fastMONAI 0.6.0__tar.gz → 0.7.0__tar.gz

{fastmonai-0.6.0/fastMONAI.egg-info → fastmonai-0.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fastMONAI
-Version: 0.6.0
+Version: 0.7.0
 Summary: fastMONAI library
 Home-page: https://github.com/MMIV-ML/fastMONAI
 Author: Satheshkumar Kaliyugarasan
@@ -12,18 +12,17 @@ Classifier: Intended Audience :: Developers
 Classifier: Natural Language :: English
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
 Classifier: License :: OSI Approved :: Apache Software License
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: fastai==2.8.3
-Requires-Dist: monai==1.5.0
-Requires-Dist: torchio==0.20.19
+Requires-Dist: fastai==2.8.6
+Requires-Dist: monai==1.5.2
+Requires-Dist: torchio==0.21.2
 Requires-Dist: xlrd>=1.2.0
-Requires-Dist: scikit-image==0.25.2
+Requires-Dist: scikit-image==0.26.0
 Requires-Dist: imagedata==3.8.14
-Requires-Dist: mlflow==3.3.1
+Requires-Dist: mlflow==3.9.0
 Requires-Dist: huggingface-hub
 Requires-Dist: gdown
 Requires-Dist: gradio
@@ -31,7 +30,7 @@ Requires-Dist: opencv-python
 Requires-Dist: plum-dispatch
 Provides-Extra: dev
 Requires-Dist: ipywidgets; extra == "dev"
-Requires-Dist: nbdev; extra == "dev"
+Requires-Dist: nbdev<3; extra == "dev"
 Requires-Dist: tabulate; extra == "dev"
 Requires-Dist: quarto; extra == "dev"
 Dynamic: author

fastmonai-0.7.0/fastMONAI/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.7.0"

{fastmonai-0.6.0 → fastmonai-0.7.0}/fastMONAI/_modidx.py

@@ -55,10 +55,10 @@ d = { 'settings': { 'branch': 'main',
                                                                                                   'fastMONAI/external_data.py'),
                                          'fastMONAI.external_data.download_spine_test_data': ( 'external_data.html#download_spine_test_data',
                                                                                                'fastMONAI/external_data.py')},
-            'fastMONAI.research_utils': { 'fastMONAI.research_utils.pred_postprocess': ( 'research_utils.html#pred_postprocess',
-                                                                                         'fastMONAI/research_utils.py')},
             'fastMONAI.utils': { 'fastMONAI.utils.MLflowUIManager': ('utils.html#mlflowuimanager', 'fastMONAI/utils.py'),
                                  '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.check_mlflow_installed': ( 'utils.html#mlflowuimanager.check_mlflow_installed',
                                                                                              'fastMONAI/utils.py'),
                                  'fastMONAI.utils.MLflowUIManager.find_available_port': ( 'utils.html#mlflowuimanager.find_available_port',
@@ -79,6 +79,8 @@ d = { 'settings': { 'branch': 'main',
                                                                                                    'fastMONAI/utils.py'),
                                  'fastMONAI.utils.ModelTrackingCallback._extract_training_params': ( 'utils.html#modeltrackingcallback._extract_training_params',
                                                                                                      'fastMONAI/utils.py'),
+                                 'fastMONAI.utils.ModelTrackingCallback._log_datasets': ( 'utils.html#modeltrackingcallback._log_datasets',
+                                                                                          'fastMONAI/utils.py'),
                                  'fastMONAI.utils.ModelTrackingCallback._register_pytorch_model': ( 'utils.html#modeltrackingcallback._register_pytorch_model',
                                                                                                     'fastMONAI/utils.py'),
                                  'fastMONAI.utils.ModelTrackingCallback._save_model_artifacts': ( 'utils.html#modeltrackingcallback._save_model_artifacts',
@@ -91,13 +93,23 @@ d = { 'settings': { 'branch': 'main',
                                                                                        'fastMONAI/utils.py'),
                                  'fastMONAI.utils.ModelTrackingCallback.extract_all_params': ( 'utils.html#modeltrackingcallback.extract_all_params',
                                                                                                'fastMONAI/utils.py'),
+                                 'fastMONAI.utils.ModelTrackingCallback.log_dataframe': ( 'utils.html#modeltrackingcallback.log_dataframe',
+                                                                                          'fastMONAI/utils.py'),
+                                 'fastMONAI.utils.ModelTrackingCallback.log_metrics': ( 'utils.html#modeltrackingcallback.log_metrics',
+                                                                                        'fastMONAI/utils.py'),
+                                 '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._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_patch_dataset_dfs': ( 'utils.html#_extract_patch_dataset_dfs',
+                                                                                 '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._extract_standard_dataset_dfs': ( 'utils.html#_extract_standard_dataset_dfs',
+                                                                                    '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'),
@@ -127,6 +139,8 @@ d = { 'settings': { 'branch': 'main',
                                                                                                               'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.NormalizeIntensity.encodes': ( 'vision_augment.html#normalizeintensity.encodes',
                                                                                                              'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation.NormalizeIntensity.tio_transform': ( 'vision_augment.html#normalizeintensity.tio_transform',
+                                                                                                                   '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__',
@@ -199,6 +213,8 @@ d = { 'settings': { 'branch': 'main',
                                                                                                                 'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.RandomIntensityScale.encodes': ( 'vision_augment.html#randomintensityscale.encodes',
                                                                                                                'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation.RandomIntensityScale.tio_transform': ( 'vision_augment.html#randomintensityscale.tio_transform',
+                                                                                                                     'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.RandomMotion': ( 'vision_augment.html#randommotion',
                                                                                                'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.RandomMotion.__init__': ( 'vision_augment.html#randommotion.__init__',
@@ -239,6 +255,12 @@ 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._TioNormalizeIntensity': ( 'vision_augment.html#_tionormalizeintensity',
+                                                                                                         'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation._TioNormalizeIntensity.__init__': ( 'vision_augment.html#_tionormalizeintensity.__init__',
+                                                                                                                  'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation._TioNormalizeIntensity.apply_transform': ( 'vision_augment.html#_tionormalizeintensity.apply_transform',
+                                                                                                                         'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation._TioRandomCutout': ( 'vision_augment.html#_tiorandomcutout',
                                                                                                    'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation._TioRandomCutout.__init__': ( 'vision_augment.html#_tiorandomcutout.__init__',
@@ -247,6 +269,12 @@ d = { 'settings': { 'branch': 'main',
                                                                                                                  'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation._TioRandomCutout.apply_transform': ( 'vision_augment.html#_tiorandomcutout.apply_transform',
                                                                                                                    'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation._TioRandomIntensityScale': ( 'vision_augment.html#_tiorandomintensityscale',
+                                                                                                           'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation._TioRandomIntensityScale.__init__': ( 'vision_augment.html#_tiorandomintensityscale.__init__',
+                                                                                                                    'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation._TioRandomIntensityScale.apply_transform': ( 'vision_augment.html#_tiorandomintensityscale.apply_transform',
+                                                                                                                           'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation._create_ellipsoid_mask': ( 'vision_augment.html#_create_ellipsoid_mask',
                                                                                                          'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.do_pad_or_crop': ( 'vision_augment.html#do_pad_or_crop',
@@ -443,6 +471,8 @@ d = { 'settings': { 'branch': 'main',
                                                                                                   'fastMONAI/vision_patch.py'),
                                         'fastMONAI.vision_patch.MedPatchDataLoaders.patch_config': ( 'vision_patch.html#medpatchdataloaders.patch_config',
                                                                                                      'fastMONAI/vision_patch.py'),
+                                        'fastMONAI.vision_patch.MedPatchDataLoaders.show_batch': ( 'vision_patch.html#medpatchdataloaders.show_batch',
+                                                                                                   'fastMONAI/vision_patch.py'),
                                         'fastMONAI.vision_patch.MedPatchDataLoaders.target_spacing': ( 'vision_patch.html#medpatchdataloaders.target_spacing',
                                                                                                        'fastMONAI/vision_patch.py'),
                                         'fastMONAI.vision_patch.MedPatchDataLoaders.to': ( 'vision_patch.html#medpatchdataloaders.to',

{fastmonai-0.6.0 → fastmonai-0.7.0}/fastMONAI/dataset_info.py

@@ -1,9 +1,9 @@
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/08_dataset_info.ipynb.
 
-# %% auto 0
+# %% auto #0
 __all__ = ['MedDataset', 'suggest_patch_size', 'get_class_weights']
 
-# %% ../nbs/08_dataset_info.ipynb 2
+# %% ../nbs/08_dataset_info.ipynb #027f016a-a80c-4842-b9dc-0bddb358a00c
 from .vision_core import *
 from .vision_plot import find_max_slice
 
@@ -15,7 +15,7 @@ import torch
 import glob
 import matplotlib.pyplot as plt
 
-# %% ../nbs/08_dataset_info.ipynb 3
+# %% ../nbs/08_dataset_info.ipynb #7401beac
 import warnings
 
 class MedDataset:
@@ -311,7 +311,7 @@ class MedDataset:
             self._visualize_single_case(img_path, mask_path, case_id, anatomical_plane, cmap, figsize)
             print("-" * 60)
 
-# %% ../nbs/08_dataset_info.ipynb 4
+# %% ../nbs/08_dataset_info.ipynb #wp61bidiwwd
 def suggest_patch_size(
     dataset: MedDataset,
     target_spacing: list = None,
@@ -319,12 +319,17 @@ def suggest_patch_size(
     max_patch_size: list = None,
     divisor: int = 16
 ) -> list:
-    """Suggest optimal patch size based on median image dimensions.
+    """Suggest optimal patch size based on dataset dimensions.
+
+    Uses median shape as the starting point but clamps to the minimum
+    volume size per axis, ensuring the suggested patch fits ALL volumes
+    without requiring padding during training.
 
     Algorithm:
-    1. Use median shape for robustness to outliers
-    2. Round down to nearest multiple of divisor (16 for 4+ UNet pooling layers)
-    3. Clamp to [min_patch_size, max_patch_size]
+    1. Use min(median, min_volume) per axis for safety
+    2. Round down to nearest multiple of divisor (16 for UNet compatibility)
+    3. Clamp to [min_patch_size, max_patch_size] bounds
+    4. Validate: error if min_patch_size exceeds smallest volume
 
     Args:
         dataset: MedDataset instance with analyzed images.
@@ -359,35 +364,49 @@ def suggest_patch_size(
     # 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")
 
-    # Step 1: Round down to nearest divisor
     def round_to_divisor(val, div):
         """Round down to nearest multiple of divisor."""
         return max(div, int(val // div) * div)
 
-    patch_size = [round_to_divisor(dim, divisor) for dim in median_shape]
+    # 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 2: Clamp to bounds
+    # 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)
     ]
 
-    # Edge case: image smaller than suggested patch
-    for i, (p, median_dim) in enumerate(zip(patch_size, median_shape)):
-        if median_dim < p:
+    # Step 4: Final safety check — error if bounds force patch > min volume
+    for i, (p, min_dim) in enumerate(zip(patch_size, min_shape)):
+        if p > min_dim:
+            raise ValueError(
+                f"Cannot suggest safe patch_size for dimension {i}: "
+                f"smallest volume is {min_dim:.0f} but min_patch_size={min_patch_size[i]}. "
+                f"Exclude small volumes or reduce min_patch_size."
+            )
+
+    # Warn when suggestion was reduced to fit smallest volume
+    for i, (med, mn, p) in enumerate(zip(median_shape, min_shape, patch_size)):
+        median_based = min(max_patch_size[i], round_to_divisor(med, divisor))
+        if p < median_based:
             warnings.warn(
-                f"Median dimension {i} ({median_dim:.0f}) smaller than suggested "
-                f"patch_size ({p}). Images will require padding."
+                f"Dim {i}: patch_size reduced from {median_based} to {p} "
+                f"to fit smallest volume (min={mn:.0f}, median={med:.0f})."
             )
 
     return patch_size
 
-# %% ../nbs/08_dataset_info.ipynb 6
+# %% ../nbs/08_dataset_info.ipynb #9b81f6e8-abd7-4bf6-be4c-4118986c308a
 def get_class_weights(labels: (np.array, list), class_weight: str = 'balanced') -> torch.Tensor: 
     """Calculates and returns the class weights.
 

{fastmonai-0.6.0 → fastmonai-0.7.0}/fastMONAI/external_data.py

@@ -1,10 +1,10 @@
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/09_external_data.ipynb.
 
-# %% auto 0
+# %% auto #0
 __all__ = ['MURLs', 'download_ixi_data', 'download_ixi_tiny', 'download_spine_test_data', 'download_example_spine_data',
            'download_medmnist3d_dataset', 'download_example_endometrial_cancer_data']
 
-# %% ../nbs/09_external_data.ipynb 1
+# %% ../nbs/09_external_data.ipynb #942e1644-0dac-4701-8a1e-5693f80f3ca0
 from pathlib import Path
 from glob import glob
 from numpy import load 
@@ -15,7 +15,7 @@ from torchio import ScalarImage
 import multiprocessing as mp
 from functools import partial
 
-# %% ../nbs/09_external_data.ipynb 3
+# %% ../nbs/09_external_data.ipynb #6d5600a3-9d70-4714-8cc2-8f4682a7e5a3
 class MURLs():
     """A class with external medical dataset URLs."""
 
@@ -32,7 +32,7 @@ class MURLs():
     EXAMPLE_EC_DATA = 'https://drive.google.com/uc?id=1P_J8MfzbfObTkAyWfY-LlEC_IA_NjYn-'
     EXAMPLE_MULTI_EC_DATA = 'https://drive.google.com/uc?id=1yOmbA9-nKfzzsfysgp9OcPw8GAarXPvE'
 
-# %% ../nbs/09_external_data.ipynb 4
+# %% ../nbs/09_external_data.ipynb #cb4c061a-d7f5-4ba0-9e7b-ee0c6ec480b0
 def _process_ixi_xls(xls_path: (str, Path), img_path: Path) -> pd.DataFrame:
     """Private method to process the demographic information for the IXI dataset.
 
@@ -74,7 +74,7 @@ def _process_ixi_xls(xls_path: (str, Path), img_path: Path) -> pd.DataFrame:
     
     return df
 
-# %% ../nbs/09_external_data.ipynb 6
+# %% ../nbs/09_external_data.ipynb #6714a68f-1378-46b3-aeff-ef940213ac2f
 def download_ixi_data(path: (str, Path) = '../data') -> Path:
     """Download T1 scans and demographic information from the IXI dataset.
     
@@ -108,7 +108,7 @@ def download_ixi_data(path: (str, Path) = '../data') -> Path:
 
     return path
 
-# %% ../nbs/09_external_data.ipynb 8
+# %% ../nbs/09_external_data.ipynb #7753da8a-93e8-4bf3-8f78-bb158b4280d0
 def download_ixi_tiny(path: (str, Path) = '../data') -> Path:
     """Download the tiny version of the IXI dataset provided by TorchIO.
 
@@ -132,7 +132,7 @@ def download_ixi_tiny(path: (str, Path) = '../data') -> Path:
     
     return path
 
-# %% ../nbs/09_external_data.ipynb 10
+# %% ../nbs/09_external_data.ipynb #b466174a-4b49-4a8f-92c6-1e5e3ca9fc2a
 def _create_spine_df(dir: Path) -> pd.DataFrame:
     """Create a pandas DataFrame containing information about spinal images.
 
@@ -159,7 +159,7 @@ def _create_spine_df(dir: Path) -> pd.DataFrame:
 
     return pd.DataFrame(test_data)
 
-# %% ../nbs/09_external_data.ipynb 11
+# %% ../nbs/09_external_data.ipynb #26256dca-d9df-43f6-b8eb-f36ce2a445dc
 def download_spine_test_data(path: (str, Path) = '../data') -> pd.DataFrame:
     """Downloads T2w scans from the study 'Fully Automatic Localization and 
     Segmentation of 3D Vertebral Bodies from CT/MR Images via a Learning-Based 
@@ -184,7 +184,7 @@ def download_spine_test_data(path: (str, Path) = '../data') -> pd.DataFrame:
     
     return _create_spine_df(Path(path) / study)
 
-# %% ../nbs/09_external_data.ipynb 12
+# %% ../nbs/09_external_data.ipynb #93b77ec9-a93a-42cc-b707-4e1e75063533
 def download_example_spine_data(path: (str, Path) = '../data') -> Path:
     """Downloads example T2w scan and corresponding predicted mask.
     
@@ -207,7 +207,7 @@ def download_example_spine_data(path: (str, Path) = '../data') -> Path:
     
     return Path(path) / study
 
-# %% ../nbs/09_external_data.ipynb 14
+# %% ../nbs/09_external_data.ipynb #89f60f76-5e5d-4a40-b49a-617ec2d35731
 def _process_medmnist_img(path, idx_arr):
     """Save tensor as NIfTI."""
     
@@ -217,7 +217,7 @@ def _process_medmnist_img(path, idx_arr):
     img.save(fn)
     return str(fn)
 
-# %% ../nbs/09_external_data.ipynb 15
+# %% ../nbs/09_external_data.ipynb #b0199679-707b-445d-8467-3d342246322a
 def _df_sort_and_add_columns(df, label_list, is_val):
     """Sort the dataframe based on img_idx and add labels and if it is validation data column."""
     
@@ -228,7 +228,7 @@ def _df_sort_and_add_columns(df, label_list, is_val):
     
     return df 
 
-# %% ../nbs/09_external_data.ipynb 16
+# %% ../nbs/09_external_data.ipynb #d82157b8-ab69-4a38-9323-af4b58c6b54a
 def _create_nodule_df(pool, output_dir, imgs, labels, is_val=False): 
     """Create dataframe for MedMNIST data."""
     
@@ -238,13 +238,13 @@ def _create_nodule_df(pool, output_dir, imgs, labels, is_val=False):
     df = pd.DataFrame(list(zip(img_path_list, img_idx)), columns=['img_path','img_idx'])        
     return  _df_sort_and_add_columns(df, labels, is_val)
 
-# %% ../nbs/09_external_data.ipynb 17
+# %% ../nbs/09_external_data.ipynb #04095111-a38f-4d00-a0fb-2dbfac263eb6
 def _dataset_available_locally(path: Path):
     """Checks if the dataset exists in the local directory."""
     
     return path.exists() and any(path.iterdir())
 
-# %% ../nbs/09_external_data.ipynb 18
+# %% ../nbs/09_external_data.ipynb #a1b456f0-8e14-42c6-a1cd-a332312145ff
 def download_medmnist3d_dataset(study: str, path: (str, Path) = '../data',
                                 max_workers: int = 1, skip_download: bool = True):
     """Downloads and processes a particular MedMNIST3D dataset.
@@ -301,7 +301,7 @@ def download_medmnist3d_dataset(study: str, path: (str, Path) = '../data',
 
     return train_val_df, test_df
 
-# %% ../nbs/09_external_data.ipynb 20
+# %% ../nbs/09_external_data.ipynb #67491c4a-8491-4b10-8f03-87ffa012fee0
 def download_example_endometrial_cancer_data(path: (str, Path) = '../data', multi_channel: bool = True):
     """Download example data for endometrial cancer.