pyalfe.pipeline

pyalfe.pipeline#

class pyalfe.pipeline.PipelineRunner(steps)[source]#

Bases: object

run(accession: str) → None[source]#
class pyalfe.pipeline.PyALFEPipelineRunner(initialization: Initialization, skullstripping: Skullstripping, t1_preprocessing: T1Preprocessing, cross_modality_registration: CrossModalityRegistration, flair_segmentation: SingleModalitySegmentation, enhancement_segmentation: MultiModalitySegmentation, tissue_segmentation: SingleModalitySegmentation, t1_postprocessing: T1Postprocessing, t1_registration: T1Registration, resampling: Resampling, quantification: Quantification)[source]#

Bases: PipelineRunner

The pyalfe pipeline runner.

initialization#

The initialization task object.

Type:

Initialization

skullstripping#

The skulstripping task object.

Type:

Skullstripping

t1_preprocessing#

The t1 preprocessing task object.

Type:

T1Preprocessing

cross_modality_registration#

The cross modality registration object.

Type:

CrossModalityRegistration

flair_segmentation#

The flair segmentation object.

Type:

SingleModalitySegmentation

enhancement_segmentation#

The enhancement segmentation object.

Type:

MultiModalitySegmentation

tissue_segmentation#

The tissue segmentation object.

Type:

SingleModalitySegmentation

t1_postprocessing#

The t1 postprocessing object.

Type:

T1Postprocessing

t1_registration#

The t1 registration object.

Type:

T1Registration

resampling#

The resampling object.

Type:

Resampling

quantification#

The quantification object.

Type:

Quantification

class pyalfe.pipeline.DicomProcessingPipelineRunner(dicom_processing: DicomProcessing)[source]#

Bases: PipelineRunner

The Dicom processing pipeline runner

dicom_processing#

The dicom processing object.

Type:

DicomProcessing