Changesets: Slicer

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2145-support-for-installing-extension-from-file 374a7cae

2013-08-27 15:24:23

jcfr

Details Diff 		COMP: Add macro "slicerMacroBuildLoadableModule"

Both macros "slicerMacroBuildQtModule" and "slicerMacroBuildLoadableModule"
can be used. At this point, no warning message is displayed if the
deprecated macro is used.

Fixes 0002648

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22342 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerMacroBuildQtModule.cmake Diff File
mod - Extensions/Testing/SuperBuildExtensionTemplate/SuperLoadableModuleTemplate/CMakeLists.txt Diff File
mod - Modules/Loadable/Annotations/CMakeLists.txt Diff File
mod - Modules/Loadable/Cameras/CMakeLists.txt Diff File
mod - Modules/Loadable/Colors/CMakeLists.txt Diff File
mod - Modules/Loadable/CropVolume/CMakeLists.txt Diff File
mod - Modules/Loadable/Data/CMakeLists.txt Diff File
mod - Modules/Loadable/DoubleArrays/CMakeLists.txt Diff File
mod - Modules/Loadable/Markups/CMakeLists.txt Diff File
mod - Modules/Loadable/Measurements/CMakeLists.txt Diff File
mod - Modules/Loadable/Models/CMakeLists.txt Diff File
mod - Modules/Loadable/MultiVolumeRendering/CMakeLists.txt Diff File
mod - Modules/Loadable/Reformat/CMakeLists.txt Diff File
mod - Modules/Loadable/SceneViews/CMakeLists.txt Diff File
mod - Modules/Loadable/SlicerWelcome/CMakeLists.txt Diff File
mod - Modules/Loadable/TractographyDisplay/CMakeLists.txt Diff File
mod - Modules/Loadable/TractographyInteractiveSeeding/CMakeLists.txt Diff File
mod - Modules/Loadable/Transforms/CMakeLists.txt Diff File
mod - Modules/Loadable/Units/CMakeLists.txt Diff File
mod - Modules/Loadable/ViewControllers/CMakeLists.txt Diff File
mod - Modules/Loadable/VolumeRendering/CMakeLists.txt Diff File
mod - Modules/Loadable/Volumes/CMakeLists.txt Diff File

2145-support-for-installing-extension-from-file 744e0184

2013-08-27 15:24:18

jcfr

Details Diff 		STYLE: Fix authorship of qSlicerScriptedFileWriter

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22341 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCore/qSlicerScriptedFileWriter.h Diff File

2145-support-for-installing-extension-from-file 642177da

2013-08-27 14:51:25

naucoin

Details Diff 		STYLE: remove debugging print out, fix doc category

Remove a qDebug call that is just informational about
the system settings for the markups.
Change the documentation category to Informatics.

Issue 0002740



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22340 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/Documentation/Markups.xml Diff File
mod - Modules/Loadable/Markups/qSlicerMarkupsModuleWidget.cxx Diff File

2145-support-for-installing-extension-from-file eee567c0

2013-08-27 14:43:26

naucoin

Details Diff 		BUG: stop the dropping of fiducials dragged outside of 2d viewport

Check if the viewport coordinates have been restricted as well as if the display
coordinates were changed, as the second check wasn't fine grained enough
to detect when a restriction was made on a slow/small drag outside
of the viewport. This would lead to the fiducial being dropped
when it was outside the viewport.
Now the fiducial is stopped at the edge of the 2d viewport. When the
mouse comes back toward the view port, there is an offset between the
mouse position and the moving fiducial, but barring more user feedback,
we decided to leave this as is.

Issue 0003318


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22339 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/MRMLDM/vtkMRMLMarkupsDisplayableManager2D.cxx Diff File
mod - Modules/Loadable/Markups/MRMLDM/vtkMRMLMarkupsDisplayableManager2D.h Diff File
mod - Modules/Loadable/Markups/MRMLDM/vtkMRMLMarkupsFiducialDisplayableManager2D.cxx Diff File

2145-support-for-installing-extension-from-file a26497c3

2013-08-26 23:29:57

jcfr

Details Diff 		ENH: Add qSlicerScriptedFileWriter interface

User can now register python based file writer.

For example:

# File MyCustomSceneExporter.py

import json
import os
import zipfile
import contextlib
import datetime
import vtk, slicer

class MyCustomSceneExporter:
def __init__(self, parent):
parent.title = "[...]"
parent.categories = ["..."]
parent.dependencies = []
parent.contributors = ["..."]
parent.helpText = """[...]"""
parent.acknowledgementText = """[...]"""
self.parent = parent

class MyCustomSceneExporterFileWriter:
def __init__(self, parent):
self.parent = parent

def description(self):
return 'Custom Scene File'

def fileType(self):
return 'SceneFile'

def canWriteObject(self, obj):
return isinstance(obj, slicer.vtkMRMLScene)

def extensions(self, obj):
return ['CustomScene File (*.customscene.zip)']

def write(self, properties):
self.exportModels(properties['fileName'])
return True

[...]

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22338 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCore/CMakeLists.txt Diff File
add - Base/QTCore/qSlicerScriptedFileWriter.cxx Diff File
add - Base/QTCore/qSlicerScriptedFileWriter.h Diff File
mod - Base/QTGUI/qSlicerScriptedLoadableModule.cxx Diff File
mod - Base/QTGUI/qSlicerScriptedLoadableModule.h Diff File

2145-support-for-installing-extension-from-file b0302280

2013-08-26 23:29:53

jcfr

Details Diff 		BUG: Consider specific file writer before generic one.

Ideally the file reader/writer should be reworked to have a more
consistent API. More specifically after the user select a file type
in the "save dialog", the corresponding "file writer id" should be
passed down the qSlicerCoreIOManager::saveScene/saveNodes methods.

This would prevent confusion for the user. Indeed, if a writer fails a
clear error message would be displated and the system wouldn't try an other
possible writer.

See issue 0003322

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22337 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCore/qSlicerCoreIOManager.cxx Diff File

2145-support-for-installing-extension-from-file af9fa03b

2013-08-26 23:29:50

jcfr

Details Diff 		BUG: Exposes RepresentationType and InterpolationType enums to python

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22336 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLDisplayNode.h Diff File

2145-support-for-installing-extension-from-file 5afd3704

2013-08-26 23:29:48

jcfr

Details Diff 		BUG: Fix serialization of display node representation property

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22335 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLDisplayNode.cxx Diff File

2145-support-for-installing-extension-from-file b291f333

2013-08-26 20:09:40

pieper

Details Diff 		BUG: 0003315 allow editor extensions to define custom cursor

The mechanism for editor extensions to declare their cursor had
already existed, but it was being ignored.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22334 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/EditorLib/EditBox.py Diff File

2145-support-for-installing-extension-from-file ac77ddbb

2013-08-26 19:46:19

naucoin

Details Diff 		BUG: remove fiducial settings from the tutorial self test GUI

Remove left over code from copying the add many fiducials self test.
Replaced them with screen shot parameters to help with making the tutorial,
a check box to turn them on (off by default) and a slider to set the scale
(1 by default).
Tweaked the test: make sure that the fiducial list is named the same
as when a user would create one. Make the slices visible in 3D.

Issue 0003328



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22333 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/Testing/Python/NeurosurgicalPlanningTutorialMarkupsSelfTest.py Diff File

2145-support-for-installing-extension-from-file 795a2283

2013-08-26 19:38:20

naucoin

Details Diff 		BUG: confirm delete of markups

Add a message box to tell the user how many markups they
are about to delete and let them cancel. Option to
not show the message again.

COMP: cleaned up unused variable warnings

Fixes issue 0003324



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22332 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/qSlicerMarkupsModuleWidget.cxx Diff File

2145-support-for-installing-extension-from-file eecc44de

2013-08-26 13:38:52

naucoin

Details Diff 		BUG: show the color indices rather than row number

The Color GUI was showing a row number starting from 1
when displaying color table entries, which are 0 indexed.
This led to a mismatch between the value shown in the
data probe (and in the actual color node) versus
what the user was being shown to be the color index.

Overloaded the headerData method to, in the case of the
vertical header display role to return the row index
minus 1. The MRML color model defines a ColorEntryRole
but it's still off by 1 from the color index.

Testing of copying a color node exposed the fact that the
new color node was not showing up in the Data module nor
in the Save Data dialog, so updated CopyNode in the color
logic to turn off the hide from editors flag on the new node.

Issue 0001892


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22331 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Logic/vtkMRMLColorLogic.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLColorModel.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLColorModel.h Diff File

2145-support-for-installing-extension-from-file c99f6ba1

2013-08-26 12:18:24

pieper

Details Diff 		ENH: 0003284 don't let user edit some dicom fields

As of r22329 the name of the volume can be set via the table widget,
but editing the other fields makes no sense, so we disable it.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22330 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOM/DICOMLib/DICOMWidgets.py Diff File

2145-support-for-installing-extension-from-file 4abdead3

2013-08-26 12:05:37

pieper

Details Diff 		ENH: Editing laodable names in DICOM widget can now lead to renaming of
the loaded loadables.

Closes 0003284

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22329 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOM/DICOMLib/DICOMWidgets.py Diff File

2145-support-for-installing-extension-from-file c056e1fd

2013-08-25 13:37:35

alexy

Details Diff 		BUG: 2816. Store SceneViews data in MRB file even if not present in the main scene for the case when the Scene Views are read from the scene file, the data pointer is NULL in this case.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22328 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Logic/vtkMRMLApplicationLogic.cxx Diff File

2145-support-for-installing-extension-from-file 60b88fb0

2013-08-24 14:56:58

alexy

Details Diff 		BUG: Fixed gcc compile error. Removed redundant 'extension' argument

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22327 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Logic/vtkMRMLApplicationLogic.cxx Diff File
mod - Libs/MRML/Logic/vtkMRMLApplicationLogic.h Diff File

2145-support-for-installing-extension-from-file ea2d585c

2013-08-24 04:44:52

lassoan

Details Diff 		COMP: Fixed build error in vtkMRMLApplicationLogic

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22326 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Logic/vtkMRMLApplicationLogic.h Diff File

2145-support-for-installing-extension-from-file 4103bccd

2013-08-23 14:58:17

alexy

Details Diff 		BUG: 2816. Made data present in SceneViews to be stored in MRB file even if not present in the main scene.
Restructured vtkMRMLApplicationLogic::SaveSceneToSlicerDataBundleDirectory() code, made it more modular.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22325 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Logic/vtkMRMLApplicationLogic.cxx Diff File
mod - Libs/MRML/Logic/vtkMRMLApplicationLogic.h Diff File

2145-support-for-installing-extension-from-file 2a70e149

2013-08-23 10:52:46

naucoin

Details Diff 		BUG: fix memory leak of vtkCollection

Clear and delete the node collection to remove a memory leak
from the snapshot dialog.

Fixes Issue 0003314



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22324 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Annotations/GUI/qSlicerAnnotationModuleSnapShotDialog.cxx Diff File

2145-support-for-installing-extension-from-file fdf40d7a

2013-08-22 21:31:27

naucoin

Details Diff 		BUG: Update Endoscopy module to support Markups

Added a backward compatibility call of GetNumberOfFiducials to the
Markups fiducial node.

See issue 0002606

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22323 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/Endoscopy/Endoscopy.py Diff File

2145-support-for-installing-extension-from-file 557f5686

2013-08-22 21:31:24

naucoin

Details Diff 		ENH: Update TractographyInteractiveSeeding module to support Markups

Allow usage of Markups fiducials or Annotations fiducials.

See issue 0002606

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22322 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/TractographyInteractiveSeeding/Logic/CMakeLists.txt Diff File
mod - Modules/Loadable/TractographyInteractiveSeeding/Logic/vtkSlicerTractographyInteractiveSeedingLogic.cxx Diff File
mod - Modules/Loadable/TractographyInteractiveSeeding/Resources/UI/qSlicerTractographyInteractiveSeedingModuleWidget.ui Diff File
mod - Modules/Loadable/TractographyInteractiveSeeding/qSlicerTractographyInteractiveSeedingModuleWidget.cxx Diff File

2145-support-for-installing-extension-from-file 4a98f205

2013-08-22 21:31:19

naucoin

Details Diff 		ENH: Replace Annotations with Markups in default favorite modules list.

See issue 0002606

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22321 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/qSlicerSettingsModulesPanel.cxx Diff File

2145-support-for-installing-extension-from-file c6ab6690

2013-08-22 21:31:16

naucoin

Details Diff 		ENH: Deprecating annotation fiducials

Edit properties in the Data module will go to the Markups module for
both Markups and Annotations fiducials, so that annotation fids
can be converted.

Unregister the Annotations fiducials IO, Markups can read .acsv files.
Add a label in the Annotations GUI that fiducials can be found in the Markups module.

See issue 0002606

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22320 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/qSlicerApplication.cxx Diff File
mod - Modules/Loadable/Annotations/Resources/UI/qSlicerAnnotationModuleWidget.ui Diff File
mod - Modules/Loadable/Annotations/qSlicerAnnotationsModule.cxx Diff File

2145-support-for-installing-extension-from-file 7ab790ee

2013-08-22 21:25:04

naucoin

Details Diff 		ENH: Support passing Markup fiducials to CLIs

Use the coordinate system flag to support RAS or LPS coordinates
for the points.

See issue 0002606

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22319 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCLI/qSlicerCLIModuleUIHelper.cxx Diff File
mod - Base/QTCLI/vtkSlicerCLIModuleLogic.cxx Diff File

2145-support-for-installing-extension-from-file e81463bf

2013-08-22 21:25:00

naucoin

Details Diff 		ENH: Add annotation and markup file loading

Add utility methods to allow loading Markup fiducials
from the python console, as well as a backward
compatible Annotation reader

See issue 0002606

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22318 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Python/slicer/util.py Diff File
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