Slicer merge requestshttps://gitlab.kitware.com/sjh26/Slicer/-/merge_requests2018-08-28T12:39:17-04:00https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/961COMP: Update CTK to fix missing include.2018-08-28T12:39:17-04:00phcerdanCOMP: Update CTK to fix missing include.$ git shortlog --no-merges 650ec821d091fe9e74d47..8cc690cc7b0399b49
Pablo Hernandez-Cerdan (1):
BUG: Fix missing include QItemSelection$ git shortlog --no-merges 650ec821d091fe9e74d47..8cc690cc7b0399b49
Pablo Hernandez-Cerdan (1):
BUG: Fix missing include QItemSelectionhttps://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/962COMP: Fix "was hidden" warning -Woverloaded-virtual2018-05-29T16:06:50-04:00phcerdanCOMP: Fix "was hidden" warning -Woverloaded-virtualUpdate() function in derived class was hiding methods from
base class: Update(foo), Update(foo, bar), etc.
This is because the way cpp lookup works, more info:
https://stackoverflow.com/questions/6727087/c-virtual-function-being-hidden
...Update() function in derived class was hiding methods from
base class: Update(foo), Update(foo, bar), etc.
This is because the way cpp lookup works, more info:
https://stackoverflow.com/questions/6727087/c-virtual-function-being-hidden
```
vtkAlgorithm.h warning: ‘virtual void vtkAlgorithm::Update(int)’ was hidden [-Woverloaded-virtual]
vtkAlgorithm.h:569:15: warning: ‘virtual int vtkAlgorithm::Update(vtkInformation*)’ was hidden [-Woverloaded-virtual]
virtual int Update(vtkInformation* requests);
^~~~~~
vtkITKImageThresholdCalculator.h:80:8: warning: by ‘virtual void vtkITKImageThresholdCalculator::Update()’ [-Woverloaded-virtual]
void Update() VTK_OVERRIDE;
^~~~~~
```https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/963BUG: Update VTK to fix volume clip bug and improve threading management2018-08-12T23:03:16-04:00Sam HorvathBUG: Update VTK to fix volume clip bug and improve threading management*Created by: jcfr*
This PR should **NOT** be integrated integrated. First, remaining issues discussed in [kitware/vtk#4338](https://gitlab.kitware.com/vtk/vtk/merge_requests/4338?commit_id=5c6bde06d788ea82e91b90bc1b95205a934f8eb7#note_4...*Created by: jcfr*
This PR should **NOT** be integrated integrated. First, remaining issues discussed in [kitware/vtk#4338](https://gitlab.kitware.com/vtk/vtk/merge_requests/4338?commit_id=5c6bde06d788ea82e91b90bc1b95205a934f8eb7#note_416096) should be addressed.
Cc: @lassoan
Highlighted list of changes
---------------------------
* https://gitlab.kitware.com/vtk/vtk/merge_requests/4338/commits (from Allison Vacanti <allison.vacanti@kitware.com>)
Fix volume clip bug and add regression test.
When clipping a volume using in-shader clipping planes, it was possible for the starting point of the ray cast to lie beyond the data volume. The raycast code is written such that the first sample is always taken before testing termination criteria, and in these cases we would always take a single sample outside of the volume, leading to artifacts.
Fixed this behavior by checking that the starting position calculated by AdjustSampleRangeForClipping is indeed
inside of the volume bounds and aborting the raycast if it is not.
The existing TestGPURayCastClipping test would have caught this, except that the vase.vti volume used for testing
has all 0's at the boundaries, so the rendering was correct even with the edge-clamp repetition outside of the volume
(the faulty samples always computed RGBA=vec4(0)). I replaced the vase.vti of this test with a wavelet with finite
boundary values that will catch this problem if there's a regression.
* https://gitlab.kitware.com/vtk/vtk/merge_requests/4175/commits (from David Gobbi)
Resolve "Multithreader creates many unnecessary threads"
Creating threads is expensive, so creating threads that do nothing should be avoided.
- Limit number of threads in vtkImageHistogram
- Remove redundant UpdateExtent calculation.
- Use vector to allocate arrays instead of new
- 17279: Limit num threads to num pieces.
Complete list of changes
------------------------
$ git shortlog 10e8cdc..9095631 --no-merges
Alessandro Genova (6):
Add a test for the axis->setPrecision(0) issue on Windows
Increase the font size of the axis label
Fix the Precision = 0 bug on MSVC compilers
Address compiler warning
Cleanup comments and unused includes
Resolve last compiler warning
Allison Vacanti (3):
Retain renderer to recompute right rendered rectangle.
Populate DataArraySelection objects for vtm files.
Fix volume clip bug and add regression test.
Andreas Buykx (2):
Fix issue #17211: crash on pick of composite data
Backport fix for issue #17211 to release.
Andrew Bauer (7):
Fixing issues with the HyperTreeGrid and improving documentation.
Hypertreegrid cleanup.
Update the HyperTreeGridSource to work in parallel.
Fixing vtkImageData::FindPoint() bug
Fixing typo in error message.
Fixing bug with unstructured grid ghost cell generator.
Fixing issue with writing structured XML field data
Aron Helser (5):
Remove MomentInvariants filter, prep to make remote
Remote Modules, add MomentInvariants, and ParallelMI
Remote: change ParallelMoments to use branch
Remote: parallel code included in single module
MomentInvariants final remote repo location and hash
Berk Geveci (2):
Introduced new composite datasets for partitioned data.
Fixed bug in the XML structured data writer.
Bill Lorensen (1):
Add NumberToString conversion class.
Brad King (10):
ParallelMomentInvariants: Exclude from all pending fixes
cmake: Set policy CMP0075 explicitly to avoid warnings
CTestCustom: Drop unused Utilities/ matches
pre-commit: Add support for ExternalData SHA512 objects
git-gitlab-push: Add support for ExternalData SHA512 objects
ExternalData: Switch from MD5 to SHA512 for new content links
ExternalData: Add URLs to fetch from Girder on data.kitware.com
ExternalData: Drop URLs using midas3.kitware.com
ExternalData: Update URLs for vtk.org to use https
ArchiveTestingDataOnGirder: Switch default to VTK collection
Carson Brownlee (2):
fixing unnecessary volume updates in ospray on updates to tf.
Fix material params with textures and add principled materials.
Cory Quammen (9):
Use slightly clearer name for variables
Stop drawing line segments outside image buffer bounds
Use vtkMath::Min/Max instead of std::min/max
Fix logic when tolerance is 0
Clamp tolerance to range [0.0, VTK_DOUBLE_MAX]
Set the field type for block selections
Change algorithm for computing selections
Rename vtkSelectionOperator to vtkSelector
Change type of InsidednessArrayName member variable
Dan Lipsa (22):
Fix SegY3D reader.
Use SegYReader for both 2D and 3D data.
Fix RequestInformation
Use X,Y coordinates instead of inline,crossline.
Use X, Y for SegY 3D.
Test changed because of switch to XY coordinate system.
Simplify computation.
Use crossline, inline, sampleCountPerTrace order to match OpendTect.
Clean up 2D reader and apply options to both readers.
Add an option to create a StructuredGrid for a 3D SegY dataset.
Update Progress.
Flip data if increment is negative.
Fix ParaView parameters and remove printouts.
Make StructuredGrid the default for 3D data.
Fix SegY warnings.
Fix uninitialized variables.
Fix warnings.
Add SEGY to StandAlong group and warning fixes.
Override and vector init warnings.
Use a standard 4 byte unsigned int instead of long.
Add cstdint include.
Fix leaks on FileName.
David E. DeMarle (12):
work around a bug where multiple threads delete image together
silently ignore objects that lack requested valuepass array
Increment version to VTK 8.1.1
fix a memory leak and vtkstyle this for member
Plug a vtk2osp leak and avoid a copy while exposing more formats.
A change to the texture has to cause a redraw.
Take advantage of zero copy textures in ospray.
Fix a huge memory leak.
dont leak the light either
don't leak ospray buffer either
use osp release not delete with osp volumes to prevent crashes
suppress and fix comp warnings
David Gobbi (11):
17265: Fix OpenGL2 vtkImageResliceMapper OOB issue
17279: Limit num threads to num pieces.
Use vector to allocate arrays instead of new
Remove redundant UpdateExtent calculation.
Limit number of threads in vtkImageHistogram
17265: Fix OpenGL2 vtkImageResliceMapper OOB issue
Fix thin border around vtkImageResliceMapper
Backport 'reslicemapper-border' to release branch.
Fix misuse of purportedly boolean Border.
Fix documentation, use K for slice index.
Fix typo in comments, xform to sform
Francois Budin (1):
Check that context exists before trying to pop context.
Joachim Pouderoux (1):
Fix destructor override warning
John Tourtellott (1):
Added GDAL reprojection filter from vtkMap
Julien Schueller (1):
Cast in vtkGetLibraryPathForSymbol macro
KWSys Upstream (2):
KWSys 2018-04-23 (aa0f06ec)
KWSys 2018-04-24 (85c211d6)
Ken Martin (26):
clean up the state API and fix Qt widget
do not use glDGetDouble on OpenGL ES
add an option for a floor to the vtkSkybox class
fix an access violation happening in StructureGridGeom filter
fix uninitialized index in DataArray.cxx
fix case where depth buffer was underflowing
fix crash when scene has scalar values
remove failihg part of test
improve the picking on the pointgaussian mapper
significantly improve performance for many blocks
fix an access violation happening in StructureGridGeom filter
add better support for using mesa when needed on windows
add support for writing larger unstructured grids
make sure we configure CTestCustom.cmake.in
fix handling of large textures
dataset mapper was not forwarding relative coincident parameters
remove old 32bit simulator for ios
add an executable to do opengl detection
fix issues with the array calc and string arrays
fixed case where the array name differed from
Remove vtkProbeOpebGLSupport executable from Mobile
comparison was being done for the wrong case
fix ios build issues
remove remaining opengl32 status methods
fix buffer overrun
cleanup and improve sphere and stick mappers in opengl
Kitware Robot (1):
ExternalData: Convert content links from MD5 to SHA512
Lucas Gandel (5):
Add WindowStereoTypeChangedEvent fired by vtkRenderWindow
Fix memory exception with checkerboard stereo
Invoke WindowResizeEvent on vtkWindow::SetSize() call
Fix viewport size before FXAA pass on OSX
Improve QVTKOpenGLWidget and add QVTKOpenGLWindow class based on QOpenGLWindow
Maik Froechtenicht (4):
Fix for vtkTriangle::TrianglesIntersect() Issue #17092
Undo copy vars for handover, format
Fix for vtkTriangle::TrianglesIntersect() Issue #17092
Fix for vtkTriangle::TrianglesIntersect() Issue #17092
Mathieu Westphal (2):
Set vtkInteractionStylePython-TestStyleRubberBandZoomPerspective to run serial
Adding new StepTime related features to LPT
Matt McCormick (1):
ArchiveTestingDataOnGirder: Add script to upload to data.kitware.com
Michael Migliore (3):
Add option in OpenFOAM reader to copy data to cell zones
Add capacity to add a point outside of the current polyline
Add tone mapping render pass
Nicolas Vuaille (3):
Introduce Molecule Append filter
Molecule to polydata conversion
Improve pointSetToMolecule : optionally convert lines into bonds
Norman Juchler (2):
Fix for QVTKRenderWindowInteractor for better support of retina displays
Style improvement for my fix in QVTKRenderWindowInteractor
Robert Maynard (1):
Update Accelerators/Vtkm to not produce any cpp check warnings
Sankhesh Jhaveri (12):
Module Geovis GDAL
Fix compile warnings for module GeovisGDAL
Volume 2D transfer function issue causing undefined variable shader errors
Fixed raster reprojection filter for celldata and GDAL 2
Include GDAL header directory for module vtkGeovisGDAL
Fix unused parameter and unused variable warnings in vtkGeovisGDAL
Add API for GDAL reader to provide projection string in PROJ.4 format
Ability to directly provide the PROJ.4 string to vtkGeoProjection
Fix crash due to unitialized pointer
Free up GDAL created memory in a GDAL safe way
Fix unused variable warnings in vtkGeovisGDAL module
Fix compiler warning in GDAL vector reader
Scott Wittenburg (1):
Keep track of threads/workers and kill them explicitly
Seacas Upstream (1):
exodusII 2018-05-07 (e4638682)
Sean McBride (1):
Added a #warning on code that I’m pretty sure is dead
Sebastien Jourdain (4):
Add ThreadedImageWriter
Improve ThreadedWriter test
Try to improve TestThreadedWriter
Remove ThreadedWriter timing failure
Shawn Waldon (23):
Add vtkFrustumSelector a selection operator for frustum selection
vtkExtractSelection2: compiles but only partly implemented
vtkExtractSelection2: selection with frustums compiles
Move selection operator to Filters/Extraction
Add test for combining extraction nodes via expression
Refactor vtkSelectionOperator to use vtkDataObject API
Change selection operator to return a boolean success value
Handle selecting points with containing cells
Add missing include
Give the selection array the expected name
Fix compile error
Update test to set association for cell selection
Fix typos
Ensure output array has correct name
Handle INVERSE property on selection nodes
Handle legacy 1-component 2 tuple threshold selection arrays
Change TestExtraction to test both old and new filters
vtkExtractSelection2: add support for extracting rows from a vtkTable
Add test of extracting rows
Fix dashboard errors and warnings
Deprecate and rename old vtkExtractSelection filter
Add API documentation
Unmark New() as legacy
Steven Hahn (2):
Use public instead of protected member functions
Use public instead of protected member functions
Sujin Philip (3):
Update VTK-m
Update to latest VTK-m master
Fix some warnings in Accelerators/Vtkm
Tim Rowley (1):
Add cell valued unstructured volume support to OSPRay mapper
Todd Martin (5):
Add custom wrap compiler directive
Fix definition name
Add macro size hints
Eliminate Windows name mangling workaround for GCCXML wrap
Remove redundant code
Utkarsh Ayachit (39):
Handle CFG files with other statements.
put code blocks to simplify debugging
Fix a shadowed var warning.
extend grammar to include '-' in file names.
updates to fix position file motions.
Ensures output has as many rows as timesteps.
Use `vtkCharArray` for mask array
Add new doubleconversion 3rd party module.
Update vtkNumberToString API to overcome build issues
use correct package name when locating sustem doubleconversion.
update thirdparty repo to point to the official fork.
avoid segfault during app exit.
Extend vtkSelection to support expressions.
add missing return
Add vtkValueSelector
use vtkValueSelector in vtkExtractSelection2 (and its test)
Add vtkLocationSelector to extract selected locations.
Update TestExtractionExpression to test vtkLocationSelector.
Update TestExtractionExpression to test threshold filter.
fixes after API changes
Misc vtkExtractSelection2 improvements
simplify `vtkExtractSelection2::GetAttributeTypeOfSelection`
exclude 3rd party warnings.
vtkNumberToString doesn't need to delete assignment operator.
add missing include.
Don't use VTK_LEGACY with out set/get macros.
vtkExtractSelection: remove unreachable code.
fix missing `std::to_string` error
fix warnings: remove testing of legacy filter
fix missing `override` warnings
warnings: fix `assignment operator could not be generated`
docs: make `Return value: New reference.` explicit.
fix warnings.
exclude ospray warnings
finally fix the implicit constructor/operator warnings.
add MSVC 2013 exclusion.
disable TestNumberToString on MSVC 2013.
add tests to read/write multiblock with partial arrays
Handle mismatch is chosen and available arrays.
Will Schroeder (6):
Fast 2D clipper for image data
Avoid reading into undefined heap; optimizing comparison on unsigned char
Input is now generalized to vtkPointSet
Removed unnecessary variables
Faster computation of point inside/outside
New regression test images
Yuri (1):
Correction to when stat64 is used: FreeBSD doesn't use stat64.
double-conversion Upstream (2):
doubleconversion 2018-03-29 (0e0b255d)
doubleconversion 2018-05-11 (f3ac1585)https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/964ENH: Improve slicer.util.exit documentation2018-06-01T17:46:22-04:00Andras LassoENH: Improve slicer.util.exit documentationFixes https://issues.slicer.org/view.php?id=4470Fixes https://issues.slicer.org/view.php?id=4470https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/965COMP: Fix bundling of extension remove obsolete OpenIGTLink external project2018-06-05T16:43:00-04:00Sam HorvathCOMP: Fix bundling of extension remove obsolete OpenIGTLink external project*Created by: jcfr*
Following r26972 (ENH: Remove support for building OpenIGTLink now
available as an extension), keeping the external project is not relevant
and was causing the bundling of SlicerOpenIGTLink extension to fail.
Reporte...*Created by: jcfr*
Following r26972 (ENH: Remove support for building OpenIGTLink now
available as an extension), keeping the external project is not relevant
and was causing the bundling of SlicerOpenIGTLink extension to fail.
Reported-by: Sam Horvath <sam.horvath@kitware.com>https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/966Multi volume rendering2018-06-11T12:18:25-04:00Csaba PinterMulti volume renderingThis PR implements real multi-volume support in Slicer, using the vtkMultiVolume actor. The actor is not fully implemented, so it has limitations, such as no shading, no cropping by ROI, no per-volume visibility. For a few of these, work...This PR implements real multi-volume support in Slicer, using the vtkMultiVolume actor. The actor is not fully implemented, so it has limitations, such as no shading, no cropping by ROI, no per-volume visibility. For a few of these, workarounds have been implemented. Hence, the options is currently marked experimental in the drop-down list.
Additionally, I refactored the volume rendering options so that many of them now are in the view node instead of the display node, and added those to Application Settings.
The PR contains four commits for easier review, and I think it makes sense to keep them separate when integrating.https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/967ENH: VectorToScalar optionally extract single components.2018-07-11T16:59:57-04:00phcerdanENH: VectorToScalar optionally extract single components.This commit improves the user interface adding support for choosing
the conversion mode.
Available conversion modes are now:
* vector (RGB, RGBA) images to luminance (default mode keeping backward
compatibility with origin...This commit improves the user interface adding support for choosing
the conversion mode.
Available conversion modes are now:
* vector (RGB, RGBA) images to luminance (default mode keeping backward
compatibility with original module implementation)
* vector images to single component (user select which component to extract)
To support reusing of components by other scripted modules, a logic
and widget have also been created:
* VectorToScalarVolumeConversionModeWidget
* VectorToScalarVolumeLogic
Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/968BUG: Load python dependent widget during module instantiation2018-06-11T11:38:03-04:00Sam HorvathBUG: Load python dependent widget during module instantiation*Created by: vovythevov*
This let python module access widget/logic or any C++ classes they may
have as soon as they are instantiated. This let users do the following:
"var = slicer.qMyClassWidget.MyEnumValue" for example.*Created by: vovythevov*
This let python module access widget/logic or any C++ classes they may
have as soon as they are instantiated. This let users do the following:
"var = slicer.qMyClassWidget.MyEnumValue" for example.https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/969Segment editor rotated slice warning2018-06-14T11:04:31-04:00Andras LassoSegment editor rotated slice warningThis pull request contains improvements to the rotate to volume plane algorithm and a warning button to indicate when editing segments on oblique slices. When the warning button is clicked, slice views are rotated to segmentation labelma...This pull request contains improvements to the rotate to volume plane algorithm and a warning button to indicate when editing segments on oblique slices. When the warning button is clicked, slice views are rotated to segmentation labelmap plane.
- Warning displayed when slice views are not aligned:
![](https://user-images.githubusercontent.com/307929/41377296-a490b056-6f29-11e8-9c18-736a17754fc9.png)
- Clicking warning button aligns slice views:
![](https://user-images.githubusercontent.com/307929/41377303-a75a95f4-6f29-11e8-8520-f2de7d84b473.png)
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/970WIP: Add Pinch and Rotate gesture interactions to 3D view2018-11-13T22:02:12-05:00SunderlandkylWIP: Add Pinch and Rotate gesture interactions to 3D viewWill not be functional until VTK forwards gesture events from QVTKOpenGLWidget using QVTKInteractorAdapter.cxx. (see merge request https://gitlab.kitware.com/vtk/vtk/merge_requests/4398/)
Example video:
https://www.dropbox.com/s/6k76...Will not be functional until VTK forwards gesture events from QVTKOpenGLWidget using QVTKInteractorAdapter.cxx. (see merge request https://gitlab.kitware.com/vtk/vtk/merge_requests/4398/)
Example video:
https://www.dropbox.com/s/6k76e17d2hvcdgy/gesture_interaction.mp4?dl=0
Cc: @lassoan https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/971ENH: Update LibArchive. Fix gcc8 warnings.2018-06-17T14:44:39-04:00phcerdanENH: Update LibArchive. Fix gcc8 warnings.The gcc8 warnings were generating build errors at Debug mode,
because the aggressive Werror flag in LibArchive.
git shortlog 98a695399e8e7420635a5448aecde8b0a82fb83a..d7dea508
Arshan Khanifar (7):
flush pending chdirs prior to pr...The gcc8 warnings were generating build errors at Debug mode,
because the aggressive Werror flag in LibArchive.
git shortlog 98a695399e8e7420635a5448aecde8b0a82fb83a..d7dea508
Arshan Khanifar (7):
flush pending chdirs prior to processing mtree files
Test case for using -C in conjunction with an @mtree format file
corrected licensing, removed unnecessary variables
build fail fix, simplified logic
absolute path fix
alphabetical order
put the absolute path in quotes in case user's directory has spaces in it
BenjaminTrapani (9):
Fix bsdtar test compilation on windows with platform toolset 141
Fix missing hardlink source test windows
Fix version format to match unit test
Copy reference resource to binary directory to make it possible to debug tests via visual studio cmake
Add space after version to fix all unit tests besides sparse tests
Fix sparse tests windows
Revert "Copy reference resource to binary directory to make it possible to debug"
Fix indentation to match rest of file
Fix warnings treated as errors during x64 build
Bernard Spil (1):
fix build with LibreSSL 2.7
Brad King (1):
Do not use nanosecond file time APIs on macOS < 10.13
Chris Roberts (1):
Check libgnu for xattr functions on Haiku
Colin Percival (1):
Avoid overflow when reading corrupt cpio archive
Ed Maste (1):
ensure ar strtab is null terminated
Graham Percival (1):
Spelling fixes
Joerg Sonnenberger (12):
Don't call wmemmove if size is zero.
Revert addition of assert.
Do something sensible for empty strings to make fuzzers happy.
Match full strings, not just prefixes.
Don't allow sparse mapping entry to pass beyond 63bit.
Place a limit on the mtree line length to make fuzzers happy.
Ensure that the AES extension header is large enough.
Avoid a read off-by-one error for UTF16 names in RAR archives.
Fix case in comment.
Match archive.h for la_int64_t vs int64_t
Fix archive freeing bug in bsdcat.
Check size of the extended time field in zip archives
John Starks (2):
Windows: set errno on CreateFileW failure
zip: Allow backslash as path separator
Martin Matuska (8):
Merge pull request #926 from emaste/libarchive
archive_write_ar_data(): replace strncpy() with memcpy()
bsdtar manpage: unify descriptions of compression options
Fix build on FreeBSD with NFS4 ACLs without ACL_ENTRY_INHERITED
Remove lzop package from Darwin testing
Unbreak write test for libzstd 1.3.4
Merge pull request #973 from o3dwade:master
Add some gzip header tests including RFC 1952 compression level flag
Martin Matuška (1):
Merge pull request #968 from trollixx/cmake-lz4-option
Mike Frysinger (1):
delete dead ppmd7 alloc callbacks (#893)
Oleg Shparber (2):
cmake: Add ENABLE_LZ4 option
cmake: Fix missing override for LZO2_FOUND
Omar Farooq (1):
Adding compression level support for gzip
Pablo Hernandez-Cerdan (1):
Fix gcc 8 warning about strncpy
Paul Spangler (2):
archive_write_disk_{posix,windows}.c: Don't modify attributes for existing directories when ARCHIVE_EXTRACT_NO_OVERWRITE is set
Simplify test case per PR comments
Sean Purcell (14):
Add Zstandard read support
Add Zstandard write support
Small zstd fixes
Add zstd test suite
Whitespace fixes
Fix zstd reader and change variable scopes
Fix compile errors with cmake and when zstd isn't present
Skip zstd write tests when library not present
Don't try to use libzstd versions without streaming API
Build with zstd on TravisCI on OS X
zstd: Address comments by @terrelln
zstd: Don't bid on skippable frames
Fix alphabetical order, other small fixes
Fix zstd memory allocation and null checks
Tim Kientzle (19):
Libarchive 3.3.3dev
Issue #924: fix capitalization of bcrypt.h header
Merge pull request #929 from cperciva/master
Merge pull request #930 from Tarsnap/spelling-upload
Merge pull request #934 from tonytheodore/cflags-private
Merge pull request #905 from iburinoc/zstd
Merge pull request #943 from jrmarino/master
Issue #947: Reference archive_write_set_options in archive_write.3
Merge pull request #912 from korli/libnetwork
Merge pull request #961 from zweger/master
Merge pull request #964 from legnaleurc/fix_fallthrough
Merge pull request #970 from jstarks/zip_path_separator
Merge pull request #966 from jstarks/windows_disk_read_error
Merge pull request #962 from spanglerco/existing-dir-owner
Merge pull request #986 from BenjaminTrapani/windows-fixes
Merge pull request #989 from trollixx/cmake-fix-lzo2
Merge pull request #993 from ArshanKhanifar/issue-991
Merge pull request #1005 from Sp1l/master
Merge pull request #1024 from phcerdan/fix_strncpy_warning
Tony Theodore (1):
libarchive.pc.in: add Cflags.private for static linking
Wei-Cheng Pan (1):
Fix -Werror=implicit-fallthrough= for GCC 7.
Zack Weger (1):
Clear the ZIP format name before constructing a new one, so it isn't appended to the format name of the previous entry
jrmarino (1):
Recognize ".tzst" extension as ".tar.zst"
ngie (1):
Fix a potential NULL pointer dereference of `tar` in archive_read_support_format_tar when HAVE_COPYFILE_H is defined (#959)https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/972COMP: Fix minor warnings generated with gcc82018-06-18T10:47:51-04:00phcerdanCOMP: Fix minor warnings generated with gcc8- Catch by value instead of reference.
- Multi-line comment without /* */ notation.
```
[77/796] Building CXX object Libs/MRML/Core/CM...LCore.dir/vtkMRMLSegmentationStorageNode.cxx.o
/Software/Slicer/Slicer-src/Libs/MRML/Logic/vtk...- Catch by value instead of reference.
- Multi-line comment without /* */ notation.
```
[77/796] Building CXX object Libs/MRML/Core/CM...LCore.dir/vtkMRMLSegmentationStorageNode.cxx.o
/Software/Slicer/Slicer-src/Libs/MRML/Logic/vtkMRMLSliceLogic.cxx:85:5: warning: multi-line comment [-Wcomment]
// foreground \
^
/Software/Slicer/Slicer-src/Libs/MRML/Logic/vtkMRMLSliceLogic.cxx:98:5: warning: multi-line comment [-Wcomment]
// foreground > AddSubForegroundCast \
^
/Software/Slicer/Slicer-src/Libs/MRML/Logic/vtkMRMLSliceLogic.cxx:103:5: warning: multi-line comment [-Wcomment]
// ... AddSubOutputCast > AddSubExtractRGB \
^
```https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/973ENH: Add Set/Get and XML macros for iterable STL container properties2018-06-27T09:55:51-04:00SunderlandkylENH: Add Set/Get and XML macros for iterable STL container propertiesAdds macros to Read/Write/Print/Copy iterable properties.
Example usage:
- Numeric container:
`vtkMRMLWriteXMLStdVectorMacro(property, Property, std::deque<int>);`
- String container:
`vtkMRMLWriteXMLStdStringVectorMacro(prope...Adds macros to Read/Write/Print/Copy iterable properties.
Example usage:
- Numeric container:
`vtkMRMLWriteXMLStdVectorMacro(property, Property, std::deque<int>);`
- String container:
`vtkMRMLWriteXMLStdStringVectorMacro(property, Property, std::vector);`
See also this related merge request in VTK: https://gitlab.kitware.com/vtk/vtk/merge_requests/4427
It's not required for this change, but it adds some convenience macros for setting/getting STL containers.
Also added generic Set/Get macros that work with STL containers.
Currently, STL containers cannot use the generic vtkSetMacro/vtkGetMacro types since those macros require a "<<" operator within vtkDebugMacro
https://github.com/openigtlink/SlicerOpenIGTLink/pull/36
cc: @lassoan https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/974ENH: Improvements in the Sample Data module2018-06-19T16:56:30-04:00Csaba PinterENH: Improvements in the Sample Data module- Made possible to load multiple files with multiple loaders
- Add Development category that only shows up in Developer mode
- Add one dataset in the Development category: TinyPatient, containing a 10x10x10 CT and a binary labelmap seg...- Made possible to load multiple files with multiple loaders
- Add Development category that only shows up in Developer mode
- Add one dataset in the Development category: TinyPatient, containing a 10x10x10 CT and a binary labelmap segmentation with two segments. Very useful for testing
- Stop trying to download data after five attempts (it could get into infinite loop)https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/975ENH: Add widget to specify labelmap geometry in segmentations2018-07-21T14:44:51-04:00Csaba PinterENH: Add widget to specify labelmap geometry in segmentations- Add qMRMLSegmentationGeometryWidget that allows the user to specify a volume/segmentation/model/ROI as source, and set geometry details
- For segmentation with labelmap master it is possible to set isotropic spacing and oversampling...- Add qMRMLSegmentationGeometryWidget that allows the user to specify a volume/segmentation/model/ROI as source, and set geometry details
- For segmentation with labelmap master it is possible to set isotropic spacing and oversampling factor. Spacing cannot be set manually in these cases
- For model, ROI, or segmentation with poly data master the parent transform is used for orientation, user input for spacing, and the bounding box for origin and extent
- Add qMRMLSegmentationGeometryDialog that has a geometry widget in it, and OK and Cancel buttons if editing is enabled, and an OK button otherwise. If resampling is requested, then besides setting the reference image geometry conversion parameter, the existing segments are resampled to the specified geometry
- Add button in row of master volume in Segment Editor widget that opens the geometry dialog
- Replace button in conversion parameters dialog for specifying reference image geometry. Before it was a simple dialog that allowed selecting a volume, now the new geometry dialog shows up
- Add python test for testing all kinds of scenarios for segmentation labelmap geometry calculation
- Crash fixed in vtkCalculateOversamplingFactor: when factor was very low, invalid extent was calculated and then crashed when calculating spacing based on thathttps://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/976ENH: update DCMTK2018-07-16T22:30:35-04:00Sam HorvathENH: update DCMTK*Created by: fedorov*
The updated version includes some patches that were earlier in the CTK fork, and an important bug fix that prevented output for DICOM Segmentation objects with the number of pixels in the frame not divisible by 8.
...*Created by: fedorov*
The updated version includes some patches that were earlier in the CTK fork, and an important bug fix that prevented output for DICOM Segmentation objects with the number of pixels in the frame not divisible by 8.
List of changes:
```
$ git shortlog DCMTK-3.6.3..29f9de10c
Jan Schlamelcher (13):
Updated version information for 3.6.3+ development.
Enhanced combined date time range matching.
Added a missing test for universal matching.
Minor language and coding style fixes in dcmwlm.
Fixed an issue in dcmwlm / universal matching.
Introduced a subset of std::filesystem for ofstd.
Minor fixes for previous commit.
More fixes for ofstd filesystem.
Enhanced Doxygen documentation.
Introduced support for compile time assertions.
Enhanced ofstd filesystem's unit test.
Simplified and enhanced dcmwlm's code.
Fixed C++11 incompatibility in yesterday's commit.
Joerg Riesmeier (70):
Enhanced verboseness of getDecompressedColorModel.
Fixed typos.
Added comment on missing timer start.
Added comment on unhandled attributes.
Use default timeout for first PDU to be read.
Fixed name of retired Storage SOP Class.
Removed all references to "CVS".
Updated copyright date.
Fixed issue with DSRTree<T>::swap().
Added support for TID 4019 to TID 1419.
Increased buffer size to avoid possible overflow.
Added reference to documentation of TID 4019.
Fixed double declaration of local variable.
Increased buffer size to avoid possible overflow.
Added PatientRadiationDoseSRStorage to man page.
Moved assignment operator to source file.
Added check for self-assignment.
Added constructors and assignment operator.
Fixed inaccurate name specifier of nested class.
Enhanced code examples for module "dcmsr".
Fixed partly wrong API documentation.
Minor fix to API documentation.
Fixed typos and removed trailing spaces.
Removed space character at beginning of a line.
Updated data dictionary for DICOM 2018a.
Updated mapping of Body Part Examined to codes.
Fixed classification of command line options.
Fixed reference to outdated macro name.
Removed double declaration of local variable.
Made log output more consistent.
Fixed outdated log message.
Enhanced API documentation of DcmObject::getVM().
Reverted to version before last commit.
Next try to keep SunPro Studio 12.x quiet.
Fixed wrong use of preprocessor directive #elif.
Initialize struct with ={} instead of ={0}.
Fixed typo in preprocessor directive.
Fixed typo.
Made mapping between VR name and enum more robust.
Added new method getNumberOfValues().
Made use of new method getNumberOfValues().
Updated documentation on CP-1704 (Final Text).
Made clear that an empty code is not valid.
Added tree node filter "has Concept Name".
Set observation date/time for all content items.
Fixed invalid patient's birthdate in demo data.
Report warning on missing file meta information.
Added quotation marks around "isinf/isnan(0.)".
Avoided "double typecast" in comparison operators.
Added missing comparison operators "==" and "!=".
Added support for recently approved CPs.
Updated data dictionary for DICOM 2018b.
Updated code definitions for DICOM 2018b.
Updated Context Group classes for DICOM 2018b.
Added support for Encapsulated STL Storage SOP.
Fixed possible "use after scope" issue.
Fixed typos, tab characters, trailing spaces, etc.
Removed addOption() flag AF_NoWarning.
Fixed possible issue with scaled overlays.
Introduced header file for common exit codes.
Fixed wrong reference to "dcmsend" tool.
Fixed "unused result warning" on fwrite() calls.
Fixed bug introduced with last commit.
Adapted code for recent API change (DEBUG mode).
Fixed issue with undefined CMAKE_SYSTEM_VERSION.
Fixed typos in API documentation of new classes.
Fixed typos in comments.
Added support for recently approved CPs.
CP-1765 retired DICOMDIR reference to CDA/XML.
Fixed issue with incorrect rendering of overlays.
Marco Eichelberg (61):
Fixed heap buffer overflow in dcmpschk.
Changed OFSockAddr::size() return type to socklen_t.
Fixed MSVC x64 type conversion warning.
Fixed MSVC x64 type conversion warning.
Fixed undefined behavior warning on 32-bit platforms.
DcmTagKey comparison operators now return OFBool.
Added line feed at EOF to fix Sun C++ warning.
Fixed use of operator delete[], reported by clang.
Include <sys/timeb.h> only if really needed.
Fixed minor warnings reported by SunPro Studio
Fixed heap buffer overflow in dcmpstat module.
Minor changes to fix warnings on MacOS.
Fixed include path for OpenSSL
Fixed two bugs in DNS lookup code.
Fixed heap overflow issue caused by invalid datasets.
Fixed minor warning on MacOS
Regenerated vrscan code with flex-2.6.4.
Fixed warning introduced by flex-2.6.4 on Win32.
Fixed compile error on current version of MinGW.
Fixed compile error on current version of MinGW.
Use readdir() instead of readdir_r() if safe.
Removed default clause in DcmItem::newDicomElement().
Permit external access to byte offsets in DICOM file.
Added OpenSSL version check to configure/CMake.
Updated OpenSSL version test to 1.0.2 as minimum.
Reverted to OpenSSL version test to 1.0.1 as minimum.
Link OpenSSL against libdl if available.
Fixed OpenSSL version test on Windows.
Another fix for the OpenSSL version test on Windows.
Major revision of TLS code implementing Suppl. 204.
Enabled NULL ciphers on OpenSSL 1.1.0 and newer.
Fixed description regarding OpenSSL 1.1.0 and newer.
Fixed read mode for certificate files to binary.
Added Perl script that generates test files.
Added Perl script with dcmtls test suite.
Minor cleanup in echoscu.
Implemented cryptographically secure ISAAC PRNG.
Modified code to use OFRandom instead of srand/rand.
Completed conversion to OFRandom.
Replaced strcpy by OFStandard::strlcpy.
Added DLL export symbols.
Replaced strcat by OFStandard::strlcat.
Added export declaration for deny_/allow_severity.
Changes for OpenSSL without ECDH support.
Replaced strcpy by OFStandard::strlcpy.
Replaced strcpy by OFStandard::strlcpy.
Fixed minor bug introduced with last commit.
Moved declaration of global variables for libwrap.
Added logger to module dcmsign.
Changed DVPSIPCMessage::resizePayload parameter type.
Undefine isinf() macro if defined.
Fixed minor warnings.
Added missing include statement.
Fixed missing end of comment.
Fixed incorrect strlcpy buffer size.
Added OFStandard::snprintf() and vsnprintf().
Changes to permit compilation with LibreSSL.
Fixed gcc 8 warning.
Fixed typo in comment.
Introduced upper size limit for A-ASSOCIATE PDUs.
Improved poll() code in module dcmnet.
Michael Onken (33):
Fix cmake error on Linux with DCMTK_ENABLE_CXX11.
Ensure isnan/isinf macro is only defined once.
Renamed VM variables for clarity.
Fixed integer overflow in pixel buffer allocation.
Print error details if conversion fails.
Fixed uninitialized variable.
Updated importHierarchy() method API.
Again, fix API for importHierarchy() (see c8fdfb).
Fixed C++11 template specialization.
Added virtual destructors to potent. base classes.
Initialize members.
Fixed some compare() methods.
Fixed missing initializers and old-style casts.
Fixed usage of getVM() versus getNumberOfValues().
Added member initializations and copy/assignment.
Enhanced documentation.
Added import() method for FoR and FoR checks.
Removed debug output.
Fixed compare() methods.
Make sure compare() works on valid objects.
Simplified cast.
Added support for CP-1650 (support JWT User ID).
Fix posible crash if network data is malformed.
Fix possible crash if network data is malformed.
Fix underflow in networking code.
Fix possible bypass of length check.
Updated copyright for last commits.
Use POLLOUT if connect() returns EINPROGRESS.
Make some parameters const in ASC_ methods.
Fixed RGB to DICOM Lab color conversion.
Fixed binary segmentations with rows*cols%8 != 0.
Fix dcmseg test for all compilers.
Enabled doxygen docs potentially hidden by macros.
Pedro (1):
Fixed wrong return status from echoscu.
Pedro F. Arizpe-Gomez (4):
Fixed wrong return status and exit codes for echoscu.
Documented exit codes in echoscu manpage.
Made const pointers for interface of core.
CMake-language style improvements.
```https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/977BUG: Generate unique name in AddNewNodeByClass2018-06-22T20:05:29-04:00phcerdanBUG: Generate unique name in AddNewNodeByClassEven though the documentation mentioned it, the implementation
wasn't generating unique names. Fix it.Even though the documentation mentioned it, the implementation
wasn't generating unique names. Fix it.https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/978COMP: Fixed packaging of bundled superbuild extensions2018-06-26T18:53:02-04:00Csaba PinterCOMP: Fixed packaging of bundled superbuild extensionsAllows packaging superbuild extensions bundled with the Slicer installer. Tested with SlicerVirtualReality
Thanks, @jcfr, I owe you one!Allows packaging superbuild extensions bundled with the Slicer installer. Tested with SlicerVirtualReality
Thanks, @jcfr, I owe you one!https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/979ENH: Update extension template to fix packaging of bundled superbuild extension2018-06-27T10:19:36-04:00Sam HorvathENH: Update extension template to fix packaging of bundled superbuild extension*Created by: jcfr*
Co-authored-by: Csaba Pinter <csaba.pinter@queensu.ca>*Created by: jcfr*
Co-authored-by: Csaba Pinter <csaba.pinter@queensu.ca>https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/980ENH: added 3d views linking capability2018-07-30T03:36:23-04:00Davide Punzopunzodavide@hotmail.itENH: added 3d views linking capabilityAdded Link button in 3DViewController;
Added MRMLViewLogic: set the interactions;
Added MRMLViewLinkLogic: propagate the events.
next step for Slicer 4.10 (no backward compatibility): merge vtkMRMLCameraNode into vtkMRMLViewNode
...Added Link button in 3DViewController;
Added MRMLViewLogic: set the interactions;
Added MRMLViewLinkLogic: propagate the events.
next step for Slicer 4.10 (no backward compatibility): merge vtkMRMLCameraNode into vtkMRMLViewNode
see also https://github.com/NA-MIC/ProjectWeek/blob/master/PW28_2018_GranCanaria/Projects/3DViewsLinking/README.md#progress-and-next-steps point (a)