fw-gear-file-metadata-importer


Namefw-gear-file-metadata-importer JSON
Version 1.4.1 PyPI version JSON
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SummaryExtract metadata of input file to Flywheel.
upload_time2023-12-02 00:34:47
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authorFlywheel
requires_python>=3.9,<4.0
licenseMIT
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            # 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)
* EEG (BrainVision, EDF, BDF, EEGLAB)

## 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 or multiframe the following tags are extracted
and stored in `file.info.header.dicom_array`:

* `AcquisitionNumber`
* `AcquisitionTime`
* `EchoTime`
* `ImageOrientationPatient`
* `ImagePositionPatient`
* `ImageType`
* `InstanceNumber`
* `SliceLocation`
* `PhaseCount`
* `PhaseIndexes`

### Extracting additional tags

Additional tags can be extracted and indexed by ammending the list above.

To add or remove to that list, specific key/value must be set on the project
custom information (`project.info`) like below:

```json
context: 
   header:
      dicom:
         <DICOM-tag>: True
```

`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 in the `file.info.header.dicom` *and*
the `file.info.header.dicom_array` namespaces, if `False` is will be removed.

### Derived fields

The following values derived from dicom are stored in a `file.info.header.derived` dictionary

* `SpacingBetweenSlices` ( Also a type 3 tag at (0018,0088))
* `MinSliceLocation` : Minimum value of slice location
* `MaxSliceLocation` : Maximum value of slice location
* `ScanCoverage` : Span of slice location (max-min)
* `SliceAxis` : 3D unit vector connecting slice origins
* `PhaseCount` : Number of sequences of consecutive slices with uniform spacing & orientation
* `PhaseIndexes` : If PhaseCount > 1, this array maps the slices indexes to the phase index
* `fov` : "Field of view" which is 3D span in patient coords along x,y,z (empty if slice spacing is not uniform)
* `affine` : 4x4 affine transform to convert grid to patient coords (empty if slice spacing is not uniform)

Raw data

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    "description": "# File metadata importer\n\nFlywheel gear for importing metadata header of file to Flywheel.\nMetadata is stored under `file.info.header`. Currently, supporting\nthe following file types:\n\n* DICOM and DICOM Zip Archive\n* PTD (Siemens PT format)\n* NIfTI\n* ParaVision (Bruker format)\n* PAR/REC (Philips format)\n* EEG (BrainVision, EDF, BDF, EEGLAB)\n\n## Usage\n\n### Inputs\n\n* __input-file__: The input file.\n\n### Configuration\n\n* __debug__ (boolean, default: `False`): Include debug statements in log.\n* __siemens CSA__ (boolean, default: `False`): If True, extracts Siemens CSA header for Dicom.\n* __derived metadata__ (boolean, default: `True`): If True, derives additional metadata from the file header and stores them under file.info.header.derived.\n* __tag__ (string, default: `file-metadata-importer`): The tag to be added on\n  input file upon run completion.\n\n## file.info.header structure\n\n### DICOM\n\nDicom header will be stored under `file.info.header.dicom`. Additionally, if:\n\n* `input-file` is an archive (e.g dicom.zip), then `file.info.header.dicom_array` will be populated.\n* `Siemens CSA` is enabled, then `file.info.header.csa` will be populated if found.\n\n### Bruker ParaVision\n\nParaVision metadata will be stored under `file.info.header.paravision`\n\n### Siemens PTD\n\nThe raw PTD preamble will be stored under `file.info.header.ptd`\n\n## Details\n\n### DICOM\n\nBy default, the following tags are not extracted:\n\n* All private tags\n* `PixelData`\n* `Pixel Data`\n* `ContourData`\n* `EncryptedAttributesSequence`\n* `OriginalAttributesSequence`\n* `SpectroscopyData`\n\nBy default, for zip archive or multiframe the following tags are extracted\nand stored in `file.info.header.dicom_array`:\n\n* `AcquisitionNumber`\n* `AcquisitionTime`\n* `EchoTime`\n* `ImageOrientationPatient`\n* `ImagePositionPatient`\n* `ImageType`\n* `InstanceNumber`\n* `SliceLocation`\n* `PhaseCount`\n* `PhaseIndexes`\n\n### Extracting additional tags\n\nAdditional tags can be extracted and indexed by ammending the list above.\n\nTo add or remove to that list, specific key/value must be set on the project\ncustom information (`project.info`) like below:\n\n```json\ncontext: \n   header:\n      dicom:\n         <DICOM-tag>: True\n```\n\n`Key: value` should take the form of `Tag: bool` where `Tag` can either be\na Dicom keyword (e.g. `PatientID`), a Dicom hex index (e.g `00100020`) or\na Dicom private tag `GEMS_PARM_01, 0043xx01`. If `bool` is `True`,  the tag\nwill be added to the parsed tags in the `file.info.header.dicom` *and*\nthe `file.info.header.dicom_array` namespaces, if `False` is will be removed.\n\n### Derived fields\n\nThe following values derived from dicom are stored in a `file.info.header.derived` dictionary\n\n* `SpacingBetweenSlices` ( Also a type 3 tag at (0018,0088))\n* `MinSliceLocation` : Minimum value of slice location\n* `MaxSliceLocation` : Maximum value of slice location\n* `ScanCoverage` : Span of slice location (max-min)\n* `SliceAxis` : 3D unit vector connecting slice origins\n* `PhaseCount` : Number of sequences of consecutive slices with uniform spacing & orientation\n* `PhaseIndexes` : If PhaseCount > 1, this array maps the slices indexes to the phase index\n* `fov` : \"Field of view\" which is 3D span in patient coords along x,y,z (empty if slice spacing is not uniform)\n* `affine` : 4x4 affine transform to convert grid to patient coords (empty if slice spacing is not uniform)\n",
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Flywheel
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