patientImagingCRDP

class PDCP.patientImagingCRDP(codesconfig=None)

Bases: PDCP.patientImaging

This class was used to collect and process datasets where connections between CT, RTSTRUCTS,RTDOSES, PLANS are required.

Methods Summary

generate_patients_data(firstversion)

A function that collects a set of patients required and verified files (CT slices, rt structs, etc.) from the orthanc server.

verify_study(df, notes[, modality])

Within this function, the links between different modalities are identified to find connections.

Methods Documentation

generate_patients_data(firstversion)

A function that collects a set of patients required and verified files (CT slices, rt structs, etc.) from the orthanc server.

Parameters

  • orthanc_ids (list) – a list of orthanc ids

  • patients_ids (list) – a list of patient ids

Returns

  • pids (list) – the patient ids

  • comments (list) – a list of the patients comments (_SUCCESS, _ERROR, or _PATIENTIMAGESNOTFOUND)

verify_study(df, notes, modality='CT')

Within this function, the links between different modalities are identified to find connections. It is expected that each CT will have associated RTSTRUCTS which will also have associated RTPLAN (SOPinstanceUID), which will also have links to the RTDOSES. By finding these links, we try to remove any unused RTDOSES, RTSTRUCTS, CTs

To do that, the CT SeriesInstanceUID links to the RTSTRUCT through the tag: ReferencedFrameOfReferenceSequence – > SeriesInstanceUID The RTSTRUCT SOPInstanceUID links to RTPLAN instances through the tag: ReferencedStructureSetSequence –> ReferencedSOPInstanceUID The RTDOSE SOPInstanceUID links to the RTPLAN instances through the tag: ReferencedRTPlanSequence –>

By that, it is assumed that the modalities, files used in treatment will be all connected.

Any study with no connections will be discarded. Any study with multiple connections will be discarded

Parameters

  • df (Pandas dataframe) – a dataframe with the patient imaging records

  • notes (list) – a list that contians the notes, and is used to append new notes while verifying the patient files.

Returns

  • list_of_values (list of dicts) – A list of dictionaries that contain the details of associations between studies objects.

  • notes (list) – list of notes appended while verifying the patient’s imaging files.