def build_patient_forest(
orthanc: Orthanc,
max_nbr_workers: int = 100,
patient_filter: Optional[Callable] = None,
study_filter: Optional[Callable] = None,
series_filter: Optional[Callable] = None,
do_trim_forest_after_construction: bool = True) -> List[Patient]:
"""Build a patient forest
Each tree in the forest correspond to a patient. The layers in the
tree correspond to:
`Patient -> Studies -> Series -> Instances`
Note that trees are build concurrently. You may want to change the
default values. Increase this number could improve performance,
but it will take more memory.
Parameters
----------
orthanc
Orthanc object.
max_nbr_workers
Number of workers for to build the concurrent tree.
patient_filter
Patient filter (e.g. lambda patient: patient.get_id() == '03HDQ99*')
study_filter
Study filter (e.g. lambda study: study.get_id() == '*pros*')
series_filter
Series filter (e.g. lambda series: series.get_modality() == 'SR')
do_trim_forest_after_construction
If True, trim the forest after its construction.
Returns
-------
List[Patient]
List of patient tree representation.
"""
patient_identifiers = orthanc.get_patients()
with ThreadPoolExecutor(max_workers=max_nbr_workers) as patient_executor:
future_patients = patient_executor.map(
lambda patient_identifier:
_build_patient(patient_identifier, orthanc, patient_filter,
study_filter, series_filter), patient_identifiers)
patient_forest = list(future_patients)
return trim_patient_forest(
patient_forest
) if do_trim_forest_after_construction else patient_forest
def _build_series(series_information: Dict, orthanc: Orthanc,
series_filter: Optional[Callable]) -> Series:
instance_information = orthanc.get_series_instance_information(
series_information['ID'])
series = Series(series_information['ID'], orthanc, series_information)
if series_filter is not None:
if not series_filter(series):
return series
series.instances = [
Instance(i['ID'], orthanc, i) for i in instance_information
]
return series
def _build_study(study_information: Dict, orthanc: Orthanc,
study_filter: Optional[Callable],
series_filter: Optional[Callable]) -> Study:
series_information = orthanc.get_study_series_information(
study_information['ID'])
study = Study(study_information['ID'], orthanc, study_information)
if study_filter is not None:
if not study_filter(study):
return study
study.series = [
_build_series(i, orthanc, series_filter) for i in series_information
]
return study
def _build_patient(patient_identifier: str, orthanc: Orthanc,
patient_filter: Optional[Callable],
study_filter: Optional[Callable],
series_filter: Optional[Callable]) -> Patient:
study_information = orthanc.get_patient_studies_information(
patient_identifier)
patient = Patient(patient_identifier, orthanc)
if patient_filter is not None:
if not patient_filter(patient):
return patient
patient.studies = [
_build_study(i, orthanc, study_filter, series_filter)
for i in study_information
]
return patient