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WIP: Volumetric Segmentations#277

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CPBridge wants to merge 101 commits intov0.24.0devImagingDataCommons/highdicom:v0.24.0devfrom feature/seg_volumesImagingDataCommons/highdicom:feature/seg_volumesCopy head branch name to clipboard

+13,416-1,975

Commits

Commits on Feb 1, 2024

• Generalize multifframe database manager

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  d0aac71

• Add multiframe tests

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  32703b0

• Automatically populate the 3D tag

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  4ba09b5

Commits on Feb 2, 2024

• Add ability to determine whether a segmentation is a volume

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  ec26339

• Fix plane ordering bug; split spatial functions

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  f598555

Commits on Apr 12, 2024

• Generalize multifframe database manager

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  13e546b

• Add multiframe tests

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  aea5578

• Automatically populate the 3D tag

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  9df31eb

• Add ability to determine whether a segmentation is a volume

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  74b412d

• Fix plane ordering bug; split spatial functions

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  91e11ce

• Merge branch 'feature/seg_volumes' of github.com:ImagingDataCommons/highdicom into feature/seg_volumes

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  0687971

Commits on May 19, 2024

• Merge branch 'v0.23.0dev' into feature/seg_volumes

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• Spelling

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  a671b27

Commits on May 27, 2024

• Merge branch 'v0.23.0dev' into feature/seg_volumes

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  c0716a5

• Merge branch 'v0.23.0dev' into feature/seg_volumes

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  81438ad

• Fix test for multiframe

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  ba83039

• Fix test for multiframe

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  0e9aa46

Commits on Jun 10, 2024

• WIP implementation of VolumeGeometry

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  e53938e

• Remove print statements from tests

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  0a7f6ba

Commits on Jun 15, 2024

• Add some docstrings

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  8ae1900

• Merge branch 'v0.23.0dev' into feature/seg_volumes

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  587e1da

Commits on Jun 16, 2024

• Fixes to matrix transform

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• further fix

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  607b1ae

Commits on Jun 19, 2024

• Move volume to new file

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  adec6b3

Commits on Jun 20, 2024

• Add new tests

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  6f41a70

Commits on Jun 27, 2024

• Moved to VolumeArray

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Commits on Jul 4, 2024

• start on affine matrix mapping

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Commits on Jul 5, 2024

• Add channels

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• Add with_array

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  379060e

• Added concat_volumes

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  dcfdc60

Commits on Jul 15, 2024

• Rename VolumeArray -> Volume

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Commits on Jul 16, 2024

• Implment volume indexing

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  c79124b

• Add get_closest patient_orientation

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  e61119e

• WIP on flip and permute

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  e73f6a9

• Add flip volume

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  dd01046

• Add to_patient_orientation

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  2518549

• Add ability to pass Volume to segmentation constructor

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  3b00d6d

• Change set_array to setter

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  c82c8bf

• Add TODOs

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  508b537

Commits on Jul 19, 2024

• Add volread

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  7e1ff71

Commits on Jul 28, 2024

• Add ability to sort volumes with duplicate and missing positions

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  0c0946e

• Add basic reading as volume. Lots of tidy up and docs to do

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  3cd033c

Commits on Jul 29, 2024

• Fixes

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  5c247a3

• Add affine to Segmentation.get_volume

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  d6a534f

• Fix seg.get_volume affine indexing

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  f272123

• Add tests, some failing

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  23d91c3

Commits on Jul 30, 2024

• Fix indexing issues

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  2c04427

Commits on Jul 31, 2024

• Fix multiframe tests

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  960fba3

• Add intensity operations to Volume

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  341a149

Commits on Aug 2, 2024

• Add cropping and padding to volumes

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  262c712

• Fix intensity normalization methods

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  7b4e6aa

Commits on Aug 3, 2024

• add handed check/ensure

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  7abd30c

• Add some tests for volumes

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  a546466

Commits on Aug 4, 2024

• Remove source frame information from Volume

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  6efd2b8

Commits on Aug 5, 2024

• Add random crop method

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  4fde694

Commits on Aug 9, 2024

• WIP on pixel transformations

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  e0d6c8b

Commits on Aug 10, 2024

• Create new VolumeGeometry class

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  934077b

Commits on Aug 11, 2024

• Refactor multiframe to use VolumeGeometry, add VolumeGeometry.create_volume

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  e4aa391

• Add rotation_for_patient_orientation

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  241a539

Commits on Aug 18, 2024

• Add volume to volume transformer

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  a8cfe82

• WIP on match geometry

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  3aaebcd

• Add match_geometry method, tests

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  f178ac1

Commits on Aug 19, 2024

• Fix type hint

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  9c6c6f2

• Small typos and better error message

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  3ec987c

Commits on Aug 20, 2024

• Implement MultiFrameImage class

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  086a370

• Add randon flip and permute

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  282e004

• Add volume to docs

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  1e6ce19

Commits on Aug 21, 2024

• Handle pickling of multiframe images

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  82d79d2

Commits on Sep 11, 2024

• Work in progress pixel transforms

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  c4632d0

Commits on Sep 25, 2024

• Merge branch 'master' into feature/seg_volumes

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  01bb579

Commits on Oct 5, 2024

• Merge branch 'v0.24.0dev' into feature/seg_volumes

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  69e81c5

• Merge branch 'v0.24.0dev' into feature/seg_volumes

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  c8eda6a

• Fix serialization

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  ad63ad2

• Add tests for labelmap volumes

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  6b9df12

Commits on Oct 11, 2024

• Implement generalized parsing for multiframe images

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  5a2bdd6

Commits on Oct 12, 2024

• Fixes to labelmap reading

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  2a408ad

Commits on Oct 13, 2024

• Fixes for labelmap reading dtypes, add test cases

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  93999e8

• Style fixes

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  f448936

Commits on Oct 17, 2024

• Fixes to slice thickness

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  799e4e0

• Fix background segment description

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  c72cd9f

• Fixes for volume-based segment creation

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  cf1969f

Commits on Nov 2, 2024

• Move to using typing_extensions.Self

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  ced72c1

Commits on Nov 10, 2024

• Add pixel transformations to ImageFileReader

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  7321d02

Commits on Nov 23, 2024

• Implement apply methods for voi and modaiity transforms

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  e6f4e0a

• Implement apply for real world mappings

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  5bc14aa

Commits on Nov 24, 2024

• Progress on pixel transform parsing

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  4e83657

• Factor out pixel transform code

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  7d7c03e

• Add palette lut from combined array

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  4caa018

Commits on Dec 19, 2024

• Fixes to multiframe, add various pixel transforms

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  befdec2

Commits on Dec 22, 2024

• Fix volume indexing at -1

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  4fb9881

• Implement missing parts of pixel transforms

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  3d34cc8

Commits on Dec 23, 2024

• Fixes to transform class

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  862ab71

Commits on Dec 24, 2024

• Add some tests related to combined pixel transform

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  6cc5150

• add further combined pixel transform tests

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  9909cd4

• More tests and fixes for combined pixel transform

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  7a796d3

• Tests for monochrome1

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  3951eac

• More tests and fixes for pixel transforms

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  afd3d2c

• add test for rvwm with lut

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  a75954d

Commits on Dec 26, 2024

• Add ability to select VOI by string

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  760bf83

• Add ability to specify an external VOI transformation

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  a26042d

• Add ability to search RWVMs

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  983cdba