fastMONAI 0.5.0.0__py3-none-any.whl → 0.5.2__py3-none-any.whl

fastMONAI/__init__.py

@@ -1 +1 @@
-__version__ = "0.5.0.0"
+__version__ = "0.5.2"

fastMONAI/_modidx.py

@@ -1,6 +1,6 @@
 # Autogenerated by nbdev
 
-d = { 'settings': { 'branch': 'master',
+d = { 'settings': { 'branch': 'main',
                 'doc_baseurl': '/',
                 'doc_host': 'https://fastmonai.no',
                 'git_url': 'https://github.com/MMIV-ML/fastMONAI',
@@ -47,7 +47,20 @@ d = { 'settings': { 'branch': 'master',
                                                                                                '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.ModelTrackingCallback': ('utils.html#modeltrackingcallback', 'fastMONAI/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.check_mlflow_installed': ( 'utils.html#mlflowuimanager.check_mlflow_installed',
+                                                                                             'fastMONAI/utils.py'),
+                                 'fastMONAI.utils.MLflowUIManager.find_available_port': ( 'utils.html#mlflowuimanager.find_available_port',
+                                                                                          'fastMONAI/utils.py'),
+                                 'fastMONAI.utils.MLflowUIManager.is_mlflow_running': ( 'utils.html#mlflowuimanager.is_mlflow_running',
+                                                                                        'fastMONAI/utils.py'),
+                                 'fastMONAI.utils.MLflowUIManager.is_port_available': ( 'utils.html#mlflowuimanager.is_port_available',
+                                                                                        'fastMONAI/utils.py'),
+                                 'fastMONAI.utils.MLflowUIManager.start_ui': ('utils.html#mlflowuimanager.start_ui', 'fastMONAI/utils.py'),
+                                 'fastMONAI.utils.MLflowUIManager.status': ('utils.html#mlflowuimanager.status', 'fastMONAI/utils.py'),
+                                 'fastMONAI.utils.MLflowUIManager.stop': ('utils.html#mlflowuimanager.stop', 'fastMONAI/utils.py'),
+                                 'fastMONAI.utils.ModelTrackingCallback': ('utils.html#modeltrackingcallback', 'fastMONAI/utils.py'),
                                  'fastMONAI.utils.ModelTrackingCallback.__init__': ( 'utils.html#modeltrackingcallback.__init__',
                                                                                      'fastMONAI/utils.py'),
                                  'fastMONAI.utils.ModelTrackingCallback._build_config': ( 'utils.html#modeltrackingcallback._build_config',
@@ -86,6 +99,12 @@ d = { 'settings': { 'branch': 'master',
                                                                                                                'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.CustomDictTransform.encodes': ( 'vision_augment.html#customdicttransform.encodes',
                                                                                                               'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation.NormalizeIntensity': ( 'vision_augment.html#normalizeintensity',
+                                                                                                     'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation.NormalizeIntensity.__init__': ( 'vision_augment.html#normalizeintensity.__init__',
+                                                                                                              'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation.NormalizeIntensity.encodes': ( 'vision_augment.html#normalizeintensity.encodes',
+                                                                                                             '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__',
@@ -150,6 +169,12 @@ d = { 'settings': { 'branch': 'master',
                                                                                                        'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.RandomSpike.encodes': ( 'vision_augment.html#randomspike.encodes',
                                                                                                       'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation.RescaleIntensity': ( 'vision_augment.html#rescaleintensity',
+                                                                                                   'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation.RescaleIntensity.__init__': ( 'vision_augment.html#rescaleintensity.__init__',
+                                                                                                            'fastMONAI/vision_augmentation.py'),
+                                               'fastMONAI.vision_augmentation.RescaleIntensity.encodes': ( 'vision_augment.html#rescaleintensity.encodes',
+                                                                                                           'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.ZNormalization': ( 'vision_augment.html#znormalization',
                                                                                                  'fastMONAI/vision_augmentation.py'),
                                                'fastMONAI.vision_augmentation.ZNormalization.__init__': ( 'vision_augment.html#znormalization.__init__',

fastMONAI/utils.py

@@ -1,7 +1,7 @@
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/07_utils.ipynb.
 
 # %% auto 0
-__all__ = ['store_variables', 'load_variables', 'print_colab_gpu_info', 'ModelTrackingCallback']
+__all__ = ['store_variables', 'load_variables', 'print_colab_gpu_info', 'ModelTrackingCallback', 'MLflowUIManager']
 
 # %% ../nbs/07_utils.ipynb 1
 import pickle
@@ -13,6 +13,7 @@ import os
 import tempfile
 import json
 from fastai.callback.core import Callback
+from fastcore.foundation import L
 from typing import Any
 
 # %% ../nbs/07_utils.ipynb 3
@@ -165,6 +166,8 @@ class ModelTrackingCallback(Callback):
         
         # Process each metric, handling both scalars and tensors
         for name, val in zip(metric_names, raw_metric_values):
+            if val is None:
+                continue  # Skip None values during inference
             if isinstance(val, torch.Tensor):
                 if val.numel() == 1:
                     # Single value tensor (like binary dice score)
@@ -182,8 +185,9 @@ class ModelTrackingCallback(Callback):
         
         # Handle loss values
         if len(recorder.log) >= 2:
-            metrics['train_loss'] = float(recorder.log[1])
-            if len(recorder.log) >= 3:
+            if recorder.log[1] is not None:
+                metrics['train_loss'] = float(recorder.log[1])
+            if len(recorder.log) >= 3 and recorder.log[2] is not None:
                 metrics['valid_loss'] = float(recorder.log[2])
                 
         return metrics
@@ -197,10 +201,22 @@ class ModelTrackingCallback(Callback):
         if os.path.exists(weights_file):
             mlflow.log_artifact(weights_file, "model")
         
+        # Remove MLflow callbacks before exporting learner for inference
+        # This prevents the callback from being triggered during inference
+        original_cbs = self.learn.cbs.copy()  # Save original callbacks
+        
+        # Remove ModelTrackingCallback instances from learner using proper collection type
+        filtered_cbs = L([cb for cb in self.learn.cbs if not isinstance(cb, ModelTrackingCallback)])
+        self.learn.cbs = filtered_cbs
+        
+        # Export clean learner without MLflow callbacks
         learner_path = temp_dir / "learner.pkl"
         self.learn.export(str(learner_path))
         mlflow.log_artifact(str(learner_path), "model")
         
+        # Restore original callbacks for current session
+        self.learn.cbs = original_cbs
+        
         config_path = temp_dir / "inference_settings.pkl"
         store_variables(config_path, self.size, self.reorder, self.resample)
         mlflow.log_artifact(str(config_path), "config")
@@ -235,3 +251,161 @@ class ModelTrackingCallback(Callback):
             self._register_pytorch_model()
             
         print(f"MLflow run completed. Run ID: {mlflow.active_run().info.run_id}")
+
+# %% ../nbs/07_utils.ipynb 7
+import subprocess
+import threading
+import time
+import socket
+import os
+from IPython.display import display, HTML, clear_output
+from IPython.core.magic import register_line_magic
+from IPython import get_ipython
+import requests
+import shutil
+
+class MLflowUIManager:
+    def __init__(self):
+        self.process = None
+        self.thread = None
+        self.port = 5001
+        self.host = '0.0.0.0'
+        self.backend_store_uri = './mlruns'
+        
+    def is_port_available(self, port):
+        """Check if a port is available."""
+        with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
+            try:
+                s.bind(('localhost', port))
+                return True
+            except OSError:
+                return False
+    
+    def is_mlflow_running(self):
+        """Check if MLflow UI is actually responding."""
+        try:
+            response = requests.get(f'http://localhost:{self.port}', timeout=2)
+            return response.status_code == 200
+        except:
+            return False
+    
+    def find_available_port(self, start_port=5001):
+        """Find an available port starting from start_port."""
+        for port in range(start_port, start_port + 10):
+            if self.is_port_available(port):
+                return port
+        return None
+    
+    def check_mlflow_installed(self):
+        """Check if MLflow is installed."""
+        return shutil.which('mlflow') is not None
+    
+    def start_ui(self, auto_open=True, quiet=False):
+        """Start MLflow UI with better error handling and user feedback."""
+        
+        # Check if MLflow is installed
+        if not self.check_mlflow_installed():
+            if not quiet:
+                display(HTML('<div style="color: #d32f2f; font-weight: bold; font-size: 14px;">❌ MLflow not installed. Run: pip install mlflow</div>'))
+            return False
+        
+        # Find available port
+        available_port = self.find_available_port(self.port)
+        if available_port is None:
+            if not quiet:
+                display(HTML('<div style="color: #d32f2f; font-weight: bold; font-size: 14px;">❌ No available ports found (5001-5010)</div>'))
+            return False
+        
+        self.port = available_port
+        
+        # Start MLflow UI in a separate thread
+        def run_mlflow():
+            try:
+                self.process = subprocess.Popen([
+                    'mlflow', 'ui', 
+                    '--host', self.host,
+                    '--port', str(self.port),
+                    '--backend-store-uri', self.backend_store_uri
+                ], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+                self.process.wait()
+            except Exception as e:
+                if not quiet:
+                    display(HTML(f'<div style="color: #d32f2f; font-weight: bold; font-size: 14px;">❌ Error: {str(e)}</div>'))
+        
+        self.thread = threading.Thread(target=run_mlflow, daemon=True)
+        self.thread.start()
+        
+        # Wait and check if server started successfully
+        max_wait = 10
+        for i in range(max_wait):
+            time.sleep(1)
+            if self.is_mlflow_running():
+                if quiet:
+                    # Bright, visible link for quiet mode
+                    display(HTML(f'''
+                        <a href="http://localhost:{self.port}" target="_blank" 
+                           style="color: #1976d2; font-weight: bold; font-size: 16px; text-decoration: underline;">
+                           🔗 MLflow UI (Port {self.port})
+                        </a>
+                    '''))
+                else:
+                    # Success message with high contrast colors
+                    display(HTML(f'''
+                        <div style="background-color: #c8e6c9; border: 2px solid #388e3c; padding: 15px; border-radius: 8px; margin: 10px 0;">
+                            <div style="color: #1b5e20; font-weight: bold; font-size: 16px; margin-bottom: 10px;">
+                                ✅ MLflow UI is running successfully!
+                            </div>
+                            <a href="http://localhost:{self.port}" target="_blank" 
+                               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;">
+                                🔗 Open MLflow UI
+                            </a>
+                            <div style="margin-top: 10px;">
+                                <div style="color: #424242; font-size: 13px;">URL: http://localhost:{self.port}</div>
+                            </div>
+                        </div>
+                    '''))
+                return True
+        
+        # If we get here, server didn't start properly
+        if not quiet:
+            display(HTML('<div style="color: #d32f2f; font-weight: bold; font-size: 14px;">❌ Failed to start MLflow UI</div>'))
+        return False
+    
+    def stop(self):
+        """Stop the MLflow UI server."""
+        if self.process:
+            self.process.terminate()
+            self.process = None
+            display(HTML('''
+                <div style="background-color: #ffecb3; border: 2px solid #f57c00; padding: 10px; border-radius: 6px;">
+                    <span style="color: #e65100; font-weight: bold; font-size: 14px;">🛑 MLflow UI stopped</span>
+                </div>
+            '''))
+        else:
+            display(HTML('''
+                <div style="background-color: #f0f0f0; border: 2px solid #757575; padding: 10px; border-radius: 6px;">
+                    <span style="color: #424242; font-weight: bold; font-size: 14px;">ℹ️ MLflow UI is not currently running</span>
+                </div>
+            '''))
+    
+    def status(self):
+        """Check MLflow UI status."""
+        if self.is_mlflow_running():
+            display(HTML(f'''
+                <div style="background-color: #c8e6c9; border: 2px solid #388e3c; padding: 10px; border-radius: 6px;">
+                    <div style="color: #1b5e20; font-weight: bold; font-size: 14px;">✅ MLflow UI is running</div>
+                    <a href="http://localhost:{self.port}" target="_blank" 
+                       style="color: #1976d2; font-weight: bold; text-decoration: underline;">
+                       http://localhost:{self.port}
+                    </a>
+                </div>
+            '''))
+        else:
+            display(HTML('''
+                <div style="background-color: #ffcdd2; border: 2px solid #d32f2f; padding: 10px; border-radius: 6px;">
+                    <div style="color: #b71c1c; font-weight: bold; font-size: 14px;">❌ MLflow UI is not running</div>
+                    <div style="color: #424242; font-size: 13px; margin-top: 5px;">
+                        Run <code style="background-color: #f5f5f5; padding: 2px 4px; border-radius: 3px;">mlflow_ui.start_ui()</code> to start it.
+                    </div>
+                </div>
+            '''))

fastMONAI/vision_augmentation.py

@@ -1,14 +1,16 @@
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/03_vision_augment.ipynb.
 
 # %% auto 0
-__all__ = ['CustomDictTransform', 'do_pad_or_crop', 'PadOrCrop', 'ZNormalization', 'BraTSMaskConverter', 'BinaryConverter',
-           'RandomGhosting', 'RandomSpike', 'RandomNoise', 'RandomBiasField', 'RandomBlur', 'RandomGamma',
-           'RandomMotion', 'RandomElasticDeformation', 'RandomAffine', 'RandomFlip', 'OneOf']
+__all__ = ['CustomDictTransform', 'do_pad_or_crop', 'PadOrCrop', 'ZNormalization', 'RescaleIntensity', 'NormalizeIntensity',
+           'BraTSMaskConverter', 'BinaryConverter', 'RandomGhosting', 'RandomSpike', 'RandomNoise', 'RandomBiasField',
+           'RandomBlur', 'RandomGamma', 'RandomMotion', 'RandomElasticDeformation', 'RandomAffine', 'RandomFlip',
+           'OneOf']
 
 # %% ../nbs/03_vision_augment.ipynb 2
 from fastai.data.all import *
 from .vision_core import *
 import torchio as tio
+from monai.transforms import NormalizeIntensity as MonaiNormalizeIntensity
 
 # %% ../nbs/03_vision_augment.ipynb 5
 class CustomDictTransform(ItemTransform):
@@ -84,9 +86,29 @@ class ZNormalization(DisplayedTransform):
         self.channel_wise = channel_wise
 
     def encodes(self, o: MedImage):
-        if self.channel_wise:
-            o = torch.stack([self.z_normalization(c[None])[0] for c in o])
-        else: o = self.z_normalization(o) 
+        try:
+            if self.channel_wise:
+                o = torch.stack([self.z_normalization(c[None])[0] for c in o])
+            else: 
+                o = self.z_normalization(o)
+        except RuntimeError as e:
+            if "Standard deviation is 0" in str(e):
+                # Calculate mean for debugging information
+                mean = float(o.mean())
+                
+                error_msg = (
+                    f"Standard deviation is 0 for image (mean={mean:.3f}).\n"
+                    f"This indicates uniform pixel values.\n\n"
+                    f"Possible causes:\n"
+                    f"• Corrupted or blank image\n"
+                    f"• Oversaturated regions\n"  
+                    f"• Background-only regions\n"
+                    f"• All-zero mask being processed as image\n\n"
+                    f"Suggested solutions:\n"
+                    f"• Check image quality and acquisition\n"
+                    f"• Verify image vs mask data loading"
+                )
+                raise RuntimeError(error_msg) from e
 
         return MedImage.create(o)
 
@@ -94,6 +116,68 @@ class ZNormalization(DisplayedTransform):
         return o
 
 # %% ../nbs/03_vision_augment.ipynb 10
+class RescaleIntensity(DisplayedTransform):
+    """Apply TorchIO RescaleIntensity for robust intensity scaling.
+    
+    Args:
+        out_min_max (tuple[float, float]): Output intensity range (min, max)
+        in_min_max (tuple[float, float]): Input intensity range (min, max) 
+    
+    Example for CT images:
+        # Normalize CT from air (-1000 HU) to bone (1000 HU) into range (-1, 1)
+        transform = RescaleIntensity(out_min_max=(-1, 1), in_min_max=(-1000, 1000))
+    """
+    
+    order = 0
+    
+    def __init__(self, out_min_max: tuple[float, float], in_min_max: tuple[float, float]):
+        self.rescale = tio.RescaleIntensity(out_min_max=out_min_max, in_min_max=in_min_max)
+    
+    def encodes(self, o: MedImage):
+        return MedImage.create(self.rescale(o))
+        
+    def encodes(self, o: MedMask):
+        return o
+
+# %% ../nbs/03_vision_augment.ipynb 11
+class NormalizeIntensity(DisplayedTransform):
+    """Apply MONAI NormalizeIntensity.
+    
+    Args:
+        nonzero (bool): Only normalize non-zero values (default: True)
+        channel_wise (bool): Apply normalization per channel (default: True)
+        subtrahend (float, optional): Value to subtract  
+        divisor (float, optional): Value to divide by
+    """
+    
+    order = 0
+    
+    def __init__(self, nonzero: bool = True, channel_wise: bool = True, 
+                 subtrahend: float = None, divisor: float = None):
+        self.nonzero = nonzero
+        self.channel_wise = channel_wise
+        self.subtrahend = subtrahend
+        self.divisor = divisor
+        
+        self.transform = MonaiNormalizeIntensity(
+            nonzero=nonzero,
+            channel_wise=False,  # Always 'False', we handle channel-wise manually
+            subtrahend=subtrahend,
+            divisor=divisor
+        )
+    
+    def encodes(self, o: MedImage):
+        if self.channel_wise:
+            result = torch.stack([self.transform(c[None])[0] for c in o])
+        else:
+            result = torch.Tensor(self.transform(o))
+        
+        return MedImage.create(result)
+    
+    def encodes(self, o: MedMask):
+        return o
+
+# %% ../nbs/03_vision_augment.ipynb 12
 class BraTSMaskConverter(DisplayedTransform):
     '''Convert BraTS masks.'''
 
@@ -105,7 +189,7 @@ class BraTSMaskConverter(DisplayedTransform):
         o = torch.where(o==4, 3., o)
         return MedMask.create(o)
 
-# %% ../nbs/03_vision_augment.ipynb 11
+# %% ../nbs/03_vision_augment.ipynb 13
 class BinaryConverter(DisplayedTransform):
     '''Convert to binary mask.'''
 
@@ -118,7 +202,7 @@ class BinaryConverter(DisplayedTransform):
         o = torch.where(o>0, 1., 0)
         return MedMask.create(o)
 
-# %% ../nbs/03_vision_augment.ipynb 12
+# %% ../nbs/03_vision_augment.ipynb 14
 class RandomGhosting(DisplayedTransform):
     """Apply TorchIO `RandomGhosting`."""
     
@@ -133,7 +217,7 @@ class RandomGhosting(DisplayedTransform):
     def encodes(self, o: MedMask):
         return o
 
-# %% ../nbs/03_vision_augment.ipynb 13
+# %% ../nbs/03_vision_augment.ipynb 15
 class RandomSpike(DisplayedTransform):
     '''Apply TorchIO `RandomSpike`.'''
     
@@ -148,7 +232,7 @@ class RandomSpike(DisplayedTransform):
     def encodes(self, o:MedMask):
         return o
 
-# %% ../nbs/03_vision_augment.ipynb 14
+# %% ../nbs/03_vision_augment.ipynb 16
 class RandomNoise(DisplayedTransform):
     '''Apply TorchIO `RandomNoise`.'''
 
@@ -163,7 +247,7 @@ class RandomNoise(DisplayedTransform):
     def encodes(self, o: MedMask):
         return o
 
-# %% ../nbs/03_vision_augment.ipynb 15
+# %% ../nbs/03_vision_augment.ipynb 17
 class RandomBiasField(DisplayedTransform):
     '''Apply TorchIO `RandomBiasField`.'''
 
@@ -178,7 +262,7 @@ class RandomBiasField(DisplayedTransform):
     def encodes(self, o: MedMask):
         return o
 
-# %% ../nbs/03_vision_augment.ipynb 16
+# %% ../nbs/03_vision_augment.ipynb 18
 class RandomBlur(DisplayedTransform):
     '''Apply TorchIO `RandomBiasField`.'''
 
@@ -193,7 +277,7 @@ class RandomBlur(DisplayedTransform):
     def encodes(self, o: MedMask):
         return o
 
-# %% ../nbs/03_vision_augment.ipynb 17
+# %% ../nbs/03_vision_augment.ipynb 19
 class RandomGamma(DisplayedTransform):
     '''Apply TorchIO `RandomGamma`.'''
 
@@ -209,7 +293,7 @@ class RandomGamma(DisplayedTransform):
     def encodes(self, o: MedMask):
         return o
 
-# %% ../nbs/03_vision_augment.ipynb 18
+# %% ../nbs/03_vision_augment.ipynb 20
 class RandomMotion(DisplayedTransform):
     """Apply TorchIO `RandomMotion`."""
 
@@ -237,7 +321,7 @@ class RandomMotion(DisplayedTransform):
     def encodes(self, o: MedMask):
         return o
 
-# %% ../nbs/03_vision_augment.ipynb 20
+# %% ../nbs/03_vision_augment.ipynb 22
 class RandomElasticDeformation(CustomDictTransform):
     """Apply TorchIO `RandomElasticDeformation`."""
 
@@ -250,7 +334,7 @@ class RandomElasticDeformation(CustomDictTransform):
             image_interpolation=image_interpolation,
             p=p))
 
-# %% ../nbs/03_vision_augment.ipynb 21
+# %% ../nbs/03_vision_augment.ipynb 23
 class RandomAffine(CustomDictTransform):
     """Apply TorchIO `RandomAffine`."""
 
@@ -266,14 +350,14 @@ class RandomAffine(CustomDictTransform):
             default_pad_value=default_pad_value,
             p=p))
 
-# %% ../nbs/03_vision_augment.ipynb 22
+# %% ../nbs/03_vision_augment.ipynb 24
 class RandomFlip(CustomDictTransform):
     """Apply TorchIO `RandomFlip`."""
 
     def __init__(self, axes='LR', p=0.5):
         super().__init__(tio.RandomFlip(axes=axes, flip_probability=p))
 
-# %% ../nbs/03_vision_augment.ipynb 23
+# %% ../nbs/03_vision_augment.ipynb 25
 class OneOf(CustomDictTransform):
     """Apply only one of the given transforms using TorchIO `OneOf`."""
 

{fastmonai-0.5.0.0.dist-info → fastmonai-0.5.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fastMONAI
-Version: 0.5.0.0
+Version: 0.5.2
 Summary: fastMONAI library
 Home-page: https://github.com/MMIV-ML/fastMONAI
 Author: Satheshkumar Kaliyugarasan
@@ -53,7 +53,7 @@ Dynamic: summary
 
 <!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
 
-![](https://raw.githubusercontent.com/skaliy/skaliy.github.io/master/assets/fastmonai_v1.png)
+![](https://raw.githubusercontent.com/skaliy/skaliy.github.io/main/assets/fastmonai_v1.png)
 
 ![CI](https://github.com/MMIV-ML/fastMONAI/workflows/CI/badge.svg)
 [![Docs](https://github.com/MMIV-ML/fastMONAI/actions/workflows/deploy.yaml/badge.svg)](https://fastmonai.no)
@@ -120,15 +120,15 @@ https://fastmonai.no for more information.
 
 | Notebook | 1-Click Notebook |
 |:---|----|
-| [10a_tutorial_classification.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/master/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/master/nbs/10a_tutorial_classification.ipynb) |
-| [10b_tutorial_regression.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/master/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/master/nbs/10b_tutorial_regression.ipynb) |
-| [10c_tutorial_binary_segmentation.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/master/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/master/nbs/10c_tutorial_binary_segmentation.ipynb) |
-| [10d_tutorial_multiclass_segmentation.ipynb](https://nbviewer.org/github/MMIV-ML/fastMONAI/blob/master/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/master/nbs/10d_tutorial_multiclass_segmentation.ipynb) |
+| [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) |
+| [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) |
+| [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) |
+| [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) |
 
 # How to contribute
 
 We welcome contributions! See
-[CONTRIBUTING.md](https://github.com/MMIV-ML/fastMONAI/blob/master/CONTRIBUTING.md)
+[CONTRIBUTING.md](https://github.com/MMIV-ML/fastMONAI/blob/main/CONTRIBUTING.md)
 
 # Citing fastMONAI
 

fastmonai-0.5.2.dist-info/RECORD

@@ -0,0 +1,20 @@
+fastMONAI/__init__.py,sha256=isJrmDBLRag7Zc2UK9ZovWGOv7ji1Oh-zJtJMNJFkXw,22
+fastMONAI/_modidx.py,sha256=pV36J9-oryTjfV9gL-lXJqoCH9SCQFGsa_NIRdkUlYI,39527
+fastMONAI/dataset_info.py,sha256=aJ-utYZ1OrA32RIQbF7jHxcDE8SgOZE3Vt1AojxnvZc,5026
+fastMONAI/external_data.py,sha256=IVj9GbIRFh9bTFkIa2wySUObSnNfZiaVtuzFxOFAi0Q,12219
+fastMONAI/research_utils.py,sha256=LZu62g8BQAVYS4dD7qDsKHJXZnDd1uLkJ6LoaMDhUhk,590
+fastMONAI/utils.py,sha256=jG8SiYebcrPJsmnmMZh4SokWRj7McdJ_gftINnfcE1A,16590
+fastMONAI/vision_all.py,sha256=_l6F8ZlUaPYcplNG6mg1-1xssYforByEe4zECbPzTck,359
+fastMONAI/vision_augmentation.py,sha256=-4LsLuPi55bh0KduB6EPTzudG63japebszdtN5FtFC0,12281
+fastMONAI/vision_core.py,sha256=k4RUBzZuh9W8J4zbcVzXCKfJxkKCsBDG0oSRMwiCNp0,13848
+fastMONAI/vision_data.py,sha256=VCB3hyBN7dYuLiYGSGeuWlBTMvb2cLVo_sbENrRWe5Q,11510
+fastMONAI/vision_inference.py,sha256=3SaJbKGbgaf9ON9PH5DtvfNlhAurov_Idnrlp4jyU9w,6625
+fastMONAI/vision_loss.py,sha256=NrHnk1yD4EBKsp6aippppXU4l-mwmsZOqE_bsZP3ZNI,3591
+fastMONAI/vision_metrics.py,sha256=CVxdOBPaMJT6Mo5jF3WoQj6a3C-_FsnBicMAU_ZrFS8,3549
+fastMONAI/vision_plot.py,sha256=-X_nNBXx7lYCZSFBIN1587ZTA3T_-2ASBM4K31wU660,3792
+fastmonai-0.5.2.dist-info/licenses/LICENSE,sha256=xV8xoN4VOL0uw9X8RSs2IMuD_Ss_a9yAbtGNeBWZwnw,11337
+fastmonai-0.5.2.dist-info/METADATA,sha256=ygTsuppVUZJZbXO9vaRhoaQnztQ7PwoaXU3KZcZbK3s,7074
+fastmonai-0.5.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+fastmonai-0.5.2.dist-info/entry_points.txt,sha256=mVBsykSXMairzzk3hJaQ8c-UiwUZqGnn4aFZ24CpsBM,40
+fastmonai-0.5.2.dist-info/top_level.txt,sha256=o8y7SWF9odtnIT3jvYtUn9okbJRlaAMCy7oPFCeQvQ8,10
+fastmonai-0.5.2.dist-info/RECORD,,

fastmonai-0.5.0.0.dist-info/RECORD

@@ -1,20 +0,0 @@
-fastMONAI/__init__.py,sha256=T19ge-mjTQc59d5RqcDcri4stPYuQEaLR3cFKwPhDfI,24
-fastMONAI/_modidx.py,sha256=sVdaZs4ZogSisNkxAN1n96jaayoJqsrODsf9xodrL14,36080
-fastMONAI/dataset_info.py,sha256=aJ-utYZ1OrA32RIQbF7jHxcDE8SgOZE3Vt1AojxnvZc,5026
-fastMONAI/external_data.py,sha256=IVj9GbIRFh9bTFkIa2wySUObSnNfZiaVtuzFxOFAi0Q,12219
-fastMONAI/research_utils.py,sha256=LZu62g8BQAVYS4dD7qDsKHJXZnDd1uLkJ6LoaMDhUhk,590
-fastMONAI/utils.py,sha256=Gr5IGb3v-tfpdFotoIaSAECPXDZS3ECOBSdvQx5vb-A,8647
-fastMONAI/vision_all.py,sha256=_l6F8ZlUaPYcplNG6mg1-1xssYforByEe4zECbPzTck,359
-fastMONAI/vision_augmentation.py,sha256=lAlrLm8jbXRmk9a6e8_o_CNTS6Pyp-KKNXwjpelUUJc,9070
-fastMONAI/vision_core.py,sha256=k4RUBzZuh9W8J4zbcVzXCKfJxkKCsBDG0oSRMwiCNp0,13848
-fastMONAI/vision_data.py,sha256=VCB3hyBN7dYuLiYGSGeuWlBTMvb2cLVo_sbENrRWe5Q,11510
-fastMONAI/vision_inference.py,sha256=3SaJbKGbgaf9ON9PH5DtvfNlhAurov_Idnrlp4jyU9w,6625
-fastMONAI/vision_loss.py,sha256=NrHnk1yD4EBKsp6aippppXU4l-mwmsZOqE_bsZP3ZNI,3591
-fastMONAI/vision_metrics.py,sha256=CVxdOBPaMJT6Mo5jF3WoQj6a3C-_FsnBicMAU_ZrFS8,3549
-fastMONAI/vision_plot.py,sha256=-X_nNBXx7lYCZSFBIN1587ZTA3T_-2ASBM4K31wU660,3792
-fastmonai-0.5.0.0.dist-info/licenses/LICENSE,sha256=xV8xoN4VOL0uw9X8RSs2IMuD_Ss_a9yAbtGNeBWZwnw,11337
-fastmonai-0.5.0.0.dist-info/METADATA,sha256=eO5N4RAweItcte4WhnzMkrfn4d-Vbbs19hZjqxU_TZI,7096
-fastmonai-0.5.0.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-fastmonai-0.5.0.0.dist-info/entry_points.txt,sha256=mVBsykSXMairzzk3hJaQ8c-UiwUZqGnn4aFZ24CpsBM,40
-fastmonai-0.5.0.0.dist-info/top_level.txt,sha256=o8y7SWF9odtnIT3jvYtUn9okbJRlaAMCy7oPFCeQvQ8,10
-fastmonai-0.5.0.0.dist-info/RECORD,,