to fail when there are memory leaks.


Revision 11613 - Directory Listing
Modified Wed Jan 13 20:01:03 2010 UTC (7 years, 9 months ago) by naucoin
PERF: adding more model maker tests, check that generate all and a range of labels works

Revision 11612 - Directory Listing
Modified Tue Jan 12 22:09:47 2010 UTC (7 years, 9 months ago) by naucoin
ENH: add a minimum heap size argument

Revision 11601 - Directory Listing
Modified Tue Jan 12 17:58:25 2010 UTC (7 years, 9 months ago) by jcfr
COMP: SlicerQT - Slicer3_USE_QT is now define using #cmakedefine Slicer3_USE_QT in vtkSlicerConfigure.h.in

Note: It was previously defined using ADD_DEFINITIONS(-DSlicer3_USE_QT) in CMake/Slicer3FindQT.cmake

Revision 11584 - Directory Listing
Modified Sun Jan 10 05:04:49 2010 UTC (7 years, 9 months ago) by finetjul
ENH: SlicerQt: Use polymorphism with the slicer module factories to factorize code. Still in qSlicerModuleFactory, remove instantiate from register (loadable modules where instantiated when registered): this was done to retrieve the module title at the registration time. The module title is now valid after a module is instantiated. (Behavior is consistent between the core modules and the loadable modules, you don't want them to have different behavior. When a module is registered: registerCoreModule, registerLoadableModule, registerCmdLineModules), a unique name is generated. When a module is instantiated, it can be used thanks to the module title.
More factorization could be done...

Revision 11569 - Directory Listing
Modified Fri Jan 8 18:05:37 2010 UTC (7 years, 9 months ago) by naucoin
BUG: java class is writing to stderr, capture that so can return 0

Revision 11568 - Directory Listing
Modified Fri Jan 8 15:48:37 2010 UTC (7 years, 9 months ago) by hjohnson
COMP:  To include this into other packages, it is necessary to set this to a local config file.

Revision 11559 - Directory Listing
Modified Fri Jan 8 01:30:36 2010 UTC (7 years, 9 months ago) by naucoin
ENH: copy the spectre wrapper file

Revision 11558 - Directory Listing
Modified Fri Jan 8 01:30:04 2010 UTC (7 years, 9 months ago) by naucoin
ENH: this will run with tclsh now

Revision 11557 - Directory Listing
Modified Fri Jan 8 01:12:21 2010 UTC (7 years, 9 months ago) by naucoin
ENH: first pass at the wrapper for SPECTRE. Todo: find MIPAV program and plugin dirs, they're hard coded right now. TODO: figure out why not getting the java exit 0 back on successful completion

Revision 11555 - Directory Listing
Modified Fri Jan 8 00:01:06 2010 UTC (7 years, 9 months ago) by hjohnson
ENH:  When Review Statistics is turned on, the long image type with HistogramMatching exposes an ITK bug that is currently being fixed for itk 3.18.

Revision 11552 - Directory Listing
Modified Thu Jan 7 22:31:38 2010 UTC (7 years, 9 months ago) by casey.goodlett
BUG: Handle negative spacing values and correctly differentiate moving and fixed image schedules.

Revision 11549 - Directory Listing
Modified Thu Jan 7 20:53:26 2010 UTC (7 years, 9 months ago) by casey.goodlett
COMP: Speed up compliation time of command line modules by linking Executable against shared library instead of recompiling.

Revision 11538 - Directory Listing
Modified Wed Jan 6 18:25:55 2010 UTC (7 years, 9 months ago) by pieper
ENH: allow python script filenames to passed on the command line either implicitly (no argument) or with the --script option

Revision 11537 - Directory Listing
Modified Wed Jan 6 15:14:51 2010 UTC (7 years, 9 months ago) by casey.goodlett
COMP: Speed up compilation of CLI Tests by linking to loadable module instead of recompiling when possible.

Revision 11535 - Directory Listing
Modified Wed Jan 6 00:47:42 2010 UTC (7 years, 9 months ago) by casey.goodlett
COMP: Speed up compilation time of OrientImage command line module test by linking to shared library instead of including source and recompiling.

Revision 11533 - Directory Listing
Modified Tue Jan 5 23:59:24 2010 UTC (7 years, 9 months ago) by millerjv
ENH: Load default parameter sets

Revision 11508 - Directory Listing
Modified Mon Jan 4 19:10:35 2010 UTC (7 years, 9 months ago) by ibanez
ENH: Removing .NoDartCoverage files and replacing them with the
     CTEST_CUSTOM_COVERAGE_EXCLUDE variable in the CTestCustom.cmake.in file.



Revision 11505 - Directory Listing
Modified Mon Jan 4 16:41:47 2010 UTC (7 years, 9 months ago) by ibanez
BUG: Checking the case in which the imageIO class failed to be created.


Revision 11501 - Directory Listing
Modified Mon Jan 4 01:54:07 2010 UTC (7 years, 9 months ago) by partyd
ENH: add install rule for qSlicerQT.

Revision 11474 - Directory Listing
Modified Thu Dec 31 20:59:51 2009 UTC (7 years, 9 months ago) by naucoin
ENH: register executables to extensions for the module factory, if find an exec for an extension when testing modules by executing files. For now, always return NULL as using this method of specifying an itksys process results in an immediate return the process being null

Revision 11454 - Directory Listing
Modified Wed Dec 30 12:47:15 2009 UTC (7 years, 9 months ago) by ibanez
COMP: The EXPORT symbol should go after the "class" keyword.


Revision 11445 - Directory Listing
Modified Wed Dec 30 05:15:49 2009 UTC (7 years, 9 months ago) by casey.goodlett
COMP: Fix problems compiling and running tests on other platforms for RegisterImagesMultiRes.

1) Use LAUNCH_EXE for tests so all libraries can be found
2) Use ${CMAKE_BUILD_TYPE} in path for windows builds
3) Create a Win32Header file for classes that are linked in multiple libraries (Application Module and test Module)

Revision 11434 - Directory Listing
Modified Tue Dec 29 20:44:37 2009 UTC (7 years, 9 months ago) by naucoin
COMP: defining M_PI for windows machines, try to disambiguate sqrt

Revision 11431 - Directory Listing
Modified Tue Dec 29 20:40:00 2009 UTC (7 years, 9 months ago) by pieper
BUG: fix test that was always failing (the test didn't exit, so it would always time out)

Revision 11427 - Directory Listing
Modified Tue Dec 29 19:48:40 2009 UTC (7 years, 9 months ago) by finetjul
BUG: On linux, QCoreApplication::arguments() returns an empty QStringList as arc/argv are set to 0/0 when instanciating QCoreApplication in vtkSlicerApplication. the program name shall be pass directly from Slicer3.cxx

Revision 11422 - Directory Listing
Modified Tue Dec 29 15:09:00 2009 UTC (7 years, 9 months ago) by casey.goodlett
ENH: Add tests for RegisterImagesMultiRes.

This adds tests to cover the new transforms and helper methods used by RegisterImagesMultiRes.  Also included are wxMaxima files that were used to develop tests for the transforms.

Revision 11407 - Directory Listing
Modified Tue Dec 29 06:09:23 2009 UTC (7 years, 9 months ago) by finetjul
BUG: SlicerQt: Between Slicer3 and SlicerQt, set loadableModuleSearchPaths and commandLineModuleSearchPaths using the same functions (qSlicerCoreApplication::initializeLoadableModulesPaths and qSlicerCoreApplication::initializeCmdLineModulesPaths). 
BUG: SlicerQt: Windows Only. In order to have initializeLoadableModulesPaths and initializeCmdLineModulesPaths working correctly with the Debug/Release/RelWithDebInfo... file hierarchy, qSlicerCoreApplicationPrivate::IntDir must be set meaning that discoverSlicerBinDirectory must be called and meaning that discoverSlicerHomeDirectory is called to. In SlicerQt, this is done via qSlicerCoreApplication::initialize(). But qSlicerCoreApplication::initialize() can't be called for Slicer3 (using KWWidgets). This is why a new method is added initializePaths. discoverSlicerHomeDirectory makes sure that discoverSlicerBinDirectory is called (to set IntDir) even if the env variable is already found (the case using KWWidgets because it is done at the beginning of Slicer3_main).

Revision 11382 - Directory Listing
Modified Fri Dec 25 23:59:02 2009 UTC (7 years, 9 months ago) by ibanez
ENH: Now enabling the vtkDebugLeaks feature of exiting with an error if there are any memory leaks.
     This is done by calling the SetExitError() method with a "true" argument. In this way, tests
     that report memory leaks will also be reported as failing when run locally.


Revision 11379 - Directory Listing
Modified Wed Dec 23 22:36:24 2009 UTC (7 years, 9 months ago) by ibanez
BUG: Early call to PrintCurrentLeaks() is not a proper mechanism for verifying the number of memory leaks.
     Removing the call to  vtkDebugLeaks::PrintCurrentLeaks();


Revision 11378 - Directory Listing
Modified Wed Dec 23 21:15:07 2009 UTC (7 years, 9 months ago) by ibanez
ENH: Adding tests suggested by Steve Pieper on
http://massmail.spl.harvard.edu/pipermail/slicer-devel/2009/003795.html


Revision 11376 - Directory Listing
Modified Tue Dec 22 23:19:16 2009 UTC (7 years, 9 months ago) by ibanez
BUG: Fixing the message regarding the number of memory leaks on exit.
     The previous message incorrectly implied that PrintCurrentLeaks()
     was returning the current number of memory leaks, but in reality
     it returns 0 or 1. (1 when there are memory leaks).


Revision 11375 - Directory Listing
Modified Tue Dec 22 23:01:21 2009 UTC (7 years, 9 months ago) by ibanez
BUG: Removing embarrassing accidental commit of code 
     that was inteded only for local debugging.
     The call to Slicer3_Tcl_Eval() was accidentally commented out.


Revision 11372 - Directory Listing
Modified Tue Dec 22 02:39:20 2009 UTC (7 years, 9 months ago) by finetjul
COMP: Remove warning C4099 with MSVC.

Revision 11362 - Directory Listing
Modified Mon Dec 21 21:14:08 2009 UTC (7 years, 9 months ago) by ibanez
ENH: Adding .NoDartCoverage files inside the Testing subdirectories
     in order to exclude them from the computation of code coverage.


Revision 11353 - Directory Listing
Modified Sat Dec 19 23:05:39 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Remove Application/SlicerQT/qSlicerQT{Configure,Wind32Header} files

The file Slicer3/qSlicerExport.h.in is now configured accordingly.

Revision 11351 - Directory Listing
Modified Sat Dec 19 17:41:09 2009 UTC (7 years, 10 months ago) by ibanez
ENH: Forcing the Slicer3 application to return a failure code if it terminates with vtkDebugLeaks.


Revision 11335 - Directory Listing
Modified Fri Dec 18 02:26:12 2009 UTC (7 years, 10 months ago) by hjohnson
ENH:  Separated special building for Slicer from separate builds.

Revision 11326 - Directory Listing
Modified Wed Dec 16 11:28:15 2009 UTC (7 years, 10 months ago) by jcfr
BUG: SlicerQT - Review how/when the moduleManager is instantiated in Slicer3

Added back method: setModuleManager to qSlicerCoreApplication
Also added method setInitialized

Update qSlicerCoreApplicationTest1

Revision 11288 - Directory Listing
Modified Tue Dec 15 09:01:52 2009 UTC (7 years, 10 months ago) by jcfr
COMP: Slicer3/Base/GUI, Slicer3/Applications/GUI included only if Slicer3_USE_KWWIDGETS is ON

Revision 11274 - Directory Listing
Modified Mon Dec 14 19:14:57 2009 UTC (7 years, 10 months ago) by ibanez
ENH: Fixing configuration for Testing, adding CXX_TEST_PATH variable in the top CMakeLists.txt file, to indicate where the executables of tests should go.


Revision 11270 - Directory Listing
Modified Mon Dec 14 04:20:26 2009 UTC (7 years, 10 months ago) by jcfr
COMP: SlicerQT - On WIN32, the forwarded executable of SlicerQT wasn't built.

On Win32, SlicerQT_FORWARD_PATH_INSTALL was starting with a comma and was
causing a built error.

Revision 11255 - Directory Listing
Modified Fri Dec 11 17:32:02 2009 UTC (7 years, 10 months ago) by jcfr
STYLE: Update CMakeLists.txt
 - Move testing code in the CMakeLists located under Testing.
 - Ensure that SlicerQT was build appropriately and without dependency on SlicerBaseGUI

Revision 11253 - Directory Listing
Modified Fri Dec 11 04:44:27 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - SlicerModuleSelectorWidget now display module titles ordered alphabetically.

Revision 11250 - Directory Listing
Modified Fri Dec 11 01:43:50 2009 UTC (7 years, 10 months ago) by jcfr
ENH: Update vtkEventBroker to follow a more robust singleton pattern.

Since we are sure to have on instance per-process, all client should call
vtkEventBroker::GetInstance() and no bother using New/Delete

It follow now the nifty counter idiom:
http://en.wikibooks.org/wiki/More_C%2B%2B_Idioms/Nifty_Counter

Largely inspired from the code of:
VTK/Common/vtkOutputWindow
VTK/Utilities/kwsys/SystemTools

It's also possible to use New (that way reference counting will be used)
Doing so the caller will be responsible to call the matching Delete.
For example, in Slicer3.cxx, TCL interpreter got a reference using New.
For that reason, we call the corresponding Delete.

It's also worth reading:
http://www.parashift.com/c++-faq-lite/ctors.html#faq-10.12

Revision 11244 - Directory Listing
Modified Thu Dec 10 19:32:05 2009 UTC (7 years, 10 months ago) by taox
ENH: added support for non-diffusion weighted images.

Revision 11242 - Directory Listing
Modified Thu Dec 10 16:23:07 2009 UTC (7 years, 10 months ago) by casey.goodlett
ENH: Add module to compute a transform two corresponding fiducial lists.  The two lists are expected to be ordered such that the same index in each list is expected to contain corresponding points.  Currently the module supports translations, rigid transformations, and similiarity transformations.

Revision 11230 - Directory Listing
Modified Wed Dec 9 08:36:55 2009 UTC (7 years, 10 months ago) by jcfr
ENH: Update CMakeLists.txt, use FILE(MAKE_DIRECTORY ..) instead of deprecated MAKE_DIRECTORY(..)

Revision 11226 - Directory Listing
Modified Tue Dec 8 23:34:28 2009 UTC (7 years, 10 months ago) by jcfr
ENH: In CMakeLists.txt, change deprecated SUBDIRS command into ADD_SUBDIRECTORY

See http://cmake.org/cmake/help/cmake-2-8-docs.html#command:subdirs

when subdirs command was taking a list of directory, change it
using the following pattern:

Before:
subdirs(sagarmatha kumbhu eiger)

After:
SET(dirs
  sagarmatha
  kumbhu
  eiger
  )
FOREACH(dir ${dirs})
  ADD_SUBDIRECTORY(${dir})
ENDFOREACH(dir)

Revision 11213 - Directory Listing
Modified Tue Dec 8 09:10:30 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - In qSlicerMainWindow, connect Undo/Redo action using the helper macro

Revision 11212 - Directory Listing
Modified Tue Dec 8 09:10:26 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - In qSlicerMainWindowCore, declare and define the slots for Undo/Redo action

Revision 11211 - Directory Listing
Modified Tue Dec 8 09:10:21 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Add helper macro qSlicerMainWindow_connect to qSlicerMainWindow

This macro allow to easily connect an MainWindow action with the
corresponding slot in qSlicerCoreWindow

Revision 11209 - Directory Listing
Modified Tue Dec 8 04:15:18 2009 UTC (7 years, 10 months ago) by jcfr
ENH: Update CMakeLists.txt - CMake 2.6 is now required

The following line have been added:

CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
IF(COMMAND CMAKE_POLICY)
  CMAKE_POLICY(SET CMP0003 NEW)
ENDIF(COMMAND CMAKE_POLICY)
MARK_AS_ADVANCED(CMAKE_BACKWARDS_COMPATIBILITY)

Revision 11206 - Directory Listing
Modified Tue Dec 8 04:13:00 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Remove all methods prefixed with 'ByName'

For example moduleManager got two methods:
 1) getModule(const QString& moduleTitle)
 2) getModuleByName(const QString& moduleName)

The first one has been removed

The signature of the second one changed from:
  - getModuleByName(const QString& moduleName)
to:
  - getModule(const QString& moduleName)

Revision 11201 - Directory Listing
Modified Mon Dec 7 23:50:58 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Remove 'setModule()/module()' function from qSlicerAbstractModuleWidget:
and add name()/setName() function.

In qSlicerModulePanel, pass moduleName instead of a pointer to qSlicerAbstractModule

Revision 11200 - Directory Listing
Modified Mon Dec 7 23:50:50 2009 UTC (7 years, 10 months ago) by jcfr
BUG: SlicerQT - In qSlicerMainWindow, add layout to 'Manipulate Slicer' and 'Manipulate 3D view' collapsibleButton

Revision 11192 - Directory Listing
Modified Mon Dec 7 01:00:22 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Updated qSllicerMainWindow UI file.

Renamed 'Hide Main Panel' action to 'Main Panel' and set the action as checkable
Same for 'Hide Bottom Panel'

Connect action show 'Main Panel' with PanelDockWidget

Change PanelDockWidget options (set allDockWidgetFeature to On)

Revision 11191 - Directory Listing
Modified Mon Dec 7 01:00:17 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - ModuleSelector is now instantiated in qSlicerMainWindow and added to the MainToolbar

Revision 11184 - Directory Listing
Modified Sun Dec 6 22:57:52 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Update SlicerQT/Main.cxx - Instead of connecting the
moduleSelector with the moduleManager, connect it with the modulePanel.

Revision 11182 - Directory Listing
Modified Sun Dec 6 22:57:44 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - In qSlicerMainWindowCore, connect ShowModuleActionMapper with slot qSlicerModulePanel::setModuleByName

Revision 11179 - Directory Listing
Modified Sun Dec 6 22:57:31 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Add modulePanel() method to qSlicerMainWindow

Revision 11178 - Directory Listing
Modified Sun Dec 6 22:57:27 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Add modulePanel to qSlicerMainWindow

Revision 11171 - Directory Listing
Modified Sun Dec 6 04:16:44 2009 UTC (7 years, 10 months ago) by hjohnson
ENH:  Moved DicomToNrrd to its own directory to make it easier to build stand alone.

Revision 11169 - Directory Listing
Modified Sat Dec 5 16:09:41 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Refactor QTCLI to consider qSlicerAbstractModuleWidget

qSlicerAbstractModuleWidget has also a new method 'module()' allowing
to obtain the module object associated with a  moduleWidget.


The API of qSlicerModulePanel (and based class) has been updated to
use qSlicerAbstractModuleWidget.

Revision 11168 - Directory Listing
Modified Sat Dec 5 16:09:32 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Refactor existing QTModules - Now using the qSlicerAsbtractModuleWidget
to have a better separation of the UI and the processing logic.

Revision 11167 - Directory Listing
Modified Sat Dec 5 16:09:22 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Refactor Modules - Added qSlicerAsbtractModuleWidget

QTModules and CLI module are disabled for now

The class qSlicerAbstractModule now inherit from QObject.
All UI specific code has been moved to qSlicerAbstractModuleWidget.

qSlicerAbstractModule provide a function named 'widgetRepresentation'
allowing to obtain the corresponding widget.

Revision 11165 - Directory Listing
Modified Sat Dec 5 16:09:01 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - In qSlicerMainWindowCorePrivate, onModuleLoaded doesn't rely anymore
on isShowModuleActionVisibleByDefault().

There is a QStringList named ToolBarModuleList allowing to specify the list
of modules we want to see in the Toolbar.

Revision 11163 - Directory Listing
Modified Sat Dec 5 04:29:02 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Module are available again in the ModuleToolbar

Created qSlicerMainWindowCore_p.h containing two slots:
  - onModuleLoaded
  - onModuleAboutToBeUnloaded

qSlicerCoreModuleManager now emit the signals:
  - moduleLoaded
  - moduleAboutToBeUnloaded

Signal from qSlicerCoremoduleManager and slot from qSlicerMainWindowCore are
connected in the constructor of qSlicerWindowCore.

Revision 11161 - Directory Listing
Modified Sat Dec 5 03:28:22 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Update SlicerQT/CMakeLists.txt - Remove SlicerBaseGUI from SlicerBase_LIBRARIES

The application 'SlicerQT' was build against SlicerBase_LIBRARIES.

The SlicerBaseGUI libraries was also included. This is a hack
allowing to remove the item 'SlicerBaseGUI' from the list Slicer3_Base_LIBRARIES.

That way, the GUI libs isn't build anymore when SlicerQT is build.

See below:

[  0%] Built target ModuleDescriptionParser
[  3%] Built target FreeSurfer
[ 10%] Built target vtkTeem
[ 17%] Built target qCTKWidgets
[ 17%] Built target SlicerBaseCLI
[ 28%] Built target vtkITK
[ 71%] Built target MRML
[ 75%] Built target qMRMLWidgets
[ 85%] Built target SlicerBaseLogic
[ 89%] Built target qSlicerBaseQTBase
[ 92%] Built target qSlicerBaseQTCoreModules
[ 92%] Built target qSlicerBaseQTCLI
[ 92%] Built target qSlicerBaseQTCore
[ 96%] Built target qSlicerBaseQTGUI
[100%] Built target qSlicerQT
[100%] Built target SlicerQT-real
[100%] Built target SlicerQT

Revision 11160 - Directory Listing
Modified Sat Dec 5 03:28:15 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Added Base/QTCore directory.

The classes qSlicerModuleFactory and qSlicerCoreApplication have been moved
into Base/QTCore

The class qSlicerModuleManager has been split into:
   * a base class named: qSlicerCoreModuleManager. That class allows to:
           - load, unload, getModuleByName, getModuleByTitle, ...

   * a class named: qSlicerModuleManager
           - which provides the same functionnality as the former one.

qSlicerCoreModuleManager is located in Base/QtCore
qSlicerModuleManager is located in Base/QtGUI

Note also that, qSlicerModuleManager was using the same singleton as
vtkIOManager. A class, named qSlicerSingleton, containing this usefull
singleton pattern has been copied into Slicer3/Attic.

Since qSlicerModuleManager or qSlicerCoreModuleManager are not singleton
anymore. qSlicerCoreApplication will hold a pointer to it.

qSlicerCoreApplication contains now:
  - setModuleManager(qSlicerCoreModuleManager* moduleManager) that will be
available in both qSlicerApplication and qSlicerCoreApplication.
  - coreModuleManager() returning the object

qSlicerApplication contains now:
  - mnoduleManager method returning the result of coreModuleManager casted
to qSlicerModuleManager.

Note: In this commit, the update of the ModuleToolBar by the moduleManager
has been disabled.

Revision 11158 - Directory Listing
Modified Sat Dec 5 00:13:18 2009 UTC (7 years, 10 months ago) by lauren
ENH: batch tensor calc, in progress

Revision 11151 - Directory Listing
Modified Fri Dec 4 16:32:31 2009 UTC (7 years, 10 months ago) by jcfr
BUG: SlicerQT - Fix SlicerQT CMakeLists.txt

There was a problem in the configuration of SlicerQT-forward.c.in.
A multi-line macro wasn't expanded properly.

Revision 11149 - Directory Listing
Modified Fri Dec 4 09:04:32 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Add method discoverSlicerHomeDirectory and discoverSlicerBinDirectory to qSlcierCoreApplication

SlicerHome directory is now auto-discovered in SlicerQT.
The environement variable Slicer3_HOME is also set if not yet done by
the launcher.

Revision 11144 - Directory Listing
Modified Thu Dec 3 20:22:40 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Add SlicerQT-real and SlicerQT to the build process

Revision 11136 - Directory Listing
Modified Thu Dec 3 16:58:59 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Update 'SlicerQT' application, reference to the ModuleToolBar is now passed to the ModuleManager

Revision 11125 - Directory Listing
Modified Thu Dec 3 07:53:18 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - In SlicerQT/Main.cxx, clear splash screen message when done loading modules.

Revision 11124 - Directory Listing
Modified Thu Dec 3 07:53:15 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Add icons (also remove the 1 pixel border, make them transparent and indexed) to Base/QTGUI, QTModules/Volumes and Base/QTCoreModules/

Revision 11118 - Directory Listing
Modified Wed Dec 2 18:54:35 2009 UTC (7 years, 10 months ago) by fedorov
BUG: previously committed wrong file by mistake


Revision 11117 - Directory Listing
Modified Wed Dec 2 17:57:40 2009 UTC (7 years, 10 months ago) by fedorov
ENH: switched ImageLabelCombine to use ITK to fix bug 711. The module operates
on input voxels.


Revision 11116 - Directory Listing
Modified Wed Dec 2 16:10:08 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Add a basic splashscreen to SlicerQT application

Revision 11115 - Directory Listing
Modified Wed Dec 2 16:10:03 2009 UTC (7 years, 10 months ago) by jcfr
BUG: SlicerQT - The resource files weren't compiled and added to the source correctly

Revision 11112 - Directory Listing
Modified Wed Dec 2 09:10:17 2009 UTC (7 years, 10 months ago) by jcfr
STYLE: SlicerQT - Clean Application/SlicerQT/Main.cxx

Revision 11111 - Directory Listing
Modified Wed Dec 2 06:27:45 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Add debug message to Slicer3.cxx

Revision 11110 - Directory Listing
Modified Wed Dec 2 06:27:40 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Update the SlicerQt application to use the module selector widget.

Revision 11103 - Directory Listing
Modified Wed Dec 2 04:10:14 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - All classes are now using qCTKPimpl, Remove qSlicerMacros.h, Add macro QCTK_CONSTRUCTOR_NO_ARG_CXX and QCTK_CONSTRUCTOR_1_ARG_CXX to qCTKPimpl.
STYLE: SlicerQT - The header inclusion has also been cleaned and documented.

Revision 11094 - Directory Listing
Modified Tue Dec 1 15:03:25 2009 UTC (7 years, 10 months ago) by jcfr
ENH: SlicerQT - Update Main.cxx of Slicer 'pure QT' application.

Revision 11089 - Directory Listing
Modified Tue Dec 1 14:42:17 2009 UTC (7 years, 10 months ago) by finetjul
COMP: Replace qCTKCollapsibleWidget2 by qCTKCollapsibleButton

Revision 11049 - Directory Listing
Modified Wed Nov 25 19:48:37 2009 UTC (7 years, 10 months ago) by taox
ENH: work with philips multi-frame dataset.

Revision 11048 - Directory Listing
Modified Wed Nov 25 19:47:47 2009 UTC (7 years, 10 months ago) by taox
ENH: work with philips multi-frame dataset.

Revision 11046 - Directory Listing
Modified Wed Nov 25 14:40:54 2009 UTC (7 years, 10 months ago) by taox
ENH: updated help information and document on the web.

Revision 11043 - Directory Listing
Modified Tue Nov 24 19:45:44 2009 UTC (7 years, 10 months ago) by casey.goodlett
ENH: Merge improvments into RegisterImagesMultiRes.  There are a few important improvements available here.

(1) Better heuristic for downsampling images of different resolutions and spacing.  The actual heuristic is implemented in DownsampleHeuristics.h.  This should enable the algorithm to work a much wider range of images (including different resolution of fixed and moving images).

(2) Heuristic for computing optimizer scales so the user only has to select one global step size (in units of voxels).  The image is then used to compute the scalings for each component of the transform.

(3) support for saving the output transform in addition to the resampled image



Revision 11029 - Directory Listing
Modified Tue Nov 24 13:22:44 2009 UTC (7 years, 10 months ago) by hjohnson
BUG:  Copy and paste error had moved the location of DicomToNrrd.

Revision 11019 - Directory Listing
Modified Mon Nov 23 21:54:47 2009 UTC (7 years, 10 months ago) by pieper
BUG: fix the Edit Properties menu item in the Data module

Revision 11018 - Directory Listing
Modified Mon Nov 23 15:54:32 2009 UTC (7 years, 10 months ago) by naucoin
BUG: take out the DWIDicomLoadTest

Revision 11017 - Directory Listing
Modified Mon Nov 23 15:52:47 2009 UTC (7 years, 10 months ago) by naucoin
BUG: take out the install command for DWIDicomLoad

Revision 11014 - Directory Listing
Modified Mon Nov 23 13:23:57 2009 UTC (7 years, 10 months ago) by taox
ENH: remove DWIDicomLoader, which does not work correctly. use DICOMToNrrdConverter to convert diffusion weighted images in DICOM format into NRRD format so that slicer can load it for processing. 

Revision 11013 - Directory Listing
Modified Mon Nov 23 13:23:47 2009 UTC (7 years, 10 months ago) by taox
ENH: remove DWIDicomLoader, which does not work correctly. use DICOMToNrrdConverter to convert diffusion weighted images in DICOM format into NRRD format so that slicer can load it for processing. 

Revision 11008 - Directory Listing
Modified Thu Nov 19 22:37:19 2009 UTC (7 years, 11 months ago) by hjohnson
BUG:  From experimention I've determined that Siemens oblique data always assumes an identity measurement frame for the reported gradient orientations.

Revision 11003 - Directory Listing
Modified Thu Nov 19 15:59:00 2009 UTC (7 years, 11 months ago) by taox
BUG: change the default space into LPS so converting from DICOM is more straightforward. Somehow GE diffusion gradient directions ARE (yes, they are!) represented in RAS and need the special treatment. For this version, useLPS does not make a difference for Philips and Siemens datasets. But for GE dataset, setting useLPS will generate WRONG results.

Revision 10995 - Directory Listing
Modified Thu Nov 19 14:05:35 2009 UTC (7 years, 11 months ago) by jcfr
ENH: SlicerQT - Update qSlicerMainWindow to use the new qCTKCollapsibleWidget2.
ENH: SlicerQT - Clean vtkSlicerApplicationGUI, vtkSlicerModuleChooseGUI, vtkSlicerApplication and add InitializeQtCommandLineModules  method
ENH: SlicerQT - Update qSlicerModuleLogic class
ENH: SlicerQT - Update QTCLI, add vtkCommandLineModuleNode, add UI resource file, update qSlicerCLIModuleLogic
ENH: SlicerQT - Rename initializer() to setup()
ENH: SlicerQT - In qSlicerModulePanel, rename signals. Split existing addModule method into AddModule, RemoveModule and SetModule. Add method clear.
ENH: SlicerQT - In CTK Factory, add uninstanciate method. Add QObject factory.
ENH: SlicerQT - Add macro qSlicerCxxInternalBckPtrConstructor1Macro
ENH: SlicerQT - Add appLogic and setAppLogic to qSlicerWidget.

Revision 10987 - Directory Listing
Modified Wed Nov 18 22:24:35 2009 UTC (7 years, 11 months ago) by hjohnson
ENH: Fixed DicomToNrrd to work with Siemens and Philips data.

Revision 10976 - Directory Listing
Modified Tue Nov 17 21:38:53 2009 UTC (7 years, 11 months ago) by taox
ENH: a better way to parse tag/values. Data generated are the same as the previous version.

Revision 10975 - Directory Listing
Modified Tue Nov 17 19:05:32 2009 UTC (7 years, 11 months ago) by taox
BUG: fixed space, measurement frame, diffusion gradient directions. Now, it works for GE, Siemens, and Philips datasets. 

Revision 10973 - Directory Listing
Modified Tue Nov 17 16:27:54 2009 UTC (7 years, 11 months ago) by taox
ENH: Better dicom tag/value parsing -- shortened code by ~100 lines. 
Siemens data needs MeasurementFrame == LPSDirCos. This is tested on IOWA datasets and Slicer/Testing/Data/Input/DWIDicom and produces correct tensor AND fiber bundles.

Revision 10970 - Directory Listing
Modified Tue Nov 17 14:52:54 2009 UTC (7 years, 11 months ago) by casey.goodlett
COMP: Specify overload of log to use on windows.

Revision 10969 - Directory Listing
Modified Tue Nov 17 14:47:56 2009 UTC (7 years, 11 months ago) by casey.goodlett
COMP: Use std::log instead of log in MultiRes RegisterImages.

Revision 10968 - Directory Listing
Modified Tue Nov 17 14:45:22 2009 UTC (7 years, 11 months ago) by casey.goodlett
COMP: Fix compile errors for multires RegisterImages on windows.

Revision 10967 - Directory Listing
Modified Tue Nov 17 04:00:20 2009 UTC (7 years, 11 months ago) by hjohnson
ENH:  Separated MeasurementFrame setting from the dicom direction cosine settins for Siemens and Philips scanners.

Revision 10965 - Directory Listing
Modified Mon Nov 16 23:28:35 2009 UTC (7 years, 11 months ago) by casey.goodlett
ENH: Add experimental module Register Images MultiRes.  This registration module uses a new set of euler angle based transforms and multi-resolution optimization.

Revision 10959 - Directory Listing
Modified Mon Nov 16 19:45:44 2009 UTC (7 years, 11 months ago) by taox
BUG: to work with the recent changes in DicomToNRRDConverter.

Revision 10946 - Directory Listing
Modified Thu Nov 12 20:00:35 2009 UTC (7 years, 11 months ago) by taox
ENH: start to merge Hans' changes.

Revision 10945 - Directory Listing
Modified Thu Nov 12 18:01:56 2009 UTC (7 years, 11 months ago) by taox
BUG: incomplete check-in.

Revision 10944 - Directory Listing
Modified Thu Nov 12 17:51:14 2009 UTC (7 years, 11 months ago) by taox
ENH: Added two command line arguments.

Revision 10943 - Directory Listing
Modified Thu Nov 12 15:00:35 2009 UTC (7 years, 11 months ago) by taox
ENH: work with recent version of GE software (15.0 and 20.0). In 15.0 value representations of diffusion related tags were changed to DS, and in 20 changed to IS.

Revision 10926 - Directory Listing
Modified Wed Nov 11 01:34:11 2009 UTC (7 years, 11 months ago) by jcfr
ENH: SlicerQT - Split Base/GUIQT into Base/QTBase and Base/QTGUI

Revision 10917 - Directory Listing
Modified Tue Nov 10 17:41:41 2009 UTC (7 years, 11 months ago) by jcfr
ENH: SlicerQT - Added qCTKAbstractLibraryFactory allowing to resolve symbols within loadable command line module.
ENH: SlicerQT - Updated qSlicerModuleFactory and Slicer3.cxx to use Library factory.
ENH: SlicerQT - Added qSlicerMacros file. Convenient macro allowing to set the constructor/destructor, and accessors of Slicer classes.
ENH: SlicerQT - Added qSlicerModuleLogic class
ENH: SlicerQT - Added Base/GUIQT/CmdLineModule.
ENH: SlicerQT - Added Base/GUIQT/qSlicerUtils class
FIX: SlicerQT - Clean code, comment extra debug statements

Revision 10896 - Directory Listing
Modified Fri Nov 6 23:19:25 2009 UTC (7 years, 11 months ago) by pieper
BUG: remove conflicting command line flag (thanks Alex Z.)

Revision 10895 - Directory Listing
Modified Fri Nov 6 23:06:21 2009 UTC (7 years, 11 months ago) by jcfr
ENH: SlicerQT - Added folder Applications/SlicerQT

Revision 10894 - Directory Listing
Modified Fri Nov 6 22:59:12 2009 UTC (7 years, 11 months ago) by jcfr
ENH: SlicerQt - Major refactoring. Module are now initialized within the overloaded function 'initializer'. qCTKFactory classed is now the base for Plugin and Object factory. Other kind of factory can easily be implemented. Module title should be set in the CMakeLists.txt of each QT module.

Revision 10849 - Directory Listing
Modified Tue Nov 3 20:54:00 2009 UTC (7 years, 11 months ago) by casey.goodlett
ENH: When setting the metric set it for rigid, affine, and bspline not just rigid.

Revision 10843 - Directory Listing
Modified Mon Nov 2 15:38:46 2009 UTC (7 years, 11 months ago) by jcfr
BUG: QtSlicer - Remove macro qSlicerGetModuleTitleDefinitionMacro/qSlicerGetModuleTitleDeclrationMacro and add the virtual method moduleTitle. In vtkSlicerApplication, rename method InitializeQtModule to InitializeQtCoreModule and add method InitializeQtCoreModules. Update QTModules and add the QtPlugin declaration. Update the appropriate header and cmake files in order to install the Qt loadable modules into a separate directory named 'QTLoadableModules'

Revision 10835 - Directory Listing
Modified Sun Nov 1 20:02:56 2009 UTC (7 years, 11 months ago) by finetjul
ENH: SlicerQT: Add the camera module

Revision 10809 - Directory Listing
Modified Fri Oct 30 15:12:26 2009 UTC (7 years, 11 months ago) by jcfr
BUG: QtSlicer - Rename qSlicerModuleTransform into qSlicerTransformsModule

Revision 10795 - Directory Listing
Modified Thu Oct 29 22:36:10 2009 UTC (7 years, 11 months ago) by barre
ENH: support for new cameras and new views. Port from Slicer 3.4 branch. As mentioned on the mailing list, apologies for instabilities while these core changes are further tested. Fiducials do not seem to follow camera for example, this will be fixed. Send bugs to sebastien.barre@kitware.com; Thank you.

Revision 10789 - Directory Listing
Modified Thu Oct 29 19:43:24 2009 UTC (7 years, 11 months ago) by jcfr
ENH: QtSlicer - Add method 'InitializeQtModule' to vtkSlicerApplication. Add method 'SetQtModuleVisible' and 'SetCurrentQtModuleVisible' to vtkSlicerApplicationGUI. Refactor and clean code to use these two function. Remove all code related to the previously added compilation directive 'Slicer_USE_KWWIDGET'. Update qSlicerAbstractModule to extend from qSlicerWidget. Now the title of a Qt module is defined in the corresponding declaration/definition using macro 'qSlicerGetModuleTitleDeclarationMacro' and 'qSlicerGetModuleTitleDefinitionMacro(_CLASSTYPE, _TITLE)'. Add method initPalette(), initFont() and loadStyleSheet() to qSlicerApplication. Qt Transform module now provide the 'invert' button.

Revision 10740 - Directory Listing
Modified Fri Oct 23 20:25:34 2009 UTC (7 years, 11 months ago) by pieper
BUG: fix for bug 668

Revision 10730 - Directory Listing
Modified Thu Oct 22 16:57:20 2009 UTC (7 years, 11 months ago) by jcfr
ENH: QtSlicer - Add vtkSlicerEmptyModuleGUI module that will be place holder for module implemented only in QT and not in Kw. Some refactoring of the Qt module snapping has been done, the QT module is positionned and resized according to the KWwindows main notebook KwWidget

Revision 10702 - Directory Listing
Modified Tue Oct 20 16:27:25 2009 UTC (8 years ago) by pieper
BUG: add missing scene observers to application gui

Revision 10686 - Directory Listing
Modified Mon Oct 19 16:07:11 2009 UTC (8 years ago) by pieper
BUG: make sure gui is up to data during startup

Revision 10663 - Directory Listing
Modified Thu Oct 15 21:30:58 2009 UTC (8 years ago) by pieper
ENH: send stings to stdout and exit with return code

Revision 10627 - Directory Listing
Modified Sat Oct 10 15:21:14 2009 UTC (8 years ago) by jcfr
ENH: QtSlicer - Add module factory and module manager classes allowing to instanciate and manage modules either from qSlicerApplication or vtkSlicerApplication. Add qSlicerKwUIWrapper widget that will encapsulates the KwWidget-Qt UI integration

Revision 10608 - Directory Listing
Modified Thu Oct 8 20:31:08 2009 UTC (8 years ago) by pieper
COMP: warning fixes

Revision 10606 - Directory Listing
Modified Thu Oct 8 20:12:02 2009 UTC (8 years ago) by finetjul
ENH: QtSlicer: fix crash when running Slicer with Qt, QApplication needs to be initialized with an argc that is valid its whole lifetime. Make sure the module is opened at the right time and at the correct position (above the kwwidget module). Remove the module window title and window bar.

Revision 10581 - Directory Listing
Modified Wed Oct 7 11:47:33 2009 UTC (8 years ago) by jcfr
ENH: Initial commit of the QtSlicer port. Added subdirs Base/GUI2, Libs/QCTKWidgets and Libs/QMRMLWidgets. Updated Application/GUI/Slicer3 and Base/GUI/vtkSlicerApplication to be able to initialize and start QtModule. CMakeLists.txt also updated to consider the script CMake/Slicer3FindQT.cmake

Revision 10579 - Directory Listing
Modified Tue Oct 6 20:51:51 2009 UTC (8 years ago) by naucoin
STYLE: updated help string when updated the web page

Revision 10569 - Directory Listing
Modified Fri Oct 2 20:07:09 2009 UTC (8 years ago) by pieper
BUG: move file system check until after app gui has been initialized

Revision 10549 - Directory Listing
Modified Wed Sep 30 18:36:56 2009 UTC (8 years ago) by naucoin
ENH: commented out subdir for java example

Revision 10548 - Directory Listing
Modified Wed Sep 30 18:36:11 2009 UTC (8 years ago) by naucoin
ENH: a sample Java command line plug in module, should only try to compile itself if it finds a java compiler when building, otherwise installs a jar file. TODO: figure out why it's not found on start up in Win32

Revision 10547 - Directory Listing
Modified Tue Sep 29 22:54:42 2009 UTC (8 years ago) by pieper
ENH: use maps to index the observation structures in order to significantly improve access time (e.g. for CloseScene with large numbers of nodes)

Revision 10515 - Directory Listing
Modified Tue Sep 22 15:45:40 2009 UTC (8 years ago) by casey.goodlett
ENH: Add capability to add a label image as a mask for the fixed images.  Samples used to compute the image match metric are only drawn within this mask.

Revision 10511 - Directory Listing
Modified Mon Sep 21 22:53:39 2009 UTC (8 years ago) by fedorov
BUG: remove constraint on maximum number of samples


Revision 10487 - Directory Listing
Modified Thu Sep 17 19:39:50 2009 UTC (8 years, 1 month ago) by casey.goodlett
COMP: Be sure that copy information from image works in both old and new versions of ITK.

Revision 10469 - Directory Listing
Modified Sat Sep 12 17:51:37 2009 UTC (8 years, 1 month ago) by aylward
COMP: Unused params



Revision 10466 - Directory Listing
Modified Sat Sep 12 16:56:35 2009 UTC (8 years, 1 month ago) by aylward
BUG: Need to link modules with ITK



Revision 10464 - Directory Listing
Modified Fri Sep 11 20:07:20 2009 UTC (8 years, 1 month ago) by casey.goodlett
ENH: Tweak a few parameters

Revision 10462 - Directory Listing
Modified Fri Sep 11 18:53:54 2009 UTC (8 years, 1 month ago) by casey.goodlett
COMP: Forgot a few lines in the CMakeLists.txt for the previous checkin

Revision 10461 - Directory Listing
Modified Fri Sep 11 18:50:39 2009 UTC (8 years, 1 month ago) by casey.goodlett
ENH: Add two new prototype modules to fall in a hierarchy of registration modules that will solve specific use cases.  As a first step included are RegisterFollowupBrainMR and RegisterBrainMRToTemplate.  These modules present a simplified view of the options in Register Images for those use cases.

Revision 10443 - Directory Listing
Modified Thu Sep 10 18:11:33 2009 UTC (8 years, 1 month ago) by pieper
COMP: apply patches from Attila Nagy for Solaris builds

Revision 10441 - Directory Listing
Modified Thu Sep 10 16:37:19 2009 UTC (8 years, 1 month ago) by fedorov
BUG: interpolation was unintentionally removed by the previous commit 
STYLE: misleading comment removed


Revision 10440 - Directory Listing
Modified Thu Sep 10 14:15:31 2009 UTC (8 years, 1 month ago) by pieper
COMP: move namespace directive to C++ code to avoid windows compile error

Revision 10439 - Directory Listing
Modified Wed Sep 9 23:05:27 2009 UTC (8 years, 1 month ago) by fedorov
BUG: incorrect pixel typing could lead to changes in the image
intensity for some modules used with some data types (eg, char vs uchar) --
propagating the change from 3-4 branch


Revision 10433 - Directory Listing
Modified Wed Sep 9 19:09:08 2009 UTC (8 years, 1 month ago) by casey.goodlett
BUG: Make the default parameters in the constructor the same as
specified in the XML file for the Slicer GUI.  This will make the
default paramters for the command line version the same as when run
from the GUI.

STYLE: Convert pointer initalizatino from 0 to NULL.


Revision 10432 - Directory Listing
Modified Wed Sep 9 18:59:35 2009 UTC (8 years, 1 month ago) by pieper
BUG: handle signed and unsigned integers correctly

Revision 10426 - Directory Listing
Modified Tue Sep 8 20:52:14 2009 UTC (8 years, 1 month ago) by hjohnson
COMP: With the conversion to CMake version 2.6, the variables CMAKE_RUNTIME_OUTPUT_DIRECTORY CMAKE_LIBRARY_OUTPUT_DIRECTORY CMAKE_ARCHIVE_OUTPUT_DIRECTORY should be used instead of EXECUTABLE_OUTPUT_PATH and LIBRARY_OUTPUT_PATH.

Revision 10421 - Directory Listing
Modified Tue Sep 8 15:00:32 2009 UTC (8 years, 1 month ago) by pieper
BUG: add missing call to SetShiftNegativeEigenvalues

Revision 10420 - Directory Listing
Modified Tue Sep 8 01:22:39 2009 UTC (8 years, 1 month ago) by aylward
BUG: Commandline args to generateTestData changed



Revision 10418 - Directory Listing
Modified Mon Sep 7 13:40:19 2009 UTC (8 years, 1 month ago) by aylward
COMP: Message about long tests should be an "Attention" statement and not a "Warning" statement to avoid ctest flagging as a build configuration warning on dashboards



Revision 10412 - Directory Listing
Modified Fri Sep 4 14:57:55 2009 UTC (8 years, 1 month ago) by aylward
ENH: Updated to support testing when used by external projects.   Also added argument to ResampleImage function to specify DefaultPixelValue used by resampler.



Revision 10407 - Directory Listing
Modified Tue Sep 1 21:19:09 2009 UTC (8 years, 1 month ago) by alexy
ENH: Qt GAD module

Revision 10379 - Directory Listing
Modified Thu Aug 27 21:45:54 2009 UTC (8 years, 1 month ago) by pieper
ENH: expose teem option to shift negative eigenvalues per request from Mahnaz and Jim.  Off by default per discussion with Casey

Revision 10358 - Directory Listing
Modified Wed Aug 26 17:42:55 2009 UTC (8 years, 1 month ago) by fedorov
ENH: removed the test from the trunk


Revision 10300 - Directory Listing
Modified Tue Aug 18 21:41:06 2009 UTC (8 years, 2 months ago) by alexy
ENH: Qt support

Revision 10297 - Directory Listing
Modified Tue Aug 18 17:59:57 2009 UTC (8 years, 2 months ago) by casey.goodlett
ENH: switch transform save and load to use the appropriate slicer routines.

Revision 10296 - Directory Listing
Modified Tue Aug 18 17:36:32 2009 UTC (8 years, 2 months ago) by casey.goodlett
ENH: switch landmark initalization to use fiducials list instead of float-vector.

Revision 10287 - Directory Listing
Modified Tue Aug 18 13:44:09 2009 UTC (8 years, 2 months ago) by pieper
ENH: add replace value option for pixels outside of mask area

Revision 10286 - Directory Listing
Modified Tue Aug 18 13:17:05 2009 UTC (8 years, 2 months ago) by casey.goodlett
ENH: Merge latest version of RegisterImagesModule.  This includes better support for landmark initalization.


Revision 10264 - Directory Listing
Modified Fri Aug 14 21:07:00 2009 UTC (8 years, 2 months ago) by pieper
BUG: allow subsequent scripted module packages to load if one of them fails

Revision 10226 - Directory Listing
Modified Wed Aug 12 18:12:21 2009 UTC (8 years, 2 months ago) by naucoin
ENH: add a new param to the MultiplyTest

Revision 10206 - Directory Listing
Modified Mon Aug 10 17:43:21 2009 UTC (8 years, 2 months ago) by pieper
BUG: be sure to run select module command after GUI is built, but before any scripts or other actions specified on the command line are run - otherwise the GUI may be destroyed before the module is loaded

Revision 10204 - Directory Listing
Modified Mon Aug 10 15:09:28 2009 UTC (8 years, 2 months ago) by naucoin
COMP: use floor for windows

Revision 10200 - Directory Listing
Modified Sun Aug 9 20:26:01 2009 UTC (8 years, 2 months ago) by fedorov
ENH: added 0-order interpolation for operations on labels


Revision 10190 - Directory Listing
Modified Fri Aug 7 20:30:50 2009 UTC (8 years, 2 months ago) by wjp@bwh.harvard.edu
ENH: Merging changes from Release branch into trunk to catch failed writes indicating file system is full, and giving options to clear Temp and Cache dirs

Revision 10187 - Directory Listing
Modified Fri Aug 7 20:11:27 2009 UTC (8 years, 2 months ago) by naucoin
BUG: more error checking to avoid crashing on a non ideal input model

Revision 10184 - Directory Listing
Modified Fri Aug 7 18:35:53 2009 UTC (8 years, 2 months ago) by naucoin
ENH: add a right hand mesh flag (PK to verify it's used properly), add arrays rather than just over writing scalars, check for already existing arrays to avoid some re-computation (more to do)

Revision 10181 - Directory Listing
Modified Fri Aug 7 13:55:38 2009 UTC (8 years, 2 months ago) by pieper
COMP: fix warning about non-virtual destructor

Revision 10179 - Directory Listing
Modified Thu Aug 6 16:39:15 2009 UTC (8 years, 2 months ago) by pieper
COMP: fix compile warnings

Revision 10173 - Directory Listing
Modified Wed Aug 5 21:02:53 2009 UTC (8 years, 2 months ago) by pieper
BUG: turn off exit confimation prompt when querying for module paths

Revision 10165 - Directory Listing
Modified Mon Aug 3 16:58:29 2009 UTC (8 years, 2 months ago) by pieper
ENH: allow launcher to query module paths from registry so dependencies can be set before launching the application

Revision 10122 - Directory Listing
Modified Thu Jul 30 19:09:12 2009 UTC (8 years, 2 months ago) by naucoin
ENH: move the options to an advanced section of the xml file. Moved some error output to cerr. Name the output arrays so they can be selected and checked later on

Revision 10121 - Directory Listing
Modified Thu Jul 30 18:04:19 2009 UTC (8 years, 2 months ago) by naucoin
BUG: use resize instead of assigning for the meshdata valarrays, as it was resulting in a size of 0 on linux64

Revision 10120 - Directory Listing
Modified Thu Jul 30 17:28:44 2009 UTC (8 years, 2 months ago) by naucoin
BUG: more error checking. ENH: adding filter watchers

Revision 10119 - Directory Listing
Modified Thu Jul 30 17:21:51 2009 UTC (8 years, 2 months ago) by taox
ENH: compute Euler angles and output.

Revision 10118 - Directory Listing
Modified Thu Jul 30 16:44:37 2009 UTC (8 years, 2 months ago) by naucoin
BUG: added error checking

Revision 10114 - Directory Listing
Modified Thu Jul 30 02:40:08 2009 UTC (8 years, 2 months ago) by tgl
ENH use a token in the module paths so that the current Slicer3 SVN revision number can be used to differentiate available extensions

Revision 10095 - Directory Listing
Modified Wed Jul 29 15:05:28 2009 UTC (8 years, 2 months ago) by millerjv
ENH: documentation

Revision 10094 - Directory Listing
Modified Wed Jul 29 15:05:01 2009 UTC (8 years, 2 months ago) by millerjv
ENH: Added interpolation control

Revision 10093 - Directory Listing
Modified Wed Jul 29 14:41:40 2009 UTC (8 years, 2 months ago) by millerjv
ENH: using resampling to get the second image into the coordinate frame of the first. This gets us progress, abort, and the linear fastpath through the resampling

Revision 10083 - Directory Listing
Modified Tue Jul 28 21:57:45 2009 UTC (8 years, 2 months ago) by millerjv
BUG: modified Add, Subtract, Multiply to work in physical space

Revision 10075 - Directory Listing
Modified Tue Jul 28 20:08:28 2009 UTC (8 years, 2 months ago) by millerjv
BUG: 600. Not sure why the Mac does not catch the exception properly. Changed the code so that Add always returns an image the same size as the first image. The resulting image will be the same as the first image wherever the images do not overlap but will be the sum of the images where they do overlap.  All this is done in pixel space, ignoring origin, spacing, and orientations

Revision 10062 - Directory Listing
Modified Tue Jul 28 16:07:14 2009 UTC (8 years, 2 months ago) by pieper
BUG: remove code that should have been replaced by previous merge from release branch

Revision 10037 - Directory Listing
Modified Mon Jul 27 15:46:19 2009 UTC (8 years, 2 months ago) by naucoin
STYLE: fixed documentation link

Revision 10016 - Directory Listing
Modified Fri Jul 24 15:09:59 2009 UTC (8 years, 2 months ago) by alexy
BUG-FIXED: 0000594
Check the interpolated point using IsInsideBuffer

Revision 10006 - Directory Listing
Modified Wed Jul 22 18:03:51 2009 UTC (8 years, 2 months ago) by millerjv
ENH: Ordering registration modules

Revision 10002 - Directory Listing
Modified Wed Jul 22 15:12:48 2009 UTC (8 years, 2 months ago) by millerjv
ENH: port from Slicer-3-4 branch to trunk

Revision 9863 - Directory Listing
Modified Tue Jul 7 14:03:36 2009 UTC (8 years, 3 months ago) by taox
ENH: loading dicom header the hard way.

Revision 9825 - Directory Listing
Modified Tue Jun 30 13:01:59 2009 UTC (8 years, 3 months ago) by millerjv
ENH: Pass diffusion weighted, diffusion tensor, and general vector images through memory to shared object command line modules instead of files. \nNOTE: RAS to LPS conversions are performed on the measurement frames which should be correct for DW and DT data.  However, general vector images are probably not handled properly here (or elsewhere in Slicer) where an RAS to LPS conversion should modify components of each vector (flip the sign on x and y components.

Revision 9763 - Directory Listing
Modified Tue Jun 23 15:04:34 2009 UTC (8 years, 3 months ago) by tgl
ENH rename ModuleCachePath to ExtensionsInstallPath

Revision 9753 - Directory Listing
Modified Mon Jun 22 15:31:00 2009 UTC (8 years, 3 months ago) by sylvain
ENH: remove old files for the MRI Bias Field Correction module. This module is now in the Slicer3/Module directory. The interface of the new module has been reworked and the code has been improved.

Revision 9704 - Directory Listing
Modified Tue Jun 16 15:21:45 2009 UTC (8 years, 4 months ago) by taox
ENH: support siemens mosaic image in IS order.

Revision 9699 - Directory Listing
Modified Mon Jun 15 20:37:16 2009 UTC (8 years, 4 months ago) by pieper
BUG: merge compile fix for vs 2003 .NET from 3.4 branch

Revision 9698 - Directory Listing
Modified Mon Jun 15 20:26:32 2009 UTC (8 years, 4 months ago) by pieper
BUG: fix license text (with Stephen Aylward's permission)

Revision 9689 - Directory Listing
Modified Fri Jun 12 20:15:31 2009 UTC (8 years, 4 months ago) by pieper
BUG: merge fixes from 3.4 release branch (module selection in test mode) plus suppress python warning in some cases

Revision 9677 - Directory Listing
Modified Wed Jun 10 21:42:23 2009 UTC (8 years, 4 months ago) by pieper
BUG: fix license issues

Revision 9676 - Directory Listing
Modified Wed Jun 10 21:29:33 2009 UTC (8 years, 4 months ago) by pieper
BUG: add license info

Revision 9670 - Directory Listing
Modified Tue Jun 9 22:09:46 2009 UTC (8 years, 4 months ago) by naucoin
BUG: cast so compiles on windows

Revision 9657 - Directory Listing
Modified Sun Jun 7 05:46:02 2009 UTC (8 years, 4 months ago) by sylvain
ENH: add generic module for bias field correction of mri images. this module contains a threshold component to create a mask. the bias field correction is only applied under the mask. this has the advantage to improve the result and speed up the processing.

Revision 9652 - Directory Listing
Modified Sat Jun 6 03:03:02 2009 UTC (8 years, 4 months ago) by sylvain
ENH: add link to Slicer wiki documentation in the ackowledgement menu

Revision 9639 - Directory Listing
Modified Wed Jun 3 06:27:14 2009 UTC (8 years, 4 months ago) by sylvain
ENH: enable the compilation of the module N3 MRI Bias Field Correction.

Revision 9585 - Directory Listing
Modified Thu May 21 19:06:48 2009 UTC (8 years, 4 months ago) by wjp@bwh.harvard.edu
BUG: cleaning up leaks

Revision 9556 - Directory Listing
Modified Tue May 19 19:39:07 2009 UTC (8 years, 5 months ago) by naucoin
BUG: make debug a flag accessible via the command line

Revision 9525 - Directory Listing
Modified Mon May 18 19:05:18 2009 UTC (8 years, 5 months ago) by pieper
STYLE: include info the tooltip about output format

Revision 9524 - Directory Listing
Modified Mon May 18 18:39:42 2009 UTC (8 years, 5 months ago) by pieper
BUG: allow non-axial input files by resampling fixed and moving to axial before registration

Revision 9511 - Directory Listing
Modified Sat May 16 16:00:18 2009 UTC (8 years, 5 months ago) by fedorov
BUG: debug image writes were accidentally commited earlier


Revision 9498 - Directory Listing
Modified Fri May 15 12:23:57 2009 UTC (8 years, 5 months ago) by pieper
BUG: add namespace for mac compile

Revision 9497 - Directory Listing
Modified Fri May 15 12:22:17 2009 UTC (8 years, 5 months ago) by pieper
BUG: add namespace for mac compile

Revision 9487 - Directory Listing
Modified Thu May 14 17:12:17 2009 UTC (8 years, 5 months ago) by fedorov
STYLE: fixed misleading comment and prescribed full output for ctest


Revision 9481 - Directory Listing
Modified Wed May 13 22:23:53 2009 UTC (8 years, 5 months ago) by naucoin
ENH: Added multiply filter and test

Revision 9480 - Directory Listing
Modified Wed May 13 21:46:01 2009 UTC (8 years, 5 months ago) by naucoin
STYLE: updating the descriptions

Revision 9479 - Directory Listing
Modified Wed May 13 21:39:43 2009 UTC (8 years, 5 months ago) by naucoin
ENH: Adding an image mask CLI and test

Revision 9478 - Directory Listing
Modified Wed May 13 21:16:00 2009 UTC (8 years, 5 months ago) by naucoin
STYLE: fix a filter watcher comment string

Revision 9475 - Directory Listing
Modified Wed May 13 18:13:44 2009 UTC (8 years, 5 months ago) by naucoin
ENH: add the image cast CLI

Revision 9473 - Directory Listing
Modified Wed May 13 18:05:03 2009 UTC (8 years, 5 months ago) by naucoin
BUG: taking out non completed test

Revision 9472 - Directory Listing
Modified Wed May 13 18:00:34 2009 UTC (8 years, 5 months ago) by naucoin
ENH: Cast volume CLI plus test

Revision 9468 - Directory Listing
Modified Tue May 12 20:19:43 2009 UTC (8 years, 5 months ago) by pieper
BUG: fix for bug 582 - go to home module on startup in --no-modules mode

Revision 9458 - Directory Listing
Modified Mon May 11 23:10:36 2009 UTC (8 years, 5 months ago) by finetjul
ENH: Fix the name of the "Resample Images" directory parameter. Suffix it with "directory".

Revision 9442 - Directory Listing
Modified Sat May 9 14:42:25 2009 UTC (8 years, 5 months ago) by alexy
BUG-FIXED: clear undo/redo stack after creating everything

Revision 9419 - Directory Listing
Modified Thu May 7 02:09:01 2009 UTC (8 years, 5 months ago) by sylvain
ENH: add module to perform Bias Field Correction for MRI images following the method Non-parametric Non-uniform Intensity Normalization (N3) described by Sled et al in IEEE TMI 1998.

Revision 9417 - Directory Listing
Modified Wed May 6 21:55:14 2009 UTC (8 years, 5 months ago) by sylvain
ENH: add module for bias field correction in MRI images. It estimates the spatial inhomogeneity of intensities due to MRI coil distorsion and applies a function to the image intensity to compensate this inhomogeneity field. This module is based on the method described in the paper of Styner et al. IEEE TMI 2000.

Revision 9407 - Directory Listing
Modified Tue May 5 14:15:26 2009 UTC (8 years, 5 months ago) by pieper
BUG: fix some I/O issues and node selector setup

Revision 9404 - Directory Listing
Modified Mon May 4 21:15:13 2009 UTC (8 years, 5 months ago) by finetjul
ENH: RegisterImagesBatchMake module now iterates over the number of Rigid, Affine and BSpline iterations

Revision 9398 - Directory Listing
Modified Sun May 3 16:26:05 2009 UTC (8 years, 5 months ago) by alexy
ENH: removed EndoNavTracking

Revision 9397 - Directory Listing
Modified Sun May 3 16:24:35 2009 UTC (8 years, 5 months ago) by alexy
BUG-FIXED: create missing filenames in snapshot's storage nodes

Revision 9360 - Directory Listing
Modified Thu Apr 30 00:41:42 2009 UTC (8 years, 5 months ago) by fedorov
ENH: modified RegistrationTest02 to compare the result with a "ground truth"
transform (transform obtained by running registration in GUI mode with the
same set of parameters)


Revision 9358 - Directory Listing
Modified Thu Apr 30 00:11:51 2009 UTC (8 years, 5 months ago) by fedorov
ENH: added testing mode for RigidRegistration module


Revision 9357 - Directory Listing
Modified Wed Apr 29 20:59:51 2009 UTC (8 years, 5 months ago) by pieper
COMP: merge warning fixes from 3.4 release branch to trunk

Revision 9335 - Directory Listing
Modified Mon Apr 27 20:57:11 2009 UTC (8 years, 5 months ago) by pieper
COMP: fix compile warnings

Revision 9299 - Directory Listing
Modified Thu Apr 23 18:32:12 2009 UTC (8 years, 5 months ago) by pieper
BUG: rearrange logic to work with CMake 2.6.0

Revision 9288 - Directory Listing
Modified Thu Apr 23 15:34:44 2009 UTC (8 years, 5 months ago) by taox
BUG: used different element sizes for morphology operation, which can potentially create holds in areas around high surface curvature.

Revision 9279 - Directory Listing
Modified Wed Apr 22 20:53:28 2009 UTC (8 years, 5 months ago) by pieper
BUG: fix leaks and compile warnings

Revision 9278 - Directory Listing
Modified Wed Apr 22 20:35:28 2009 UTC (8 years, 5 months ago) by pieper
COMP: only include RegisterImages if we have a 3.12 build, when optimized registration will be part of ITK proper, or when using an earlier version that was built with the proper experimental code enabled

Revision 9275 - Directory Listing
Modified Wed Apr 22 16:25:05 2009 UTC (8 years, 5 months ago) by pieper
COMP: fix logic for deciding if RegisterImages can be included in the build

Revision 9270 - Directory Listing
Modified Tue Apr 21 17:29:50 2009 UTC (8 years, 5 months ago) by taox
ENH: compute and write out window/level for proper display.

Revision 9269 - Directory Listing
Modified Tue Apr 21 16:30:07 2009 UTC (8 years, 5 months ago) by taox
ENH: added test for new module PolyDataToLabelmap. Test data and baseline result were checked in.

Revision 9268 - Directory Listing
Modified Tue Apr 21 16:28:27 2009 UTC (8 years, 5 months ago) by taox
ENH: added new module PolyDataToLabelmap, which convert a closed surface model (in vtk xml format) into a label map.

Revision 9246 - Directory Listing
Modified Thu Apr 16 19:35:22 2009 UTC (8 years, 6 months ago) by pieper
BUG: fix leak by deleting scene before dispoing of EventBroker singleton

Revision 9245 - Directory Listing
Modified Thu Apr 16 18:30:54 2009 UTC (8 years, 6 months ago) by pieper
BUG: don't call delete on the smart pointer

Revision 9243 - Directory Listing
Modified Thu Apr 16 17:51:00 2009 UTC (8 years, 6 months ago) by hayes
BUG: Changed logical AND to OR

Revision 9230 - Directory Listing
Modified Wed Apr 15 22:07:43 2009 UTC (8 years, 6 months ago) by naucoin
BUG: check for empty directory and return instead of crashing

Revision 9206 - Directory Listing
Modified Wed Apr 15 10:29:13 2009 UTC (8 years, 6 months ago) by wjp@bwh.harvard.edu
BUG: null pointer checking on loadable module setup

Revision 9202 - Directory Listing
Modified Tue Apr 14 22:17:57 2009 UTC (8 years, 6 months ago) by alexy
BUG-FIXED: fixed crash in CLI on checking relative file path, changed ImageLabelCombine


Revision 9198 - Directory Listing
Modified Tue Apr 14 19:36:41 2009 UTC (8 years, 6 months ago) by hayes
BUG: Changed logical OR to AND

Revision 9189 - Directory Listing
Modified Tue Apr 14 15:54:25 2009 UTC (8 years, 6 months ago) by pieper
BUG: don't try to set home module when in test mode

Revision 9181 - Directory Listing
Modified Tue Apr 14 00:15:32 2009 UTC (8 years, 6 months ago) by naucoin
BUG: took out applying the transform, changed module name to ACPC Transform, updated docs

Revision 9177 - Directory Listing
Modified Mon Apr 13 20:38:10 2009 UTC (8 years, 6 months ago) by wjp@bwh.harvard.edu
BUG: fixing the crash with lazybuild

Revision 9173 - Directory Listing
Modified Mon Apr 13 19:33:56 2009 UTC (8 years, 6 months ago) by wjp@bwh.harvard.edu
BUG: added mechanism for loadable modules to build lazily

Revision 9170 - Directory Listing
Modified Mon Apr 13 19:08:00 2009 UTC (8 years, 6 months ago) by pieper
BUG: avoid crash when starting in --no-modules mode

Revision 9162 - Directory Listing
Modified Sat Apr 11 22:08:47 2009 UTC (8 years, 6 months ago) by pieper
BUG: revert change that was committed by mistake

Revision 9160 - Directory Listing
Modified Sat Apr 11 16:58:58 2009 UTC (8 years, 6 months ago) by alexy
BUG-FIXED: 519 prevent scalar volume reader from reading non-scalar volumes.

Revision 9157 - Directory Listing
Modified Fri Apr 10 21:21:00 2009 UTC (8 years, 6 months ago) by wjp@bwh.harvard.edu
ENH: added SlicerWelcome module at startup options in app registry.

Revision 9150 - Directory Listing
Modified Fri Apr 10 20:11:49 2009 UTC (8 years, 6 months ago) by pieper
BUG: revert incorrect code

Revision 9147 - Directory Listing
Modified Fri Apr 10 18:55:41 2009 UTC (8 years, 6 months ago) by naucoin
BUG: remove unused var

Revision 9144 - Directory Listing
Modified Fri Apr 10 18:10:05 2009 UTC (8 years, 6 months ago) by naucoin
BUG: removing compiler warnings, RunCondor and ParseBuffer are void methods

Revision 9136 - Directory Listing
Modified Fri Apr 10 17:33:12 2009 UTC (8 years, 6 months ago) by millerjv
BUG: Attempt to fix bug #488 and perhaps #440 but forcing functions in plugins to have file scope.  Turns out not to be cause of the bug but since it is probably a good idea to have the code structured like this, I am checking it in.

Revision 9135 - Directory Listing
Modified Fri Apr 10 16:16:04 2009 UTC (8 years, 6 months ago) by millerjv
COMP: warnings

Revision 9133 - Directory Listing
Modified Fri Apr 10 15:20:53 2009 UTC (8 years, 6 months ago) by naucoin
BUG: need quotes around the home module in case it has a space in it's name -Model Maker was failing as a home module on start up

Revision 9125 - Directory Listing
Modified Fri Apr 10 03:23:48 2009 UTC (8 years, 6 months ago) by tgl
ENH add binary directory to store execution location

Revision 9122 - Directory Listing
Modified Thu Apr 9 18:22:32 2009 UTC (8 years, 6 months ago) by pieper
BUG: move switch to home module before scripts and exec commands since they are meant to happen after the GUI has finished being created

Revision 9110 - Directory Listing
Modified Wed Apr 8 22:42:32 2009 UTC (8 years, 6 months ago) by pieper
BUG: add command line arguments to file executed from command line and turn off some debug statements and avoid one leak

Revision 9109 - Directory Listing
Modified Wed Apr 8 22:06:45 2009 UTC (8 years, 6 months ago) by naucoin
BUG: hide all the label options just have generate all as the default

Revision 9105 - Directory Listing
Modified Wed Apr 8 18:54:14 2009 UTC (8 years, 6 months ago) by pieper
BUG: fix typo

Revision 9102 - Directory Listing
Modified Wed Apr 8 18:20:08 2009 UTC (8 years, 6 months ago) by naucoin
BUG: be a bit more clear about where the models are, and if you need to import a scene file because you didn't specify a model hierarchy node

Revision 9101 - Directory Listing
Modified Wed Apr 8 18:09:40 2009 UTC (8 years, 6 months ago) by pieper
BUG: avoid calling GUI creation code before application has finished initializing

Revision 9094 - Directory Listing
Modified Tue Apr 7 17:14:56 2009 UTC (8 years, 6 months ago) by pieper
COMP: fix for windows compilation

Revision 9073 - Directory Listing
Modified Mon Apr 6 14:29:28 2009 UTC (8 years, 6 months ago) by finetjul
ENH: Fix the parameter names of the RegisterImages BatchMake module

Revision 9072 - Directory Listing
Modified Mon Apr 6 14:19:36 2009 UTC (8 years, 6 months ago) by finetjul
BUG: Register Images BatchMake module had a wrong title

Revision 9071 - Directory Listing
Modified Mon Apr 6 13:50:52 2009 UTC (8 years, 6 months ago) by finetjul
ENH: Add ResampleVolume BatchMake Module

Revision 9070 - Directory Listing
Modified Mon Apr 6 13:45:29 2009 UTC (8 years, 6 months ago) by finetjul
ENH: BatchMake: Remove wrong directory name


Revision 9069 - Directory Listing
Modified Mon Apr 6 13:39:23 2009 UTC (8 years, 6 months ago) by finetjul
ENH: Add ResampleVolume BatchMake Module


Revision 9068 - Directory Listing
Modified Mon Apr 6 13:35:57 2009 UTC (8 years, 6 months ago) by finetjul
ENH: Add ResampleVolume BatchMake Module


Revision 9057 - Directory Listing
Modified Sun Apr 5 17:41:45 2009 UTC (8 years, 6 months ago) by alexy
BUG-FIXED: check the RAS matrix for null

Revision 9055 - Directory Listing
Modified Sun Apr 5 14:41:47 2009 UTC (8 years, 6 months ago) by pieper
COMP: remove reference to missing subdirectory

Revision 9049 - Directory Listing
Modified Sat Apr 4 22:21:49 2009 UTC (8 years, 6 months ago) by finetjul
ENH: ResampleVolumeBatchMake is the BatchMake version of the ResampleVolume module


Revision 9048 - Directory Listing
Modified Sat Apr 4 22:21:34 2009 UTC (8 years, 6 months ago) by finetjul
ENH: ResampleVolumeBatchMake is the BatchMake version of the ResampleVolume module


Revision 9047 - Directory Listing
Modified Sat Apr 4 22:21:20 2009 UTC (8 years, 6 months ago) by finetjul
ENH: ResampleVolumeBatchMake is the BatchMake version of the ResampleVolume module


Revision 9046 - Directory Listing
Modified Sat Apr 4 22:20:50 2009 UTC (8 years, 6 months ago) by finetjul
ENH: ENH: ResampleVolumeBatchMake is the BatchMake version of the ResampleVolume module

Revision 9045 - Directory Listing
Modified Sat Apr 4 22:16:58 2009 UTC (8 years, 6 months ago) by finetjul
ENH: ResampleVolumeBatchMake is the BatchMake version of the ResampleVolume module


Revision 9044 - Directory Listing
Modified Sat Apr 4 22:16:38 2009 UTC (8 years, 6 months ago) by finetjul
ENH: ResampleVolumeBatchMake is the BatchMake version of the ResampleVolume module


Revision 9031 - Directory Listing
Modified Fri Apr 3 10:11:14 2009 UTC (8 years, 6 months ago) by lantiga
ENH: Add ScriptedModuleInfo to Slicer Python module in order to access it programmatically or from the Python console

Revision 8979 - Directory Listing
Modified Thu Mar 26 15:29:29 2009 UTC (8 years, 6 months ago) by pieper
BUG: change Measurement to Measure to comply with the Westin published naming conventions

Revision 8915 - Directory Listing
Modified Thu Mar 19 19:44:58 2009 UTC (8 years, 7 months ago) by pieper
ENH: fix module menu layout to match the documentation on the wiki

Revision 8912 - Directory Listing
Modified Thu Mar 19 18:02:06 2009 UTC (8 years, 7 months ago) by pieper
BUG: remove older code (use python stochastic tractography instead)

Revision 8901 - Directory Listing
Modified Wed Mar 18 02:36:21 2009 UTC (8 years, 7 months ago) by blezek
BUG: EndoNavTracking not yet checked in

Revision 8900 - Directory Listing
Modified Wed Mar 18 00:14:23 2009 UTC (8 years, 7 months ago) by alexy
ENH: added Line/Tube selection to Fiducial Seeding
BUG 475

Revision 8878 - Directory Listing
Modified Sat Mar 14 19:58:21 2009 UTC (8 years, 7 months ago) by aylward
ENH: Reduced compile time when 2D image support isn't needed



Revision 8873 - Directory Listing
Modified Fri Mar 13 03:43:54 2009 UTC (8 years, 7 months ago) by lorensen
ENH: Added documentation url.


Revision 8872 - Directory Listing
Modified Fri Mar 13 03:02:29 2009 UTC (8 years, 7 months ago) by lorensen
COMP: VS7 could not compile with ImageType::ConstPointer. Substituted TImage::ConstPointer.

Revision 8858 - Directory Listing
Modified Mon Mar 9 16:41:58 2009 UTC (8 years, 7 months ago) by pieper
BUG: add missing fiducial/point example

Revision 8814 - Directory Listing
Modified Mon Mar 2 16:32:21 2009 UTC (8 years, 7 months ago) by millerjv
ENH: make deformation field output a hidden parameter to keep it out of the Slicer3 GUI

Revision 8812 - Directory Listing
Modified Mon Mar 2 16:23:31 2009 UTC (8 years, 7 months ago) by pieper
BUG: fix out of date reference to a module

Revision 8811 - Directory Listing
Modified Mon Mar 2 16:21:51 2009 UTC (8 years, 7 months ago) by pieper
COMP: remove orphaned module

Revision 8810 - Directory Listing
Modified Mon Mar 2 14:28:33 2009 UTC (8 years, 7 months ago) by pieper
COMP: avoid warnings when building python (avoid mismatch betweent the way Python defines _LARGEFILE_SOURCE compared to the way kwsys defines it

Revision 8804 - Directory Listing
Modified Mon Mar 2 02:45:57 2009 UTC (8 years, 7 months ago) by millerjv
ENH: add an index to module

Revision 8803 - Directory Listing
Modified Mon Mar 2 02:29:50 2009 UTC (8 years, 7 months ago) by millerjv
ENH: Added an "Index" to Modules to facilitate module list order within a category (menu).  Modules within a category are now sorted by index and then by name. Builtin modules can override the method GetIndex() to prescribe a position. Command line modules can use the <index> tag to indicate an order.  Modules with an index are always displayed before modules without an index (default index is the maximum value of a short, i.e. the last position).




Revision 8784 - Directory Listing
Modified Sat Feb 28 21:43:09 2009 UTC (8 years, 7 months ago) by pieper
BUG: check for gui pointer being null to handle gui-less extensions

Revision 8780 - Directory Listing
Modified Fri Feb 27 22:28:47 2009 UTC (8 years, 7 months ago) by millerjv
BUG: Crosshair is now click-to-drag. You can drag the center or the horizontal or vertical lines in the basic crosshair

Revision 8770 - Directory Listing
Modified Fri Feb 27 19:38:17 2009 UTC (8 years, 7 months ago) by pieper
COMP: allow GUIless loadable modules

Revision 8761 - Directory Listing
Modified Thu Feb 26 22:38:28 2009 UTC (8 years, 7 months ago) by pieper
BUG: fix typos and display/tooltip issues in GUI

Revision 8757 - Directory Listing
Modified Thu Feb 26 21:09:47 2009 UTC (8 years, 7 months ago) by lorensen
COMP: Better description of filter.

Revision 8753 - Directory Listing
Modified Thu Feb 26 19:49:48 2009 UTC (8 years, 7 months ago) by pieper
COMP: remove UtahBSpline and TestGridTransformRegistration in preparation for release

Revision 8744 - Directory Listing
Modified Wed Feb 25 17:01:33 2009 UTC (8 years, 7 months ago) by naucoin
COMP: removing compiler warnings, unused variables

Revision 8676 - Directory Listing
Modified Wed Feb 18 00:54:03 2009 UTC (8 years, 8 months ago) by pieper
BUG: avoid multithreading of the vtkTensorMask due to instability

Revision 8673 - Directory Listing
Modified Tue Feb 17 17:45:25 2009 UTC (8 years, 8 months ago) by pieper
BUG: add ability to set default pixel value when running the resampler

Revision 8655 - Directory Listing
Modified Mon Feb 16 21:12:09 2009 UTC (8 years, 8 months ago) by alexy
ENH: added help and about pages. Fixed loading man made MRML scene with partial volume information

Revision 8644 - Directory Listing
Modified Mon Feb 16 17:42:51 2009 UTC (8 years, 8 months ago) by lorensen
ENH: Added cubic bspline interpolator.

Revision 8643 - Directory Listing
Modified Mon Feb 16 17:17:03 2009 UTC (8 years, 8 months ago) by lorensen
STYLE: improved documentation.

Revision 8642 - Directory Listing
Modified Mon Feb 16 17:15:45 2009 UTC (8 years, 8 months ago) by lorensen
BUG: flawed logic for interpolation selection. ENH: Added nearest neighbor. STYLE: Improved documentation.

Revision 8641 - Directory Listing
Modified Sat Feb 14 21:28:08 2009 UTC (8 years, 8 months ago) by lorensen
BUG: now does sinc interpolation.

Revision 8635 - Directory Listing
Modified Fri Feb 13 17:22:56 2009 UTC (8 years, 8 months ago) by naucoin
STYLE: point to 3.4 docs

Revision 8630 - Directory Listing
Modified Thu Feb 12 21:22:26 2009 UTC (8 years, 8 months ago) by pieper
BUG: fixes to python internals to support scripted wizards

Revision 8625 - Directory Listing
Modified Wed Feb 11 22:48:16 2009 UTC (8 years, 8 months ago) by pieper
BUG: first pass of python and numpy builds from source (fixes but that they weren't building before).  Still turned off by default until more testing is done

Revision 8623 - Directory Listing
Modified Wed Feb 11 22:33:54 2009 UTC (8 years, 8 months ago) by taox
ENH: Update test for DicomToNRRDConverter

Revision 8600 - Directory Listing
Modified Sun Feb 8 18:39:35 2009 UTC (8 years, 8 months ago) by lorensen
STYLE: enhanced documentation.

Revision 8599 - Directory Listing
Modified Sun Feb 8 18:38:34 2009 UTC (8 years, 8 months ago) by lorensen
BUG: memory leak.

Revision 8596 - Directory Listing
Modified Sat Feb 7 21:41:39 2009 UTC (8 years, 8 months ago) by lorensen
STYLE: change doc url.

Revision 8595 - Directory Listing
Modified Sat Feb 7 21:06:06 2009 UTC (8 years, 8 months ago) by lorensen
ENH: added documentation-url.

Revision 8593 - Directory Listing
Modified Sat Feb 7 18:27:01 2009 UTC (8 years, 8 months ago) by lorensen
STYLE: corrected itk example from which this filter was derived.

Revision 8589 - Directory Listing
Modified Fri Feb 6 18:31:22 2009 UTC (8 years, 8 months ago) by pkarasev3
BUG: repaired memory leaks in module

Revision 8535 - Directory Listing
Modified Wed Feb 4 18:04:28 2009 UTC (8 years, 8 months ago) by pieper
BUG: fix a leak when evaluating code sent on the command line

Revision 8528 - Directory Listing
Modified Wed Feb 4 04:23:04 2009 UTC (8 years, 8 months ago) by pkarasev3
BUG: better name for what appears in the gui; do not use acronym

Revision 8503 - Directory Listing
Modified Tue Feb 3 13:09:02 2009 UTC (8 years, 8 months ago) by taox
ENH: Added support for Philips, from Vince. Made change to the test to use the new command line argument.

Revision 8500 - Directory Listing
Modified Mon Feb 2 20:23:12 2009 UTC (8 years, 8 months ago) by taox
ENH: Added support for Philips, from Vince.

Revision 8483 - Directory Listing
Modified Wed Jan 28 17:38:48 2009 UTC (8 years, 8 months ago) by naucoin
STYLE: update description and documentation url with changes to model hierarchy node and mrml scene requirements

Revision 8482 - Directory Listing
Modified Wed Jan 28 17:28:35 2009 UTC (8 years, 8 months ago) by naucoin
ENH: if there is no scene file passed in, create one and a model hierarchy node. Makes it easier to run on the command line, will create a scene file with the prefix of the InputVolume and the extension mrml

Revision 8449 - Directory Listing
Modified Fri Jan 23 21:11:07 2009 UTC (8 years, 8 months ago) by pieper
ENH: error checking on file read

Revision 8431 - Directory Listing
Modified Tue Jan 20 23:14:39 2009 UTC (8 years, 8 months ago) by pieper
ENH: add module path to the shared library load path so that modules can be executed when they depend on their on libs they supply in their module directory

Revision 8408 - Directory Listing
Modified Mon Jan 19 17:41:20 2009 UTC (8 years, 9 months ago) by fedorov
BUG: Need to investigate alternative approaches to registration
regression testing. 


Revision 8401 - Directory Listing
Modified Fri Jan 16 16:46:37 2009 UTC (8 years, 9 months ago) by fedorov
ENH: Added rigid registration test and baseline image for regression
testing (meningioma data)


Revision 8398 - Directory Listing
Modified Thu Jan 15 23:28:58 2009 UTC (8 years, 9 months ago) by pieper
COMP: fix install target for batchmake modules

Revision 8368 - Directory Listing
Modified Tue Jan 13 13:40:25 2009 UTC (8 years, 9 months ago) by lorensen
BUG: improper or missing vtkSmartPointer usage.

Revision 8367 - Directory Listing
Modified Tue Jan 13 13:35:20 2009 UTC (8 years, 9 months ago) by lorensen
BUG: Missing vtkEventBroker::GetInstance()->Delete() was causing leak.

Revision 8355 - Directory Listing
Modified Mon Jan 12 17:38:49 2009 UTC (8 years, 9 months ago) by lorensen
BUG: memory leak.

Revision 8351 - Directory Listing
Modified Sun Jan 11 13:53:12 2009 UTC (8 years, 9 months ago) by lorensen
BUG: No return(EXIT_SUCCESS) was present.

Revision 8350 - Directory Listing
Modified Sun Jan 11 05:21:21 2009 UTC (8 years, 9 months ago) by lorensen
BUG: improper use of vtkSmartPointer.

Revision 8343 - Directory Listing
Modified Sat Jan 10 15:35:35 2009 UTC (8 years, 9 months ago) by lorensen
ENH: Changed name of test.

Revision 8338 - Directory Listing
Modified Fri Jan 9 21:51:37 2009 UTC (8 years, 9 months ago) by pieper
BUG: fix name of test of test by removing incorrectly named file

Revision 8333 - Directory Listing
Modified Fri Jan 9 15:32:45 2009 UTC (8 years, 9 months ago) by lorensen
ENH: New test for DiffusionTensorMathematics

Revision 8331 - Directory Listing
Modified Fri Jan 9 14:33:38 2009 UTC (8 years, 9 months ago) by lorensen
ENH: New test for DiffusionTensorMathematics

Revision 8320 - Directory Listing
Modified Thu Jan 8 16:28:31 2009 UTC (8 years, 9 months ago) by naucoin
ENH: adding the itkThresholdImageFilter and test

Revision 8317 - Directory Listing
Modified Thu Jan 8 14:02:10 2009 UTC (8 years, 9 months ago) by lorensen
ENH: New test for DiffusionTensorEstimation.

Revision 8297 - Directory Listing
Modified Wed Jan 7 20:49:10 2009 UTC (8 years, 9 months ago) by lorensen
ENH: New test for ResampleVolume2

Revision 8287 - Directory Listing
Modified Wed Jan 7 01:35:17 2009 UTC (8 years, 9 months ago) by lantiga
ENH: adding ExecPython and EvalPython options to the Slicer executable

Revision 8276 - Directory Listing
Modified Tue Jan 6 15:43:36 2009 UTC (8 years, 9 months ago) by taox
BUG: The order of first and second dimensions was wrong.

Revision 8266 - Directory Listing
Modified Mon Jan 5 17:48:57 2009 UTC (8 years, 9 months ago) by lorensen
ENH: new regression test for OtsuThresholdImageFilter.
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