datamint 1.8.0__py3-none-any.whl → 1.9.0__py3-none-any.whl

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)
 
@@ -437,7 +443,7 @@ 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.")

{datamint-1.8.0.dist-info → datamint-1.9.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: datamint
-Version: 1.8.0
+Version: 1.9.0
 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.dist-info → datamint-1.9.0.dist-info}/RECORD

@@ -4,7 +4,7 @@ datamint/apihandler/api_handler.py,sha256=cdVSddrFCKlF_BJ81LO1aJ0OP49rssjpNEFzJ6
 datamint/apihandler/base_api_handler.py,sha256=GQuJS3FFjxPi-2vkJtbHeNKywoa-PWa3Qvw3NGRzxug,12206
 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=03eDLFYHzaQi-cv5aonKj7j0KowGK6sU5F_TCx3tRlU,59183
+datamint/apihandler/root_api_handler.py,sha256=_vgIjqt7jb1yUkhyMez1Tg-vs4xmExby4TqWnfQG4OI,59320
 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=J62xBDTaLxwBFWDmuXhzgbmZfPWaAZLr7CKsbqgTI7U,31389
@@ -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-1.8.0.dist-info/METADATA,sha256=wkOXaU-02ah0wNosREQqODM-H9NmdEw1L3sQ3F9gFW8,4100
-datamint-1.8.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-datamint-1.8.0.dist-info/entry_points.txt,sha256=mn5H6jPjO-rY0W0CAZ6Z_KKWhMLvyVaSpoqk77jlTI4,145
-datamint-1.8.0.dist-info/RECORD,,
+datamint-1.9.0.dist-info/METADATA,sha256=M1oMNcVYjTVV8tfZcxxcPFijib04QC8Zz9VBQLR7tXg,4100
+datamint-1.9.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+datamint-1.9.0.dist-info/entry_points.txt,sha256=mn5H6jPjO-rY0W0CAZ6Z_KKWhMLvyVaSpoqk77jlTI4,145
+datamint-1.9.0.dist-info/RECORD,,