Code

Release v2.3.0#97

Code

Merged

alexzwanenburg merged 122 commits intomasteroncoray/mirp:masterfrom v2.3.0oncoray/mirp:v2.3.0Copy head branch name to clipboardSep 18, 2024

+9,725-5,686

Commits

Commits on Jul 5, 2024

• Create new feature backend

  Show description for 10f030d
  alexzwanenburg

  committed
  10f030d

  Copy full SHA for 10f030d

• Update histogram.py

  alexzwanenburg

  committed
  9138fa7

  Copy full SHA for 9138fa7

• Further work on feature back-end.

  alexzwanenburg

  committed
  bab6805

  Copy full SHA for bab6805

Commits on Jul 8, 2024

• Move rep utility function from _featuresets.utilities to _features.utilities

  alexzwanenburg

  committed
  cedcb1b

  Copy full SHA for cedcb1b

• WIP on feature backend

  alexzwanenburg

  committed
  67c0d9c

  Copy full SHA for 67c0d9c

• Further WIP on feature backend.

  Show description for 3c91e54
  alexzwanenburg

  committed
  3c91e54

  Copy full SHA for 3c91e54

• Fixed missing semicolon.

  alexzwanenburg

  committed
  f2fb56d

  Copy full SHA for f2fb56d

• Added RLM-LRE and RLM-LGRE features.

  alexzwanenburg

  committed
  13ead79

  Copy full SHA for 13ead79

Commits on Jul 10, 2024

• Moved code related to the RLM matrix to rlm_matrix.py

  alexzwanenburg

  committed
  f9ef84a

  Copy full SHA for f9ef84a

• Added remaining RLM features

  alexzwanenburg

  committed
  76333b0

  Copy full SHA for 76333b0

• WIP on integrating features into the workflow.

  alexzwanenburg

  committed
  9c6d311

  Copy full SHA for 9c6d311

• Integrated conversion to feature tables.

  alexzwanenburg

  committed
  395eb58

  Copy full SHA for 395eb58

• Debugging RLM.

  alexzwanenburg

  committed
  19a757b

  Copy full SHA for 19a757b

Commits on Jul 11, 2024

• DataFrame objects are now correctly generated from feature objects.

  alexzwanenburg

  committed
  48074d5

  Copy full SHA for 48074d5

• Matrices are now correctly initialised prior to processing

  alexzwanenburg

  committed
  28c5715

  Copy full SHA for 28c5715

• Feature order in class_dict is now maintained.

  alexzwanenburg

  committed
  2d352e7

  Copy full SHA for 2d352e7

• Allow for passing additional values to set_values_from_matrix

  alexzwanenburg

  committed
  e2d0a8f

  Copy full SHA for e2d0a8f

• Added _lookup_intensity helper method.

  alexzwanenburg

  committed
  e3ba710

  Copy full SHA for e3ba710

• Initial implementation of MatrixCM

  alexzwanenburg

  committed
  a3827f3

  Copy full SHA for a3827f3

• Initial implementations for CM-features.

  alexzwanenburg

  committed
  31f4e00

  Copy full SHA for 31f4e00

• CM features can now be passed to the workflow.

  alexzwanenburg

  committed
  1c803ee

  Copy full SHA for 1c803ee

• Work in progress on CM features.

  alexzwanenburg

  committed
  d1d57ac

  Copy full SHA for d1d57ac

• Temporary changes to test.

  alexzwanenburg

  committed
  882f904

  Copy full SHA for 882f904

• Added more features.

  alexzwanenburg

  committed
  2558da0

  Copy full SHA for 2558da0

Commits on Jul 12, 2024

• Added remaining CM features.

  alexzwanenburg

  committed
  e46f9c3

  Copy full SHA for e46f9c3

• CM features can now be computed correctly.

  alexzwanenburg

  committed
  163e527

  Copy full SHA for 163e527

• Stubs for size zone matrix features.

  alexzwanenburg

  committed
  81e75b1

  Copy full SHA for 81e75b1

• Change signature of Matrix.compute to facilitate size zone matrices

  alexzwanenburg

  committed
  5b28413

  Copy full SHA for 5b28413

• Implemented MatrixSZM.compute method.

  alexzwanenburg

  committed
  09c5802

  Copy full SHA for 09c5802

• Update MatrixSZM.set_values_from_matrix

  alexzwanenburg

  committed
  8ee4c87

  Copy full SHA for 8ee4c87

• Re-enable SZM tests.

  alexzwanenburg

  committed
  b3b3a74

  Copy full SHA for b3b3a74

• First implementation of SZM features.

  alexzwanenburg

  committed
  6b10411

  Copy full SHA for 6b10411

• Implemented features for DZM.

  alexzwanenburg

  committed
  a431a8d

  Copy full SHA for a431a8d

Commits on Jul 15, 2024

• WIP on NGTDM features.

  alexzwanenburg

  committed
  be33a7f

  Copy full SHA for be33a7f

Commits on Jul 16, 2024

• Updated NGTDM to function correctly.

  alexzwanenburg

  committed
  4e40d64

  Copy full SHA for 4e40d64

• Implemented NGLDM.

  alexzwanenburg

  committed
  d6124a3

  Copy full SHA for d6124a3

• Added intensity histogram features.

  alexzwanenburg

  committed
  3a0d832

  Copy full SHA for 3a0d832

• WIP for statistics features.

  alexzwanenburg

  committed
  8b0ac7a

  Copy full SHA for 8b0ac7a

Commits on Jul 17, 2024

• Implemented statistical features.

  alexzwanenburg

  committed
  f74c8eb

  Copy full SHA for f74c8eb

• WIP for morphological features.

  alexzwanenburg

  committed
  214d79d

  Copy full SHA for 214d79d

Commits on Jul 30, 2024

• Further work on morphological features.

  alexzwanenburg

  committed
  6c7010f

  Copy full SHA for 6c7010f

Commits on Jul 31, 2024

• Morphological features have been re-implemented.

  alexzwanenburg

  committed
  f907df1

  Copy full SHA for f907df1

• implemented framework for local intensity features

  alexzwanenburg

  committed
  3103971

  Copy full SHA for 3103971

Commits on Aug 1, 2024

• Re-implemented local intensity features.

  alexzwanenburg

  committed
  fe076e7

  Copy full SHA for fe076e7

• Scaffolding for ivh features.

  alexzwanenburg

  committed
  4c745a1

  Copy full SHA for 4c745a1

Commits on Aug 2, 2024

• WIP on IVH features.

  alexzwanenburg

  committed
  2f4bca0

  Copy full SHA for 2f4bca0

• Re-implemented IVH.

  alexzwanenburg

  committed
  a68a784

  Copy full SHA for a68a784

• Removed unused import.

  alexzwanenburg

  committed
  4d0f61b

  Copy full SHA for 4d0f61b

Commits on Aug 5, 2024

• Added update_ibsi_compliance method.

  alexzwanenburg

  committed
  0e6859e

  Copy full SHA for 0e6859e

• Added _data_key methods.

  alexzwanenburg

  committed
  bf6ce0d

  Copy full SHA for bf6ce0d

• Use lru_cache with max_size as 1 to limit memory use.

  alexzwanenburg

  committed
  bd8e1bf

  Copy full SHA for bd8e1bf

Commits on Aug 6, 2024

• Switch from cache to lru_cache

  alexzwanenburg

  committed
  79ad519

  Copy full SHA for 79ad519

• Remove _data_key again.

  alexzwanenburg

  committed
  6ac3cc3

  Copy full SHA for 6ac3cc3

• Added clear_local_cache that checks for deleting contained data.

  alexzwanenburg

  committed
  3d1e2ca

  Copy full SHA for 3d1e2ca

• Avoid warnings on _get_data by replacing it with _get_spatial_data

  alexzwanenburg

  committed
  717913c

  Copy full SHA for 717913c

• Removed print statements for caching.

  alexzwanenburg

  committed
  59f48b0

  Copy full SHA for 59f48b0

• Update typing of ibsi_compliant attribute.

  alexzwanenburg

  committed
  fd404b9

  Copy full SHA for fd404b9

• Added ibsi_compliant and ibsi_id to filters and image objects.

  alexzwanenburg

  committed
  d900a2c

  Copy full SHA for d900a2c

• Add checks on IBSI-compliance.

  alexzwanenburg

  committed
  1bea771

  Copy full SHA for 1bea771

• Remove outdated code.

  alexzwanenburg

  committed
  ece6792

  Copy full SHA for ece6792

• Remove redundant code.

  alexzwanenburg

  committed
  9736976

  Copy full SHA for 9736976

• Update design.rst

  alexzwanenburg

  committed
  1ebff74

  Copy full SHA for 1ebff74

• Added is_ibsi_compliant method to check ibsi-compliance.

  alexzwanenburg

  committed
  5ea03bc

  Copy full SHA for 5ea03bc

• Fixes to IVH feature computation.

  alexzwanenburg

  committed
  32f3dfc

  Copy full SHA for 32f3dfc

• Filtered images are now indicated in feature names.

  alexzwanenburg

  committed
  cab6e45

  Copy full SHA for cab6e45

• Fortified feature computation against empty masks.

  alexzwanenburg

  committed
  e408583

  Copy full SHA for e408583

• Report changes to feature backend.

  alexzwanenburg

  committed
  d0539ba

  Copy full SHA for d0539ba

Commits on Aug 8, 2024

• Added parametric map and more segmentation example data from DICOM4QI

  alexzwanenburg

  committed
  f75c7e6

  Copy full SHA for f75c7e6

• Simplify __init__ of image files.

  alexzwanenburg

  committed
  be83298

  Copy full SHA for be83298

• Initial implementation for processing ADC data.

  alexzwanenburg

  committed
  e569dd5

  Copy full SHA for e569dd5

Commits on Aug 9, 2024

• Add unit test for ADC image parameter export.

  alexzwanenburg

  committed
  5d67be9

  Copy full SHA for 5d67be9

• WIP on adding multi-frame dicom objects.

  alexzwanenburg

  committed
  6ed1e50

  Copy full SHA for 6ed1e50

Commits on Aug 11, 2024

• WIP on multi-frame dicom objects

  alexzwanenburg

  committed
  67bdfca

  Copy full SHA for 67bdfca

Commits on Aug 12, 2024

• get_pydicom_meta_tag can now inspect functional groups.

  alexzwanenburg

  committed
  372bf6c

  Copy full SHA for 372bf6c

• Extend signature for several _complete_* methods

  alexzwanenburg

  committed
  1fec911

  Copy full SHA for 1fec911

• ImageDicomFile.create() now calls to update_from_template to instantiate dicom file objects.

  alexzwanenburg

  committed
  b21a3f9

  Copy full SHA for b21a3f9

• Update _complete_* methods to work with functional groups.

  alexzwanenburg

  committed
  4992300

  Copy full SHA for 4992300

• Added_complete_image_orientation for multi-frame dicom.

  alexzwanenburg

  committed
  2ce3d05

  Copy full SHA for 2ce3d05

• Fixed an incorrect tag reference.

  alexzwanenburg

  committed
  d1e1c39

  Copy full SHA for d1e1c39

• Updated _complete_* method for multi-frame stacks.

  alexzwanenburg

  committed
  285fca9

  Copy full SHA for 285fca9

• Add load_data for multi-frame dicom/

  alexzwanenburg

  committed
  6430c6d

  Copy full SHA for 6430c6d

• Do not create deep copies of image_data and image_metadata.

  alexzwanenburg

  committed
  318ca8d

  Copy full SHA for 318ca8d

• Update check for MR-ADC to be more specific.

  alexzwanenburg

  committed
  1385bff

  Copy full SHA for 1385bff

• WIP on multi-frame DICOM.

  alexzwanenburg

  committed
  b133d98

  Copy full SHA for b133d98

Commits on Aug 13, 2024

• Added multi-frame info for MR and CT.

  alexzwanenburg

  committed
  bd7423c

  Copy full SHA for bd7423c

• Added PET DICOM multi-frame

  alexzwanenburg

  committed
  ddedd8d

  Copy full SHA for ddedd8d

• Added multi-frame ADC tests.

  alexzwanenburg

  committed
  5c398d6

  Copy full SHA for 5c398d6

• Added mention of ADC maps to document.

  alexzwanenburg

  committed
  6f963b7

  Copy full SHA for 6f963b7

Commits on Aug 14, 2024

• Set default slope and intercept if even the shared function groups lack these tags.

  alexzwanenburg

  committed
  22c66d7

  Copy full SHA for 22c66d7

• Update NEWS.md

  alexzwanenburg

  committed
  cd6d89e

  Copy full SHA for cd6d89e

• Added test data for planar imaging.

  alexzwanenburg

  committed
  3029d49

  Copy full SHA for 3029d49

Commits on Aug 15, 2024

• Added MRI-DCE test data.

  alexzwanenburg

  committed
  9eec1f9

  Copy full SHA for 9eec1f9

• Remove unusedsingle frame object.

  alexzwanenburg

  committed
  c7d75d5

  Copy full SHA for c7d75d5

• WIP on planar images such as digital x-rays.

  alexzwanenburg

  committed
  908b850

  Copy full SHA for 908b850

Commits on Aug 16, 2024

• Basic implementation of planar imaging now functions.

  alexzwanenburg

  committed
  3b63775

  Copy full SHA for 3b63775

• Working implementation for digital x-ray parameters.

  alexzwanenburg

  committed
  20e9e8e

  Copy full SHA for 20e9e8e

• Added image type again and patient orientation to exported parameters.

  alexzwanenburg

  committed
  dfc99b7

  Copy full SHA for dfc99b7

• Added tests for exporting metadata from MG and CR data.

  alexzwanenburg

  committed
  a0539a1

  Copy full SHA for a0539a1

• Update documentation to show off planar imaging.

  alexzwanenburg

  committed
  e8c3b0c

  Copy full SHA for e8c3b0c

• Update NEWS.md

  alexzwanenburg

  committed
  f638f73

  Copy full SHA for f638f73

Commits on Aug 17, 2024

• Early work on replacing by_slice by separate_slices attribute.

  alexzwanenburg

  committed
  d930344

  Copy full SHA for d930344

Commits on Aug 20, 2024

• Replaced by_slice by separate_slices in image filters.

  alexzwanenburg

  committed
  3e1dd67

  Copy full SHA for 3e1dd67

• Update by_slice in interpolate and related functions.

  alexzwanenburg

  committed
  b74942b

  Copy full SHA for b74942b

• Adapted use of by_slice by alter_mask and underlying functions.

  alexzwanenburg

  committed
  f82f103

  Copy full SHA for f82f103

• Updated by_slice in randomise_mask

  alexzwanenburg

  committed
  0dc7445

  Copy full SHA for 0dc7445

• Updated by_slice in split_masks

  alexzwanenburg

  committed
  a73b086

  Copy full SHA for a73b086

• Updated by_slice in decimate

  alexzwanenburg

  committed
  a3d6110

  Copy full SHA for a3d6110

• Update by_slice in dilate.

  alexzwanenburg

  committed
  6e9614c

  Copy full SHA for 6e9614c

• Checks on image modalities are now conducted correctly in flat files.

  alexzwanenburg

  committed
  f9c1638

  Copy full SHA for f9c1638

• PET modality is now consistently named "pt" for DICOM objects.

  alexzwanenburg

  committed
  99a071b

  Copy full SHA for 99a071b

Commits on Aug 21, 2024

• Fixed outdated tests due to change in error message.

  alexzwanenburg

  committed
  bf96ba6

  Copy full SHA for bf96ba6

• Fixes numpy deprecation warnings related to np.cross.

  alexzwanenburg

  committed
  e3dd3ae

  Copy full SHA for e3dd3ae

Commits on Aug 23, 2024

• Implementation for processing DCE-MR images.

  alexzwanenburg

  committed
  d1bd96e

  Copy full SHA for d1bd96e

• Updated processing of SEG files to be more consistent with multi-frame images.

  alexzwanenburg

  committed
  af5debb

  Copy full SHA for af5debb

• Updated test_dce_mr_image_methods test.

  alexzwanenburg

  committed
  1a2081b

  Copy full SHA for 1a2081b

• DCE exports no additional parameters.

  alexzwanenburg

  committed
  febb54c

  Copy full SHA for febb54c

• Updated documentation.

  alexzwanenburg

  committed
  d33e7a7

  Copy full SHA for d33e7a7

Commits on Sep 18, 2024

• Incremented version.

  alexzwanenburg

  committed
  6d06ece

  Copy full SHA for 6d06ece

• Removed block on ray version.

  alexzwanenburg

  committed
  71bab0b

  Copy full SHA for 71bab0b

• Mention support for python version 3.12

  alexzwanenburg

  committed
  aa545a7

  Copy full SHA for aa545a7

• Added missing DICOM tag.

  alexzwanenburg

  committed
  3a766b9

  Copy full SHA for 3a766b9

• Update documentation.

  alexzwanenburg

  committed
  53f12d1

  Copy full SHA for 53f12d1