Add new resource attributes and increase performance

pyorthanc/__init__.py

@@ -1,16 +1,17 @@
+from . import errors, util
+from ._filtering import build_patient_forest, find, trim_patients
+from ._find import find_instances, find_patients, find_series, find_studies, query_orthanc
+from ._modality import Modality, RemoteModality
+from ._resources import Instance, Patient, Series, Study
 from .async_client import AsyncOrthanc
 from .client import Orthanc
-from .filtering import build_patient_forest, find, trim_patients
-from .find import find_instances, find_patients, find_series, find_studies, query_orthanc
-from .remote import RemoteModality
-from .resources import Instance, Patient, Series, Study
 from .retrieve import retrieve_and_write_instance, retrieve_and_write_patient, retrieve_and_write_patients, \
     retrieve_and_write_series, retrieve_and_write_study
 
-
 __all__ = [
     'AsyncOrthanc',
     'Orthanc',
+    'Modality',
     'RemoteModality',
     'Patient',
     'Study',
@@ -29,4 +30,6 @@
     'retrieve_and_write_study',
     'retrieve_and_write_series',
     'retrieve_and_write_instance',
+    'util',
+    'errors',
 ]

pyorthanc/filtering.py → pyorthanc/_filtering.py

@@ -4,10 +4,10 @@
 
 from .async_client import AsyncOrthanc
 from .client import Orthanc
-from .resources.instance import Instance
-from .resources.patient import Patient
-from .resources.series import Series
-from .resources.study import Study
+from ._resources.instance import Instance
+from ._resources.patient import Patient
+from ._resources.series import Series
+from ._resources.study import Study
 from .util import async_to_sync
 
 

pyorthanc/find.py → pyorthanc/_find.py

@@ -1,11 +1,11 @@
 from typing import Dict, List, Union
 
 from .client import Orthanc
-from .resources.instance import Instance
-from .resources.patient import Patient
-from .resources.resource import Resource
-from .resources.series import Series
-from .resources.study import Study
+from ._resources.instance import Instance
+from ._resources.patient import Patient
+from ._resources.resource import Resource
+from ._resources.series import Series
+from ._resources.study import Study
 
 DEFAULT_RESOURCES_LIMIT = 1_000
 

pyorthanc/remote.py → pyorthanc/_modality.py

@@ -5,9 +5,8 @@
 from .client import Orthanc
 
 
-class RemoteModality:
-    """Wrapper around Orthanc API when dealing with a (remote) modality.
-    """
+class Modality:
+    """Wrapper around Orthanc API when dealing with a modality."""
 
     def __init__(self, client: Orthanc, modality: str) -> None:
         """Constructor
@@ -23,7 +22,7 @@ def __init__(self, client: Orthanc, modality: str) -> None:
         self.modality = modality
 
     def echo(self) -> bool:
-        """C-Echo to remote modality
+        """C-Echo to modality
 
         Returns
         -------
@@ -60,12 +59,12 @@ def query(self, data: Dict) -> Dict:
         ...         }
         ... }
 
-        >>> remote_modality = RemoteModality(
+        >>> modality = Modality(
         ...     client=Orthanc('http://localhost:8042'),
         ...     modality='sample'
         ... )
 
-        >>> remote_modality.query(data)
+        >>> modality.query(data)
         """
         return dict(self.client.post_modalities_id_query(self.modality, json=data))
 
@@ -88,13 +87,13 @@ def move(self, query_identifier: str, cmove_data: Dict) -> Dict:
 
         Examples
         --------
-        >>> remote_modality = RemoteModality(Orthanc('http://localhost:8042'), 'modality')
-        >>> query_id = remote_modality.query(
+        >>> modality = Modality(Orthanc('http://localhost:8042'), 'modality')
+        >>> query_id = modality.query(
         ...     data={'Level': 'Series',
         ...           'Query': {'PatientID': '',
         ...                     'Modality':'SR'}})
 
-        >>> remote_modality.move(
+        >>> modality.move(
         ...     query_identifier=query_id['ID'],
         ...     cmove_data={'TargetAet': 'TARGETAET'}
         ... )
@@ -103,7 +102,7 @@ def move(self, query_identifier: str, cmove_data: Dict) -> Dict:
         return dict(self.client.post_queries_id_retrieve(query_identifier, json=cmove_data))
 
     def store(self, instance_or_series_id: str) -> Dict:
-        """Store series or instance to remote modality.
+        """Store series or instance to modality.
 
         Parameters
         ----------
@@ -130,3 +129,4 @@ def get_query_answers(self) -> Dict:
         return answers
 
 
+RemoteModality = Modality

pyorthanc/resources/instance.py → pyorthanc/_resources/instance.py

@@ -39,14 +39,8 @@ def get_dicom_file_content(self) -> bytes:
 
     @property
     def uid(self) -> str:
-        """Get SOPInstanceUID
-
-        Returns
-        -------
-        str
-            SOPInstanceUID
-        """
-        return self.get_main_information()['MainDicomTags']['SOPInstanceUID']
+        """Get SOPInstanceUID"""
+        return self._get_main_dicom_tag_value('SOPInstanceUID')
 
     def get_main_information(self) -> Dict:
         """Get instance information
@@ -96,57 +90,72 @@ def creation_date(self) -> datetime:
         return util.make_datetime_from_dicom_date(date_string, time_string)
 
     @property
-    def series_id(self) -> str:
-        """Get the parent series identifier
-
-        Returns
-        -------
-        str
-            The parent series identifier.
-        """
+    def series_identifier(self) -> str:
+        """Get the parent series identifier"""
         return self.get_main_information()['ParentSeries']
+
+    @property
+    def acquisition_number(self) -> int:
+        return int(self._get_main_dicom_tag_value('AcquisitionNumber'))
+
+    @property
+    def image_index(self) -> int:
+        return int(self._get_main_dicom_tag_value('ImageIndex'))
 
     @property
-    def first_level_tags(self) -> Any:
-        """Get first level tags
+    def image_orientation_patient(self) -> List[float]:
+        orientation = self._get_main_dicom_tag_value('ImageOrientationPatient')
 
-        Returns
-        -------
-        Any
-            First level tags.
-        """
+        return [float(i) for i in orientation.split('\\')]
+
+    @property
+    def image_position_patient(self) -> List[float]:
+        position = self._get_main_dicom_tag_value('ImagePositionPatient')
+
+        return [float(i) for i in position.split('\\')]
+
+    @property
+    def image_comments(self) -> str:
+        return self._get_main_dicom_tag_value('ImageComments')
+
+    @property
+    def instance_number(self) -> int:
+        return int(self._get_main_dicom_tag_value('InstanceNumber'))
+
+    @property
+    def number_of_frames(self) -> int:
+        return int(self._get_main_dicom_tag_value('NumberOfFrames'))
+
+    @property
+    def temporal_position_identifier(self) -> str:
+        return self._get_main_dicom_tag_value('TemporalPositionIdentifier')
+
+    @property
+    def first_level_tags(self) -> Any:
+        """Get first level tags"""
         return self.client.get_instances_id_content_tags_path(self.id_, '')
 
     @property
     def tags(self) -> Dict:
-        """Get tags
-
-        Returns
-        -------
-        Dict
-            Tags in the form of a dictionary.
-        """
+        """Get tags"""
         return dict(self.client.get_instances_id_tags(self.id_))
 
     @property
     def simplified_tags(self) -> Dict:
-        """Get simplified tags
-
-        Returns
-        -------
-        Dict
-            Simplified tags in the form of a dictionary.
-        """
+        """Get simplified tags"""
         return dict(self.client.get_instances_id_tags(self.id_, params={'simplify': True}))
 
     @property
     def labels(self) -> List[str]:
+        """Get instance labels"""
         return self.get_main_information()['Labels']
 
     def add_label(self, label: str) -> None:
+        """Add label to resource"""
         self.client.put_instances_id_labels_label(self.id_, label)
 
     def remove_label(self, label):
+        """Remove label from resource"""
         self.client.delete_instances_id_labels_label(self.id_, label)
 
     def get_content_by_tag(self, tag: str) -> Any:

pyorthanc/resources/patient.py → pyorthanc/_resources/patient.py

@@ -33,36 +33,29 @@ def get_main_information(self) -> Dict:
 
     @property
     def patient_id(self) -> str:
-        """Get patient ID
-
-        Returns
-        -------
-        str
-            Patient ID
-        """
-        return self.get_main_information()['MainDicomTags']['PatientID']
+        """Get patient ID"""
+        return self._get_main_dicom_tag_value('PatientID')
 
     @property
     def name(self) -> str:
-        """Get patient name
+        """Get patient name"""
+        return self._get_main_dicom_tag_value('PatientName')
 
-        Returns
-        -------
-        str
-            Patient name
-        """
-        return self.get_main_information()['MainDicomTags']['PatientName']
+    @property
+    def birth_date(self) -> datetime:
+        """Get patient birthdate"""
+        date = self._get_main_dicom_tag_value('PatientBirthDate')
+
+        return util.make_datetime_from_dicom_date(date)
 
     @property
     def sex(self) -> str:
-        """Get patient sex
+        """Get patient sex"""
+        return self._get_main_dicom_tag_value('PatientSex')
 
-        Returns
-        -------
-        str
-            Patient sex
-        """
-        return self.get_main_information()['MainDicomTags']['PatientSex']
+    @property
+    def other_patient_ids(self) -> str:
+        return self._get_main_dicom_tag_value('OtherPatientIDs').split('\\')
 
     @property
     def is_stable(self):
@@ -224,14 +217,14 @@ def studies(self) -> List[Study]:
         """
         if self.lock:
             if self._child_resources is None:
-                studies_information = self.client.get_patients_id_studies(self.id_)
-                self._child_resources = [Study(i['ID'], self.client, self.lock) for i in studies_information]
+                studies_ids = self.get_main_information()['Studies']
+                self._child_resources = [Study(i, self.client, self.lock) for i in studies_ids]
 
             return self._child_resources
 
-        studies_information = self.client.get_patients_id_studies(self.id_)
+        studies_ids = self.get_main_information()['Studies']
 
-        return [Study(i['ID'], self.client, self.lock) for i in studies_information]
+        return [Study(i, self.client, self.lock) for i in studies_ids]
 
     def anonymize(self, remove: List = None, replace: Dict = None, keep: List = None, force: bool = False) -> 'Patient':
         """Anonymize patient

pyorthanc/resources/resource.py → pyorthanc/_resources/resource.py

@@ -1,5 +1,6 @@
-from typing import Dict, List, Optional
+from typing import Any, Dict, List, Optional
 
+from .. import errors
 from ..client import Orthanc
 
 
@@ -41,6 +42,12 @@ def identifier(self) -> str:
     def get_main_information(self):
         raise NotImplementedError
 
+    def _get_main_dicom_tag_value(self, tag: str) -> Any:
+        try:
+            return self.get_main_information()['MainDicomTags'][tag]
+        except KeyError:
+            raise errors.TagDoesNotExistError(f'{self} has no {tag} tag.')
+
     def __eq__(self, other: 'Resource') -> bool:
         return self.id_ == other.id_