Changesets: Import 2017-06-07 23:51:09
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master 97118990 2015-09-16 11:47:06 Details Diff |
ENH: Update CTK (includes PythonQt crash fix, DICOM browser enhancement) Fixes Issue 0004045 (py_StandaloneEditorWidgetTest crashes on exit in PythonQt) Fixes Issue 0003792 (unable to remove one series of an exam in the dicom menu) // ------------------------- commit cbf890f8eda122b8dca8e67d2bf75e85640ab297 Author: Max Smolens <max.smolens@kitware.com> Date: Tue Sep 15 15:45:30 2015 -0400 Fix PythonQtSignalReceiver crash during cleanup This commit fixes a crash during PythonQt::cleanup(). While destroying the PythonQtPrivate instance, any remaining PythonQtSignalReceivers that are kept alive only by their parent object will be destroyed. The crash occurs when PythonQtSignalReceiver's destructor calls back into PythonQtPrivate::removeSignalEmitter() when the PythonQtPrivate instance is mostly destroyed. Includes test case that crashes without the fix. // ------------------------- // ------------------------- commit ea653d2cfc5be6dc846a5a54f75543af7dfd4445 Author: Nicole Aucoin <nicole@bwh.harvard.edu> Date: Mon Aug 3 18:51:07 2015 -0400 ENH: add ability to delete individual series, studies, patients Add to the browser Remove button the information that it will delete all selected series, studies, patients. Add support for right click custom context menus in the patient, study, series tables. Translate the local points to global ones in terms of the table view and signal right clicked with the global position so that the browser can position the context menu appropriately. Add the context menu to the DICOM browser to allow deleting at just one level, with number of items selected information, and a confirmation message box with descriptive information that can be set to not be shown again. Added a test for the DICOM browser, with the ability to open it in interactive mode to test the right clicks. Add query wrappers for the DICOM database to get the patient name as well as descriptions for series and study. They will return empty strings on failure. Use the new queries to give more meaningful information on the right click pop up menu in the DICOM browser. Added a test for the new DICOM database accessors. Slicer bug: http://www.na-mic.org/Bug/view.php?id=3792 When Slicer makes a custom DICOM browser, it moves the table views directly into the new window, extracting them from the DICOM table. With this change, the table view takes care of mapping the point to global, the table manager propagates the signal as a table specific XRightClicked signal, and the browser responds to it with a table specific context menu. Slicer Issue 0003792 // ------------------------- From: Max Smolens <max.smolens@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24554 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/External_CTK.cmake | Diff File | ||
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master bd557aa8 2015-09-15 19:01:13 Details Diff |
STYLE: Facilitate integration with python IDE This commit introduces slicer/kits.py and rename slicer/__init__.py.in to slicer/__init__,py. This will facilitate integration with IDE like PyCharm when simply adding the "Slicer/Base/Python" folder as dependent project for scripted module. Ideally, on platform supporting it, python script shouldn't be copied into the build directory. Instead they should be symlinked similarly to what is done with the option "develop" of setup.py or the option "--editable" of pip. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24553 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Base/Python/CMakeLists.txt | Diff File | ||
| add - Base/Python/slicer/kits.py.in | Diff File | ||
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master 673e8327 2015-09-15 18:44:42 Details Diff |
STYLE: DataProbe: Refactor adding functions to generate text descriptions This commits adds the functions to facilitate the customization of the text displayed in the data probe in extension. Function added are: * generateViewDescription(self, xyz, ras, sliceNode, sliceLogic) * generateLayerName(self, slicerLayerLogic) * generateIJKPixelDescription(self, ijk, slicerLayerLogic) * generateIJKPixelValueDescription(self, ijk, slicerLayerLogic) Co-authored-by: Davide Punzo <punzodavide@hotmail.it> From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24552 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Scripted/DataProbe/DataProbe.py | Diff File | ||
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master ff9efe95 2015-09-15 18:44:40 Details Diff |
STYLE: DataProbe: Rename function to indicate it is "private" From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24551 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Scripted/DataProbe/DataProbe.py | Diff File | ||
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master e27a10ae 2015-09-15 18:44:38 Details Diff |
STYLE: DataProbe: Simplify constructor This commit removes unneeded test for widget "type". Initially introduced in r18030 (ENH: remove ThreeDViews and SlicesControllerToolbar) on Sept 12th 2011. From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24550 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Scripted/DataProbe/DataProbe.py | Diff File | ||
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master 1595806a 2015-09-15 18:44:36 Details Diff |
STYLE: DataProbe: Remove redundant code This commit removes redundant call to "onShowImage(False)" from "addView()". It is already done in function "createSmall()" called by in the constructor of DataProbeInfoWidget itself instantiated in "addView()" function mentioned above. From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24549 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Scripted/DataProbe/DataProbe.py | Diff File | ||
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master 6e2c9593 2015-09-15 18:44:34 Details Diff |
STYLE: DataProbe: Refactor code introducing "_createMagnifiedPixmap()" From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24548 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Scripted/DataProbe/DataProbe.py | Diff File | ||
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master 27de5a06 2015-09-15 18:44:32 Details Diff |
STYLE: DataProbe: Remove unused code setting 'currentLayoutName' ivar This commit removes code initially introduced in r22253 (BUG: 0003262 update data probe on non-mouse-move events) that later became obsolete with r23387 (ENH: Added mouse cursor position to vtkMRMLCrosshairNode.) From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24547 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Scripted/DataProbe/DataProbe.py | Diff File | ||
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master 4f2e9dc4 2015-09-15 18:40:18 Details Diff |
BUG: Finalize transition to ITK MGH IO fixing mgh test. See 0003410 Fix failing test py_nomainwindow_test_slicer_mgh. This commit fixes a regression introduced by r24539 (ENH: Convert to using ITK version of MGHIO ) by explicitly adding MGHIO to list of IO modules that should be loaded by ITKFactoryRegistration library. Thanks: Bradley Lowekamp <blowekamp@mail.nih.gov> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24546 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/ITKFactoryRegistration/CMakeLists.txt | Diff File | ||
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master d5b9cece 2015-09-14 18:16:20 Details Diff |
STYLE: UnitsLogic: Improve AddUnitNodeToScene doxygen From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24545 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Units/Logic/vtkSlicerUnitsLogic.h | Diff File | ||
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master 0beb6ddb 2015-09-14 18:16:19 Details Diff |
ENH: Extend Units logic API adding "GetDisplayCoefficient()" Executing the following python snippet before and after integrating this commit confirmed that value associated with "length" units are converted to suitable values for display. 8<---8<---8<---8<---8<---8<---8<---8<---8<---8<--- import math l = slicer.modules.units.logic() s = l.GetUnitsScene() units = ['Meter', 'Centimeter', 'Millimeter', 'Micrometer', 'Nanometer'] print("X mm -> %s", units) for v in range(-5, 5): value_in_mm = math.pow(10, v) converted_values = [] for unit in units: n = s.GetNodesByName(unit).GetItemAsObject(0) n.SetPrecision(6) converted_values.append(n.GetDisplayStringFromValue(value_in_mm)) print("10^%d mm -> %s" % (v, converted_values)) 8<---8<---8<---8<---8<---8<---8<---8<---8<---8<--- Output before and after: 10^-5 mm -> [' 0.000000 m', ' 0.000001 cm', ' 0.000010 mm', ' 0.010000 \xb5m', ' 10.000000 nm'] 10^-4 mm -> [' 0.000000 m', ' 0.000010 cm', ' 0.000100 mm', ' 0.100000 \xb5m', ' 100.000000 nm'] 10^-3 mm -> [' 0.000001 m', ' 0.000100 cm', ' 0.001000 mm', ' 1.000000 \xb5m', ' 1000.000000 nm'] 10^-2 mm -> [' 0.000010 m', ' 0.001000 cm', ' 0.010000 mm', ' 10.000000 \xb5m', ' 10000.000000 nm'] 10^-1 mm -> [' 0.000100 m', ' 0.010000 cm', ' 0.100000 mm', ' 100.000000 \xb5m', ' 100000.000000 nm'] 10^0 mm -> [' 0.001000 m', ' 0.100000 cm', ' 1.000000 mm', ' 1000.000000 \xb5m', ' 1000000.000000 nm'] 10^1 mm -> [' 0.010000 m', ' 1.000000 cm', ' 10.000000 mm', ' 10000.000000 \xb5m', ' 10000000.000000 nm'] 10^2 mm -> [' 0.100000 m', ' 10.000000 cm', ' 100.000000 mm', ' 100000.000000 \xb5m', ' 100000000.000000 nm'] 10^3 mm -> [' 1.000000 m', ' 100.000000 cm', ' 1000.000000 mm', ' 1000000.000000 \xb5m', ' 1000000000.000000 nm'] 10^4 mm -> [' 10.000000 m', ' 1000.000000 cm', ' 10000.000000 mm', ' 10000000.000000 \xb5m', ' 10000000000.000000 nm'] From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24544 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Units/Logic/vtkSlicerUnitsLogic.cxx | Diff File | ||
| mod - Modules/Loadable/Units/Logic/vtkSlicerUnitsLogic.h | Diff File | ||
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master 8f1a365a 2015-09-14 18:16:17 Details Diff |
ENH: Extend Units logic API adding "GetSIPrefixCoefficient()" From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24543 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Units/Logic/vtkSlicerUnitsLogic.cxx | Diff File | ||
| mod - Modules/Loadable/Units/Logic/vtkSlicerUnitsLogic.h | Diff File | ||
| mod - Modules/Loadable/Units/Testing/Cxx/vtkSlicerUnitsLogicTest1.cxx | Diff File | ||
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master 8903ca4f 2015-09-14 18:16:15 Details Diff |
STYLE: Fix doxygen in vtkSlicerUnitsLogic From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24542 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Units/Logic/vtkSlicerUnitsLogic.h | Diff File | ||
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master d9f522cc 2015-09-14 18:16:13 Details Diff |
BUG: MRMLUnitNode: Ensure value to string conversion account for precision Fixes 0004044 By calling "strstream.setf(ios::fixed,ios::floatfield)", it guarantees that the returned string will have a number of decimals equal to the precision (instead of a number of digit equal to precision). This prevents the cut of decimals when we have big numbers. Running the following python snippet in the python interactor before and after integrating this commit illustrates the problem and confirm it is fixed. 8<---8<---8<---8<---8<---8<---8<---8<---8<---8<--- import math l = slicer.modules.units.logic() s = l.GetUnitsScene() n = s.GetNodesByName("Metre per second").GetItemAsObject(0) n.SetPrecision(3) for v in range(-5, 5): print("10^%d -> %s" % (v, n.GetDisplayStringFromValue(math.pow(10, v)))) 8<---8<---8<---8<---8<---8<---8<---8<---8<---8<--- Before the change: 10^-5 -> 1e-05 m/s 10^-4 -> 0.0001 m/s 10^-3 -> 0.001 m/s 10^-2 -> 0.01 m/s 10^-1 -> 0.1 m/s 10^0 -> 1 m/s 10^1 -> 10 m/s 10^2 -> 100 m/s 10^3 -> 1e+03 m/s 10^4 -> 1e+04 m/s After the change: 10^-5 -> 0.000 m/s 10^-4 -> 0.000 m/s 10^-3 -> 0.001 m/s 10^-2 -> 0.010 m/s 10^-1 -> 0.100 m/s 10^0 -> 1.000 m/s 10^1 -> 10.000 m/s 10^2 -> 100.000 m/s 10^3 -> 1000.000 m/s 10^4 -> 10000.000 m/s Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> From: Davide Punzo <punzodavide@hotmail.it> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24541 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/vtkMRMLUnitNode.cxx | Diff File | ||
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master f1201a58 2015-09-14 17:58:53 Details Diff |
ENH: Update BRAINSTools to version 4.5.0 Version 4.5.0 is a bug fix for DWIConvert to facilitate generating multi-shell data from Siemens scanners where the --useBMatrix override flag was used (i.e. VB13 data). From: Hans Johnson <hans-johnson@uiowa.edu> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24540 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master d1a2328d 2015-09-14 17:04:20 Details Diff |
ENH: Convert to using ITK version of MGHIO The ITK supplied version of MGHIO is a derivative work that originated in Slicer. The ITK version has more widespread use in non-slicer envirnments and can be used and maintained by a larger community. From: Hans Johnson <hans-johnson@uiowa.edu> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24539 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/CMakeLists.txt | Diff File | ||
| rm - Libs/MGHImageIO/CMakeLists.txt | Diff File | ||
| rm - Libs/MGHImageIO/itkMGHIOPlugin.cxx | Diff File | ||
| rm - Libs/MGHImageIO/itkMGHIOPlugin.h | Diff File | ||
| rm - Libs/MGHImageIO/itkMGHIOWin32Header.h | Diff File | ||
| rm - Libs/MGHImageIO/itkMGHImageIO.cxx | Diff File | ||
| rm - Libs/MGHImageIO/itkMGHImageIO.h | Diff File | ||
| rm - Libs/MGHImageIO/itkMGHImageIOConfigure.h.in | Diff File | ||
| rm - Libs/MGHImageIO/itkMGHImageIOFactory.cxx | Diff File | ||
| rm - Libs/MGHImageIO/itkMGHImageIOFactory.h | Diff File | ||
| mod - SuperBuild/External_ITKv4.cmake | Diff File | ||
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master 45d353d7 2015-09-14 16:50:08 Details Diff |
ENH: Update CTK to include PythonQt cleanup fixes Fixes crash on exit in py_nomainwindow_DCMTKPrivateDictTest. // ------------------------------------------- commit commontk/CTK@ffc7f7a9 Author: Max Smolens <max.smolens@kitware.com> Date: Fri Sep 11 16:52:23 2015 -0400 ctkAbstractPythonManager: revert change to clean up PythonQt before finalizing the Python interpreter This commit reverts commontk/CTK@77a24f2 The original change worked in conjunction with fixes in PythonQt to avoid various crashes while destroying the ctkAbstractPythonManager, for example by calling Py_DECREF after the Python interpreter was finalized. Further testing shows that a better fix is indeed to finalize first to ensure clean destruction of PythonQt objects, and to make PythonQt's clean up step more robust by handling a finalized interpreter. An example of code which necessitates this change is creating an instance of class Foo: class Foo(object): def __init__(self): self.timer = qt.QTimer() def __del__(self): self.timer.setSingleShot(True) During Py_Finalize(), the Foo instance's __del__ method is called, which in turn calls a method on a Qt object. For this to succeed, PythonQt's data must still be in place. // ------------------------------------------- From: Max Smolens <max.smolens@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24538 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/External_CTK.cmake | Diff File | ||
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master 042c3080 2015-09-14 13:23:55 Details Diff |
ENH: Display module name in qSlicerCLIProgressBar This commit allows to display the name of the CLI module node in the top left corner of the progressbar. This new feature follows the same implementation than for the status visibility and the progressbar visibility. By default the CLI Module node name is always hidden. Rational : When creating a python module running a pipeline of CLI modules, we usually link our main progressbar to the current CLI node. This practice helps following the progress of one module, but was lacking information regarding our progress in the whole pipeline. Displaying the name of the CLI module node above the progressbar allows for more explicit information. From: Alexis Girault <alexis.girault@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24537 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Base/QTCLI/qSlicerCLIProgressBar.cxx | Diff File | ||
| mod - Base/QTCLI/qSlicerCLIProgressBar.h | Diff File | ||
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master 7eefd19f 2015-09-12 23:42:59 Details Diff |
BUG: UnitLogic: Fix display coefficient associated with "velocity" unit. This commit fixes a regression introduced in r24413 (ENH: Adding extra units support (frequency, velocity and intensity) ) From: Davide Punzo <punzodavide@hotmail.it> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24536 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Units/Logic/vtkSlicerUnitsLogic.cxx | Diff File | ||
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master d73197ff 2015-09-12 23:42:57 Details Diff |
BUG: MRMLUnitWidget: Connect correct signal This commit fixes an issue introduced in r22190 (ENH: Improve qMRMLUnitWidget interface). From: Davide Punzo <punzodavide@hotmail.it> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24535 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Units/Widgets/qMRMLUnitWidget.cxx | Diff File | ||
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master e1cfc9dc 2015-09-12 23:42:54 Details Diff |
STYLE: Fix doxygen in vtkMRMLUnitNode.h From: Davide Punzo <punzodavide@hotmail.it> git-svn-id: http://svn.slicer.org/Slicer4/trunk@24534 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/vtkMRMLUnitNode.h | Diff File | ||
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master fa09fe40 2015-09-12 23:19:13 Details Diff |
ENH: Added method to convert any transform to a grid transform Useful for creating transforms that are compatible with software that cannot use inverse transforms or can only use grid transforms. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24533 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Base/Logic/vtkSlicerTransformLogic.cxx | Diff File | ||
| mod - Base/Logic/vtkSlicerTransformLogic.h | Diff File | ||
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master f41f3fac 2015-09-12 22:46:00 Details Diff |
COMP: Fix module library build macros to consider already set variables This commit fixes the build of SlicerRt extensions. It basically removes the hack introduced in r24530 (COMP: Set loadable module _INCLUDE_DIRS variables in Slicer project) and fixes the build of extensions already setting the <ProjectName>_INLCUDE_DIRS variable in their Qt and VTK module library CMakeLists.txt. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24532 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - CMake/SlicerMacroBuildModuleQtLibrary.cmake | Diff File | ||
| mod - CMake/SlicerMacroBuildModuleVTKLibrary.cmake | Diff File | ||
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master 4e00f0d0 2015-09-12 22:45:58 Details Diff |
COMP: Facilitate build of few more CLIs as external module This commit will facilitate the building of DiffusionWeightedVolumeMasking and ExecutionModelTour CLIs as external module. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24531 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/CLI/DiffusionWeightedVolumeMasking/CMakeLists.txt | Diff File | ||
| mod - Modules/CLI/ExecutionModelTour/CMakeLists.txt | Diff File | ||
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master 00ff318f 2015-09-10 02:22:23 Details Diff |
COMP: Set loadable module _INCLUDE_DIRS variables in Slicer project This commit fixes a regression introduced in previous commit by ensuring vtkSlicerTractographyDisplayModuleMRML_INCLUDE_DIRS variable is also defined in the Slicer project itself. Before this commit similar variables were only defined after including SlicerConfig.cmake (by calling "find_package(Slicer)"). Note that since SubjectHierarchy Logic and MRML libraries are setting the _INCLUDE_DIRS to a specific values, an exception is adding to the SlicerMacroBuildModuleVTKLibrary macro. Alternatively, missing include directories could have been added to each SH plugin but the same update would have to be done for extension building SH plugin. git-svn-id: http://svn.slicer.org/Slicer4/trunk@24530 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - CMake/SlicerGenerateSlicerConfig.cmake | Diff File | ||
| mod - CMake/SlicerMacroBuildModuleQtLibrary.cmake | Diff File | ||
| mod - CMake/SlicerMacroBuildModuleVTKLibrary.cmake | Diff File | ||
| mod - Modules/Loadable/Markups/SubjectHierarchyPlugins/CMakeLists.txt | Diff File | ||
| mod - Modules/Loadable/Models/SubjectHierarchyPlugins/CMakeLists.txt | Diff File | ||
| mod - Modules/Loadable/SceneViews/SubjectHierarchyPlugins/CMakeLists.txt | Diff File | ||
| mod - Modules/Loadable/SubjectHierarchy/Widgets/CMakeLists.txt | Diff File | ||
| mod - Modules/Loadable/Transforms/SubjectHierarchyPlugins/CMakeLists.txt | Diff File | ||
| mod - Modules/Loadable/Volumes/SubjectHierarchyPlugins/CMakeLists.txt | Diff File | ||
| mod - Modules/Scripted/DICOMLib/Logic/CMakeLists.txt | Diff File | ||
| mod - Modules/Scripted/DICOMLib/SubjectHierarchyPlugins/CMakeLists.txt | Diff File | ||
| mod - Modules/Scripted/DICOMLib/Widgets/CMakeLists.txt | Diff File | ||
