fw-gear-file-metadata-importer 1.2.3

Extract metadata of input file to Flywheel.

File metadata importer

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

• DICOM and DICOM Zip Archive
• PTD (Siemens PT format)
• NIfTI
• ParaVision (Bruker format)
• PAR/REC (Philips format)

Usage

Inputs

• input-file: The input file.

Configuration

• debug (boolean, default: False): Include debug statements in log.
• siemens CSA (boolean, default: False): If True, extracts Siemens CSA header for Dicom.
• derived metadata (boolean, default: True): If True, derives additional metadata from the file header and stores them under file.info.header.derived.
• tag (string, default: file-metadata-importer): The tag to be added on input file upon run completion.

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.

Bruker ParaVision

ParaVision metadata will be stored under file.info.header.paravision

Siemens PTD

The raw PTD preamble will be stored under file.info.header.ptd

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.