fw-gear-file-metadata-importer 0.1.0

Extract metadata of input file to Flywheel.

File metadata import

Flywheel gear for importing metadata header of file to Flywheel. Metadata is stored under file.info.header. Currently, supporting the following file types:

• DICOM

Usage

Inputs

• input-file: The input file.

Configuration

• debug (boolean, default False): Include debug statements in log.
• Siemens CSA (boolean, default False): If True extract Siemens CSA header for Dicom.

file.info.header structure

DICOM

Dicom header will be stored under file.info.header.dicom. Additionally, if:

• input-file is an archive (e.g dicom.zip), then file.info.header.dicom_array will be populated.
• Siemens CSA is enabled, then file.info.header.csa will be populated if found.

Details

DICOM

By default, the following tags are not extracted:

• All private tags
• PixelData
• Pixel Data
• ContourData
• EncryptedAttributesSequence
• OriginalAttributesSequence
• SpectroscopyData

By default, for zip archive the following tags are extracted and stored in file.info.header.dicom_array:

• AcquisitionNumber
• AcquisitionTime
• EchoTime
• ImageOrientationPatient
• ImagePositionPatient
• ImageType
• InstanceNumber
• SliceLocation

These deny/allow lists can be amended by defining a specific key/value in the project level custom information under context.header.dicom. Key: value should take the form of Tag: bool where Tag can either be a Dicom keyword (e.g. PatientID), a Dicom hex index (e.g 00100020) or a Dicom private tag GEMS_PARM_01, 0043xx01. If bool is True, the tag will be added to the parsed tags , if False is will be removed.