pymedphys/pymedphys: v0.32.0

"Stable" API changes

(Won't truly be stable until after a 1.0.0 release)

Bug fixes

• Fixed bug in the PyMedPhys trf decoding logic where leaf pairs 77, 78, 79, and 80 on the Y2 bank were decoded into having the wrong sign.
  • See issue #968 and pull request #970 for more details.

Breaking changes

• config.toml has undergone a few breaking changes.
  • See the example for a working config file.
  • See below for a comparison highlighting the key differences.

# Previous version
[[site]]
name = "rccc"
escan_directory = '\\pdc\Shared\Scanned Documents\RT\PhysChecks\Logfile PDFs'

    [[site.linac]]
    name = "2619"
    icom_live_directory = '\\rccc-physicssvr\iComLogFiles\live\192.168.100.200'


# New version
[[site]]
name = "rccc"

    [site.export-directories]
    escan = '\\pdc\Shared\Scanned Documents\RT\PhysChecks\Logfile PDFs'
    anonymised_monaco = 'S:\DataExchange\anonymised-monaco'
    icom_live = '\\rccc-physicssvr\iComLogFiles\live'

    [[site.linac]]
    name = "2619"
    ip = '192.168.100.200'

New Features

• Two new optional keywords were added to pymedphys.dicom.anonymise. These are replacement_strategy and identifying_keywords. This was designed to support alternative anonymisation methods. The API to the anonymise function is being flagged for a rework and simplification for which a breaking change is likely to occur in the near future.
• Added ability to configure logging via config.toml.

Data file changes

Refers to the data files accessible via pymedphys.data_path, pymedphys.zip_data_paths, and pymedphys.zenodo_data_paths.

• The data file pinnacle_test_data_no_image.zip was removed and its contents were moved into pinnacle_test_data.zip.
• Data files treatment-record-anonymisation.zip, negative-mu-density.trf, and trf-references-and-baselines.zip were added.

Beta API changes

Nil

Experimental API changes New Features

• Added pseudonymisation as an experimental extension of anonymise.
  • This API is undergoing refinement, however in its current form it is accessible via pymedphys.experimental.pseudonymisation.pseudonymisation_dispatch and pymedphys.experimental.pseudonymisation.get_default_pseudonymisation_keywords. These are designed to be passed to the new keywords replacement_strategy and identifying_keywords within pymedphys.dicom.anonymise.
  • The pseudonymisation strategy uses SHA3_256 hashing for text and UIDs, date shifting for dates, and jittering for Age. The intent is to enable sets of data that are correlated to remain correlated, and to prevent uncorrelated patient/study/series from clashing.

• Added experimental pseudonymisation CLI. Callable via pymedphys experimental dicom anonymise --pseudo path/to/dicom.dcm

• Added pymedphys experimental gui. This is a testing ground for new GUIs that are intended to appear within pymedphys gui in the future. The GUIs exposed under this experimental scope are minimally tested.

  • At this point in time, the new GUIs include a GUI index, an electron insert factor prediction tool, and a Monaco anonymisation tool.

Bug Fixes

• Pinnacle Export Tool now allows for the trial to be set using the CLI. See issue #973 and pull request #995 for more details.
• Fixed bug where the dose grid in the Pinnacle Export Tool was only correct when patients were in HFS. See #929 for more details.