fastMONAI 0.5.0.0__tar.gz → 0.5.2__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.
- {fastmonai-0.5.0.0/fastMONAI.egg-info → fastmonai-0.5.2}/PKG-INFO +7 -7
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/README.md +6 -6
- fastmonai-0.5.2/fastMONAI/__init__.py +1 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI/_modidx.py +27 -2
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI/utils.py +177 -3
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI/vision_augmentation.py +102 -18
- {fastmonai-0.5.0.0 → fastmonai-0.5.2/fastMONAI.egg-info}/PKG-INFO +7 -7
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/pyproject.toml +1 -1
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/settings.ini +2 -2
- fastmonai-0.5.0.0/fastMONAI/__init__.py +0 -1
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/CONTRIBUTING.md +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/LICENSE +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/MANIFEST.in +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI/dataset_info.py +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI/external_data.py +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI/research_utils.py +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI/vision_all.py +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI/vision_core.py +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI/vision_data.py +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI/vision_inference.py +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI/vision_loss.py +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI/vision_metrics.py +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI/vision_plot.py +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI.egg-info/SOURCES.txt +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI.egg-info/dependency_links.txt +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI.egg-info/entry_points.txt +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI.egg-info/not-zip-safe +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI.egg-info/requires.txt +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/fastMONAI.egg-info/top_level.txt +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/setup.cfg +0 -0
- {fastmonai-0.5.0.0 → fastmonai-0.5.2}/setup.py +0 -0
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Metadata-Version: 2.4
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Name: fastMONAI
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Version: 0.5.
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Version: 0.5.2
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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
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<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
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[](https://fastmonai.no)
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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/
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| [10b_tutorial_regression.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/
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| [10c_tutorial_binary_segmentation.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/
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| [10d_tutorial_multiclass_segmentation.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/
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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. | [](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”). | [](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). | [](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). | [](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/10d_tutorial_multiclass_segmentation.ipynb) |
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# How to contribute
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We welcome contributions! See
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[CONTRIBUTING.md](https://github.com/MMIV-ML/fastMONAI/blob/
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[CONTRIBUTING.md](https://github.com/MMIV-ML/fastMONAI/blob/main/CONTRIBUTING.md)
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# Citing fastMONAI
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[](https://fastmonai.no)
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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. | [](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”). | [](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). | [](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). | [](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/10d_tutorial_multiclass_segmentation.ipynb) |
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# How to contribute
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We welcome contributions! See
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[CONTRIBUTING.md](https://github.com/MMIV-ML/fastMONAI/blob/
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[CONTRIBUTING.md](https://github.com/MMIV-ML/fastMONAI/blob/main/CONTRIBUTING.md)
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# Citing fastMONAI
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__version__ = "0.5.2"
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# Autogenerated by nbdev
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d = { 'settings': { 'branch': '
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d = { 'settings': { 'branch': 'main',
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'doc_baseurl': '/',
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'doc_host': 'https://fastmonai.no',
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'git_url': 'https://github.com/MMIV-ML/fastMONAI',
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'fastMONAI/external_data.py')},
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'fastMONAI.research_utils': { 'fastMONAI.research_utils.pred_postprocess': ( 'research_utils.html#pred_postprocess',
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'fastMONAI.utils': { 'fastMONAI.utils.
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'fastMONAI.utils': { 'fastMONAI.utils.MLflowUIManager': ('utils.html#mlflowuimanager', 'fastMONAI/utils.py'),
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'fastMONAI.utils.MLflowUIManager.__init__': ('utils.html#mlflowuimanager.__init__', 'fastMONAI/utils.py'),
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'fastMONAI.utils.MLflowUIManager.check_mlflow_installed': ( 'utils.html#mlflowuimanager.check_mlflow_installed',
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'fastMONAI/utils.py'),
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'fastMONAI.utils.MLflowUIManager.find_available_port': ( 'utils.html#mlflowuimanager.find_available_port',
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'fastMONAI/utils.py'),
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'fastMONAI.utils.MLflowUIManager.is_mlflow_running': ( 'utils.html#mlflowuimanager.is_mlflow_running',
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'fastMONAI/utils.py'),
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'fastMONAI.utils.MLflowUIManager.is_port_available': ( 'utils.html#mlflowuimanager.is_port_available',
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'fastMONAI/utils.py'),
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'fastMONAI.utils.MLflowUIManager.start_ui': ('utils.html#mlflowuimanager.start_ui', 'fastMONAI/utils.py'),
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'fastMONAI.utils.MLflowUIManager.status': ('utils.html#mlflowuimanager.status', 'fastMONAI/utils.py'),
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'fastMONAI.utils.MLflowUIManager.stop': ('utils.html#mlflowuimanager.stop', 'fastMONAI/utils.py'),
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'fastMONAI.utils.ModelTrackingCallback': ('utils.html#modeltrackingcallback', 'fastMONAI/utils.py'),
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'fastMONAI.utils.ModelTrackingCallback.__init__': ( 'utils.html#modeltrackingcallback.__init__',
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'fastMONAI/utils.py'),
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'fastMONAI.utils.ModelTrackingCallback._build_config': ( 'utils.html#modeltrackingcallback._build_config',
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'fastMONAI.vision_augmentation.CustomDictTransform.encodes': ( 'vision_augment.html#customdicttransform.encodes',
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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.NormalizeIntensity.encodes': ( 'vision_augment.html#normalizeintensity.encodes',
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'fastMONAI.vision_augmentation.OneOf': ( 'vision_augment.html#oneof',
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'fastMONAI.vision_augmentation.OneOf.__init__': ( 'vision_augment.html#oneof.__init__',
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'fastMONAI.vision_augmentation.RandomSpike.encodes': ( 'vision_augment.html#randomspike.encodes',
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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.ZNormalization': ( 'vision_augment.html#znormalization',
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'fastMONAI.vision_augmentation.ZNormalization.__init__': ( 'vision_augment.html#znormalization.__init__',
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__all__ = ['store_variables', 'load_variables', 'print_colab_gpu_info', 'ModelTrackingCallback']
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__all__ = ['store_variables', 'load_variables', 'print_colab_gpu_info', 'ModelTrackingCallback', 'MLflowUIManager']
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import socket
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from IPython.core.magic import register_line_magic
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class MLflowUIManager:
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def __init__(self):
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try:
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def is_mlflow_running(self):
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try:
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response = requests.get(f'http://localhost:{self.port}', timeout=2)
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except:
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def find_available_port(self, start_port=5001):
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for port in range(start_port, start_port + 10):
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return port
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return None
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def check_mlflow_installed(self):
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def start_ui(self, auto_open=True, quiet=False):
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"""Start MLflow UI with better error handling and user feedback."""
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if not self.check_mlflow_installed():
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if not quiet:
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display(HTML('<div style="color: #d32f2f; font-weight: bold; font-size: 14px;">❌ MLflow not installed. Run: pip install mlflow</div>'))
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return False
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# Find available port
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available_port = self.find_available_port(self.port)
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if available_port is None:
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if not quiet:
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display(HTML('<div style="color: #d32f2f; font-weight: bold; font-size: 14px;">❌ No available ports found (5001-5010)</div>'))
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return False
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self.port = available_port
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# Start MLflow UI in a separate thread
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def run_mlflow():
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try:
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self.process = subprocess.Popen([
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'mlflow', 'ui',
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'--host', self.host,
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'--port', str(self.port),
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'--backend-store-uri', self.backend_store_uri
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], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
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self.process.wait()
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except Exception as e:
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if not quiet:
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display(HTML(f'<div style="color: #d32f2f; font-weight: bold; font-size: 14px;">❌ Error: {str(e)}</div>'))
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self.thread = threading.Thread(target=run_mlflow, daemon=True)
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self.thread.start()
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max_wait = 10
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for i in range(max_wait):
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time.sleep(1)
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if quiet:
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# Bright, visible link for quiet mode
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display(HTML(f'''
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<a href="http://localhost:{self.port}" target="_blank"
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style="color: #1976d2; font-weight: bold; font-size: 16px; text-decoration: underline;">
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🔗 MLflow UI (Port {self.port})
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</a>
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'''))
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else:
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# Success message with high contrast colors
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display(HTML(f'''
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<div style="background-color: #c8e6c9; border: 2px solid #388e3c; padding: 15px; border-radius: 8px; margin: 10px 0;">
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<div style="color: #1b5e20; font-weight: bold; font-size: 16px; margin-bottom: 10px;">
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✅ MLflow UI is running successfully!
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</div>
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<a href="http://localhost:{self.port}" target="_blank"
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|
+
style="background-color: #1976d2; color: white; padding: 12px 24px; text-decoration: none; border-radius: 6px; font-weight: bold; font-size: 14px; display: inline-block; margin: 5px 0;">
|
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|
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🔗 Open MLflow UI
|
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|
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</a>
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<div style="margin-top: 10px;">
|
|
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|
+
<div style="color: #424242; font-size: 13px;">URL: http://localhost:{self.port}</div>
|
|
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|
+
</div>
|
|
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|
+
</div>
|
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|
+
'''))
|
|
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|
+
return True
|
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+
|
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369
|
+
# If we get here, server didn't start properly
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|
+
if not quiet:
|
|
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|
+
display(HTML('<div style="color: #d32f2f; font-weight: bold; font-size: 14px;">❌ Failed to start MLflow UI</div>'))
|
|
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|
+
return False
|
|
373
|
+
|
|
374
|
+
def stop(self):
|
|
375
|
+
"""Stop the MLflow UI server."""
|
|
376
|
+
if self.process:
|
|
377
|
+
self.process.terminate()
|
|
378
|
+
self.process = None
|
|
379
|
+
display(HTML('''
|
|
380
|
+
<div style="background-color: #ffecb3; border: 2px solid #f57c00; padding: 10px; border-radius: 6px;">
|
|
381
|
+
<span style="color: #e65100; font-weight: bold; font-size: 14px;">🛑 MLflow UI stopped</span>
|
|
382
|
+
</div>
|
|
383
|
+
'''))
|
|
384
|
+
else:
|
|
385
|
+
display(HTML('''
|
|
386
|
+
<div style="background-color: #f0f0f0; border: 2px solid #757575; padding: 10px; border-radius: 6px;">
|
|
387
|
+
<span style="color: #424242; font-weight: bold; font-size: 14px;">ℹ️ MLflow UI is not currently running</span>
|
|
388
|
+
</div>
|
|
389
|
+
'''))
|
|
390
|
+
|
|
391
|
+
def status(self):
|
|
392
|
+
"""Check MLflow UI status."""
|
|
393
|
+
if self.is_mlflow_running():
|
|
394
|
+
display(HTML(f'''
|
|
395
|
+
<div style="background-color: #c8e6c9; border: 2px solid #388e3c; padding: 10px; border-radius: 6px;">
|
|
396
|
+
<div style="color: #1b5e20; font-weight: bold; font-size: 14px;">✅ MLflow UI is running</div>
|
|
397
|
+
<a href="http://localhost:{self.port}" target="_blank"
|
|
398
|
+
style="color: #1976d2; font-weight: bold; text-decoration: underline;">
|
|
399
|
+
http://localhost:{self.port}
|
|
400
|
+
</a>
|
|
401
|
+
</div>
|
|
402
|
+
'''))
|
|
403
|
+
else:
|
|
404
|
+
display(HTML('''
|
|
405
|
+
<div style="background-color: #ffcdd2; border: 2px solid #d32f2f; padding: 10px; border-radius: 6px;">
|
|
406
|
+
<div style="color: #b71c1c; font-weight: bold; font-size: 14px;">❌ MLflow UI is not running</div>
|
|
407
|
+
<div style="color: #424242; font-size: 13px; margin-top: 5px;">
|
|
408
|
+
Run <code style="background-color: #f5f5f5; padding: 2px 4px; border-radius: 3px;">mlflow_ui.start_ui()</code> to start it.
|
|
409
|
+
</div>
|
|
410
|
+
</div>
|
|
411
|
+
'''))
|
|
@@ -1,14 +1,16 @@
|
|
|
1
1
|
# AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/03_vision_augment.ipynb.
|
|
2
2
|
|
|
3
3
|
# %% auto 0
|
|
4
|
-
__all__ = ['CustomDictTransform', 'do_pad_or_crop', 'PadOrCrop', 'ZNormalization', '
|
|
5
|
-
'
|
|
6
|
-
'RandomMotion', 'RandomElasticDeformation', 'RandomAffine', 'RandomFlip',
|
|
4
|
+
__all__ = ['CustomDictTransform', 'do_pad_or_crop', 'PadOrCrop', 'ZNormalization', 'RescaleIntensity', 'NormalizeIntensity',
|
|
5
|
+
'BraTSMaskConverter', 'BinaryConverter', 'RandomGhosting', 'RandomSpike', 'RandomNoise', 'RandomBiasField',
|
|
6
|
+
'RandomBlur', 'RandomGamma', 'RandomMotion', 'RandomElasticDeformation', 'RandomAffine', 'RandomFlip',
|
|
7
|
+
'OneOf']
|
|
7
8
|
|
|
8
9
|
# %% ../nbs/03_vision_augment.ipynb 2
|
|
9
10
|
from fastai.data.all import *
|
|
10
11
|
from .vision_core import *
|
|
11
12
|
import torchio as tio
|
|
13
|
+
from monai.transforms import NormalizeIntensity as MonaiNormalizeIntensity
|
|
12
14
|
|
|
13
15
|
# %% ../nbs/03_vision_augment.ipynb 5
|
|
14
16
|
class CustomDictTransform(ItemTransform):
|
|
@@ -84,9 +86,29 @@ class ZNormalization(DisplayedTransform):
|
|
|
84
86
|
self.channel_wise = channel_wise
|
|
85
87
|
|
|
86
88
|
def encodes(self, o: MedImage):
|
|
87
|
-
|
|
88
|
-
|
|
89
|
-
|
|
89
|
+
try:
|
|
90
|
+
if self.channel_wise:
|
|
91
|
+
o = torch.stack([self.z_normalization(c[None])[0] for c in o])
|
|
92
|
+
else:
|
|
93
|
+
o = self.z_normalization(o)
|
|
94
|
+
except RuntimeError as e:
|
|
95
|
+
if "Standard deviation is 0" in str(e):
|
|
96
|
+
# Calculate mean for debugging information
|
|
97
|
+
mean = float(o.mean())
|
|
98
|
+
|
|
99
|
+
error_msg = (
|
|
100
|
+
f"Standard deviation is 0 for image (mean={mean:.3f}).\n"
|
|
101
|
+
f"This indicates uniform pixel values.\n\n"
|
|
102
|
+
f"Possible causes:\n"
|
|
103
|
+
f"• Corrupted or blank image\n"
|
|
104
|
+
f"• Oversaturated regions\n"
|
|
105
|
+
f"• Background-only regions\n"
|
|
106
|
+
f"• All-zero mask being processed as image\n\n"
|
|
107
|
+
f"Suggested solutions:\n"
|
|
108
|
+
f"• Check image quality and acquisition\n"
|
|
109
|
+
f"• Verify image vs mask data loading"
|
|
110
|
+
)
|
|
111
|
+
raise RuntimeError(error_msg) from e
|
|
90
112
|
|
|
91
113
|
return MedImage.create(o)
|
|
92
114
|
|
|
@@ -94,6 +116,68 @@ class ZNormalization(DisplayedTransform):
|
|
|
94
116
|
return o
|
|
95
117
|
|
|
96
118
|
# %% ../nbs/03_vision_augment.ipynb 10
|
|
119
|
+
class RescaleIntensity(DisplayedTransform):
|
|
120
|
+
"""Apply TorchIO RescaleIntensity for robust intensity scaling.
|
|
121
|
+
|
|
122
|
+
Args:
|
|
123
|
+
out_min_max (tuple[float, float]): Output intensity range (min, max)
|
|
124
|
+
in_min_max (tuple[float, float]): Input intensity range (min, max)
|
|
125
|
+
|
|
126
|
+
Example for CT images:
|
|
127
|
+
# Normalize CT from air (-1000 HU) to bone (1000 HU) into range (-1, 1)
|
|
128
|
+
transform = RescaleIntensity(out_min_max=(-1, 1), in_min_max=(-1000, 1000))
|
|
129
|
+
"""
|
|
130
|
+
|
|
131
|
+
order = 0
|
|
132
|
+
|
|
133
|
+
def __init__(self, out_min_max: tuple[float, float], in_min_max: tuple[float, float]):
|
|
134
|
+
self.rescale = tio.RescaleIntensity(out_min_max=out_min_max, in_min_max=in_min_max)
|
|
135
|
+
|
|
136
|
+
def encodes(self, o: MedImage):
|
|
137
|
+
return MedImage.create(self.rescale(o))
|
|
138
|
+
|
|
139
|
+
def encodes(self, o: MedMask):
|
|
140
|
+
return o
|
|
141
|
+
|
|
142
|
+
# %% ../nbs/03_vision_augment.ipynb 11
|
|
143
|
+
class NormalizeIntensity(DisplayedTransform):
|
|
144
|
+
"""Apply MONAI NormalizeIntensity.
|
|
145
|
+
|
|
146
|
+
Args:
|
|
147
|
+
nonzero (bool): Only normalize non-zero values (default: True)
|
|
148
|
+
channel_wise (bool): Apply normalization per channel (default: True)
|
|
149
|
+
subtrahend (float, optional): Value to subtract
|
|
150
|
+
divisor (float, optional): Value to divide by
|
|
151
|
+
"""
|
|
152
|
+
|
|
153
|
+
order = 0
|
|
154
|
+
|
|
155
|
+
def __init__(self, nonzero: bool = True, channel_wise: bool = True,
|
|
156
|
+
subtrahend: float = None, divisor: float = None):
|
|
157
|
+
self.nonzero = nonzero
|
|
158
|
+
self.channel_wise = channel_wise
|
|
159
|
+
self.subtrahend = subtrahend
|
|
160
|
+
self.divisor = divisor
|
|
161
|
+
|
|
162
|
+
self.transform = MonaiNormalizeIntensity(
|
|
163
|
+
nonzero=nonzero,
|
|
164
|
+
channel_wise=False, # Always 'False', we handle channel-wise manually
|
|
165
|
+
subtrahend=subtrahend,
|
|
166
|
+
divisor=divisor
|
|
167
|
+
)
|
|
168
|
+
|
|
169
|
+
def encodes(self, o: MedImage):
|
|
170
|
+
if self.channel_wise:
|
|
171
|
+
result = torch.stack([self.transform(c[None])[0] for c in o])
|
|
172
|
+
else:
|
|
173
|
+
result = torch.Tensor(self.transform(o))
|
|
174
|
+
|
|
175
|
+
return MedImage.create(result)
|
|
176
|
+
|
|
177
|
+
def encodes(self, o: MedMask):
|
|
178
|
+
return o
|
|
179
|
+
|
|
180
|
+
# %% ../nbs/03_vision_augment.ipynb 12
|
|
97
181
|
class BraTSMaskConverter(DisplayedTransform):
|
|
98
182
|
'''Convert BraTS masks.'''
|
|
99
183
|
|
|
@@ -105,7 +189,7 @@ class BraTSMaskConverter(DisplayedTransform):
|
|
|
105
189
|
o = torch.where(o==4, 3., o)
|
|
106
190
|
return MedMask.create(o)
|
|
107
191
|
|
|
108
|
-
# %% ../nbs/03_vision_augment.ipynb
|
|
192
|
+
# %% ../nbs/03_vision_augment.ipynb 13
|
|
109
193
|
class BinaryConverter(DisplayedTransform):
|
|
110
194
|
'''Convert to binary mask.'''
|
|
111
195
|
|
|
@@ -118,7 +202,7 @@ class BinaryConverter(DisplayedTransform):
|
|
|
118
202
|
o = torch.where(o>0, 1., 0)
|
|
119
203
|
return MedMask.create(o)
|
|
120
204
|
|
|
121
|
-
# %% ../nbs/03_vision_augment.ipynb
|
|
205
|
+
# %% ../nbs/03_vision_augment.ipynb 14
|
|
122
206
|
class RandomGhosting(DisplayedTransform):
|
|
123
207
|
"""Apply TorchIO `RandomGhosting`."""
|
|
124
208
|
|
|
@@ -133,7 +217,7 @@ class RandomGhosting(DisplayedTransform):
|
|
|
133
217
|
def encodes(self, o: MedMask):
|
|
134
218
|
return o
|
|
135
219
|
|
|
136
|
-
# %% ../nbs/03_vision_augment.ipynb
|
|
220
|
+
# %% ../nbs/03_vision_augment.ipynb 15
|
|
137
221
|
class RandomSpike(DisplayedTransform):
|
|
138
222
|
'''Apply TorchIO `RandomSpike`.'''
|
|
139
223
|
|
|
@@ -148,7 +232,7 @@ class RandomSpike(DisplayedTransform):
|
|
|
148
232
|
def encodes(self, o:MedMask):
|
|
149
233
|
return o
|
|
150
234
|
|
|
151
|
-
# %% ../nbs/03_vision_augment.ipynb
|
|
235
|
+
# %% ../nbs/03_vision_augment.ipynb 16
|
|
152
236
|
class RandomNoise(DisplayedTransform):
|
|
153
237
|
'''Apply TorchIO `RandomNoise`.'''
|
|
154
238
|
|
|
@@ -163,7 +247,7 @@ class RandomNoise(DisplayedTransform):
|
|
|
163
247
|
def encodes(self, o: MedMask):
|
|
164
248
|
return o
|
|
165
249
|
|
|
166
|
-
# %% ../nbs/03_vision_augment.ipynb
|
|
250
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Metadata-Version: 2.4
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Name: fastMONAI
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Version: 0.5.
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Version: 0.5.2
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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
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<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
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[](https://fastmonai.no)
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| Notebook | 1-Click Notebook |
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|:---|----|
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| [10b_tutorial_regression.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/
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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. | [](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”). | [](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). | [](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). | [](https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/main/nbs/10d_tutorial_multiclass_segmentation.ipynb) |
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# How to contribute
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We welcome contributions! See
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[CONTRIBUTING.md](https://github.com/MMIV-ML/fastMONAI/blob/
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[CONTRIBUTING.md](https://github.com/MMIV-ML/fastMONAI/blob/main/CONTRIBUTING.md)
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# Citing fastMONAI
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[project]
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name="fastMONAI"
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dynamic = [ "keywords", "description", "version", "dependencies", "optional-dependencies", "readme", "license", "authors", "classifiers", "entry-points", "scripts", "urls"]
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[tool.uv]
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### Python Library ###
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lib_name = fastMONAI
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version = 0.5.2
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### OPTIONAL ###
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requirements = fastai==2.8.3 monai==1.5.0 torchio==0.20.19 xlrd>=1.2.0 scikit-image==0.25.2 imagedata==3.8.4 mlflow==3.3.1 huggingface-hub gdown gradio opencv-python plum-dispatch
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### Documentation ###
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host = github
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repo = fastMONAI
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branch = main
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custom_sidebar = True
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jupyter_hooks = True
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clean_ids = False
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