datamint 1.8.0__tar.gz → 1.9.1__tar.gz

{datamint-1.8.0 → datamint-1.9.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: datamint
-Version: 1.8.0
+Version: 1.9.1
 Summary: A library for interacting with the Datamint API, designed for efficient data management, processing and Deep Learning workflows.
 Requires-Python: >=3.10
 Classifier: Programming Language :: Python :: 3
@@ -19,7 +19,7 @@ Requires-Dist: humanize (>=4.0.0,<5.0.0)
 Requires-Dist: lazy-loader (>=0.3.0)
 Requires-Dist: lightning
 Requires-Dist: matplotlib
-Requires-Dist: medimgkit (>=0.3.1)
+Requires-Dist: medimgkit (>=0.4.4)
 Requires-Dist: nest-asyncio (>=1.0.0,<2.0.0)
 Requires-Dist: nibabel (>=4.0.0)
 Requires-Dist: numpy

{datamint-1.8.0 → datamint-1.9.1}/datamint/apihandler/root_api_handler.py

@@ -8,7 +8,7 @@ import asyncio
 import aiohttp
 from medimgkit.dicom_utils import anonymize_dicom, to_bytesio, is_dicom, is_dicom_report
 from medimgkit import dicom_utils, standardize_mimetype
-from medimgkit.io_utils import is_io_object
+from medimgkit.io_utils import is_io_object, peek
 from medimgkit.format_detection import guess_typez, guess_extension, DEFAULT_MIME_TYPE
 from medimgkit.nifti_utils import DEFAULT_NIFTI_MIME, NIFTI_MIMES
 import pydicom
@@ -103,16 +103,22 @@ class RootAPIHandler(BaseAPIHandler):
         filename = os.path.basename(name)
         _LOGGER.debug(f"File name '{filename}' mimetype: {mimetype}")
 
-        if anonymize:
-            if is_a_dicom_file == True or is_dicom(file_path):
-                ds = pydicom.dcmread(file_path)
+        if is_a_dicom_file == True or is_dicom(file_path):
+            if tags is None:
+                tags = []
+            else:
+                tags = list(tags)
+            ds = pydicom.dcmread(file_path)
+            if anonymize:
                 _LOGGER.info(f"Anonymizing {file_path}")
                 ds = anonymize_dicom(ds, retain_codes=anonymize_retain_codes)
-                # make the dicom `ds` object a file-like object in order to avoid unnecessary disk writes
-                f = to_bytesio(ds, name)
-            else:
-                _LOGGER.warning(f"File {file_path} is not a dicom file. Skipping anonymization.")
-                f = _open_io(file_path)
+            lat = dicom_utils.get_dicom_laterality(ds)
+            if lat == 'L':
+                tags.append("left")
+            elif lat == 'R':
+                tags.append("right")
+            # make the dicom `ds` object a file-like object in order to avoid unnecessary disk writes
+            f = to_bytesio(ds, name)
         else:
             f = _open_io(file_path)
 
@@ -423,8 +429,21 @@ class RootAPIHandler(BaseAPIHandler):
 
         # Discard DICOM reports
         if discard_dicom_reports:
-            files_path = [f for f in files_path if not is_dicom_report(f)]
             old_size = len(files_path)
+            # Create filtered lists maintaining index correspondence
+            filtered_files = []
+            filtered_metadata = []
+            
+            for i, f in enumerate(files_path):
+                if not is_dicom_report(f):
+                    filtered_files.append(f)
+                    if metadata is not None:
+                        filtered_metadata.append(metadata[i])
+            
+            files_path = filtered_files
+            if metadata is not None:
+                metadata = filtered_metadata
+                
             if old_size is not None and old_size != len(files_path):
                 _LOGGER.info(f"Discarded {old_size - len(files_path)} DICOM report files from upload.")
 
@@ -437,7 +456,7 @@ class RootAPIHandler(BaseAPIHandler):
         if assemble_dicoms:
             files_path, assembled = self._assemble_dicoms(files_path)
             assemble_dicoms = assembled
-
+        
         if segmentation_files is not None:
             if assemble_dicoms:
                 raise NotImplementedError("Segmentation files cannot be uploaded when assembling dicoms yet.")
@@ -1093,16 +1112,46 @@ class RootAPIHandler(BaseAPIHandler):
         """
         if isinstance(resource_ids, str):
             resource_ids = [resource_ids]
-        for rid in resource_ids:
-            url = f"{self._get_endpoint_url(RootAPIHandler.ENDPOINT_RESOURCES)}/{rid}"
-            request_params = {'method': 'DELETE',
-                              'url': url
-                              }
-            try:
-                self._run_request(request_params)
-            except ResourceNotFoundError as e:
-                e.set_params('resource', {'resource_id': rid})
-                raise e
+
+        async def _delete_all_resources_async():
+            async with aiohttp.ClientSession() as session:
+                tasks = [
+                    self._delete_resource_async(resource_id, session)
+                    for resource_id in resource_ids
+                ]
+                await asyncio.gather(*tasks)
+
+        loop = asyncio.get_event_loop()
+        loop.run_until_complete(_delete_all_resources_async())
+            
+    
+    async def _delete_resource_async(self,
+                                   resource_id: str,
+                                   session: aiohttp.ClientSession | None = None) -> None:
+        """
+        Asynchronously delete a resource by its unique id.
+
+        Args:
+            resource_id (str): The resource unique id.
+            session (aiohttp.ClientSession | None): The aiohttp session to use for the request.
+
+        Raises:
+            ResourceNotFoundError: If the resource does not exist.
+        """
+        if session is not None and not isinstance(session, aiohttp.ClientSession):
+            raise ValueError("session must be an aiohttp.ClientSession object.")
+
+        url = f"{self._get_endpoint_url(RootAPIHandler.ENDPOINT_RESOURCES)}/{resource_id}"
+        request_params = {
+            'method': 'DELETE',
+            'url': url
+        }
+
+        try:
+            await self._run_request_async(request_params, session)
+        except ResourceNotFoundError as e:
+            e.set_params('resource', {'resource_id': resource_id})
+            raise e
 
     def get_datasets(self) -> list[dict]:
         """

{datamint-1.8.0 → datamint-1.9.1}/pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "datamint"
 description = "A library for interacting with the Datamint API, designed for efficient data management, processing and Deep Learning workflows."
-version = "1.8.0"
+version = "1.9.1"
 dynamic = ["dependencies"]
 requires-python = ">=3.10"
 readme = "README.md"
@@ -40,7 +40,7 @@ matplotlib = "*"
 lightning = "*"
 albumentations = ">=2.0.0"
 lazy-loader = ">=0.3.0"
-medimgkit = ">=0.3.1"
+medimgkit = ">=0.4.4"
 # For compatibility with the datamintapi package
 datamintapi = "0.0.*"
 # Extra dependencies for docs