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SlicerDMRI v1.0.0

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@jhlegarreta jhlegarreta released this 10 Dec 18:17
· 6 commits to master since this release
v1.0.0
4c4b00b
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SlicerDMRI v1.0.0: release all recent enhancements and bug fixes. Tested
against 3D Slicer 2cf6f14.

Summary of changes:

  • Fix miscellaneous bugs, especially related to fiber bundle reader crash
    after changes in recent VTK versions, fix testing data URLs and MRML
    file elements.
  • Adopt f-strings.
  • Fix miscellaneous warnings.

tract1 and FA property querying and tract measurement tests failures
to be addressed in future releases.

What's Changed

  • ENH: Added edit node support to tractography interactive seeding by @cpinter in #75
  • BUG/ENH: use enums for UI<->SeedingNode settings by @ihnorton in #77
  • COMP: fix Tract.DisplayableMgr registration by @ihnorton in #83
  • ENH: add average length to FiberTractMeasurements by @ihnorton in #84
  • Ensure displayable manager are registered with Slicer >= 4.9 by @jcfr in #85
  • WIP ENH: add MeanDiffusivity to scalar maps CLI by @ihnorton in #86
  • BUG: fix tract color-by-orientation modes by @ihnorton in #87
  • BUG: fix color-by-tensorproperty after by-orientation by @ihnorton in #88
  • BUG/STYLE: fix crash during some MRML reloads, and confusing shadowed… by @ihnorton in #89
  • ENH: add MeanDiffusivity to FiberTractMeasurements CLI by @ihnorton in #90
  • ENH: add test for FBTractMeasure with scalar-only polydata by @ihnorton in #91
  • BUG: fix Extract FBNode by Annotation ROI (1/2) by @ihnorton in #93
  • WIP: refactor vtkMRMLFiberBundleNode (2/2) by @ihnorton in #94
  • COMP: support Qt5 by @ihnorton in #95
  • ENH: FBNode: observe producer modification events in order to update … by @ihnorton in #96
  • Add DWI DICOM plugin by @ihnorton in #97
  • ENH: use line display as default by @ihnorton in #99
  • Add PLY export module by @ihnorton in #101
  • ENH: rename vtkNRRDReader,vtkNRRDWriter -> vtkTeemNRRD{R,W} by @ihnorton in #103
  • PLY export updates by @ihnorton in #104
  • ENH: add option to limit exported scalar range to the node's range by @ihnorton in #105
  • BUG: fix crash in FB2LabelMap due to mismatched NumPy/VTK dtype size by @ihnorton in #106
  • ENH: properly support PLY export of color-by-solid by @ihnorton in #107
  • Add TractographyDownsample module by @ihnorton in #108
  • BUG: fix Tractography Display 'Interactive Edit' feature by @ihnorton in #109
  • ENH: add '--baseline_clamp' option, and tests for ExtractDWIShells by @ihnorton in #112
  • COMP: reduce mac build warnings by adding VTK_OVERRIDE annotations by @ihnorton in #113
  • Add Module templates by @ihnorton in #115
  • Tract template by @zhangfanmark in #118
  • Dicom TR improvements by @ihnorton in #119
  • Add support for all Supp. 181 measurement codes based on array name by @ihnorton in #120
  • COMP: update header includes to fix build by @ihnorton in #122
  • Improve and simplify buildsystem, and add support for python 3.x by @jcfr in #123
  • BUG: Replace saferef with weakref by @jamesobutler in #125
  • COMP: Disable Broken tests on Windows by @sjh26 in #131
  • COMP: disable another test breaking on windows by @pieper in #133
  • BUG: fix crash trying to load trk file by @pieper in #139
  • BUG: explicitly flag all vtk fiber bundles RAS by @pieper in #137
  • COMP: Add support for building against VTK 8.2.0 or 9.0.0 by @jcfr in #141
  • BUG: avoid crash or assert on bad load arguments by @pieper in #140
  • COMP: fix several of the tests by @pieper in #142
  • Fixed vendor name bug and removed erroneous tags by @mikebind in #143
  • use custom function to select fiber boundle by @simonoxen in #149
  • BUG: fix tracts for vtk9 by @pieper in #151
  • STYLE: remove unused EditorLib import by @simonoxen in #152
  • COMP: fix copydata ambiguity and missing math.h by @pieper in #153
  • ENH: refactor TractographyDownsample, add batch feature by @pieper in #154
  • COMP: Fix build error with C++17 by @lassoan in #157
  • Support for disabling register dmri module templates by @jcfr in #159
  • Fix warnings by @jcfr in #160
  • Fix implicit fallthrough warning related issues by @jcfr in #161
  • Save tracts in LPS coordinate system by @lassoan in #162
  • Fix registration of Tractography displayable manager and remove support for Qt4 and Slicer 4 by @jcfr in #163
  • ENH: Switch ROI selection from Annotations to Markups #158 by @pieper in #164
  • COMP: fix missing method link error by @pieper in #166
  • ENH: Use SetVisibility2D instead of SetSliceIntersectionVisibility by @jhlegarreta in #168
  • BUG: add fiber storage node to the scene by @pieper in #173
  • ENH: Add GitHub actions build, test workflow file for CI by @jhlegarreta in #172
  • COMP: Simplify TractographyDisplay Python tests removing obsolete workaround by @jcfr in #178
  • Re-organize and optimize GitHub Actions workflow by @jcfr in #177
  • DOC: Increase consistency in SlicerDMRI citation message by @jhlegarreta in #176
  • DOC: Sync the license file with the current Slicer license file content by @jhlegarreta in #175
  • DOC: Add the Build, test GHA workflow status badge to the README file by @jhlegarreta in #174
  • DOC: Add release version badge to README file by @jhlegarreta in #183
  • ENH: Add ColorLegendDisplayNode support to vtkMRMLFiberBundleDisplayNode by @MichaelColonel in #185
  • DOC: Update the extension's homepage by @jhlegarreta in #180
  • COMP: Call explicitly .c_str() to get a const char* by @jhlegarreta in #190
  • COMP: Prefer using vtkExtractSelection by @jhlegarreta in #193
  • COMP: Prefer snprintf to avoid buffer overruns by @jhlegarreta in #194
  • COMP: Fix sizeof argument in snprintf call by @jhlegarreta in #196
  • ENH: Test build by @jhlegarreta in #191
  • ENH: Add a GHA workflow file to build and deploy Doxygen documentation by @jhlegarreta in #195
  • BUG: Fix input scene update in vtkMRMLFiberBundleNodeTest1 by @jhlegarreta in #213
  • STYLE: Fix grammar in logged message by @jhlegarreta in #200
  • BUG: Fix weakref method warning by @jhlegarreta in #214
  • BUG: Fix data download URLs and Slicer display message call by @jhlegarreta in #203
  • STYLE: Remove deprecated Python import statements by @jhlegarreta in #199
  • STYLE: Use toStdString().c_str() instead of toLatin1() for char* by @jhlegarreta in #204
  • COMP: Fix CodeSequenceMacro implict declaration warning by @jhlegarreta in #217
  • COMP: Fix vtkHyperPoint implicit declaration warning by @jhlegarreta in #218
  • COMP: Fix vtkTractographyPoint implicit declaration warning by @jhlegarreta in #219
  • COMP: Remove unused topCluster var from FiberTractMeasurements by @jhlegarreta in #220
  • DOC: Add a link to the Doxygen documentation GitHub Pages URL in README by @jhlegarreta in #222
  • BUG: Fix fiber bundle reader crash by @lassoan in #208
  • COMP: Use SetNthControlPointPosition instead of SetNthFiducialPosition by @jhlegarreta in #209
  • STYLE: Prefer using f-strings by @jhlegarreta in #198
  • ENH: Remove unnecessary stat serialization whitespaces around separator by @jhlegarreta in #171
  • Update README.md by @ljod in #223
  • BUG: Fix syntax errors raised after introducing f-strings by @jhlegarreta in #224
  • BUG: Fix syntax errors raised after introducing f-strings (follow-up) by @jhlegarreta in #225
  • ENH: Adapt tract measure baselines to whitespace removal by @jhlegarreta in #226

New Contributors

Full Changelog: 2017.03.12...v1.0.0

Contributors

pieper, jcfr, and 11 other contributors
Assets 2