rpt_dosi.db
===========

.. py:module:: rpt_dosi.db


Classes
-------

.. autoapisummary::

   rpt_dosi.db.PatientTreatmentDatabase
   rpt_dosi.db.CycleTreatmentDatabase
   rpt_dosi.db.TimepointTreatmentDatabase


Functions
---------

.. autoapisummary::

   rpt_dosi.db.db_get_time_interval
   rpt_dosi.db.create_test_db
   rpt_dosi.db.compute_time_activity_curve


Module Contents
---------------

.. py:function:: db_get_time_interval(cycle, acquisition)

.. py:class:: PatientTreatmentDatabase(filename, create=False, sync_metadata_image=False)

   Bases: :py:obj:`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/ ...


   .. py:attribute:: _metadata_fields


   .. py:attribute:: patient_id
      :value: None



   .. py:attribute:: body_weight_kg
      :value: None



   .. py:attribute:: cycles


   .. py:attribute:: _db_file_path
      :value: None



   .. py:attribute:: _db_data_path
      :value: None



   .. py:method:: info()


   .. py:property:: db_data_path


   .. py:property:: db_file_path


   .. py:method:: __str__()


   .. py:method:: number_of_timepoints()


   .. py:method:: number_of_rois()


   .. py:method:: number_of_images()


   .. py:method:: get_cycle(cycle_id)


   .. py:method:: __getitem__(key)


   .. py:method:: add_cycle(cycle)


   .. py:method:: remove_cycle(cycle_id)


   .. py:method:: add_new_cycle(cycle_id)


   .. py:method:: add_dicom_ct(cycle_id, tp_id, folder_path)


   .. py:method:: write(filename=None, sync_metadata_image=True, sync_policy='auto')


   .. py:method:: write_metadata_images()


   .. py:method:: sync_metadata_images(sync_policy='auto')


   .. py:method:: read(filename, sync_metadata_image)


   .. py:method:: to_dict()

      Store the metadata attributes to a dictionary.



   .. py:method:: from_dict(data)

      Set the metadata attributes of the instance from a dictionary.



   .. py:method:: check_folders_exist()


   .. py:method:: check_files_exist()


   .. py:method:: check_files_metadata()


.. py:class:: CycleTreatmentDatabase(db, cycle_id)

   Bases: :py:obj:`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.


   .. py:attribute:: _metadata_fields


   .. py:attribute:: db


   .. py:attribute:: cycle_id


   .. py:attribute:: injection_activity_mbq
      :value: None



   .. py:attribute:: _injection_datetime
      :value: None



   .. py:attribute:: injection_radionuclide
      :value: None



   .. py:attribute:: timepoints


   .. py:method:: info()


   .. py:method:: __str__()


   .. py:property:: injection_datetime


   .. py:method:: get_timepoint(tp_id)


   .. py:method:: __getitem__(key)


   .. py:method:: add_timepoint(tp)


   .. py:method:: add_new_timepoint(tp_id)


   .. py:property:: cycle_path


   .. py:method:: to_dict()

      Store the metadata attributes to a dictionary.



   .. py:method:: from_dict(data)

      Set the metadata attributes of the instance from a dictionary.



   .. py:method:: sync_metadata_images(sync_policy='auto')


   .. py:method:: write_metadata_images()


   .. py:method:: check_folders_exist()


   .. py:method:: check_files_exist()


   .. py:method:: check_files_metadata()


.. py:class:: TimepointTreatmentDatabase(cycle, tp_id)

   Bases: :py:obj:`rpt_dosi.metadata.ClassWithMetaData`


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


   .. py:attribute:: _metadata_fields


   .. py:attribute:: cycle


   .. py:attribute:: timepoint_id


   .. py:attribute:: _acquisition_datetime
      :value: None



   .. py:attribute:: images


   .. py:attribute:: rois


   .. py:method:: info()


   .. py:method:: __str__()


   .. py:method:: to_dict()

      Store the metadata attributes to a dictionary.



   .. py:method:: from_dict(data)

      Set the metadata attributes of the instance from a dictionary.



   .. py:property:: acquisition_datetime


   .. py:method:: sync_metadata_images(sync_policy='auto')


   .. py:method:: sync_metadata_image(image_name, sync_policy='auto')


   .. py:method:: sync_metadata_roi(roi_name, sync_policy='auto')


   .. py:method:: write_metadata_images()


   .. py:property:: timepoint_path


   .. py:property:: rois_path


   .. py:method:: get_roi(roi_id)


   .. py:method:: get_roi_path(roi_id)


   .. py:method:: get_metaimage(image_name)


   .. py:method:: get_image_file_path(image_name)


   .. py:property:: time_from_injection_h


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


   .. py:method:: add_image(image_name, meta_image)


   .. py:method:: add_rois(roi_list, mode='copy', exist_ok=False)


   .. py:method:: add_roi(roi)


   .. py:method:: add_roi_from_file(roi_id, input_path, mode='copy', exist_ok=False)


   .. py:method:: check_folders_exist()


   .. py:method:: check_files_exist()


   .. py:method:: check_files_metadata()


.. py:function:: create_test_db(data_folder, db_file_path)

.. py:function:: compute_time_activity_curve(cycle, roi_names, spect_name='spect')