fastMONAI 0.8.3__tar.gz → 0.8.4__tar.gz

{fastmonai-0.8.3/fastMONAI.egg-info → fastmonai-0.8.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fastMONAI
-Version: 0.8.3
+Version: 0.8.4
 Summary: fastMONAI library
 Home-page: https://github.com/MMIV-ML/fastMONAI
 Author: Satheshkumar Kaliyugarasan
@@ -25,8 +25,6 @@ Requires-Dist: imagedata==3.8.14
 Requires-Dist: mlflow==3.9.0
 Requires-Dist: huggingface-hub
 Requires-Dist: gdown
-Requires-Dist: gradio
-Requires-Dist: opencv-python
 Requires-Dist: plum-dispatch
 Provides-Extra: dev
 Requires-Dist: ipywidgets; extra == "dev"
@@ -34,6 +32,8 @@ Requires-Dist: nbdev<3; extra == "dev"
 Requires-Dist: execnb<0.2; extra == "dev"
 Requires-Dist: tabulate; extra == "dev"
 Requires-Dist: quarto; extra == "dev"
+Provides-Extra: viz
+Requires-Dist: gradio; extra == "viz"
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier
@@ -93,6 +93,9 @@ We recommend using a conda environment to avoid dependency conflicts:
 
 `pip install fastMONAI`
 
+Optional Gradio web-app demo (tutorial 11b):
+`pip install fastMONAI[viz]`.
+
 ## Development install [(GitHub)](https://github.com/MMIV-ML/fastMONAI)
 
 If you want to install an editable version of fastMONAI for development:

{fastmonai-0.8.3 → fastmonai-0.8.4}/README.md

@@ -43,6 +43,9 @@ We recommend using a conda environment to avoid dependency conflicts:
 
 `pip install fastMONAI`
 
+Optional Gradio web-app demo (tutorial 11b):
+`pip install fastMONAI[viz]`.
+
 ## Development install [(GitHub)](https://github.com/MMIV-ML/fastMONAI)
 
 If you want to install an editable version of fastMONAI for development:

fastmonai-0.8.4/fastMONAI/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.8.4"

{fastmonai-0.8.3 → fastmonai-0.8.4}/fastMONAI/_modidx.py

@@ -71,6 +71,8 @@ d = { 'settings': { 'branch': 'main',
                                  'fastMONAI.utils.MLflowUIManager.__init__': ('utils.html#mlflowuimanager.__init__', 'fastMONAI/utils.py'),
                                  'fastMONAI.utils.MLflowUIManager._find_running_mlflow': ( 'utils.html#mlflowuimanager._find_running_mlflow',
                                                                                            'fastMONAI/utils.py'),
+                                 'fastMONAI.utils.MLflowUIManager._kill_process': ( 'utils.html#mlflowuimanager._kill_process',
+                                                                                    'fastMONAI/utils.py'),
                                  'fastMONAI.utils.MLflowUIManager.check_mlflow_installed': ( 'utils.html#mlflowuimanager.check_mlflow_installed',
                                                                                              'fastMONAI/utils.py'),
                                  'fastMONAI.utils.MLflowUIManager.find_available_port': ( 'utils.html#mlflowuimanager.find_available_port',
@@ -112,16 +114,23 @@ d = { 'settings': { 'branch': 'main',
                                  'fastMONAI.utils.ModelTrackingCallback.log_metrics_table': ( 'utils.html#modeltrackingcallback.log_metrics_table',
                                                                                               'fastMONAI/utils.py'),
                                  'fastMONAI.utils._detect_patch_workflow': ('utils.html#_detect_patch_workflow', 'fastMONAI/utils.py'),
+                                 'fastMONAI.utils._die_with_parent': ('utils.html#_die_with_parent', 'fastMONAI/utils.py'),
+                                 'fastMONAI.utils._ensure_fastmonai_tracking_uri': ( 'utils.html#_ensure_fastmonai_tracking_uri',
+                                                                                     'fastMONAI/utils.py'),
                                  'fastMONAI.utils._extract_loss_name': ('utils.html#_extract_loss_name', 'fastMONAI/utils.py'),
                                  'fastMONAI.utils._extract_model_name': ('utils.html#_extract_model_name', 'fastMONAI/utils.py'),
                                  'fastMONAI.utils._extract_patch_config': ('utils.html#_extract_patch_config', 'fastMONAI/utils.py'),
                                  'fastMONAI.utils._extract_size_from_transforms': ( 'utils.html#_extract_size_from_transforms',
                                                                                     'fastMONAI/utils.py'),
                                  'fastMONAI.utils._extract_standard_config': ('utils.html#_extract_standard_config', 'fastMONAI/utils.py'),
+                                 'fastMONAI.utils._resolve_backend_store_uri': ( 'utils.html#_resolve_backend_store_uri',
+                                                                                 'fastMONAI/utils.py'),
+                                 'fastMONAI.utils._to_jsonable': ('utils.html#_to_jsonable', 'fastMONAI/utils.py'),
                                  'fastMONAI.utils.create_mlflow_callback': ('utils.html#create_mlflow_callback', 'fastMONAI/utils.py'),
                                  'fastMONAI.utils.load_patch_variables': ('utils.html#load_patch_variables', 'fastMONAI/utils.py'),
                                  'fastMONAI.utils.load_variables': ('utils.html#load_variables', 'fastMONAI/utils.py'),
                                  'fastMONAI.utils.print_colab_gpu_info': ('utils.html#print_colab_gpu_info', 'fastMONAI/utils.py'),
+                                 'fastMONAI.utils.set_mlflow_tracking_uri': ('utils.html#set_mlflow_tracking_uri', 'fastMONAI/utils.py'),
                                  'fastMONAI.utils.store_patch_variables': ('utils.html#store_patch_variables', 'fastMONAI/utils.py'),
                                  'fastMONAI.utils.store_variables': ('utils.html#store_variables', 'fastMONAI/utils.py')},
             'fastMONAI.vision_all': {},
@@ -171,6 +180,8 @@ d = { 'settings': { 'branch': 'main',
                                                                                                              'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.NormalizeIntensity.tio_transform': ( 'vision_augment.html#normalizeintensity.tio_transform',
                                                                                                                    'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation.NormalizeIntensity.to_spec': ( 'vision_augment.html#normalizeintensity.to_spec',
+                                                                                                             'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.OneOf': ( 'vision_augment.html#oneof',
                                                                                         'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.OneOf.__init__': ( 'vision_augment.html#oneof.__init__',
@@ -285,6 +296,8 @@ d = { 'settings': { 'branch': 'main',
                                                                                                            'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.RescaleIntensity.tio_transform': ( 'vision_augment.html#rescaleintensity.tio_transform',
                                                                                                                  'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation.RescaleIntensity.to_spec': ( 'vision_augment.html#rescaleintensity.to_spec',
+                                                                                                           'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.ZNormalization': ( 'vision_augment.html#znormalization',
                                                                                                  'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.ZNormalization.__init__': ( 'vision_augment.html#znormalization.__init__',
@@ -293,6 +306,8 @@ d = { 'settings': { 'branch': 'main',
                                                                                                          'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.ZNormalization.tio_transform': ( 'vision_augment.html#znormalization.tio_transform',
                                                                                                                'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation.ZNormalization.to_spec': ( 'vision_augment.html#znormalization.to_spec',
+                                                                                                         'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation._TioNormalizeIntensity': ( 'vision_augment.html#_tionormalizeintensity',
                                                                                                          'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation._TioNormalizeIntensity.__init__': ( 'vision_augment.html#_tionormalizeintensity.__init__',
@@ -321,12 +336,18 @@ d = { 'settings': { 'branch': 'main',
                                                                                                          'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation._foreground_masking': ( 'vision_augment.html#_foreground_masking',
                                                                                                       'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation.build_transform_from_spec': ( 'vision_augment.html#build_transform_from_spec',
+                                                                                                            'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.do_pad_or_crop': ( 'vision_augment.html#do_pad_or_crop',
                                                                                                  'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.gpu_patch_augmentations': ( 'vision_augment.html#gpu_patch_augmentations',
                                                                                                           'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.suggest_patch_augmentations': ( 'vision_augment.html#suggest_patch_augmentations',
-                                                                                                              'fastMONAI/vision_augmentation.py')},
+                                                                                                              'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation.transforms_from_specs': ( 'vision_augment.html#transforms_from_specs',
+                                                                                                        'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation.transforms_to_specs': ( 'vision_augment.html#transforms_to_specs',
+                                                                                                      'fastMONAI/vision_augmentation.py')},
             'fastMONAI.vision_core': { 'fastMONAI.vision_core.MedBase': ('vision_core.html#medbase', 'fastMONAI/vision_core.py'),
                                        'fastMONAI.vision_core.MedBase.__copy__': ( 'vision_core.html#medbase.__copy__',
                                                                                    'fastMONAI/vision_core.py'),

{fastmonai-0.8.3 → fastmonai-0.8.4}/fastMONAI/dataset_info.py

@@ -61,23 +61,21 @@ class MedDataset:
         self.max_workers = max_workers
         self.use_cache = use_cache
         self.cache_path = cache_path
+        self.failed_files = []
         self.df = self._create_data_frame()
 
     def _create_data_frame(self):
         """Private method that returns a dataframe with information about the dataset."""
 
-        # Handle img_list (simple list of paths)
         if self.img_list is not None:
             file_list = self.img_list
 
-        # Handle path-based initialization
         elif self.path:
             file_list = glob.glob(f'{self.path}/*{self.postfix}*')
             if not file_list:
                 print('Could not find images. Check the image path')
                 return pd.DataFrame()
 
-        # Handle dataframe-based initialization
         elif self.input_df is not None and self.mask_col in self.input_df.columns:
             file_list = self.input_df[self.mask_col].tolist()
 
@@ -85,11 +83,9 @@ class MedDataset:
             print('Error: Must provide path, img_list, or dataframe with mask_col')
             return pd.DataFrame()
 
-        # Resolve cache path
         if self.use_cache and self.cache_path is None:
             self.cache_path = self._auto_cache_path(file_list)
 
-        # Process images to extract metadata (with optional caching)
         if self.use_cache and self.cache_path is not None:
             data_info_dict = self._process_with_cache(file_list)
         else:
@@ -98,7 +94,19 @@ class MedDataset:
 
         df = pd.DataFrame(data_info_dict)
 
-        if len(df) > 0 and df.orientation.nunique() > 1 and not self.apply_reorder:
+        # DSET-1: surface failed files instead of letting NaN error rows silently
+        # corrupt downstream statistics (summary/get_suggestion/get_size_statistics/...).
+        if 'error' in df.columns:
+            failed_mask = df['error'].notna()
+            self.failed_files = df.loc[failed_mask, 'path'].tolist()
+            if self.failed_files:
+                warnings.warn(
+                    f'{len(self.failed_files)}/{len(df)} file(s) failed to load and were '
+                    f'excluded from dataset statistics. See self.failed_files.'
+                )
+            df = df.loc[~failed_mask].drop(columns=['error']).reset_index(drop=True)
+
+        if len(df) > 0 and 'orientation' in df.columns and df.orientation.nunique() > 1 and not self.apply_reorder:
             raise ValueError(
                 'Mixed orientations detected in dataset. '
                 'Please recreate MedDataset with apply_reorder=True to get correct resample values: '
@@ -137,6 +145,8 @@ class MedDataset:
 
     def summary(self):
         """Summary DataFrame of the dataset with example path for similar data."""
+        if len(self.df) == 0:
+            raise ValueError("Dataset is empty - cannot summarize")
 
         columns = ['dim_0', 'dim_1', 'dim_2', 'voxel_0', 'voxel_1', 'voxel_2', 'orientation']
 
@@ -162,6 +172,8 @@ class MedDataset:
             dict: {'target_spacing': [voxel_0, voxel_1, voxel_2]}
                   If include_patch_size=True, also includes 'patch_size': [dim_0, dim_1, dim_2]
         """
+        if len(self.df) == 0:
+            raise ValueError("Dataset is empty - cannot suggest preprocessing parameters")
         target_spacing = [float(self.df.voxel_0.mode()[0]), float(self.df.voxel_1.mode()[0]), float(self.df.voxel_2.mode()[0])]
         result = {'target_spacing': target_spacing}
 
@@ -186,10 +198,8 @@ class MedDataset:
                 # Calculate voxel volume in mm³
                 voxel_volume = o.spacing[0] * o.spacing[1] * o.spacing[2]
 
-                # Get voxel counts for each label
                 mask_labels_dict = o.count_labels()
 
-                # Calculate volumes for each label > 0 (skip background)
                 for key, voxel_count in mask_labels_dict.items():
                     label_int = int(key)
                     if label_int > 0 and voxel_count > 0:  # Skip background (label 0)
@@ -285,11 +295,13 @@ class MedDataset:
             all_results[i] = info
 
         n_cached = len(cached_results)
-        n_processed = len(files_to_process)
+        n_failed = sum(1 for info in fresh_results if 'error' in info)
+        n_processed = len(files_to_process) - n_failed
+        _fail_suffix = f', {n_failed} failed' if n_failed else ''
         if n_cached > 0:
-            print(f"MedDataset cache: {n_cached} cached, {n_processed} processed")
-        elif n_processed > 0:
-            print(f"MedDataset: processed {n_processed} files (results cached)")
+            print(f"MedDataset cache: {n_cached} cached, {n_processed} processed{_fail_suffix}")
+        elif n_processed > 0 or n_failed:
+            print(f"MedDataset: processed {n_processed} files (results cached){_fail_suffix}")
 
         return all_results
 
@@ -387,38 +399,37 @@ class MedDataset:
 
     def _visualize_single_case(self, img_path, mask_path, case_id, anatomical_plane=2, cmap='hot', figsize=(12, 5)):
         """Helper method to visualize a single case."""
+        # Snapshot global MedBase preprocessing state so visualization stays side-effect-free (ARCH-1)
+        _saved = (MedBase.target_spacing, MedBase.apply_reorder, MedBase.affine_matrix)
         try:
-            # Create MedImage and MedMask with current preprocessing settings
             suggestion = self.get_suggestion()
             MedBase.item_preprocessing(target_spacing=suggestion['target_spacing'], apply_reorder=self.apply_reorder)
 
             img = MedImage.create(img_path)
             mask = MedMask.create(mask_path)
 
-            # Find optimal slice using explicit function
             mask_data = mask.numpy()[0]  # Remove channel dimension
             optimal_slice = find_max_slice(mask_data, anatomical_plane)
 
-            # Create subplot
             fig, axes = plt.subplots(1, 2, figsize=figsize)
 
-            # Show image
             img.show(ctx=axes[0], anatomical_plane=anatomical_plane, slice_index=optimal_slice)
             axes[0].set_title(f"{case_id} - Image (slice {optimal_slice})")
 
-            # Show overlay
             img.show(ctx=axes[1], anatomical_plane=anatomical_plane, slice_index=optimal_slice)
             mask.show(ctx=axes[1], anatomical_plane=anatomical_plane, slice_index=optimal_slice,
                      alpha=0.3, cmap=cmap)
             axes[1].set_title(f"{case_id} - Overlay (slice {optimal_slice})")
 
-            # Adjust spacing to bring plots closer
             plt.subplots_adjust(wspace=0.1)
             plt.tight_layout()
             plt.show()
 
         except Exception as e:
             print(f"Failed to visualize case {case_id}: {e}")
+        finally:
+            # Restore global state: visualize_cases() must not mutate training preprocessing config
+            MedBase.target_spacing, MedBase.apply_reorder, MedBase.affine_matrix = _saved
 
     def visualize_cases(self, n_cases=4, anatomical_plane=2, cmap='hot', figsize=(12, 5)):
         """Visualize cases from the dataset.
@@ -437,7 +448,6 @@ class MedDataset:
             print("Error: No image_col specified. Cannot visualize cases.")
             return
 
-        # Check if required columns exist
         if self.image_col not in self.input_df.columns:
             print(f"Error: Column '{self.image_col}' not found in dataframe.")
             return
@@ -496,21 +506,17 @@ def suggest_patch_size(
         >>> # Use custom spacing
         >>> patch_size = suggest_patch_size(dataset, target_spacing=[1.0, 1.0, 2.0])
     """
-    # Defaults
     min_patch_size = min_patch_size or [32, 32, 32]
     max_patch_size = max_patch_size or [256, 256, 256]
 
-    # Use explicit spacing or get from dataset suggestion
     if target_spacing is None:
         suggestion = dataset.get_suggestion()
         target_spacing = suggestion['target_spacing']
 
-    # Get size statistics (resampled to target_spacing)
     stats = dataset.get_size_statistics(target_spacing)
     median_shape = stats['median']
     min_shape = stats['min']
 
-    # Handle single-image edge case
     if len(dataset.df) == 1:
         warnings.warn("Single image dataset - using image dimensions directly")
 
@@ -521,10 +527,8 @@ def suggest_patch_size(
     # Step 1: Clamp to min(median, min_volume) per axis — safety guarantee
     effective_dims = [min(med, mn) for med, mn in zip(median_shape, min_shape)]
 
-    # Step 2: Round down to nearest divisor
     patch_size = [round_to_divisor(dim, divisor) for dim in effective_dims]
 
-    # Step 3: Clamp to [min_patch_size, max_patch_size] bounds
     patch_size = [
         max(min_p, min(max_p, p))
         for p, min_p, max_p in zip(patch_size, min_patch_size, max_patch_size)
@@ -577,7 +581,6 @@ def preprocess_dataset(df, img_col, mask_col=None, output_dir='preprocessed',
             volume into memory, so reduce for large volumes.
         skip_existing: Skip files that already exist on disk (with size > 0).
     """
-    # Input validation
     if len(df) == 0:
         raise ValueError("DataFrame is empty")
     if img_col not in df.columns:
@@ -608,7 +611,6 @@ def preprocess_dataset(df, img_col, mask_col=None, output_dir='preprocessed',
         all_tfms.extend([getattr(t, 'tio_transform', t) for t in transforms])
     pipeline = tio.Compose(all_tfms) if all_tfms else None
 
-    # Create output directories
     output_dir = Path(output_dir)
     img_dir = output_dir / 'images'
     img_dir.mkdir(parents=True, exist_ok=True)
@@ -638,7 +640,6 @@ def preprocess_dataset(df, img_col, mask_col=None, output_dir='preprocessed',
             'out_img': out_img, 'out_mask': out_mask,
         })
 
-    # Process cases
     processed = 0
     failed = 0
     failed_cases = []

{fastmonai-0.8.3 → fastmonai-0.8.4}/fastMONAI/external_data.py

@@ -88,7 +88,6 @@ def download_ixi_data(path: (str, Path) = '../data') -> Path:
     path = Path(path) / 'IXI'
     img_path = path / 'T1_images'
 
-    # Check whether image data already present in img_path:
     is_extracted = False
     try:
         if len(list(img_path.iterdir())) >= 581:  # 581 imgs in the IXI dataset