Latest (updated on 2024-12-10 22:12 UTC)

Merge pull request #511 from thewtex/python-executable

COMP: Update python executable location and usage

v1.3.4

What's Changed

• Fixes for upgraded DCMTK and web-assembly build by @jadh4v in #496
• support source image references in the shared FG by @fedorov in #501

New Contributors

• @jadh4v made their first contribution in #496

Full Changelog: v1.3.3...v1.3.4

v1.3.3

What's Changed

• bug: switch to integer for the skip flag by @fedorov in #499

Full Changelog: v1.3.2...v1.3.3

v1.3.2

What's Changed

• ENH: use SegmentDescription to populate SegmentLabel by @fedorov in #488
• allow saving merged segments to all formats by @fedorov in #495

Full Changelog: v1.3.1...v1.3.2

v1.3.1

What's Changed

• Switch to framesorter class by @michaelonken in #484
• Use label id as segment numbers by @michaelonken in #485
• Fix order of pixel spacing converting ITK->DICOM by @michaelonken in #486
• Fix publishing of docker images by @fedorov #487

Full Changelog: v1.3.0...v1.3.1

v1.3.0

Major highlights of this release:

• upgrade to ITK v5
• switch to GitHub Actions from platform-specific CI solutions
• major performance improvements for DICOM SEG conversion
• added ability to save non-overlapping DICOM SEG segments into a single file

$ git shortlog v1.2.5..v1.3.0 --no-merges
Andrey Fedorov (78):
      ENH: switch to use ITKv5
      COMP: remove references to multi threader
      CI: fixing CircleCI and Appveyor
      CI: switch to VS 2015
      CI: use cmake 3.10.2 for travis-ci
      ENH: resolve conflicts
      CI: update python to 3.11
      use pip3
      ci
      CI: update VS version
      CI: update ITK package
      CI: fix typo
      CI: add back prebuilt packages paths
      CI: update ITK path
      CI: force build of SEM
      update to use ITK with XML IO
      trying to add missing modules
      use package with missing headers fixed
      update zlib package
      BUG: try to fix multithreading
      BUG: remove long type
      BUG: remove unicode type
      BUG: remove xrange
      upgrade circleci cmake
      replace deprecated dockcross image
      replace deprecated dockcross image
      try to set python 3.8 in dockcross container
      CI: remove travis-ci
      use shield badge for circleci
      ENH: write all segments to the same file
      ENH: adding parameterization for merged segments
      BUG: add segments to existing segmentation
      STYLE: remove blanks per codefactor
      ENH: fix tests
      BUG: fix overwrite of segment metadata
      fix metadata init with mergedSegments on
      WIP: use ImportImageFilter + iterators to copy frame
      CI with gh-actions
      Update cmake.yml
      Update cmake.yml
      CI: add timeout
      CI: add windows
      CI: change win python to 3.8
      CI: add 7z unpack
      CI: add win configure/build/package
      CI: separate win workflow
      CI: win only
      CI: fix name
      CI: debug
      CI: fixes
      CI: refinement of the github actions workflows
      CI: add win configure/build/package
      CI: separate win workflow
      CI: win only
      CI: fix name
      CI: debug
      CI: fixes
      CI: refinement of the github actions workflows
      CI: linux docker
      CI docker fix
      CI switch to fedorov docker for testing
      CI bump timeout
      CI: increase macos job timeout
      CI: change build step
      CI: adding upload linux package
      CI: remove invalid option
      CI: try to fix permissions
      CI: try using a dedicated token
      BUG: init badges from the QIICR project
      CI: fix destination for the linux package
      CI: add package publish for win and mac
      CI: install scikit-ci-addons
      DOC: update acks
      DOC: add reference
      CI: try new token
      CI: revert to the earlier token
      DOC: update readme and trigger GA
      CI: trying to fix macos package publishing
      BUG: specify full folder name
      BUG: fix typo
      BUG: add missing newlines
      cmake: set dcmqi version to 1.2.6
      CI: enable testing on win and mac
      CI: trying to fix release package upload
      cmake: set dcmqi version to 1.3.0

Jean-Christophe Fillion-Robin (2):
      BUG: Ensure binaries bundled into dcmqi docker image can run
      COMP: Add regression test "docker_image_test"

Michael Onken (34):
      Permit manual builds.
      Also allow manual builds on Mac OS X.
      Better name for Mac OS build job.
      Split up some build steps for debugging.
      Cache ITK, DCMTK and ZLIB for dcmqi build.
      Remove circle ci references. Consistency fixes.
      Removed old CI files, added GH CI status badges.
      Fix Windows Release publishing.
      WIP: Introduce OverlapUtil
      Separate build and publish phase in CI.
      Don't release if user is not QIICR.
      List workspace content.
      Add manual workflow run.
      Revert "Add manual workflow run."
      Revert "List workspace content."
      WIP: Fully integrated code producing first results.
      Better error handling.
      Fix Image Origin bug and speed up processing.
      Error handling.
      WIP: Fix assignment of frames to NRRD, speedup.
      ENH: Don't check functional groups (speedup)
      Only publish on master and on qiicr/dcmqi repo.
      Fix accidentially commited typo.
      Cleanups, robustness, documentation.
      Refactored converter classes.
      Fixed tests and bug, minor changes.
      Try to fix Linux docker build.
      New method for finding frame sorting coordinate.
      Return result image by image to save memory.
      Try to fix compile error on Windows.
      Another fix for windows build errors.
      Replace use of deprecated jsoncpp class.
      Fix bug when creating JSON output for merges.
      Added test for merging segments into NRRD files.

Tobias Weihs (2):
      support for new dcmtk targets
      find dcmtk and itk in exported config, removed hard coded dcmtk path

Vamsi Thiriveedhi (1):
      BUG: fix release package publishing

v1.2.5

$ git shortlog v1.2.4..v1.2.5 --no-merges
Andrey Fedorov (12):
      ENH: switch from ceil() to round() for slice number calculation
      CI: fix TravisCI
      ENH: update TravisCI badge location
      ENH: update TravisCI pointer
      ENH: update docker badge
      COMP: will it work with C++ 14?
      BUG: fix initialization of referenced instances
      COMP: use https instead of git for clones
      BUG: check for in-plane consistency of seg size
      CI: migrate to Ubuntu 20.04
      BUG: register RLE codecs before loading data
      cmake: Set DCMQI version to 1.2.5

Jean-Christophe Fillion-Robin (2):
      COMP: Fix Slicer extension build by not forcing CMAKE_CXX_STANDARD value
      COMP: Simplify setting of CMAKE_CXX_STANDARD defaulting to C++14

Tobias Weihs (3):
      install config with correct paths
      install generated internal include directory
      removed unnecessary include

v1.2.4

This is a maintenance patch release with the following fixes:

• improve precision of encoding floating point numbers
• fix incorrect handling of row/column spacing, which affected non-square segmentations with anisotropic spacint
• fix incorrect handling of segmentations that resulted in total number of pixels not divisible by 8 (DCMTK bug)
• superbuild updated to use DCMTK 3.6.6 with an additional backported commit
• cleanup of cmake to support integration with external tools, contributed by Tobias Weihs

$ git shortlog v1.2.3..v1.2.4 --no-merges
Andrey Fedorov (6):
      CI: add print for debugging
      CI: remove print
      BUG: PixelSpacing order incorrect on read
      ENH: update DCMTK to 3.6.6 patched for seg
      CI: update DCMTK package to 3.6.6_patched
      cmake: Set DCMQI version to 1.2.4

Stefan Dinkelacker (1):
      BUG: serialize floats with maximum precision

Tobias Weihs (10):
      added guard to ensure segmentation object is deleted
      #419 do not delete a shallow copied frame, only delete if necessary
      #421 added overload taking a seg object, for this overload the json meta generation is optional
      replaced nullptr by NULL macro
      cannot use auto
      no cpp11
      force DCMTK build to link dynamic runtime library to avoid mixing static vs dynamic
      added missing headers
      made include directories pointing into build directory build dependent
      added target export installing if superbuild is disabled

v1.2.3

This is a maintenance release updating the use of coded terms to SCT, and resolving minor bugs.

$ git shortlog v1.2.2..v1.2.3 --no-merges

Andras Lasso (2):
      BUG: Fix loading of single-frame segmentation
      ENH: Added detailed logging option to itkimage2segimage and segimage2itkimage

Andrey Fedorov (21):
      ENH: update to DCMTK 3.6.5
      COMP: remove use of CERR and COUT
      COMP: update DCMTK/ITK to fix static link issue
      BUG: update SRT to SCT codes
      BUG: fix SR roundtrip test by checking for SCT codes
      ENH: check both SCT and SRT codes
      ENH: add cardinality constraint to the schemas
      ENH: revise multi-segment example
      ENH: compare to epsilon instead of zero
      BUG: remove midas pointers
      BUG: create a new example
      ENH: improve seg conversion support
      BUG: fix typos
      ENH: update the documentation link
      update support options
      update readme
      ENH: initialize SegmentsOverlap for simple case
      BUG: switch to dcmtk for CIELab conversion
      ENH: switch to CIELab conversion from @dclunie
      BUG: downgrade ajv to 3.3.0
      cmake: set dcmqi version to 1.2.3

Steve Pieper (1):
      COMP: turn of SNDFILE to fix include path

afshinmessiah (6):
      Replaced the srt code with sct codes (the ones are available at snomed dictionary of pydicom)
      Added the PYTHON script which replaces srt wiht sct
      Used dcm.h macros instead of direct code strings for dcm codes. The list was incomplete for sct&ucum
      Got the reader to read both srt/sct codes
      Replaced all SRT wiht their SCT counterparts except for 4: (1)G-C306              "Measurement Method" (2)A-10044         "Non-Lesion Object Type" (3)T-00317             "FindingSite" (4)R-404A4                "Entire"
      Final step SRT to SCT conversion (1) 'G-C306'-->'370129005' (2) 'A-10044'-->'111102' (3) 'T-00317'-->'55940004' (4) 'R-404A4'-->'255503000'

v1.2.2

This is a minor release, and the last one before updating to DCMTK 3.6.5

$ git shortlog v1.2.1..v1.2.2 --no-merges
Andrey Fedorov (7):
ENH: add warning if composite context is not initialized
ENH: add SEG SegmentLabel support
ENH: improve error reporting for seg converter
ENH: improve error handling
BUG: fix and add missing codes to the Slicer terminology file
ENH: populate 3dSlicerIntegerLabel in JSON seg context
cmake: update version to v1.2.2