fw-gear-dicom-fixer 0.3.6

This gear reports on the Dicom files data elements and optionally fixes or enhances the problematic ones, generating a new archive.

Dicom Fixer

Description

This gear is responsible for reporting on the Dicom files data elements and optionally fixing/enhancing the problematic ones and generating a new archive.
This gear utilizes the tracker functionality of RawDataElements in fw-file. Namely, it houses a collection of default and custom callbacks that are applied to RawDataElements on read through pydicom. More on callback below.

Usage

Inputs

• dicom: Input dicom

Configuration

• debug (boolean, default False): Include debug statements in output.
• tag (string, default: dicom-fixer): The tag to be added on input file upon run completion.

Callbacks

fw-file callbacks:

• backslash_in_VM1_string_callback: Fix value of RawDataElement with VM=1 and VR of type string that contains an invalid \ character (\ is the array delimiter in Dicom standard) and replaces with _. Use case is to handle non-compliant Dicom implementation that let e.g. SeriesDescription value containing .
• handle_none_VR: A callback to handle VR = None.
  • Mirror the handling of pydicom pydicom.dataelement.DataElement_from_raw when VR is None but set VR to 'UN' for public tag that are not in the pydicom dictionary instead of raising a KeyError.
• handle_un_VR: A callback to handle VR=UN.
  • Mirror pydicom.dataelem.DataElement_from_raw when VR is UN but instead set VR to 'OB' when decoding value raises with the inferred VR.
• converter_exception_callback: A callback to catch NotImplementedError when raw_elem contains an invalid VR.

Custom callbacks:

• handle_incorrect_unit: Callback to fix known incorrect units
  • Currently only implemented to correct MagneticFieldStrength from milli-Tesla to Tesla.

Non-RawDataElement callbacks:

• decode_dcm: Mirrors pydicom.dataset.Dataset.decode, except it ignores decoding the OriginalAttributesSequence tag.
• is_dcm: This is a callback that works on the collection itself, filtering out and removing any files that don't look like a DICOM.
  • "Looks like a dicom" is defined as: Having at least 2 public dicom tags outside the file_meta (0x0000, and 0x0002) group.

Contributing

For more information about how to get started contributing to that gear, checkout CONTRIBUTING.md.