datamint 1.4.0__py3-none-any.whl → 1.4.1__py3-none-any.whl

datamint/client_cmd_tools/datamint_upload.py

@@ -267,7 +267,13 @@ def _find_json_metadata(file_path: str | Path) -> Optional[str]:
         Optional[str]: Path to the JSON metadata file if found, None otherwise
     """
     file_path = Path(file_path)
-    json_path = file_path.with_suffix('.json')
+    
+    # Handle .nii.gz files specially - need to remove both extensions
+    if file_path.name.endswith('.nii.gz'):
+        base_name = file_path.name[:-7]  # Remove .nii.gz
+        json_path = file_path.parent / f"{base_name}.json"
+    else:
+        json_path = file_path.with_suffix('.json')
 
     if json_path.exists() and json_path.is_file():
         _LOGGER.debug(f"Found JSON metadata file: {json_path}")
@@ -313,12 +319,11 @@ def _collect_metadata_files(files_path: list[str], auto_detect_json: bool) -> tu
     if used_json_files:
         _LOGGER.debug(f"Filtering out {len(used_json_files)} JSON metadata files from main upload list")
         filtered_metadata_files = []
-        filtered_file_index = 0
-
+        
         for original_file in files_path:
             if original_file not in used_json_files:
-                filtered_metadata_files.append(metadata_files[files_path.index(original_file)])
-                filtered_file_index += 1
+                original_index = files_path.index(original_file)
+                filtered_metadata_files.append(metadata_files[original_index])
 
         metadata_files = filtered_metadata_files
 

datamint/experiment/experiment.py

@@ -803,7 +803,7 @@ class Experiment:
         Args:
             resource_id: The resource ID of the sample.
             predictions: The predictions of the model. One binary mask for each class. Can be a numpy array of shape (H, W) or (N,H,W);
-                Or a path to a png file; Or a path to a .nii.gz file.
+                Or a path to a png file; Or a path to a .nii/.nii.gz file.
             label_name: The name of the class or a dictionary mapping pixel values to names.
                 Example: ``{1: 'Femur', 2: 'Tibia'}`` means that pixel value 1 is 'Femur' and pixel value 2 is 'Tibia'.
             frame_index: The frame index of the prediction or a list of frame indexes.

datamint/utils/io_utils.py

@@ -54,17 +54,32 @@ def read_video(file_path: str, index: int = None) -> np.ndarray:
 
 
 def read_nifti(file_path: str) -> np.ndarray:
-    imgs = nib.load(file_path).get_fdata()  # shape: (W, H, #frame) or (W, H)
-    if imgs.ndim == 2:
-        imgs = imgs.transpose(1, 0)
-        imgs = imgs[np.newaxis, np.newaxis]
-    elif imgs.ndim == 3:
-        imgs = imgs.transpose(2, 1, 0)
-        imgs = imgs[:, np.newaxis]
-    else:
-        raise ValueError(f"Unsupported number of dimensions in '{file_path}': {imgs.ndim}")
+    """
+    Read a NIfTI file and return the image data in standardized format.
+    
+    Args:
+        file_path: Path to the NIfTI file (.nii or .nii.gz)
+        
+    Returns:
+        np.ndarray: Image data with shape (#frames, C, H, W)
+    """
+    try:
+        nii_img = nib.load(file_path)
+        imgs = nii_img.get_fdata()  # shape: (W, H, #frame) or (W, H)
+        
+        if imgs.ndim == 2:
+            imgs = imgs.transpose(1, 0)  # (W, H) -> (H, W)
+            imgs = imgs[np.newaxis, np.newaxis]  # -> (1, 1, H, W)
+        elif imgs.ndim == 3:
+            imgs = imgs.transpose(2, 1, 0)  # (W, H, #frame) -> (#frame, H, W)
+            imgs = imgs[:, np.newaxis]  # -> (#frame, 1, H, W)
+        else:
+            raise ValueError(f"Unsupported number of dimensions in '{file_path}': {imgs.ndim}")
 
-    return imgs
+        return imgs
+    except Exception as e:
+        _LOGGER.error(f"Failed to read NIfTI file '{file_path}': {e}")
+        raise e
 
 
 def read_image(file_path: str) -> np.ndarray:
@@ -123,6 +138,18 @@ def read_array_normalized(file_path: str,
             else:
                 if mime_type == 'image/x.nifti' or file_path.endswith(NII_EXTS):
                     imgs = read_nifti(file_path)
+                    # For NIfTI files, try to load associated JSON metadata
+                    if return_metainfo:
+                        json_path = file_path.replace('.nii.gz', '.json').replace('.nii', '.json')
+                        if os.path.exists(json_path):
+                            try:
+                                import json
+                                with open(json_path, 'r') as f:
+                                    metainfo = json.load(f)
+                                _LOGGER.debug(f"Loaded JSON metadata from {json_path}")
+                            except Exception as e:
+                                _LOGGER.warning(f"Failed to load JSON metadata from {json_path}: {e}")
+                                metainfo = None
                 elif mime_type.startswith('image/') or file_path.endswith(IMAGE_EXTS):
                     imgs = read_image(file_path)
                 elif file_path.endswith('.npy') or mime_type == 'application/x-numpy-data':

{datamint-1.4.0.dist-info → datamint-1.4.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: datamint
-Version: 1.4.0
+Version: 1.4.1
 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

{datamint-1.4.0.dist-info → datamint-1.4.1.dist-info}/RECORD

@@ -7,7 +7,7 @@ datamint/apihandler/exp_api_handler.py,sha256=hFUgUgBc5rL7odK7gTW3MnrvMY1pVfJUpU
 datamint/apihandler/root_api_handler.py,sha256=-dy5IxDP3wJAr2ahhxKKswWfyKSzn6hHrPSYwKKW1pQ,44507
 datamint/client_cmd_tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 datamint/client_cmd_tools/datamint_config.py,sha256=NNWLBaHXYhY1fqherwg0u3bcu0r95ZJIMTH45X-bJ2Q,6279
-datamint/client_cmd_tools/datamint_upload.py,sha256=CUqOIKHZNC1KKFS_opMYsFiOALvWh1D9RPLjft_1Qu0,25668
+datamint/client_cmd_tools/datamint_upload.py,sha256=oDNt-91Naz8fQER2sk3I9x9G7C7xzQ0SjBjr0XNht1k,25900
 datamint/configs.py,sha256=Bdp6NydYwyCJ2dk19_gf_o3M2ZyQOmMHpLi8wEWNHUk,1426
 datamint/dataset/__init__.py,sha256=4PlUKSvVhdfQvvuq8jQXrkdqnot-iTTizM3aM1vgSwg,47
 datamint/dataset/base_dataset.py,sha256=EnnIeF3ZaBL2M8qEV39U0ogKptyvezBNoVOvrS12bZ8,38756
@@ -16,14 +16,14 @@ datamint/examples/__init__.py,sha256=zcYnd5nLVme9GCTPYH-1JpGo8xXK2WEYvhzcy_2alZc
 datamint/examples/example_projects.py,sha256=7Nb_EaIdzJTQa9zopqc-WhTBQWQJSoQZ_KjRS4PB4FI,2931
 datamint/experiment/__init__.py,sha256=5qQOMzoG17DEd1YnTF-vS0qiM-DGdbNh42EUo91CRhQ,34
 datamint/experiment/_patcher.py,sha256=ZgbezoevAYhJsbiJTvWPALGTcUiMT371xddcTllt3H4,23296
-datamint/experiment/experiment.py,sha256=dP3aQdG44UQss8X-YQrCKK1dM9gxjPNGr-NTAIW6GI8,44541
+datamint/experiment/experiment.py,sha256=aHK9dRFdQTi569xgUg1KqlCZLHZpDmSH3g3ndPIZvXw,44546
 datamint/logging.yaml,sha256=a5dsATpul7QHeUHB2TjABFjWaPXBMbO--dgn8GlRqwk,483
 datamint/utils/dicom_utils.py,sha256=HTuEjwXyTSMaTVGb9pFOO76q2KLTr2CxTDoCRElVHRA,26023
-datamint/utils/io_utils.py,sha256=w3loo8C29MI2ERRvrcUc-Bc9X6OcjCnZCa1RixIiEZY,5451
+datamint/utils/io_utils.py,sha256=ebP1atKkhKEf1mUU1LsVwDq0h_so7kVKkD_7hQYn_kM,6754
 datamint/utils/logging_utils.py,sha256=DvoA35ATYG3JTwfXEXYawDyKRfHeCrH0a9czfkmz8kM,1851
 datamint/utils/torchmetrics.py,sha256=lwU0nOtsSWfebyp7dvjlAggaqXtj5ohSEUXOg3L0hJE,2837
 datamint/utils/visualization.py,sha256=yaUVAOHar59VrGUjpAWv5eVvQSfztFG0eP9p5Vt3l-M,4470
-datamint-1.4.0.dist-info/METADATA,sha256=og99PrYnYzM6C7V9m3ERFdkndMM8Bpp1QfLVkzp52dI,4065
-datamint-1.4.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-datamint-1.4.0.dist-info/entry_points.txt,sha256=mn5H6jPjO-rY0W0CAZ6Z_KKWhMLvyVaSpoqk77jlTI4,145
-datamint-1.4.0.dist-info/RECORD,,
+datamint-1.4.1.dist-info/METADATA,sha256=Av01QDy0f3zl0oud-ebW6vyjk0J0P33MGWMq8wg3nMs,4065
+datamint-1.4.1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+datamint-1.4.1.dist-info/entry_points.txt,sha256=mn5H6jPjO-rY0W0CAZ6Z_KKWhMLvyVaSpoqk77jlTI4,145
+datamint-1.4.1.dist-info/RECORD,,