Extract metadata of input file to Flywheel.
Project description
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 and DICOM Zip Archive
- PTD (Siemens PT 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 extract Siemens CSA header for Dicom. - 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), thenfile.info.header.dicom_array
will be populated.Siemens CSA
is enabled, thenfile.info.header.csa
will be populated if found.
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.
Project details
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