BUG: 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 should be addressed.

Cc: @lassoan

Highlighted list of changes

• vtk/vtk!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.

• vtk/vtk!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)