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WIP: Volumetric Segmentations#277

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CPBridge merged 159 commits intov0.24.0devImagingDataCommons/highdicom:v0.24.0devfrom feature/seg_volumesImagingDataCommons/highdicom:feature/seg_volumesCopy head branch name to clipboardJan 25, 2025

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Commits on Feb 1, 2024

• Generalize multifframe database manager

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• Add multiframe tests

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• Automatically populate the 3D tag

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Commits on Feb 2, 2024

• Add ability to determine whether a segmentation is a volume

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• Fix plane ordering bug; split spatial functions

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Commits on Apr 12, 2024

• Generalize multifframe database manager

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• Add multiframe tests

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• Automatically populate the 3D tag

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• Add ability to determine whether a segmentation is a volume

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• Fix plane ordering bug; split spatial functions

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

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Commits on May 19, 2024

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

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• Spelling

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Commits on May 27, 2024

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

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

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• Fix test for multiframe

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• Fix test for multiframe

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Commits on Jun 10, 2024

• WIP implementation of VolumeGeometry

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• Remove print statements from tests

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Commits on Jun 15, 2024

• Add some docstrings

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

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Commits on Jun 16, 2024

• Fixes to matrix transform

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• further fix

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Commits on Jun 19, 2024

• Move volume to new file

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Commits on Jun 20, 2024

• Add new tests

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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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• Added concat_volumes

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Commits on Jul 15, 2024

• Rename VolumeArray -> Volume

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Commits on Jul 16, 2024

• Implment volume indexing

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• Add get_closest patient_orientation

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• WIP on flip and permute

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• Add flip volume

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• Add to_patient_orientation

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• Add ability to pass Volume to segmentation constructor

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• Change set_array to setter

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• Add TODOs

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Commits on Jul 19, 2024

• Add volread

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Commits on Jul 28, 2024

• Add ability to sort volumes with duplicate and missing positions

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

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Commits on Jul 29, 2024

• Fixes

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• Add affine to Segmentation.get_volume

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• Fix seg.get_volume affine indexing

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• Add tests, some failing

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Commits on Jul 30, 2024

• Fix indexing issues

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Commits on Jul 31, 2024

• Fix multiframe tests

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• Add intensity operations to Volume

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Commits on Aug 2, 2024

• Add cropping and padding to volumes

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• Fix intensity normalization methods

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Commits on Aug 3, 2024

• add handed check/ensure

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• Add some tests for volumes

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Commits on Aug 4, 2024

• Remove source frame information from Volume

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Commits on Aug 5, 2024

• Add random crop method

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Commits on Aug 9, 2024

• WIP on pixel transformations

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Commits on Aug 10, 2024

• Create new VolumeGeometry class

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Commits on Aug 11, 2024

• Refactor multiframe to use VolumeGeometry, add VolumeGeometry.create_volume

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• Add rotation_for_patient_orientation

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Commits on Aug 18, 2024

• Add volume to volume transformer

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• WIP on match geometry

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• Add match_geometry method, tests

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Commits on Aug 19, 2024

• Fix type hint

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• Small typos and better error message

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Commits on Aug 20, 2024

• Implement MultiFrameImage class

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• Add randon flip and permute

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• Add volume to docs

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Commits on Aug 21, 2024

• Handle pickling of multiframe images

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Commits on Sep 11, 2024

• Work in progress pixel transforms

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Commits on Sep 25, 2024

• Merge branch 'master' into feature/seg_volumes

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Commits on Oct 5, 2024

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

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

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  c8eda6a

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• Fix serialization

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• Add tests for labelmap volumes

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Commits on Oct 11, 2024

• Implement generalized parsing for multiframe images

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Commits on Oct 12, 2024

• Fixes to labelmap reading

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Commits on Oct 13, 2024

• Fixes for labelmap reading dtypes, add test cases

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  93999e8

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• Style fixes

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Commits on Oct 17, 2024

• Fixes to slice thickness

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  799e4e0

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• Fix background segment description

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• Fixes for volume-based segment creation

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Commits on Nov 2, 2024

• Move to using typing_extensions.Self

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Commits on Nov 10, 2024

• Add pixel transformations to ImageFileReader

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Commits on Nov 23, 2024

• Implement apply methods for voi and modaiity transforms

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• Implement apply for real world mappings

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Commits on Nov 24, 2024

• Progress on pixel transform parsing

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  4e83657

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• Factor out pixel transform code

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  7d7c03e

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• Add palette lut from combined array

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  4caa018

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Commits on Dec 19, 2024

• Fixes to multiframe, add various pixel transforms

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Commits on Dec 22, 2024

• Fix volume indexing at -1

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  4fb9881

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• Implement missing parts of pixel transforms

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Commits on Dec 23, 2024

• Fixes to transform class

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Commits on Dec 24, 2024

• Add some tests related to combined pixel transform

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  6cc5150

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• add further combined pixel transform tests

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  9909cd4

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• More tests and fixes for combined pixel transform

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  7a796d3

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• Tests for monochrome1

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• More tests and fixes for pixel transforms

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• add test for rvwm with lut

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Commits on Dec 26, 2024

• Add ability to select VOI by string

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• Add ability to specify an external VOI transformation

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• Add ability to search RWVMs

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Commits on Dec 28, 2024

• Move to new Image class, add frame access methods

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Commits on Dec 31, 2024

• Add new multi-channel logic

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  ce017ff

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• Fix some volume tests

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  1c7f242

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• WIP on pixel iteration

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Commits on Jan 1, 2025

• Completed generalized frame access

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• Fix dtype in modality lut

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  4524a11

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• Accommodate palette color segmentations

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  bc871c0

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• Add more tests, add checks for missing frames

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  b7c99dc

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• Add Image volume and total pixel matrix getters, fix most volume tests

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Commits on Jan 2, 2025

• Single frame images and volume from series

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  8e9be43

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• Look for ICCs in optical path sequence

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• Fix to ICC prfile

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• Allow lazy decoding for all seg methods

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  905b292

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• Fix problem with palette color LUTs and incomplete segments

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  cd976d1

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• minor typing error

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Commits on Jan 4, 2025

• Allow non-consecutive segment numbers for labelmaps, or for any existing seg

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  1bb9336

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• Fixes to labelmap parsing and tests

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  4245c43

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• New checks on valid volumes as inputs to segmentation

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• Improvements on 3D dimension organization

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Commits on Jan 5, 2025

• fixes to volume position ordering

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  cc8ea2e

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• Fixes to volumetric seg tests

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  23a95bd

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• Fix to spacing calculation

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• Allow images with no dimension indices

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• Enable single frame volumes

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Commits on Jan 8, 2025

• Implement lazy pixel retrieval

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• Tidy up of SQL related code, add volume geometry for tiled images

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  9a3f61d

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• Fix tiled geometry

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• Change sqlite_schema to sqlite_master

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• Fix to _get_bot for new pydicom version

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Commits on Jan 9, 2025

• Change default spacing tolerance to 1e-2

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  8c2c1e0

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• Fixes and test for ImageFileReader

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Commits on Jan 13, 2025

• Implement tiled volumes from image and seg

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• Add coordinate system to volume and take volume as input to segmentation

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• Check shared functional groups for extra collection items

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Commits on Jan 14, 2025

• Allow images with FoR but no coordinate system

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• Use ExtendedOffsetTable in ImageFileReader

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  e6955b4

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• Move to relative tolerance for spacing

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• Add docs for ChannelDscriptor

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Commits on Jan 15, 2025

• Various documentation tidy ups

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• Disallow creation of Image

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• Add pixel_array method to Image

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• Add geometry from components, allow passing center and patient orientation

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Commits on Jan 17, 2025

• Refactor value types

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• Improvements to refrenced instance storage

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Commits on Jan 21, 2025

• Move from eager to lazy geometry calculates, expose tolerance parameters

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  bfe2a1a

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• Linter fixes

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  a201101

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• Fix error with allow_duplicates

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  27f4ecb

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• linter and spelling fixes

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  a348d17

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• Fix exports and docs

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Commits on Jan 22, 2025

• rename pixel_transforms -> pixels

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  a1758d2

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• Better error handling for single frame images

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  cff5769

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• Add method to get affine in a different convention

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  8efa2d1

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• Rename voimue_from_image_series -> get_volume_from_series

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• docstring improvements

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• Various further documentation improvements

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Commits on Jan 23, 2025

• Fix series datasets bug

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• Fix test

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• Add further checks on geometry of series for volume

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