Index

A

AortaMBP (class in autods_pet.roi) (class in autods_pet.roi.aorta_mbp) apply_transform() (in module autods_pet.imaging.registration) assign_ds() (in module autods_pet.deauville) autods_pet.config module autods_pet.deauville module autods_pet.imaging module autods_pet.imaging.dicom module autods_pet.imaging.geometry module autods_pet.imaging.normalization module autods_pet.imaging.registration module autods_pet.imaging.segmentation module autods_pet.io module autods_pet.labels module autods_pet.manifest module autods_pet.ops module autods_pet.ops.dicom_seg module

autods_pet.ops.mask_discovery module autods_pet.ops.masks module autods_pet.ops.morphology module autods_pet.ops.save_masks module autods_pet.ops.stats module autods_pet.patient module autods_pet.pipeline module autods_pet.results module autods_pet.roi module autods_pet.roi.aorta_mbp module autods_pet.roi.brain module autods_pet.roi.liver module autods_pet.roi.long_bones module autods_pet.roi.lumbar_vb module autods_pet.roi.target_roi module

B

BrainROI (class in autods_pet.roi) (class in autods_pet.roi.brain)

C

check_same_geometry() (in module autods_pet.imaging.geometry) check_sub_geometry() (in module autods_pet.imaging.geometry) clear_cache() (autods_pet.patient.PatientCase method) collect_environment() (in module autods_pet.manifest) compute_stats() (in module autods_pet.ops) (in module autods_pet.ops.stats) compute_suvbw() (in module autods_pet.imaging) (in module autods_pet.imaging.normalization)

ConfigValidator (class in autods_pet.config) convert() (autods_pet.pipeline.DeauvillePipeline method) convert_images() (in module autods_pet.pipeline) count_voxels() (in module autods_pet.ops) (in module autods_pet.ops.stats) create_default_config() (in module autods_pet.config) ct_path (autods_pet.patient.PatientCase property)

D

deauville_csv_path (autods_pet.patient.PatientCase property) DeauvillePipeline (class in autods_pet.pipeline) DeauvilleResult (class in autods_pet.results) decay_dose() (in module autods_pet.imaging) (in module autods_pet.imaging.normalization) default_config() (in module autods_pet.config)

dicom_series_to_nifti() (in module autods_pet.imaging) (in module autods_pet.imaging.dicom) dilate_mask_mm() (in module autods_pet.ops.morphology) discover_all_masks() (in module autods_pet.ops.mask_discovery) discover_dicom_seg_masks() (in module autods_pet.ops.mask_discovery) discover_file_masks() (in module autods_pet.ops.mask_discovery) DiscoveredMask (class in autods_pet.ops.mask_discovery)

E

effective_dose() (in module autods_pet.imaging) (in module autods_pet.imaging.normalization) elastix_report_path (autods_pet.patient.PatientCase property) erode_mask_mm() (in module autods_pet.ops.morphology) error (autods_pet.results.DeauvilleResult attribute) errors (autods_pet.config.ConfigValidator property) extract() (autods_pet.pipeline.DeauvillePipeline method) (autods_pet.roi.aorta_mbp.AortaMBP method) (autods_pet.roi.AortaMBP method) (autods_pet.roi.brain.BrainROI method) (autods_pet.roi.BrainROI method) (autods_pet.roi.liver.LiverROI method) (autods_pet.roi.LiverROI method) (autods_pet.roi.long_bones.LongBonesROI method) (autods_pet.roi.LongBonesROI method) (autods_pet.roi.lumbar_vb.LumbarVB method) (autods_pet.roi.LumbarVB method) (autods_pet.roi.target_roi.TargetROI method) (autods_pet.roi.TargetROI method)

extract_ct_tags() (in module autods_pet.imaging) (in module autods_pet.imaging.dicom) extract_new_targets_only() (in module autods_pet.pipeline) extract_patient_weight() (in module autods_pet.imaging) (in module autods_pet.imaging.dicom) extract_pet_tags() (in module autods_pet.imaging) (in module autods_pet.imaging.dicom) extract_rois() (in module autods_pet.pipeline)

F

fill_holes() (in module autods_pet.ops) (in module autods_pet.ops.masks) find_dicom_files() (in module autods_pet.imaging) (in module autods_pet.imaging.dicom)

find_series_by_modality() (in module autods_pet.imaging) (in module autods_pet.imaging.dicom) format (autods_pet.ops.mask_discovery.DiscoveredMask attribute)

G

generate_metadata_template() (in module autods_pet.pipeline)

get_all_targets() (in module autods_pet.config) get_roi_config() (in module autods_pet.config)

I

input_dir (autods_pet.patient.PatientCase property) input_seg_dir (autods_pet.patient.PatientCase property)

is_dicom_seg() (in module autods_pet.ops.dicom_seg) is_valid (autods_pet.config.ConfigValidator property) issues (autods_pet.config.ConfigValidator attribute)

K

keep_largest_component() (in module autods_pet.ops) (in module autods_pet.ops.masks)

key (autods_pet.config.ValidationIssue attribute)

L

label_mask() (in module autods_pet.ops) (in module autods_pet.ops.masks) label_union() (in module autods_pet.ops) (in module autods_pet.ops.masks) level (autods_pet.config.ValidationIssue attribute) list_segments() (in module autods_pet.ops.dicom_seg) LiverROI (class in autods_pet.roi) (class in autods_pet.roi.liver) load_config() (in module autods_pet.config)

load_ct() (autods_pet.patient.PatientCase method) load_pet_registered() (autods_pet.patient.PatientCase method) load_pet_suv() (autods_pet.patient.PatientCase method) load_segmentation() (autods_pet.patient.PatientCase method) load_vert_body_seg() (autods_pet.patient.PatientCase method) LongBonesROI (class in autods_pet.roi) (class in autods_pet.roi.long_bones) LumbarVB (class in autods_pet.roi) (class in autods_pet.roi.lumbar_vb)

M

mask_volume_mm3() (in module autods_pet.ops) (in module autods_pet.ops.stats) max_in_mask() (in module autods_pet.ops) (in module autods_pet.ops.stats) mean_in_mask() (in module autods_pet.ops) (in module autods_pet.ops.stats) message (autods_pet.config.ValidationIssue attribute) metadata_path (autods_pet.patient.PatientCase property) min_in_mask() (in module autods_pet.ops) (in module autods_pet.ops.stats) module autods_pet.config autods_pet.deauville autods_pet.imaging autods_pet.imaging.dicom autods_pet.imaging.geometry autods_pet.imaging.normalization autods_pet.imaging.registration autods_pet.imaging.segmentation autods_pet.io autods_pet.labels autods_pet.manifest autods_pet.ops autods_pet.ops.dicom_seg autods_pet.ops.mask_discovery autods_pet.ops.masks autods_pet.ops.morphology autods_pet.ops.save_masks autods_pet.ops.stats autods_pet.patient autods_pet.pipeline autods_pet.results autods_pet.roi autods_pet.roi.aorta_mbp autods_pet.roi.brain autods_pet.roi.liver autods_pet.roi.long_bones autods_pet.roi.lumbar_vb autods_pet.roi.target_roi

N

normalize() (autods_pet.pipeline.DeauvillePipeline method)

normalize_pet() (in module autods_pet.pipeline)

O

output_dir (autods_pet.patient.PatientCase property)

P

parse_dicom_date() (in module autods_pet.imaging) (in module autods_pet.imaging.normalization) parse_dicom_time() (in module autods_pet.imaging) (in module autods_pet.imaging.normalization) parse_stat() (in module autods_pet.config) path (autods_pet.ops.mask_discovery.DiscoveredMask attribute) patient_id (autods_pet.results.DeauvilleResult attribute)

PatientCase (class in autods_pet.patient) percentile_in_mask() (in module autods_pet.ops) (in module autods_pet.ops.stats) pet_path (autods_pet.patient.PatientCase property) pet_registered_path (autods_pet.patient.PatientCase property) pet_series_uid (autods_pet.patient.PatientCase property) pet_suv_path (autods_pet.patient.PatientCase property)

R

read_dicom_seg() (in module autods_pet.ops.dicom_seg) read_patient_list() (in module autods_pet.io) read_referenced_series_uids() (in module autods_pet.ops.dicom_seg) refine() (autods_pet.roi.aorta_mbp.AortaMBP method) (autods_pet.roi.AortaMBP method) (autods_pet.roi.brain.BrainROI method) (autods_pet.roi.BrainROI method) (autods_pet.roi.liver.LiverROI method) (autods_pet.roi.LiverROI method) (autods_pet.roi.long_bones.LongBonesROI method) (autods_pet.roi.LongBonesROI method) (autods_pet.roi.lumbar_vb.LumbarVB method) (autods_pet.roi.LumbarVB method) refined_mask (autods_pet.results.ROIResult attribute)

register() (autods_pet.pipeline.DeauvillePipeline method) register_pet() (in module autods_pet.pipeline) resample_to_reference() (in module autods_pet.imaging.geometry) resolve_output_dir() (in module autods_pet.config) resolve_paths() (in module autods_pet.patient) resolve_patient_folder() (in module autods_pet.imaging) (in module autods_pet.imaging.dicom) rigid_register_pet_to_ct() (in module autods_pet.imaging) (in module autods_pet.imaging.registration) ROIResult (class in autods_pet.results) rois (autods_pet.results.DeauvilleResult attribute) run() (autods_pet.pipeline.DeauvillePipeline method) run_batch() (autods_pet.pipeline.DeauvillePipeline method) run_totalsegmentator() (in module autods_pet.imaging) (in module autods_pet.imaging.segmentation)

S

save_batch_csv() (in module autods_pet.pipeline) save_dataframe() (in module autods_pet.io) save_raw_masks() (in module autods_pet.ops.save_masks) save_refined_masks() (in module autods_pet.ops.save_masks) score() (autods_pet.pipeline.DeauvillePipeline method) score_deauville() (in module autods_pet.pipeline) scores (autods_pet.results.DeauvilleResult attribute) seconds_between() (in module autods_pet.imaging) (in module autods_pet.imaging.normalization) section (autods_pet.config.ValidationIssue attribute) seg_dir (autods_pet.patient.PatientCase property)

segment() (autods_pet.pipeline.DeauvillePipeline method) segment_ct() (in module autods_pet.pipeline) segment_label (autods_pet.ops.mask_discovery.DiscoveredMask attribute) segment_number (autods_pet.ops.mask_discovery.DiscoveredMask attribute) shrinkage (autods_pet.results.ROIResult attribute) shrinkage_report() (in module autods_pet.ops) (in module autods_pet.ops.stats) signed_distance_mm() (in module autods_pet.ops.morphology) stats (autods_pet.results.ROIResult attribute) subtract_mask() (in module autods_pet.ops.masks) suv_csv_path (autods_pet.patient.PatientCase property)

T

target_name (autods_pet.ops.mask_discovery.DiscoveredMask attribute) TargetROI (class in autods_pet.roi) (class in autods_pet.roi.target_roi)

to_dataframe() (autods_pet.pipeline.DeauvillePipeline static method) TOTSEG_FILENAME (in module autods_pet.imaging.segmentation)

U

update_targets() (autods_pet.pipeline.DeauvillePipeline method)

V

validate() (autods_pet.config.ConfigValidator method) ValidationIssue (class in autods_pet.config)

vert_body_seg_path (autods_pet.patient.PatientCase property) voxelwise_median() (in module autods_pet.ops) (in module autods_pet.ops.stats)

W

warnings (autods_pet.config.ConfigValidator property) write_manifest() (in module autods_pet.manifest)

write_patient_deauville_csv() (in module autods_pet.pipeline) write_patient_suv_csv() (in module autods_pet.pipeline)