pyalfe.tasks.quantification

class pyalfe.tasks.quantification.Quantification(pipeline_dir: PipelineDataDir, modalities_all: list[Modality], modalities_target: list[Modality], dominant_tissue: str | None = None)

Bases: Task

This task generates the quantification files. This is the final task in the pipeline.

pipeline_dir

The pipeline data directory object.

Type:

PipelineDataDir

modalities_all

All the modalities for processed by the pipeline.

Type:

list[Modality]

modalities_target

Target modalities that are used to defince lesions.

Type:

list[Modality]

dominant_tissue

The dominant tissue where the tumor or lesion is expected to be located at. THe options are white_matter, gray_matter, auto. If auto is chosen, then the dominant tissue is chosen to be the tissue with which the lesion most intersects with.

Type:

str

logger = <Logger Quantification (DEBUG)>

static load_nii_gz(filename)

load(filename)

load_modality_images(accession, target)

load_template_images(accession, modality)

get_radiomics(skullstripped_file, lesion_seg_file)

get_brain_volume_stats(brain_mask, tissue_seg, ventricles_seg, template_images, voxel_volume)

get_lesion_stats(lesion_seg, tissue_seg, ventricles_distance, modality_images, template_images, voxel_volume, lesion_label=1)

static get_summary_update_from_individual(individual_lesion_df)

run(accession)

Runs the task for an accession.