fastMONAI 0.5.3__tar.gz → 0.5.4__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (33) hide show
  1. {fastmonai-0.5.3/fastMONAI.egg-info → fastmonai-0.5.4}/PKG-INFO +5 -5
  2. {fastmonai-0.5.3 → fastmonai-0.5.4}/README.md +4 -4
  3. fastmonai-0.5.4/fastMONAI/__init__.py +1 -0
  4. {fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI/_modidx.py +171 -27
  5. fastmonai-0.5.4/fastMONAI/dataset_info.py +267 -0
  6. {fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI/external_data.py +1 -1
  7. {fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI/utils.py +101 -18
  8. {fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI/vision_all.py +3 -2
  9. {fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI/vision_augmentation.py +133 -29
  10. {fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI/vision_core.py +29 -132
  11. {fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI/vision_data.py +6 -6
  12. {fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI/vision_inference.py +35 -9
  13. fastmonai-0.5.4/fastMONAI/vision_metrics.py +501 -0
  14. fastmonai-0.5.4/fastMONAI/vision_patch.py +1125 -0
  15. {fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI/vision_plot.py +1 -0
  16. {fastmonai-0.5.3 → fastmonai-0.5.4/fastMONAI.egg-info}/PKG-INFO +5 -5
  17. {fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI.egg-info/SOURCES.txt +1 -0
  18. {fastmonai-0.5.3 → fastmonai-0.5.4}/settings.ini +1 -1
  19. fastmonai-0.5.3/fastMONAI/__init__.py +0 -1
  20. fastmonai-0.5.3/fastMONAI/dataset_info.py +0 -122
  21. fastmonai-0.5.3/fastMONAI/vision_metrics.py +0 -100
  22. {fastmonai-0.5.3 → fastmonai-0.5.4}/CONTRIBUTING.md +0 -0
  23. {fastmonai-0.5.3 → fastmonai-0.5.4}/LICENSE +0 -0
  24. {fastmonai-0.5.3 → fastmonai-0.5.4}/MANIFEST.in +0 -0
  25. {fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI/research_utils.py +0 -0
  26. {fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI/vision_loss.py +0 -0
  27. {fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI.egg-info/dependency_links.txt +0 -0
  28. {fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI.egg-info/entry_points.txt +0 -0
  29. {fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI.egg-info/not-zip-safe +0 -0
  30. {fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI.egg-info/requires.txt +0 -0
  31. {fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI.egg-info/top_level.txt +0 -0
  32. {fastmonai-0.5.3 → fastmonai-0.5.4}/setup.cfg +0 -0
  33. {fastmonai-0.5.3 → fastmonai-0.5.4}/setup.py +0 -0
{fastmonai-0.5.3/fastMONAI.egg-info → fastmonai-0.5.4}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: fastMONAI
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- Version: 0.5.3
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+ Version: 0.5.4
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  Summary: fastMONAI library
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  Home-page: https://github.com/MMIV-ML/fastMONAI
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  Author: Satheshkumar Kaliyugarasan
@@ -120,10 +120,10 @@ https://fastmonai.no for more information.
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  | Notebook | 1-Click Notebook |
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  |:---|----|
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- | [10a_tutorial_classification.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/10a_tutorial_classification.ipynb) <br>shows how to construct a binary classification model based on MRI data. | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/10a_tutorial_classification.ipynb) |
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- | [10b_tutorial_regression.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/10b_tutorial_regression.ipynb) <br>shows how to construct a model to predict the age of a subject from MRI scans (“brain age”). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/10b_tutorial_regression.ipynb) |
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- | [10c_tutorial_binary_segmentation.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/10c_tutorial_binary_segmentation.ipynb) <br>shows how to do binary segmentation (extract the left atrium from monomodal cardiac MRI). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/10c_tutorial_binary_segmentation.ipynb) |
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- | [10d_tutorial_multiclass_segmentation.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/10d_tutorial_multiclass_segmentation.ipynb) <br>shows how to perform segmentation from multimodal MRI (brain tumor segmentation). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/10d_tutorial_multiclass_segmentation.ipynb) |
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+ | [11b_tutorial_classification.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/11b_tutorial_classification.ipynb) <br>shows how to construct a binary classification model based on MRI data. | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/11b_tutorial_classification.ipynb) |
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+ | [11c_tutorial_regression.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/11c_tutorial_regression.ipynb) <br>shows how to construct a model to predict the age of a subject from MRI scans (“brain age”). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/11c_tutorial_regression.ipynb) |
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+ | [11d_tutorial_binary_segmentation.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/11d_tutorial_binary_segmentation.ipynb) <br>shows how to do binary segmentation (extract the left atrium from monomodal cardiac MRI). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/11d_tutorial_binary_segmentation.ipynb) |
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+ | [11e_tutorial_multiclass_segmentation.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/11e_tutorial_multiclass_segmentation.ipynb) <br>shows how to perform segmentation from multimodal MRI (brain tumor segmentation). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/11e_tutorial_multiclass_segmentation.ipynb) |
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  # How to contribute
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{fastmonai-0.5.3 → fastmonai-0.5.4}/README.md RENAMED
@@ -70,10 +70,10 @@ https://fastmonai.no for more information.
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  | Notebook | 1-Click Notebook |
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  |:---|----|
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- | [10a_tutorial_classification.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/10a_tutorial_classification.ipynb) <br>shows how to construct a binary classification model based on MRI data. | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/10a_tutorial_classification.ipynb) |
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- | [10b_tutorial_regression.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/10b_tutorial_regression.ipynb) <br>shows how to construct a model to predict the age of a subject from MRI scans (“brain age”). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/10b_tutorial_regression.ipynb) |
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- | [10c_tutorial_binary_segmentation.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/10c_tutorial_binary_segmentation.ipynb) <br>shows how to do binary segmentation (extract the left atrium from monomodal cardiac MRI). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/10c_tutorial_binary_segmentation.ipynb) |
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- | [10d_tutorial_multiclass_segmentation.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/10d_tutorial_multiclass_segmentation.ipynb) <br>shows how to perform segmentation from multimodal MRI (brain tumor segmentation). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/10d_tutorial_multiclass_segmentation.ipynb) |
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+ | [11b_tutorial_classification.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/11b_tutorial_classification.ipynb) <br>shows how to construct a binary classification model based on MRI data. | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/11b_tutorial_classification.ipynb) |
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+ | [11c_tutorial_regression.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/11c_tutorial_regression.ipynb) <br>shows how to construct a model to predict the age of a subject from MRI scans (“brain age”). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/11c_tutorial_regression.ipynb) |
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+ | [11d_tutorial_binary_segmentation.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/11d_tutorial_binary_segmentation.ipynb) <br>shows how to do binary segmentation (extract the left atrium from monomodal cardiac MRI). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/11d_tutorial_binary_segmentation.ipynb) |
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+ | [11e_tutorial_multiclass_segmentation.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/main/nbs/11e_tutorial_multiclass_segmentation.ipynb) <br>shows how to perform segmentation from multimodal MRI (brain tumor segmentation). | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/11e_tutorial_multiclass_segmentation.ipynb) |
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  # How to contribute
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fastmonai-0.5.4/fastMONAI/__init__.py ADDED
@@ -0,0 +1 @@
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+ __version__ = "0.5.4"
{fastmonai-0.5.3 → fastmonai-0.5.4}/fastMONAI/_modidx.py RENAMED
@@ -12,12 +12,18 @@ d = { 'settings': { 'branch': 'main',
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  'fastMONAI/dataset_info.py'),
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  'fastMONAI.dataset_info.MedDataset._get_data_info': ( 'dataset_info.html#meddataset._get_data_info',
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  'fastMONAI/dataset_info.py'),
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- 'fastMONAI.dataset_info.MedDataset.get_largest_img_size': ( 'dataset_info.html#meddataset.get_largest_img_size',
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- 'fastMONAI/dataset_info.py'),
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- 'fastMONAI.dataset_info.MedDataset.suggestion': ( 'dataset_info.html#meddataset.suggestion',
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- 'fastMONAI/dataset_info.py'),
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+ 'fastMONAI.dataset_info.MedDataset._visualize_single_case': ( 'dataset_info.html#meddataset._visualize_single_case',
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+ 'fastMONAI/dataset_info.py'),
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+ 'fastMONAI.dataset_info.MedDataset.calculate_target_size': ( 'dataset_info.html#meddataset.calculate_target_size',
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+ 'fastMONAI/dataset_info.py'),
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+ 'fastMONAI.dataset_info.MedDataset.get_suggestion': ( 'dataset_info.html#meddataset.get_suggestion',
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+ 'fastMONAI/dataset_info.py'),
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+ 'fastMONAI.dataset_info.MedDataset.get_volume_summary': ( 'dataset_info.html#meddataset.get_volume_summary',
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+ 'fastMONAI/dataset_info.py'),
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  'fastMONAI.dataset_info.MedDataset.summary': ( 'dataset_info.html#meddataset.summary',
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  'fastMONAI/dataset_info.py'),
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+ 'fastMONAI.dataset_info.MedDataset.visualize_cases': ( 'dataset_info.html#meddataset.visualize_cases',
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+ 'fastMONAI/dataset_info.py'),
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  'fastMONAI.dataset_info.get_class_weights': ( 'dataset_info.html#get_class_weights',
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  'fastMONAI/dataset_info.py')},
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  'fastMONAI.external_data': { 'fastMONAI.external_data.MURLs': ('external_data.html#murls', 'fastMONAI/external_data.py'),
@@ -81,8 +87,10 @@ d = { 'settings': { 'branch': 'main',
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  'fastMONAI/utils.py'),
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  'fastMONAI.utils.ModelTrackingCallback.extract_all_params': ( 'utils.html#modeltrackingcallback.extract_all_params',
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  'fastMONAI/utils.py'),
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+ 'fastMONAI.utils.load_patch_variables': ('utils.html#load_patch_variables', 'fastMONAI/utils.py'),
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  'fastMONAI.utils.load_variables': ('utils.html#load_variables', 'fastMONAI/utils.py'),
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  'fastMONAI.utils.print_colab_gpu_info': ('utils.html#print_colab_gpu_info', 'fastMONAI/utils.py'),
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+ 'fastMONAI.utils.store_patch_variables': ('utils.html#store_patch_variables', 'fastMONAI/utils.py'),
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  'fastMONAI.utils.store_variables': ('utils.html#store_variables', 'fastMONAI/utils.py')},
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  'fastMONAI.vision_all': {},
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  'fastMONAI.vision_augmentation': { 'fastMONAI.vision_augmentation.BinaryConverter': ( 'vision_augment.html#binaryconverter',
@@ -99,6 +107,8 @@ d = { 'settings': { 'branch': 'main',
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  'fastMONAI.vision_augmentation.CustomDictTransform.encodes': ( 'vision_augment.html#customdicttransform.encodes',
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+ 'fastMONAI.vision_augmentation.CustomDictTransform.tio_transform': ( 'vision_augment.html#customdicttransform.tio_transform',
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+ 'fastMONAI/vision_augmentation.py'),
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  'fastMONAI.vision_augmentation.NormalizeIntensity': ( 'vision_augment.html#normalizeintensity',
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  'fastMONAI.vision_augmentation.NormalizeIntensity.__init__': ( 'vision_augment.html#normalizeintensity.__init__',
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  'fastMONAI.vision_augmentation.PadOrCrop.encodes': ( 'vision_augment.html#padorcrop.encodes',
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+ 'fastMONAI.vision_augmentation.PadOrCrop.tio_transform': ( 'vision_augment.html#padorcrop.tio_transform',
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+ 'fastMONAI/vision_augmentation.py'),
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  'fastMONAI.vision_augmentation.RandomAffine': ( 'vision_augment.html#randomaffine',
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  'fastMONAI.vision_augmentation.RandomAffine.__init__': ( 'vision_augment.html#randomaffine.__init__',
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  'fastMONAI.vision_augmentation.RandomBiasField.encodes': ( 'vision_augment.html#randombiasfield.encodes',
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+ 'fastMONAI.vision_augmentation.RandomBiasField.tio_transform': ( 'vision_augment.html#randombiasfield.tio_transform',
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+ 'fastMONAI/vision_augmentation.py'),
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  'fastMONAI.vision_augmentation.RandomBlur': ( 'vision_augment.html#randomblur',
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  'fastMONAI.vision_augmentation.RandomBlur.__init__': ( 'vision_augment.html#randomblur.__init__',
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  'fastMONAI.vision_augmentation.RandomBlur.encodes': ( 'vision_augment.html#randomblur.encodes',
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+ 'fastMONAI.vision_augmentation.RandomBlur.tio_transform': ( 'vision_augment.html#randomblur.tio_transform',
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+ 'fastMONAI/vision_augmentation.py'),
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  'fastMONAI.vision_augmentation.RandomElasticDeformation': ( 'vision_augment.html#randomelasticdeformation',
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  'fastMONAI.vision_augmentation.RandomElasticDeformation.__init__': ( 'vision_augment.html#randomelasticdeformation.__init__',
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  'fastMONAI.vision_augmentation.RandomGamma.encodes': ( 'vision_augment.html#randomgamma.encodes',
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+ 'fastMONAI.vision_augmentation.RandomGamma.tio_transform': ( 'vision_augment.html#randomgamma.tio_transform',
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+ 'fastMONAI/vision_augmentation.py'),
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  'fastMONAI.vision_augmentation.RandomGhosting': ( 'vision_augment.html#randomghosting',
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  'fastMONAI.vision_augmentation.RandomGhosting.__init__': ( 'vision_augment.html#randomghosting.__init__',
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  'fastMONAI.vision_augmentation.RandomGhosting.encodes': ( 'vision_augment.html#randomghosting.encodes',
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+ 'fastMONAI.vision_augmentation.RandomGhosting.tio_transform': ( 'vision_augment.html#randomghosting.tio_transform',
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+ 'fastMONAI/vision_augmentation.py'),
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+ 'fastMONAI.vision_augmentation.RandomIntensityScale': ( 'vision_augment.html#randomintensityscale',
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+ 'fastMONAI/vision_augmentation.py'),
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+ 'fastMONAI.vision_augmentation.RandomIntensityScale.__init__': ( 'vision_augment.html#randomintensityscale.__init__',
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+ 'fastMONAI/vision_augmentation.py'),
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+ 'fastMONAI.vision_augmentation.RandomIntensityScale.encodes': ( 'vision_augment.html#randomintensityscale.encodes',
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+ 'fastMONAI/vision_augmentation.py'),
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  'fastMONAI.vision_augmentation.RandomMotion.__init__': ( 'vision_augment.html#randommotion.__init__',
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  'fastMONAI.vision_augmentation.RandomMotion.encodes': ( 'vision_augment.html#randommotion.encodes',
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+ 'fastMONAI.vision_augmentation.RandomMotion.tio_transform': ( 'vision_augment.html#randommotion.tio_transform',
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+ 'fastMONAI/vision_augmentation.py'),
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  'fastMONAI.vision_augmentation.RandomNoise': ( 'vision_augment.html#randomnoise',
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  'fastMONAI.vision_augmentation.RandomNoise.encodes': ( 'vision_augment.html#randomnoise.encodes',
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+ 'fastMONAI.vision_augmentation.RandomNoise.tio_transform': ( 'vision_augment.html#randomnoise.tio_transform',
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+ 'fastMONAI/vision_augmentation.py'),
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  'fastMONAI.vision_augmentation.RandomSpike': ( 'vision_augment.html#randomspike',
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  'fastMONAI.vision_augmentation.RandomSpike.__init__': ( 'vision_augment.html#randomspike.__init__',
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  'fastMONAI.vision_augmentation.RandomSpike.encodes': ( 'vision_augment.html#randomspike.encodes',
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+ 'fastMONAI.vision_augmentation.RandomSpike.tio_transform': ( 'vision_augment.html#randomspike.tio_transform',
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+ 'fastMONAI/vision_augmentation.py'),
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  'fastMONAI.vision_augmentation.RescaleIntensity': ( 'vision_augment.html#rescaleintensity',
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  'fastMONAI.vision_augmentation.RescaleIntensity.__init__': ( 'vision_augment.html#rescaleintensity.__init__',
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  'fastMONAI.vision_augmentation.RescaleIntensity.encodes': ( 'vision_augment.html#rescaleintensity.encodes',
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+ 'fastMONAI.vision_augmentation.RescaleIntensity.tio_transform': ( 'vision_augment.html#rescaleintensity.tio_transform',
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+ 'fastMONAI/vision_augmentation.py'),
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  'fastMONAI.vision_augmentation.ZNormalization': ( 'vision_augment.html#znormalization',
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  'fastMONAI.vision_augmentation.ZNormalization.__init__': ( 'vision_augment.html#znormalization.__init__',
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  'fastMONAI.vision_augmentation.ZNormalization.encodes': ( 'vision_augment.html#znormalization.encodes',
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+ 'fastMONAI.vision_augmentation.ZNormalization.tio_transform': ( 'vision_augment.html#znormalization.tio_transform',
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+ 'fastMONAI/vision_augmentation.py'),
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  'fastMONAI.vision_augmentation.do_pad_or_crop': ( 'vision_augment.html#do_pad_or_crop',
185
221
  'fastMONAI/vision_augmentation.py')},
186
222
  'fastMONAI.vision_core': { 'fastMONAI.vision_core.MedBase': ('vision_core.html#medbase', 'fastMONAI/vision_core.py'),
@@ -202,33 +238,13 @@ d = { 'settings': { 'branch': 'main',
202
238
  'fastMONAI.vision_core.MedImage': ('vision_core.html#medimage', 'fastMONAI/vision_core.py'),
203
239
  'fastMONAI.vision_core.MedMask': ('vision_core.html#medmask', 'fastMONAI/vision_core.py'),
204
240
  'fastMONAI.vision_core.MetaResolver': ('vision_core.html#metaresolver', 'fastMONAI/vision_core.py'),
205
- 'fastMONAI.vision_core.VSCodeProgressCallback': ( 'vision_core.html#vscodeprogresscallback',
206
- 'fastMONAI/vision_core.py'),
207
- 'fastMONAI.vision_core.VSCodeProgressCallback.__init__': ( 'vision_core.html#vscodeprogresscallback.__init__',
208
- 'fastMONAI/vision_core.py'),
209
- 'fastMONAI.vision_core.VSCodeProgressCallback._detect_vscode_environment': ( 'vision_core.html#vscodeprogresscallback._detect_vscode_environment',
210
- 'fastMONAI/vision_core.py'),
211
- 'fastMONAI.vision_core.VSCodeProgressCallback.after_batch': ( 'vision_core.html#vscodeprogresscallback.after_batch',
212
- 'fastMONAI/vision_core.py'),
213
- 'fastMONAI.vision_core.VSCodeProgressCallback.after_fit': ( 'vision_core.html#vscodeprogresscallback.after_fit',
214
- 'fastMONAI/vision_core.py'),
215
- 'fastMONAI.vision_core.VSCodeProgressCallback.after_validate': ( 'vision_core.html#vscodeprogresscallback.after_validate',
216
- 'fastMONAI/vision_core.py'),
217
- 'fastMONAI.vision_core.VSCodeProgressCallback.before_epoch': ( 'vision_core.html#vscodeprogresscallback.before_epoch',
218
- 'fastMONAI/vision_core.py'),
219
- 'fastMONAI.vision_core.VSCodeProgressCallback.before_fit': ( 'vision_core.html#vscodeprogresscallback.before_fit',
220
- 'fastMONAI/vision_core.py'),
221
- 'fastMONAI.vision_core.VSCodeProgressCallback.before_validate': ( 'vision_core.html#vscodeprogresscallback.before_validate',
222
- 'fastMONAI/vision_core.py'),
223
241
  'fastMONAI.vision_core._load_and_preprocess': ( 'vision_core.html#_load_and_preprocess',
224
242
  'fastMONAI/vision_core.py'),
225
243
  'fastMONAI.vision_core._multi_channel': ( 'vision_core.html#_multi_channel',
226
244
  'fastMONAI/vision_core.py'),
227
245
  'fastMONAI.vision_core._preprocess': ('vision_core.html#_preprocess', 'fastMONAI/vision_core.py'),
228
246
  'fastMONAI.vision_core.med_img_reader': ( 'vision_core.html#med_img_reader',
229
- 'fastMONAI/vision_core.py'),
230
- 'fastMONAI.vision_core.setup_vscode_progress': ( 'vision_core.html#setup_vscode_progress',
231
- 'fastMONAI/vision_core.py')},
247
+ 'fastMONAI/vision_core.py')},
232
248
  'fastMONAI.vision_data': { 'fastMONAI.vision_data.MedDataBlock': ('vision_data.html#meddatablock', 'fastMONAI/vision_data.py'),
233
249
  'fastMONAI.vision_data.MedDataBlock.__init__': ( 'vision_data.html#meddatablock.__init__',
234
250
  'fastMONAI/vision_data.py'),
@@ -259,6 +275,8 @@ d = { 'settings': { 'branch': 'main',
259
275
  'fastMONAI/vision_inference.py'),
260
276
  'fastMONAI.vision_inference.inference': ( 'vision_inference.html#inference',
261
277
  'fastMONAI/vision_inference.py'),
278
+ 'fastMONAI.vision_inference.keep_largest': ( 'vision_inference.html#keep_largest',
279
+ 'fastMONAI/vision_inference.py'),
262
280
  'fastMONAI.vision_inference.load_system_resources': ( 'vision_inference.html#load_system_resources',
263
281
  'fastMONAI/vision_inference.py'),
264
282
  'fastMONAI.vision_inference.refine_binary_pred_mask': ( 'vision_inference.html#refine_binary_pred_mask',
@@ -281,18 +299,144 @@ d = { 'settings': { 'branch': 'main',
281
299
  'fastMONAI/vision_loss.py'),
282
300
  'fastMONAI.vision_loss.TverskyFocalLoss.forward': ( 'vision_loss_functions.html#tverskyfocalloss.forward',
283
301
  'fastMONAI/vision_loss.py')},
284
- 'fastMONAI.vision_metrics': { 'fastMONAI.vision_metrics.binary_dice_score': ( 'vision_metrics.html#binary_dice_score',
302
+ 'fastMONAI.vision_metrics': { 'fastMONAI.vision_metrics.AccumulatedDice': ( 'vision_metrics.html#accumulateddice',
303
+ 'fastMONAI/vision_metrics.py'),
304
+ 'fastMONAI.vision_metrics.AccumulatedDice.__init__': ( 'vision_metrics.html#accumulateddice.__init__',
305
+ 'fastMONAI/vision_metrics.py'),
306
+ 'fastMONAI.vision_metrics.AccumulatedDice.accumulate': ( 'vision_metrics.html#accumulateddice.accumulate',
307
+ 'fastMONAI/vision_metrics.py'),
308
+ 'fastMONAI.vision_metrics.AccumulatedDice.name': ( 'vision_metrics.html#accumulateddice.name',
309
+ 'fastMONAI/vision_metrics.py'),
310
+ 'fastMONAI.vision_metrics.AccumulatedDice.reset': ( 'vision_metrics.html#accumulateddice.reset',
311
+ 'fastMONAI/vision_metrics.py'),
312
+ 'fastMONAI.vision_metrics.AccumulatedDice.value': ( 'vision_metrics.html#accumulateddice.value',
313
+ 'fastMONAI/vision_metrics.py'),
314
+ 'fastMONAI.vision_metrics.AccumulatedMultiDice': ( 'vision_metrics.html#accumulatedmultidice',
315
+ 'fastMONAI/vision_metrics.py'),
316
+ 'fastMONAI.vision_metrics.AccumulatedMultiDice.name': ( 'vision_metrics.html#accumulatedmultidice.name',
317
+ 'fastMONAI/vision_metrics.py'),
318
+ 'fastMONAI.vision_metrics.AccumulatedMultiDice.value': ( 'vision_metrics.html#accumulatedmultidice.value',
319
+ 'fastMONAI/vision_metrics.py'),
320
+ 'fastMONAI.vision_metrics.binary_dice_score': ( 'vision_metrics.html#binary_dice_score',
285
321
  'fastMONAI/vision_metrics.py'),
286
322
  'fastMONAI.vision_metrics.binary_hausdorff_distance': ( 'vision_metrics.html#binary_hausdorff_distance',
287
323
  'fastMONAI/vision_metrics.py'),
324
+ 'fastMONAI.vision_metrics.binary_lesion_detection_rate': ( 'vision_metrics.html#binary_lesion_detection_rate',
325
+ 'fastMONAI/vision_metrics.py'),
326
+ 'fastMONAI.vision_metrics.binary_precision': ( 'vision_metrics.html#binary_precision',
327
+ 'fastMONAI/vision_metrics.py'),
328
+ 'fastMONAI.vision_metrics.binary_sensitivity': ( 'vision_metrics.html#binary_sensitivity',
329
+ 'fastMONAI/vision_metrics.py'),
330
+ 'fastMONAI.vision_metrics.binary_signed_rve': ( 'vision_metrics.html#binary_signed_rve',
331
+ 'fastMONAI/vision_metrics.py'),
332
+ 'fastMONAI.vision_metrics.calculate_confusion_metrics': ( 'vision_metrics.html#calculate_confusion_metrics',
333
+ 'fastMONAI/vision_metrics.py'),
288
334
  'fastMONAI.vision_metrics.calculate_dsc': ( 'vision_metrics.html#calculate_dsc',
289
335
  'fastMONAI/vision_metrics.py'),
290
336
  'fastMONAI.vision_metrics.calculate_haus': ( 'vision_metrics.html#calculate_haus',
291
337
  'fastMONAI/vision_metrics.py'),
338
+ 'fastMONAI.vision_metrics.calculate_lesion_detection_rate': ( 'vision_metrics.html#calculate_lesion_detection_rate',
339
+ 'fastMONAI/vision_metrics.py'),
340
+ 'fastMONAI.vision_metrics.calculate_signed_rve': ( 'vision_metrics.html#calculate_signed_rve',
341
+ 'fastMONAI/vision_metrics.py'),
292
342
  'fastMONAI.vision_metrics.multi_dice_score': ( 'vision_metrics.html#multi_dice_score',
293
343
  'fastMONAI/vision_metrics.py'),
294
344
  'fastMONAI.vision_metrics.multi_hausdorff_distance': ( 'vision_metrics.html#multi_hausdorff_distance',
295
- 'fastMONAI/vision_metrics.py')},
345
+ 'fastMONAI/vision_metrics.py'),
346
+ 'fastMONAI.vision_metrics.multi_lesion_detection_rate': ( 'vision_metrics.html#multi_lesion_detection_rate',
347
+ 'fastMONAI/vision_metrics.py'),
348
+ 'fastMONAI.vision_metrics.multi_precision': ( 'vision_metrics.html#multi_precision',
349
+ 'fastMONAI/vision_metrics.py'),
350
+ 'fastMONAI.vision_metrics.multi_sensitivity': ( 'vision_metrics.html#multi_sensitivity',
351
+ 'fastMONAI/vision_metrics.py'),
352
+ 'fastMONAI.vision_metrics.multi_signed_rve': ( 'vision_metrics.html#multi_signed_rve',
353
+ 'fastMONAI/vision_metrics.py')},
354
+ 'fastMONAI.vision_patch': { 'fastMONAI.vision_patch.MedPatchDataLoader': ( 'vision_patch.html#medpatchdataloader',
355
+ 'fastMONAI/vision_patch.py'),
356
+ 'fastMONAI.vision_patch.MedPatchDataLoader.__init__': ( 'vision_patch.html#medpatchdataloader.__init__',
357
+ 'fastMONAI/vision_patch.py'),
358
+ 'fastMONAI.vision_patch.MedPatchDataLoader.__iter__': ( 'vision_patch.html#medpatchdataloader.__iter__',
359
+ 'fastMONAI/vision_patch.py'),
360
+ 'fastMONAI.vision_patch.MedPatchDataLoader.__len__': ( 'vision_patch.html#medpatchdataloader.__len__',
361
+ 'fastMONAI/vision_patch.py'),
362
+ 'fastMONAI.vision_patch.MedPatchDataLoader.dataset': ( 'vision_patch.html#medpatchdataloader.dataset',
363
+ 'fastMONAI/vision_patch.py'),
364
+ 'fastMONAI.vision_patch.MedPatchDataLoader.device': ( 'vision_patch.html#medpatchdataloader.device',
365
+ 'fastMONAI/vision_patch.py'),
366
+ 'fastMONAI.vision_patch.MedPatchDataLoader.one_batch': ( 'vision_patch.html#medpatchdataloader.one_batch',
367
+ 'fastMONAI/vision_patch.py'),
368
+ 'fastMONAI.vision_patch.MedPatchDataLoader.to': ( 'vision_patch.html#medpatchdataloader.to',
369
+ 'fastMONAI/vision_patch.py'),
370
+ 'fastMONAI.vision_patch.MedPatchDataLoaders': ( 'vision_patch.html#medpatchdataloaders',
371
+ 'fastMONAI/vision_patch.py'),
372
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.__getitem__': ( 'vision_patch.html#medpatchdataloaders.__getitem__',
373
+ 'fastMONAI/vision_patch.py'),
374
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.__init__': ( 'vision_patch.html#medpatchdataloaders.__init__',
375
+ 'fastMONAI/vision_patch.py'),
376
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.__iter__': ( 'vision_patch.html#medpatchdataloaders.__iter__',
377
+ 'fastMONAI/vision_patch.py'),
378
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.__len__': ( 'vision_patch.html#medpatchdataloaders.__len__',
379
+ 'fastMONAI/vision_patch.py'),
380
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.apply_reorder': ( 'vision_patch.html#medpatchdataloaders.apply_reorder',
381
+ 'fastMONAI/vision_patch.py'),
382
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.bs': ( 'vision_patch.html#medpatchdataloaders.bs',
383
+ 'fastMONAI/vision_patch.py'),
384
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.cpu': ( 'vision_patch.html#medpatchdataloaders.cpu',
385
+ 'fastMONAI/vision_patch.py'),
386
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.cuda': ( 'vision_patch.html#medpatchdataloaders.cuda',
387
+ 'fastMONAI/vision_patch.py'),
388
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.device': ( 'vision_patch.html#medpatchdataloaders.device',
389
+ 'fastMONAI/vision_patch.py'),
390
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.from_df': ( 'vision_patch.html#medpatchdataloaders.from_df',
391
+ 'fastMONAI/vision_patch.py'),
392
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.new_empty': ( 'vision_patch.html#medpatchdataloaders.new_empty',
393
+ 'fastMONAI/vision_patch.py'),
394
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.one_batch': ( 'vision_patch.html#medpatchdataloaders.one_batch',
395
+ 'fastMONAI/vision_patch.py'),
396
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.patch_config': ( 'vision_patch.html#medpatchdataloaders.patch_config',
397
+ 'fastMONAI/vision_patch.py'),
398
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.target_spacing': ( 'vision_patch.html#medpatchdataloaders.target_spacing',
399
+ 'fastMONAI/vision_patch.py'),
400
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.to': ( 'vision_patch.html#medpatchdataloaders.to',
401
+ 'fastMONAI/vision_patch.py'),
402
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.train': ( 'vision_patch.html#medpatchdataloaders.train',
403
+ 'fastMONAI/vision_patch.py'),
404
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.train_ds': ( 'vision_patch.html#medpatchdataloaders.train_ds',
405
+ 'fastMONAI/vision_patch.py'),
406
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.valid': ( 'vision_patch.html#medpatchdataloaders.valid',
407
+ 'fastMONAI/vision_patch.py'),
408
+ 'fastMONAI.vision_patch.MedPatchDataLoaders.valid_ds': ( 'vision_patch.html#medpatchdataloaders.valid_ds',
409
+ 'fastMONAI/vision_patch.py'),
410
+ 'fastMONAI.vision_patch.PatchConfig': ( 'vision_patch.html#patchconfig',
411
+ 'fastMONAI/vision_patch.py'),
412
+ 'fastMONAI.vision_patch.PatchConfig.__post_init__': ( 'vision_patch.html#patchconfig.__post_init__',
413
+ 'fastMONAI/vision_patch.py'),
414
+ 'fastMONAI.vision_patch.PatchInferenceEngine': ( 'vision_patch.html#patchinferenceengine',
415
+ 'fastMONAI/vision_patch.py'),
416
+ 'fastMONAI.vision_patch.PatchInferenceEngine.__init__': ( 'vision_patch.html#patchinferenceengine.__init__',
417
+ 'fastMONAI/vision_patch.py'),
418
+ 'fastMONAI.vision_patch.PatchInferenceEngine.predict': ( 'vision_patch.html#patchinferenceengine.predict',
419
+ 'fastMONAI/vision_patch.py'),
420
+ 'fastMONAI.vision_patch.PatchInferenceEngine.to': ( 'vision_patch.html#patchinferenceengine.to',
421
+ 'fastMONAI/vision_patch.py'),
422
+ 'fastMONAI.vision_patch._extract_tio_transform': ( 'vision_patch.html#_extract_tio_transform',
423
+ 'fastMONAI/vision_patch.py'),
424
+ 'fastMONAI.vision_patch._get_default_device': ( 'vision_patch.html#_get_default_device',
425
+ 'fastMONAI/vision_patch.py'),
426
+ 'fastMONAI.vision_patch._normalize_patch_overlap': ( 'vision_patch.html#_normalize_patch_overlap',
427
+ 'fastMONAI/vision_patch.py'),
428
+ 'fastMONAI.vision_patch._warn_config_override': ( 'vision_patch.html#_warn_config_override',
429
+ 'fastMONAI/vision_patch.py'),
430
+ 'fastMONAI.vision_patch.create_patch_sampler': ( 'vision_patch.html#create_patch_sampler',
431
+ 'fastMONAI/vision_patch.py'),
432
+ 'fastMONAI.vision_patch.create_subjects_dataset': ( 'vision_patch.html#create_subjects_dataset',
433
+ 'fastMONAI/vision_patch.py'),
434
+ 'fastMONAI.vision_patch.med_to_subject': ( 'vision_patch.html#med_to_subject',
435
+ 'fastMONAI/vision_patch.py'),
436
+ 'fastMONAI.vision_patch.normalize_patch_transforms': ( 'vision_patch.html#normalize_patch_transforms',
437
+ 'fastMONAI/vision_patch.py'),
438
+ 'fastMONAI.vision_patch.patch_inference': ( 'vision_patch.html#patch_inference',
439
+ 'fastMONAI/vision_patch.py')},
296
440
  'fastMONAI.vision_plot': { 'fastMONAI.vision_plot._get_slice': ('vision_plot.html#_get_slice', 'fastMONAI/vision_plot.py'),
297
441
  'fastMONAI.vision_plot.find_max_slice': ( 'vision_plot.html#find_max_slice',
298
442
  'fastMONAI/vision_plot.py'),