datamint 1.7.1__py3-none-any.whl → 1.7.3__py3-none-any.whl

datamint/apihandler/root_api_handler.py

@@ -239,14 +239,14 @@ class RootAPIHandler(BaseAPIHandler):
                         names = _infinite_gen(names)
                     frame_indices = segfiles.get('frame_index', _infinite_gen(None))
                     for f, name, frame_index in tqdm(zip(fpaths, names, frame_indices),
-                                                        desc=f"Uploading segmentations for {file_path}",
-                                                        total=len(fpaths)):
+                                                     desc=f"Uploading segmentations for {file_path}",
+                                                     total=len(fpaths)):
                         if f is not None:
                             await self._upload_segmentations_async(rid,
-                                                                    file_path=f,
-                                                                    name=name,
-                                                                    frame_index=frame_index,
-                                                                    transpose_segmentation=transpose_segmentation)
+                                                                   file_path=f,
+                                                                   name=name,
+                                                                   frame_index=frame_index,
+                                                                   transpose_segmentation=transpose_segmentation)
                 return rid
 
             tasks = [__upload_single_resource(f, segfiles, metadata_file)
@@ -368,26 +368,29 @@ class RootAPIHandler(BaseAPIHandler):
     def _is_dicom_report(file_path: str | IO) -> bool:
         """
         Check if a DICOM file is a report (e.g., Structured Report).
-        
+
         Args:
             file_path: Path to the DICOM file or file-like object.
-            
+
         Returns:
             bool: True if the DICOM file is a report, False otherwise.
         """
         try:
             if not is_dicom(file_path):
                 return False
-            
+
             ds = pydicom.dcmread(file_path, stop_before_pixels=True)
+            if hasattr(file_path, 'seek'):
+                file_path.seek(0)
             modality = getattr(ds, 'Modality', None)
-            
+
             # Common report modalities
-            report_modalities = {'SR', 'DOC', 'KO', 'PR', 'ESR'}  # SR=Structured Report, DOC=Document, KO=Key Object, PR=Presentation State
-            
+            # SR=Structured Report, DOC=Document, KO=Key Object, PR=Presentation State
+            report_modalities = {'SR', 'DOC', 'KO', 'PR', 'ESR'}
+
             return modality in report_modalities
         except Exception as e:
-            _LOGGER.debug(f"Error checking if DICOM is a report: {e}")
+            _LOGGER.warning(f"Error checking if DICOM is a report: {e}")
             return False
 
     def upload_resources(self,
@@ -443,21 +446,18 @@ class RootAPIHandler(BaseAPIHandler):
             list[str | Exception]: A list of resource IDs or errors.
         """
 
-        if discard_dicom_reports:
-            if isinstance(files_path, (str, Path)):
-                files_path = [files_path]
-            elif isinstance(files_path, pydicom.dataset.Dataset):
-                files_path = [files_path]
-
-            old_size = len(files_path)
-            files_path = [f for f in files_path if not RootAPIHandler._is_dicom_report(f)]
-            if old_size != len(files_path):
-                _LOGGER.info(f"Discarded {old_size - len(files_path)} DICOM report files from upload.")
-
         if on_error not in ['raise', 'skip']:
             raise ValueError("on_error must be either 'raise' or 'skip'")
 
         files_path, is_multiple_resources = RootAPIHandler.__process_files_parameter(files_path)
+
+        ### Discard DICOM reports
+        if discard_dicom_reports:
+            files_path = [f for f in files_path if not RootAPIHandler._is_dicom_report(f)]
+            old_size = len(files_path)
+            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.")
+
         if isinstance(metadata, (str, dict)):
             _LOGGER.debug("Converting metadatas to a list")
             metadata = [metadata]
@@ -903,7 +903,7 @@ class RootAPIHandler(BaseAPIHandler):
                                     ) -> None:
         """
         Download multiple resources and save them to the specified paths.
-        
+
         Args:
             resource_ids (list[str]): A list of resource unique ids.
             save_path (list[str] | str): A list of paths to save the files or a directory path.

{datamint-1.7.1.dist-info → datamint-1.7.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: datamint
-Version: 1.7.1
+Version: 1.7.3
 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

{datamint-1.7.1.dist-info → datamint-1.7.3.dist-info}/RECORD

@@ -4,7 +4,7 @@ datamint/apihandler/api_handler.py,sha256=cdVSddrFCKlF_BJ81LO1aJ0OP49rssjpNEFzJ6
 datamint/apihandler/base_api_handler.py,sha256=dWLiowyuP1XiGfNc-_D5oQSmJdfR0Quy0ToeJlkRA8s,11911
 datamint/apihandler/dto/annotation_dto.py,sha256=qId1RK1VO7dXrvGJ7dqJ31jBQB7Z8yy5x0tLSiMxTB4,7105
 datamint/apihandler/exp_api_handler.py,sha256=hFUgUgBc5rL7odK7gTW3MnrvMY1pVfJUpUdzRNobMQE,6226
-datamint/apihandler/root_api_handler.py,sha256=fLJpm2-0xueL0BVwBWoybPqgH0JLyDSWltPXosV4w3U,56984
+datamint/apihandler/root_api_handler.py,sha256=aPJSPYEedm3oBKyEMJAz5J2l3eh1iw_nDVloWgQoeR4,56857
 datamint/client_cmd_tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 datamint/client_cmd_tools/datamint_config.py,sha256=md7dnWrbl10lPtXKbmD9yo6onLJsajeG8Vz0ZWH1v4M,8181
 datamint/client_cmd_tools/datamint_upload.py,sha256=890USkrtaH23mNjTRYVHWce2q9jSmkUNHIP_e8fnJRM,29502
@@ -22,7 +22,7 @@ datamint/logging.yaml,sha256=a5dsATpul7QHeUHB2TjABFjWaPXBMbO--dgn8GlRqwk,483
 datamint/utils/logging_utils.py,sha256=DvoA35ATYG3JTwfXEXYawDyKRfHeCrH0a9czfkmz8kM,1851
 datamint/utils/torchmetrics.py,sha256=lwU0nOtsSWfebyp7dvjlAggaqXtj5ohSEUXOg3L0hJE,2837
 datamint/utils/visualization.py,sha256=yaUVAOHar59VrGUjpAWv5eVvQSfztFG0eP9p5Vt3l-M,4470
-datamint-1.7.1.dist-info/METADATA,sha256=ucTsLUXq0fyNqzo7b9SI_PPJ6i6oU_QpFKicso-11XQ,4090
-datamint-1.7.1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-datamint-1.7.1.dist-info/entry_points.txt,sha256=mn5H6jPjO-rY0W0CAZ6Z_KKWhMLvyVaSpoqk77jlTI4,145
-datamint-1.7.1.dist-info/RECORD,,
+datamint-1.7.3.dist-info/METADATA,sha256=YTALWrY1wwiyjk2a-4FOx_LBxTKxd__QrchCCukTcDA,4090
+datamint-1.7.3.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+datamint-1.7.3.dist-info/entry_points.txt,sha256=mn5H6jPjO-rY0W0CAZ6Z_KKWhMLvyVaSpoqk77jlTI4,145
+datamint-1.7.3.dist-info/RECORD,,