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Version 0.22.0 #269

Merged
merged 117 commits into from
Nov 9, 2023
Merged

Version 0.22.0 #269

merged 117 commits into from
Nov 9, 2023

Commits on May 15, 2023

  1. Make checks more efficient, avoid appending to pydicom.Sequence

    @CPBridge
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  2. Add check for non-unique plane positions

    @CPBridge
    CPBridge committed May 15, 2023
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  3. Tidy up

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    CPBridge committed May 15, 2023
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Commits on May 16, 2023

  1. Move compression out of the loop, in preparation for multiprocessing

    @CPBridge
    CPBridge committed May 16, 2023
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  2. Simplify SegmentSequence logic

    @CPBridge
    CPBridge committed May 16, 2023
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  3. Factored out several parts of seg constructor into methods for readib… 

    …ility
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    CPBridge committed May 16, 2023
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Commits on Jun 9, 2023

  1. Add annotation_coordinate_type property and check for 0 in get_coordi… 

    …nate
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    CPBridge committed Jun 9, 2023
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  2. Add annread function

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    CPBridge committed Jun 9, 2023
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Commits on Jun 13, 2023

  1. Fix for single channel floating point pixel array

    @CPBridge
    CPBridge committed Jun 13, 2023
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Commits on Jun 21, 2023

  1. Merge branch 'master' into ann_parsing_improvements

    @CPBridge
    CPBridge committed Jun 21, 2023
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  2. Update user guide

    @CPBridge
    CPBridge committed Jun 21, 2023
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  3. Merge branch 'master' into seg_creation_efficiency

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    CPBridge committed Jun 21, 2023
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  4. Codespell typo

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    CPBridge committed Jun 21, 2023
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Commits on Jun 22, 2023

  1. Merge pull request #230 from ImagingDataCommons/ann_parsing_improvements 

    ANN parsing improvements
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  2. Apply suggestions from code review 

    Co-authored-by: Markus D. Herrmann <[email protected]>
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    CPBridge and hackermd committed Jun 22, 2023
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Commits on Jul 5, 2023

  1. Simplification of _get_pixel_measures

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  2. Add missing Returns section to docstring

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    CPBridge committed Jul 5, 2023
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  3. Remove has_ref_frame_uid from _get_dimension_index_values

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  4. rename index_values -> dimension_index_values

    @CPBridge
    CPBridge committed Jul 5, 2023
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  5. Fix missing variable name change

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    CPBridge committed Jul 5, 2023
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Commits on Jul 6, 2023

  1. Add further explanation to _get_dimension_index_values docstring

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    CPBridge committed Jul 6, 2023
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  2. Simplify _omit_empty_frames to find indices only

    @CPBridge
    CPBridge committed Jul 6, 2023
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  3. Rewrite as list comprehension

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    CPBridge committed Jul 6, 2023
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Commits on Jul 7, 2023

  1. remove unnecessary flattens to save memory

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Commits on Jul 8, 2023

  1. Merge branch 'seg_creation_efficiency' of github.com:ImagingDataCommo… 

    …ns/highdicom into seg_creation_efficiency
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  2. Tidy up of dimension indexing code

    @CPBridge
    CPBridge committed Jul 8, 2023
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  3. Add further docstring comment for _get_segment_array

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    CPBridge committed Jul 8, 2023
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Commits on Jul 27, 2023

  1. Update src/highdicom/seg/sop.py 

    Co-authored-by: Markus D. Herrmann <[email protected]>
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    CPBridge and hackermd committed Jul 27, 2023
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  2. Apply suggestions from code review 

    Co-authored-by: Markus D. Herrmann <[email protected]>
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    CPBridge and hackermd committed Jul 27, 2023
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  3. Rename methods, fix lints

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    CPBridge committed Jul 27, 2023
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  4. Merge pull request #227 from ImagingDataCommons/seg_creation_efficiency 

    Improve Segmentation Creation Efficiency
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    CPBridge committed Jul 27, 2023
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  5. Add multithreading option to segmentation creation

    @CPBridge
    CPBridge committed Jul 27, 2023
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  6. Remove array copy, seems to be unnecessary

    @CPBridge
    CPBridge committed Jul 27, 2023
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  7. Add test

    @CPBridge
    CPBridge committed Jul 27, 2023
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  8. Add section to docs on multiprocessing

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    CPBridge committed Jul 27, 2023
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  9. Retrieve one segment array at a time: simpler and slightly faster

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    CPBridge committed Jul 27, 2023
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  10. Fix docstring for _get_segment_array

    @CPBridge
    CPBridge committed Jul 27, 2023
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  11. add ability for user to pass their own process pool

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    CPBridge committed Jul 27, 2023
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  12. Add basic tiled_full option

    @CPBridge
    CPBridge committed Jul 27, 2023
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  13. Fixes

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    CPBridge committed Jul 27, 2023
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Commits on Aug 3, 2023

  1. Test for optional parameters

    @erikogabrielsson
    erikogabrielsson committed Aug 3, 2023
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  2. Raise ValueError if duplicating "Processing Step Description"

    @erikogabrielsson
    erikogabrielsson committed Aug 3, 2023
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  3. Fix concept code name for DateTimeContentItem

    @erikogabrielsson
    erikogabrielsson committed Aug 3, 2023
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  4. Add additional properties

    @erikogabrielsson
    erikogabrielsson committed Aug 3, 2023
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  5. Tests for datetime-based content items

    @erikogabrielsson
    erikogabrielsson committed Aug 3, 2023
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  6. Fix for parsing of datetime-type content

    @erikogabrielsson
    erikogabrielsson committed Aug 3, 2023
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  7. Add specimen container and specimen type

    @erikogabrielsson
    erikogabrielsson committed Aug 3, 2023
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  8. Fix type annotation

    @erikogabrielsson
    erikogabrielsson committed Aug 3, 2023
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  9. Return simple datetime

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    erikogabrielsson committed Aug 3, 2023
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  10. Add addtitional parameters to SpecimenDescription

    @erikogabrielsson
    erikogabrielsson committed Aug 3, 2023
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  11. Fix spelling and duplicate test classes

    @erikogabrielsson
    erikogabrielsson committed Aug 3, 2023
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  12. Flake8 fixes

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    erikogabrielsson committed Aug 3, 2023
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Commits on Aug 7, 2023

  1. Merge variables used for compressed and uncompressed frames

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Commits on Aug 10, 2023

  1. Switch ordering of tiles to actually match TILED_FULL

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    CPBridge committed Aug 10, 2023
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Commits on Aug 18, 2023

  1. Refactor utils code into iter_tiled_full_frame_data

    @CPBridge
    CPBridge committed Aug 18, 2023
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  2. Fix types

    @CPBridge
    CPBridge committed Aug 18, 2023
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  3. Fix tests relating to order of dimension indices

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    CPBridge committed Aug 18, 2023
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Commits on Aug 24, 2023

  1. Basic implementation of autotiling. Need to add omitting frame logic

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Commits on Aug 31, 2023

  1. Add frame omission logic and tests

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Commits on Sep 2, 2023

  1. Work in progress implementation of constructing tiled outputs

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Commits on Sep 4, 2023

  1. Working implementation of tiled outputs, need tests

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Commits on Sep 10, 2023

  1. Add tests, fix bug with padded tiles

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Commits on Sep 11, 2023

  1. Add doc sections on total pixel matrices for seg creation and parsing

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    CPBridge committed Sep 11, 2023
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  2. Add tiled full test image, links in docs

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    CPBridge committed Sep 11, 2023
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Commits on Sep 12, 2023

  1. Minor typos in docstrings

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    CPBridge committed Sep 12, 2023
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Commits on Sep 14, 2023

  1. Add pyramid utility method

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  2. Add export of create_segmentation_pyramid

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    CPBridge committed Sep 14, 2023
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  3. Fixes to pyramid

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    CPBridge committed Sep 14, 2023
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  4. Fix error reading TILED_FULL segmentations from file

    @CPBridge
    CPBridge committed Sep 14, 2023
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  5. Merge branch 'feat/autotile' into feat/pyramid

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    CPBridge committed Sep 14, 2023
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  6. Add full docs

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Commits on Sep 15, 2023

  1. Merge pull request #245 from ImagingDataCommons/seg_multithreading 

    Multiprocessing for frame encoding in Segmentation constructor
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Commits on Sep 20, 2023

  1. Merge branch 'master' into v0.22.0dev

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  2. Merge branch 'v0.22.0dev' into feat/tiled_full

    @CPBridge
    CPBridge committed Sep 20, 2023
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  3. Fix variable name change introduced by merge

    @CPBridge
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  4. Merge branch 'feat/tiled_full' into feat/autotile

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  5. Merge branch 'feat/autotile' into feat/pyramid

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Commits on Sep 24, 2023

  1. Add docstrings to new properties

    @erikogabrielsson
    erikogabrielsson committed Sep 24, 2023
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  2. Append steps before adding preparation step sequence to dataset

    @erikogabrielsson
    erikogabrielsson committed Sep 24, 2023
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  3. Move new optional arguments to end of init

    @erikogabrielsson
    erikogabrielsson committed Sep 24, 2023
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  4. Add reference to valid container type 

    Co-authored-by: Chris Bridge <[email protected]>
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  5. Merge branch 'SpecimenPreparationStep-fixes' of https://github.com/er… 

    …ikogabrielsson/highdicom into SpecimenPreparationStep-fixes
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    erikogabrielsson committed Sep 24, 2023
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  6. Add references to CIDs

    @erikogabrielsson
    erikogabrielsson committed Sep 24, 2023
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  7. Check for type of issuer of specimen id on constructed preparation step

    @erikogabrielsson
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  8. Test date, time, and datetime conversion from dataset with pydicom co… 

    …nfig.datetime_conversion setting
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  9. Add docstrings for missed properties

    @erikogabrielsson
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  10. Fix typo in docstring

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  11. Add from_dataset for IssuerOfIdentifier

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  12. Add description of issuer_of_specimen_id argument

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Commits on Sep 25, 2023

  1. Add 'copy' parameter to from_dataset()-method 

    Co-authored-by: Chris Bridge <[email protected]>
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  2. Check that specimen_short_description is valid 

    Co-authored-by: Chris Bridge <[email protected]>
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  3. Tests for specimen_short_description

    @erikogabrielsson
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  4. Add reference to CID for specimen type argument

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  5. Convert Code specimen_type to CodedConcept

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    erikogabrielsson committed Sep 25, 2023
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  6. Remove extra line

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Commits on Oct 2, 2023

  1. Fix merge conflicts from master

    @CPBridge
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  2. Flake 8 fixes

    @CPBridge
    CPBridge committed Oct 2, 2023
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  3. Merge branch 'v0.22.0dev' into feat/autotile

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  4. Merge branch 'feat/autotile' into feat/pyramid

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Commits on Oct 3, 2023

  1. Add TotalPixelMatrixFocalPlanes

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  2. Merge branch 'feat/autotile' into feat/pyramid

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Commits on Oct 19, 2023

  1. WIP adding input checks for pyramid segs

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Commits on Oct 28, 2023

  1. WIP pyramid finalization

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  2. Merge branch 'master' into v0.22.0dev

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Commits on Nov 9, 2023

  1. Add tests for all four pyramid input combinations

    @CPBridge
    CPBridge committed Nov 9, 2023
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  2. Add pyramid doc section

    @CPBridge
    CPBridge committed Nov 9, 2023
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  3. Merge pull request #246 from erikogabrielsson/SpecimenPreparationStep… 

    …-fixes

Specimen description and preparation step fixes
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  4. Merge pull request #248 from ImagingDataCommons/feat/autotile 

    Improvements for working with tiled segmentations
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    CPBridge committed Nov 9, 2023
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  5. Merge pull request #253 from ImagingDataCommons/feat/pyramid 

    Add function to create multiresolution segmentation pyramids
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    CPBridge committed Nov 9, 2023
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  6. Version bump for release

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    CPBridge committed Nov 9, 2023
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  7. Fix codespell errors

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    CPBridge committed Nov 9, 2023
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  8. Fix wrong transfer syntax in test

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    CPBridge committed Nov 9, 2023
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  9. Merge pull request #270 from ImagingDataCommons/fix_jpegls_encode_test 

    Fix wrong transfer syntax in test
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    CPBridge committed Nov 9, 2023
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  10. doctest fix

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    CPBridge committed Nov 9, 2023
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  11. Fix for new seg tests when libjpeg not installed

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    CPBridge committed Nov 9, 2023
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  12. Workaround use of math.prod in python 3.7

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    CPBridge committed Nov 9, 2023
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  13. Flake8 fix

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    CPBridge committed Nov 9, 2023
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