2.1.1.2. rpt_dosi.db

2.1.1.2.1. Classes

PatientTreatmentDatabase	Store information about a patient treatment:
CycleTreatmentDatabase	Class to manage metadata, providing methods to convert to/from dict and JSON.
TimepointTreatmentDatabase	Store filenames, not paths, paths are computed on the fly.

2.1.1.2.2. Functions

db_get_time_interval(cycle, acquisition)
create_test_db(data_folder, db_file_path)
compute_time_activity_curve(cycle, roi_names[, spect_name])

2.1.1.2.3. Module Contents

rpt_dosi.db.db_get_time_interval(cycle, acquisition)

class rpt_dosi.db.PatientTreatmentDatabase(filename, create=False, sync_metadata_image=False)

Bases: rpt_dosi.metadata.ClassWithMetaData

Store information about a patient treatment: - all cycles, all imaging timepoints - consider a hierarchy folders patient/cycle_id/timepoint_id/images - from / to json files - when store to a json file, the database folder MUST be the one of the json file

patient/

db.json cycle1/

tp1/

ct.nii.gz spect.nii.gz

tp2/ …

cycle2/ …

_metadata_fields

patient_id = None

body_weight_kg = None

cycles

_db_file_path = None

_db_data_path = None

info()

property db_data_path

property db_file_path

__str__()

number_of_timepoints()

number_of_rois()

number_of_images()

get_cycle(cycle_id)

__getitem__(key)

add_cycle(cycle)

remove_cycle(cycle_id)

add_new_cycle(cycle_id)

add_dicom_ct(cycle_id, tp_id, folder_path)

write(filename=None, sync_metadata_image=True, sync_policy='auto')

write_metadata_images()

sync_metadata_images(sync_policy='auto')

read(filename, sync_metadata_image)

to_dict()

Store the metadata attributes to a dictionary.

from_dict(data)

Set the metadata attributes of the instance from a dictionary.

check_folders_exist()

check_files_exist()

check_files_metadata()

class rpt_dosi.db.CycleTreatmentDatabase(db, cycle_id)

Bases: rpt_dosi.metadata.ClassWithMetaData

Class to manage metadata, providing methods to convert to/from dict and JSON. The class fields that are considered as metadata are store in _metadata_fields.

_metadata_fields

db

cycle_id

injection_activity_mbq = None

_injection_datetime = None

injection_radionuclide = None

timepoints

info()

__str__()

property injection_datetime

get_timepoint(tp_id)

__getitem__(key)

add_timepoint(tp)

add_new_timepoint(tp_id)

property cycle_path

to_dict()

Store the metadata attributes to a dictionary.

from_dict(data)

Set the metadata attributes of the instance from a dictionary.

sync_metadata_images(sync_policy='auto')

write_metadata_images()

check_folders_exist()

check_files_exist()

check_files_metadata()

class rpt_dosi.db.TimepointTreatmentDatabase(cycle, tp_id)

Bases: rpt_dosi.metadata.ClassWithMetaData

Store filenames, not paths, paths are computed on the fly. The folders are build from db/cycle/timepoint

_metadata_fields

cycle

timepoint_id

_acquisition_datetime = None

images

rois

info()

__str__()

to_dict()

Store the metadata attributes to a dictionary.

from_dict(data)

Set the metadata attributes of the instance from a dictionary.

property acquisition_datetime

sync_metadata_images(sync_policy='auto')

sync_metadata_image(image_name, sync_policy='auto')

sync_metadata_roi(roi_name, sync_policy='auto')

write_metadata_images()

property timepoint_path

property rois_path

get_roi(roi_id)

get_roi_path(roi_id)

get_metaimage(image_name)

get_image_file_path(image_name)

property time_from_injection_h

add_image_from_file(image_name, input_path, image_type=None, filename=None, mode='copy', unit=None, file_exist_ok=False)

add_image(image_name, meta_image)

add_rois(roi_list, mode='copy', exist_ok=False)

add_roi(roi)

add_roi_from_file(roi_id, input_path, mode='copy', exist_ok=False)

check_folders_exist()

check_files_exist()

check_files_metadata()

rpt_dosi.db.create_test_db(data_folder, db_file_path)

rpt_dosi.db.compute_time_activity_curve(cycle, roi_names, spect_name='spect')