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master 003e3c2d

2014-09-20 02:37:40

jcfr

Details Diff 		COMP: Fix vtkITK windows build error when ITK_USE_64BITS_IDS is ON. See 0003825

Thanks to "Gib Bogle <g.bogle@auckland.ac.nz>" for reporting the issue and
testing the patch.

The build error fixed by this commit was:

32> vtkITKTimeSeriesDatabase.cxx
32>c:\slicer\libs\vtkitk\itkTimeSeriesDatabase.txx(34): error C2782: 'T itk::TSD_MAX(T,T)' : template parameter 'T' is ambiguous [C:\s\b\Slicer-build\Libs\vtkITK\vtkITK.vcxproj]
32> c:\slicer\libs\vtkitk\itkTimeSeriesDatabase.txx(19) : see declaration of 'itk::TSD_MAX'
32> could be 'itk::Size<VDimension>::SizeValueType'
32> with
32> [
32> VDimension=3
32> ]
32> or 'itk::IndexValueType'
32> c:\slicer\libs\vtkitk\itkTimeSeriesDatabase.txx(27) : while compiling class template member function 'bool itk::TimeSeriesDatabase<TPixel>::CalculateIntersection(itk::Size<VDimension>,itk::ImageRegion<VImageDimension>,itk::ImageRegion<VImageDimension> &,itk::ImageRegion<VImageDimension> &)'
32> with
32> [
32> TPixel=vtkITKTimeSeriesDatabase::OutputImagePixelType,
32> VDimension=3,
32> VImageDimension=3
32> ]
32> c:\slicer\libs\vtkitk\itkTimeSeriesDatabase.txx(344) : while compiling class template member function 'void itk::TimeSeriesDatabase<TPixel>::CreateFromFileArchetype(const char *,const char *)'
32> with
32> [
32> TPixel=vtkITKTimeSeriesDatabase::OutputImagePixelType
32> ]
32> c:\slicer\libs\vtkitk\vtkITKTimeSeriesDatabase.h(89) : see reference to class template instantiation 'itk::TimeSeriesDatabase<TPixel>' being compiled
32> with
32> [
32> TPixel=vtkITKTimeSeriesDatabase::OutputImagePixelType
32> ]
32>c:\slicer\libs\vtkitk\itkTimeSeriesDatabase.txx(41): error C2782: 'T itk::TSD_MIN(T,T)' : template parameter 'T' is ambiguous [C:\s\b\Slicer-build\Libs\vtkITK\vtkITK.vcxproj]
32> c:\slicer\libs\vtkitk\itkTimeSeriesDatabase.txx(18) : see declaration of 'itk::TSD_MIN'
32> could be 'itk::Size<VDimension>::SizeValueType'
32> with
32> [
32> VDimension=3
32> ]
32> or 'itk::IndexValueType'
32> Done Building Project "C:\s\b\Slicer-build\Libs\vtkITK\vtkITK.vcxproj" (default targets) -- FAILED.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23717 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkITK/itkTimeSeriesDatabase.txx Diff File

master 4fca425f

2014-09-20 01:17:14

jcfr

Details Diff 		BUG: Update ITKv4 - Fix GDCMImageIO and TIFFImageIO

The fix related to TIFFImageIO (InsightSoftwareConsortium/ITK@6791b4a3)
should help when building Slicer with option ITK_USE_64BITS_IDS enabled.

// -----------
$ git shortlog c768e9b..056d97b --no-merges
Arnaud Gelas (1):
BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false

Bradley Lowekamp (1):
BUG: Fix overflows computing size of read tiff image

Matthew McCormick (1):
BUG: gdcm::StringFilter recognizes backslash delimiter.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23716 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_ITKv4.cmake Diff File

master 82ba4b60

2014-09-19 22:52:48

jcfr

Details Diff 		COMP: N4ITKBiasFieldCorrection - Fix compilation error with ITK_USE_64BITS_IDS

Similar to the change to vtkITK applied in previous commit (r23714), this
commit fixes the build error happening on windows when building
the CLI module N4ITKBiasFieldCorrection with the option ITK_USE_64BITS_IDS
enabled.

From: Gib Bogle <g.bogle@auckland.ac.nz>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23715 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/CLI/N4ITKBiasFieldCorrection/N4ITKBiasFieldCorrection.cxx Diff File

master 4a1fbc8c

2014-09-19 21:57:00

jcfr

Details Diff 		COMP: Fix compilation errors with ITK_USE_64BITS_IDS

Enabling this cmake configuration flag for ITK changes the size types
used in ITK from ulong to ulong long on windows. This patch addresses
compilation errors which resulted from this change. The
itk::SizeValueType is preferred type, or a referenced typedef from the
related ITK class being used.

For reference, see :
http://slicer-devel.65872.n3.nabble.com/Building-Slicer-with-ITK-USE-64BIT-IDS-tt4032499.html
http://slicer-devel.65872.n3.nabble.com/BigTIFF-tt4032353.html

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23714 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkITK/itkTimeSeriesDatabase.txx Diff File
mod - Libs/vtkITK/vtkITKArchetypeImageSeriesScalarReader.cxx Diff File
mod - Libs/vtkITK/vtkITKArchetypeImageSeriesVectorReaderFile.cxx Diff File
mod - Libs/vtkITK/vtkITKArchetypeImageSeriesVectorReaderSeries.cxx Diff File
mod - Libs/vtkITK/vtkITKTimeSeriesDatabase.cxx Diff File

master fe93d806

2014-09-19 14:22:36

jcfr

Details Diff 		ENH: DICOM2FullBrainTractography now supports setting a new scene.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23713 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/full_tractography_workflow.py Diff File
mod - Modules/Scripted/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/workflow_support.py Diff File

master 5e7ec80d

2014-09-19 14:22:33

jcfr

Details Diff 		BUG: Reference parent when creating DICOM2FullBrainTractography workflow

Prior to this commit, the layout was incorrectly used as a the parent
widget. This was working because the function "QLayout::layout()" return
the layout that would be otherwise returned by "parent.layout().

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23712 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOM2FullBrainTractography/DICOM2FullBrainTractography.py Diff File

master d25d8370

2014-09-19 14:22:31

jcfr

Details Diff 		BUG: Fix memory leak in SlicerDICOM2FullBrainTractographyModuleGenericTest

This commit sets the parent for the workflow. Doing so will ensure the
workflow and its children will be deleted.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23711 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/workflow_support.py Diff File

master 507315e3

2014-09-18 22:25:53

jcfr

Details Diff 		COMP: Fix windows numpy build error.

This commit is an attempt to fix the following error:

File "numpy\core\setup_common.py", line 247, in long_double_representation
24> raise ValueError("Could not lock sequences (%s)" % saw)
24>ValueError: Could not lock sequences (None)

To explain the changes, the content of the file "SLICER_README.txt"
now bundled in the archive is reported below:

// ------------
This archive has originally been downloaded from sourceforge.

URL http://sourceforge.net/projects/numpy/files/NumPy/1.4.1/
MD5: 5c7b5349dc3161763f7f366ceb96516b


The patches located in the "patches" subdirectory have all been
applied and are descibed below:

0001-BLD-fix-build-error-on-Windows-with-MSVC9.-Thanks-to.patch

Generated using: git format-patch c17738a..4872cac

Applied using: Did NOT apply cleanly. File numpy/core/setup_common.py
manually updated.

The issue addressed by this patch has been reported on
the Slicer list [1] on Sept 18th 2014 and has also been
discussed on the numpy list [2] on July 10th 2011.

The error message was:

File "numpy\core\setup_common.py", line 247, in long_double_representation
24> raise ValueError("Could not lock sequences (%s)" % saw)
24>ValueError: Could not lock sequences (None)

[1] http://slicer-devel.65872.n3.nabble.com/Numpy-build-error-on-trunk-tt4032488.html
[2] http://mail.scipy.org/pipermail/numpy-discussion/2011-July/057614.html
// ------------

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23710 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_NUMPY.cmake Diff File

master 7e9694e9

2014-09-18 18:15:06

jcfr

Details Diff 		ENH: Update ITKv4 project to integrate BSpline registration improvements.

Thanks to "Andras Lasso <lasso@queensu.ca>" for testing.

From Andras:

"I’ve done some tests and it seems that with the new ITK version
computation time of BSpline registration is significantly decreased
(by a factor of about 1.5-2x), while the computed transforms look
the same.

[...]

MR brain tumor, rigid, 0.01
Nightly: 9 sec
ITK-c768e9b: 8 sec

MR brain tumor, rigid+bspline, 0.01
Nightly: 106 sec
ITK-c768e9b: 49 sec

Dental surgery CBCT, rigid, 0.002
Nightly: 14 sec
ITK-c768e9b: 15 sec

Dental surgery CBCT, rigid, 0.01
Nightly: 66 sec
ITK-c768e9b: 57 sec

Dental surgery CBCT, rigid+bspline, 0.002
Nightly: 76 sec
ITK-c768e9b: 55 sec

Dental surgery CBCT, rigid+bspline, 0.01
Nightly: 1200+ sec (could not wait for it to finish)
ITK-c768e9b: 623 sec
"

// ----------
$ git shortlog 7c3a15eb..c768e9b87c --no-merges
Arnaud Gelas (2):
BUG: fix gdcm version in GDCMImageIO.
COMP: missing cast when calling gdcm::DataElement::SetByteValue

Girish Mallya (1):
BUG: Tests added for BinaryImageToLabelMapFilter for single-row images.

Hans Johnson (9):
PERF: Revert Remove large foot print of PDF derivatives.
STYLE: Test against almost equal for floating point values
STYLE: Non-exact floating point testing
PERF: Distribute initialization per thread buffers
ENH: Remove unnecessary mutable qualifier.
STYLE: Remove comment with no meaning.
ENH: Moved accumlator logic to main MI class
ENH: Allow staggering of accumulations per thread.
PERF: Zero reset thread buffers during finalize

Matthew McCormick (6):
STYLE: Improve style in BinaryImageToLabelMapFilter.
BUG: Fix BinaryImageToLabelMapFilter on 1D image.
ENH: Improve precision of the joint PDF sum
BUG: Fix BinShrinkImageFilter for different input/output image types.
COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
COMP: Add missing wrapping for TransformIOBaseTemplate.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23709 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_ITKv4.cmake Diff File

master 145cec4d

2014-09-18 18:15:05

jcfr

Details Diff 		STYLE: Fix comment in SlicerApp/CMakeLists.txt

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23708 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/CMakeLists.txt Diff File

master a2cbc2c0

2014-09-18 18:15:03

jcfr

Details Diff 		STYLE: Fix typo "protocol" instead of "protocole"

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23707 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Extensions/Testing/SuperBuildExtensionTemplate/SuperBuild.cmake Diff File
mod - SuperBuild.cmake Diff File
mod - Utilities/Templates/Extensions/SuperBuild/SuperBuild.cmake Diff File

master c5829c95

2014-09-18 18:15:01

jcfr

Details Diff 		STYLE: Fix typo "nonexistent" instead of "non-existing "

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23706 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/ExternalProjectAddSource.cmake Diff File
mod - CMake/SlicerCPackBundleFixup.cmake.in Diff File
mod - CMake/SlicerMacroBuildScriptedModule.cmake Diff File
mod - Extensions/Testing/SuperBuildExtensionTemplate/SuperBuild/External_Foo.cmake Diff File
mod - SuperBuild/External_CTKAPPLAUNCHER.cmake Diff File
mod - SuperBuild/External_CTKResEdit.cmake Diff File
mod - SuperBuild/External_DCMTK.cmake Diff File
mod - SuperBuild/External_ITKv4.cmake Diff File
mod - SuperBuild/External_OpenIGTLink.cmake Diff File
mod - SuperBuild/External_PCRE.cmake Diff File
mod - SuperBuild/External_SimpleITK.cmake Diff File
mod - SuperBuild/External_SlicerExecutionModel.cmake Diff File
mod - SuperBuild/External_Swig.cmake Diff File
mod - SuperBuild/External_VTKv5.cmake Diff File
mod - SuperBuild/External_VTKv6.cmake Diff File
mod - SuperBuild/External_qRestAPI.cmake Diff File
mod - SuperBuild/External_teem.cmake Diff File
mod - SuperBuild/External_zlib.cmake Diff File
mod - Utilities/Scripts/SlicerWizard/Utilities.py Diff File
mod - Utilities/Templates/Extensions/SuperBuild/SuperBuild/External_Foo.cmake Diff File

master 1761cb25

2014-09-18 04:51:18

jcfr

Details Diff 		BUG: Fix crash when setting null scene on Markups widget.

This commit re-organizes the code associate with function
"onActiveMarkupMRMLNodeChanged" to prevent a crash and avoid displaying
warnings when setting a null scene.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23705 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/qSlicerMarkupsModuleWidget.cxx Diff File

master 0c20d7f1

2014-09-18 04:51:16

jcfr

Details Diff 		BUG: Update EMSegment - Do not display warning when setting a null scene.

Before this commit, setting an null scene on the EMSegent widgets was
outputting the following:

335: Warning: In /path/to/EMSegment/vtkEMSegmentLogic.cxx, line 400
335: vtkEMSegmentLogic (0x4d35da0): InitializeEventListeners: no scene to listen to!
335:
335: Warning: In /path/to/EMSegment/vtkEMSegmentLogic.cxx, line 400
335: vtkEMSegmentLogic (0x4d264c0): InitializeEventListeners: no scene to listen to!

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23704 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master 9d8d091f

2014-09-18 04:51:14

jcfr

Details Diff 		STYLE: Simplify RegisterNodes implementation in Markups and Annotation logic

This commit updates the code to use smart pointer.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23703 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Annotations/Logic/vtkSlicerAnnotationModuleLogic.cxx Diff File
mod - Modules/Loadable/Markups/Logic/vtkSlicerMarkupsLogic.cxx Diff File

master cfbb44e6

2014-09-17 19:14:12

jcfr

Details Diff 		BUG: Create zip archive and move tcl binaries onto slicer.kitware.com

This should help address issue preventing binaries from being downloaded
on some version of Windows. The error reported was:

// -----------
1>------ Build started: Project: tcl, Configuration: Release x64 ------

1>Performing download step (SVN checkout) for 'tcl'

1>svn: E175002: Unable to connect to a repository at URL 'http://svn.slicer.org/Slicer3-lib-mirrors/trunk/Binaries/Windows/tcl85-x64-build'

1>svn: E175002: Unexpected HTTP status 413 'Request Entity Too Large' on '/Slicer3-lib-mirrors/trunk/Binaries/Windows/tcl85-x64-build'

1>Project : error PRJ0019: A tool returned an error code from "Performing download step (SVN checkout) for 'tcl'"

1>Build log was saved at "file://c:\build\s3d\tcl.dir\Release\BuildLog.htm"
// --------------

For more details, see http://slicer-devel.65872.n3.nabble.com/SVN-TCL-donwload-issue-tt4032460.html

Thanks to "Bradley Lowekamp <blowekamp@mail.nih.gov>" for reporting the problem.

Solution suggested by "Steve Pieper <pieper@bwh.harvard.edu>"

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23702 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_tcl.cmake Diff File

master 4925ffa8

2014-09-17 19:14:10

jcfr

Details Diff 		ENH: Relocate numpy and teem source archives onto slicer.kitware.com

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23701 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_NUMPY.cmake Diff File
mod - SuperBuild/External_teem.cmake Diff File

master e4f2656a

2014-09-17 18:28:42

jcfr

Details Diff 		ENH: Simplify vtkMRMLFiberBundleNode::Add(Line/Tube/Glyph)DisplayNode methods

This commit update the functions Add(Line/Tube/Glyph)DisplayNode methods
to return null if no scene has been set. Doing so will prevent memory leak
ensuring new node are always added to the scene.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23700 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/TractographyDisplay/MRML/vtkMRMLFiberBundleNode.cxx Diff File

master eddcd201

2014-09-17 18:28:40

jcfr

Details Diff 		ENH: Simplify vtkSeedTracts::TransformStreamlinesToRASAndAppendToPolyData

This commit updates the function to use vtkNew and simplifies the code
by removing redundant calls.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23699 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkTeem/vtkSeedTracts.cxx Diff File

master dd3a5331

2014-09-17 18:28:38

jcfr

Details Diff 		STYLE: Use vtkNew in vtkSeedTract/vtkDiffusionTensorGlyph/...

This commit simplifies code using vtkNew where it makes sense.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23698 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkTeem/vtkDiffusionTensorGlyph.cxx Diff File
mod - Libs/vtkTeem/vtkSeedTracts.cxx Diff File
mod - Modules/Loadable/TractographyDisplay/MRML/vtkMRMLFiberBundleNode.cxx Diff File
mod - Modules/Loadable/TractographyInteractiveSeeding/Logic/vtkSlicerTractographyInteractiveSeedingLogic.cxx Diff File

master 631a4103

2014-09-17 15:59:43

pieper

Details Diff 		ENH: improve dicom warning and tooltip for loadables

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23697 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOMPlugins/DICOMScalarVolumePlugin.py Diff File

master 7329f08d

2014-09-17 15:59:41

pieper

Details Diff 		BUG: 0003847 create subseries based on image orientation in DICOM

Because the image orientation patient value can include a
comma, the logic to track the distinct values in a collection
of files failed to recognize different orientation values.
This led the only available loading option in slicer being one
with a mix of orientations, leading to incorrect geometry.
This fix allows the plugin to generate independent loadables
for each orientation, thus removing the incorrect behavior.

The issue remains that the loadable with the geometry warning
is still the highest confidence loadable which could lead
to errors. Will address that independently.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23696 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOMPlugins/DICOMScalarVolumePlugin.py Diff File

master a31d8b56

2014-09-17 08:40:45

jcfr

Details Diff 		BUG: Update diffusion tensor reader to force origin/spacing. Fixes 0003845

This commit fixes a regression introduced in r23122 and forces the
origin/spacing for VTK 6 similarly to what was done for VTK 5.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23695 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkITK/vtkITKArchetypeDiffusionTensorImageReaderFile.cxx Diff File

master dc4f20d3

2014-09-17 08:40:43

jcfr

Details Diff 		BUG: Fix return value in diffusion tensor reader "RequestData()"

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23694 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkITK/vtkITKArchetypeDiffusionTensorImageReaderFile.cxx Diff File

master 00835541

2014-09-17 08:40:42

jcfr

Details Diff 		ENH: Simplify Diffusion tensor reader using FindPoint with both VTK 5 and 6

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23693 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkITK/vtkITKArchetypeDiffusionTensorImageReaderFile.cxx Diff File
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