Feat/niftii

pyorthanc/_resources/instance.py

@@ -42,13 +42,15 @@ def get_dicom_file_content(self) -> bytes:
         """
         return self.client.get_instances_id_file(self.id_)
 
-    def download(self, filepath: Union[str, BinaryIO], with_progres: bool = False) -> None:
+    def download(self, filepath: Union[str, BinaryIO], with_progres: bool = False, file_format: str = 'dcm') -> None:
         """Download the DICOM file to a target path or buffer
 
         This method is an alternative to the `.get_dicom_file_content()` method for large files.
         The `.get_dicom_file_content()` method will pull all the data in a single GET call,
         while `.download()` stream the data to a file or a buffer.
         Favor the `.download()` method to avoid timeout and memory issues.
+        file_format option accepts 'dcm', 'nii', 'nii.gz'
+
 
         Examples
         --------
@@ -68,9 +70,19 @@ def download(self, filepath: Union[str, BinaryIO], with_progres: bool = False) -
         # Now do whatever you want to do
         buffer.seek(0)
         dicom_bytes = buffer.read()
+
+        # download instance in nii.gz format
+        instance.download('instance.nii.gz', file_format='nii.gz')
+
         ```
         """
-        self._download_file(f'{self.client.url}/instances/{self.id_}/file', filepath, with_progres)
+        if file_format.lower() not in ['dcm', 'nii', 'nii.gz']:
+            raise ValueError(
+                f"format should be one of ['dcm, 'nii', 'nii.gz'], "
+                f"got '{file_format}' instead."
+            )
+
+        self._download_file(f'{self.client.url}/instances/{self.id_}', filepath, with_progres, file_format)
 
     @property
     def uid(self) -> str:

pyorthanc/_resources/patient.py

@@ -139,7 +139,7 @@ def download(self, filepath: Union[str, BinaryIO], with_progres: bool = False) -
         zip_bytes = buffer.read()
         ```
         """
-        self._download_file(f'{self.client.url}/patients/{self.id_}/archive', filepath, with_progres)
+        self._download_file(f'{self.client.url}/patients/{self.id_}', filepath, with_progres, 'zip')
 
     def get_patient_module(self, simplify: bool = False, short: bool = False) -> Dict:
         """Get patient module in a simplified version

pyorthanc/_resources/resource.py

@@ -1,10 +1,12 @@
 import abc
 from typing import Any, BinaryIO, Dict, List, Optional, Union
 
+from httpx import HTTPError
 from httpx._types import QueryParamTypes
 
 from .. import errors, util
 from ..client import Orthanc
+from ..errors import PluginNotEnabledError
 
 
 class Resource:
@@ -76,11 +78,38 @@ def _make_response_format_params(self, simplify: bool = False, short: bool = Fal
 
         return params
 
+    def _is_neuro_plugin_installed(self):
+        try:
+            _ = self.client.get_plugins_id(id_='neuro')
+            return True
+        except HTTPError:
+            return False
+
     def _download_file(
             self, url: str,
             filepath: Union[str, BinaryIO],
             with_progress: bool = False,
+            file_format: str = 'zip',
             params: Optional[QueryParamTypes] = None):
+
+        if file_format.lower() == 'zip':
+            url = f'{url}/archive'
+        elif file_format.lower() == 'dcm':
+            url = f'{url}/file'
+        elif file_format.lower() in ['nii', 'nii.gz']:
+            if not self._is_neuro_plugin_installed():
+                raise PluginNotEnabledError(
+                    'Neuro plugin is not installed or enabled on Orthanc instance. More information on https://orthanc.uclouvain.be/book/plugins/neuro.html'
+                )
+            url = f'{url}/nifti'
+            if file_format.lower() == 'nii.gz':
+                url += '?compress'
+        else:
+            raise ValueError(
+                f"format should be one of ['dcm, 'zip', 'nii', 'nii.gz'], "
+                f"got '{file_format}' instead."
+            )
+
         # Check if filepath is a path or a file object.
         if isinstance(filepath, str):
             is_file_object = False

pyorthanc/_resources/series.py

@@ -584,13 +584,14 @@ def get_zip(self) -> bytes:
         """
         return self.client.get_series_id_archive(self.id_)
 
-    def download(self, filepath: Union[str, BinaryIO], with_progres: bool = False) -> None:
+    def download(self, filepath: Union[str, BinaryIO], with_progres: bool = False, file_format: str = 'zip') -> None:
         """Download the zip file to a target path or buffer
 
         This method is an alternative to the `.get_zip()` method for large files.
         The `.get_zip()` method will pull all the data in a single GET call,
         while `.download()` stream the data to a file or a buffer.
         Favor the `.download()` method to avoid timeout and memory issues.
+        file_format option accepts 'zip', 'nii', 'nii.gz'
 
         Examples
         --------
@@ -610,9 +611,17 @@ def download(self, filepath: Union[str, BinaryIO], with_progres: bool = False) -
         # Now do whatever you want to do
         buffer.seek(0)
         zip_bytes = buffer.read()
+
+        # download series in nii.gz format
+        a_series.download('series.nii.gz', file_format='nii.gz')
         ```
         """
-        self._download_file(f'{self.client.url}/series/{self.id_}/archive', filepath, with_progres)
+        if file_format.lower() not in ['zip', 'nii', 'nii.gz']:
+            raise ValueError(
+                f"format should be one of ['zip', 'nii', 'nii.gz'], "
+                f"got '{file_format}' instead."
+            )
+        self._download_file(f'{self.client.url}/series/{self.id_}', filepath, with_progres, file_format)
 
     def get_shared_tags(self, simplify: bool = False, short: bool = False) -> Dict:
         """Retrieve the shared tags of the series"""

pyorthanc/_resources/study.py

@@ -563,7 +563,7 @@ def download(self, filepath: Union[str, BinaryIO], with_progres: bool = False) -
         zip_bytes = buffer.read()
         ```
         """
-        self._download_file(f'{self.client.url}/studies/{self.id_}/archive', filepath, with_progres)
+        self._download_file(f'{self.client.url}/studies/{self.id_}', filepath, with_progres, 'zip')
 
     def get_shared_tags(self, simplify: bool = False, short: bool = False) -> Dict:
         """Retrieve the shared tags of the study"""

pyorthanc/errors.py

@@ -8,3 +8,7 @@ class ModificationError(Exception):
 
 class NotInInternalEnvironmentError(Exception):
     pass
+
+
+class PluginNotEnabledError(Exception):
+    pass