fastMONAI 0.3.1__py3-none-any.whl → 0.3.3__py3-none-any.whl

fastMONAI/vision_metrics.py

@@ -11,50 +11,67 @@ from monai.metrics import compute_hausdorff_distance, compute_dice
 from .vision_data import pred_to_binary_mask, batch_pred_to_multiclass_mask
 
 # %% ../nbs/05_vision_metrics.ipynb 3
-def calculate_dsc(pred, targ):
-    ''' MONAI `compute_meandice`'''
+def calculate_dsc(pred: torch.Tensor, targ: torch.Tensor) -> torch.Tensor:
+    """MONAI `compute_meandice`"""
 
     return torch.Tensor([compute_dice(p[None], t[None]) for p, t in list(zip(pred,targ))])
 
 # %% ../nbs/05_vision_metrics.ipynb 4
-def calculate_haus(pred, targ):
-    ''' MONAI `compute_hausdorff_distance`'''
+def calculate_haus(pred: torch.Tensor, targ: torch.Tensor) -> torch.Tensor:
+    """MONAI `compute_hausdorff_distance`"""
 
     return torch.Tensor([compute_hausdorff_distance(p[None], t[None]) for p, t in list(zip(pred,targ))])
 
 # %% ../nbs/05_vision_metrics.ipynb 5
-def binary_dice_score(act, # Activation tensor [B, C, W, H, D]
-                      targ # Target masks [B, C, W, H, D]
-                     ) -> torch.Tensor:
-    '''Calculate the mean Dice score for binary semantic segmentation tasks.'''
-
+def binary_dice_score(act: torch.tensor, targ: torch.Tensor) -> torch.Tensor:
+    """Calculates the mean Dice score for binary semantic segmentation tasks.
+    
+    Args:
+        act: Activation tensor with dimensions [B, C, W, H, D].
+        targ: Target masks with dimensions [B, C, W, H, D].
+
+    Returns:
+        Mean Dice score.
+    """
     pred = pred_to_binary_mask(act)
     dsc = calculate_dsc(pred.cpu(), targ.cpu())
 
     return torch.mean(dsc)
 
 # %% ../nbs/05_vision_metrics.ipynb 6
-def multi_dice_score(act, # Activation values [B, C, W, H, D]
-                     targ # Target masks [B, C, W, H, D]
-                    ) -> torch.Tensor:
-    '''Calculate the mean Dice score for each class in multi-class semantic segmentation tasks.'''
+def multi_dice_score(act: torch.Tensor, targ: torch.Tensor) -> torch.Tensor:
+    """Calculate the mean Dice score for each class in multi-class semantic 
+    segmentation tasks.
 
+    Args:
+        act: Activation tensor with dimensions [B, C, W, H, D].
+        targ: Target masks with dimensions [B, C, W, H, D].
 
+    Returns:
+        Mean Dice score for each class.
+    """
     pred, n_classes = batch_pred_to_multiclass_mask(act)
     binary_dice_scores = []
 
     for c in range(1, n_classes):
-        c_pred, c_targ = torch.where(pred==c, 1, 0), torch.where(targ==c, 1, 0)
+        c_pred, c_targ = torch.where(pred == c, 1, 0), torch.where(targ == c, 1, 0)
         dsc = calculate_dsc(c_pred, c_targ)
-        binary_dice_scores.append(np.nanmean(dsc)) #TODO update torch to get torch.nanmean() to work
+        binary_dice_scores.append(np.nanmean(dsc)) # #TODO update torch to get torch.nanmean() to work
 
     return torch.Tensor(binary_dice_scores)
 
 # %% ../nbs/05_vision_metrics.ipynb 7
-def binary_hausdorff_distance(act, # Activation tensor [B, C, W, H, D]
-                              targ # Target masks [B, C, W, H, D]
-                             ) -> torch.Tensor:
-    '''Calculate the mean Hausdorff distance for binary semantic segmentation tasks.'''
+def binary_hausdorff_distance(act: torch.Tensor, targ: torch.Tensor) -> torch.Tensor:
+    """Calculate the mean Hausdorff distance for binary semantic segmentation tasks.
+    
+    Args:
+        act: Activation tensor with dimensions [B, C, W, H, D].
+        targ: Target masks with dimensions [B, C, W, H, D].
+
+    Returns:
+        Mean Hausdorff distance.
+    """
+    
 
     pred = pred_to_binary_mask(act)
 
@@ -62,10 +79,16 @@ def binary_hausdorff_distance(act, # Activation tensor [B, C, W, H, D]
     return torch.mean(haus)
 
 # %% ../nbs/05_vision_metrics.ipynb 8
-def multi_hausdorff_distance(act, # Activation tensor [B, C, W, H, D]
-                             targ # Target masks [B, C, W, H, D]
-                            ) -> torch.Tensor :
-    '''Calculate the mean Hausdorff distance for each class in multi-class semantic segmentation tasks.'''
+def multi_hausdorff_distance(act: torch.Tensor, targ: torch.Tensor) -> torch.Tensor :
+    """Calculate the mean Hausdorff distance for each class in multi-class semantic segmentation tasks.
+    
+    Args:
+        act: Activation tensor with dimensions [B, C, W, H, D].
+        targ: Target masks with dimensions [B, C, W, H, D].
+
+    Returns:
+        Mean Hausdorff distance for each class.
+    """
 
     pred, n_classes = batch_pred_to_multiclass_mask(act)
     binary_haus = []

fastMONAI/vision_plot.py

@@ -9,8 +9,7 @@ from torchio.visualization import rotate
 
 # %% ../nbs/00_vision_plot.ipynb 3
 def _get_slice(image, channel: int, indices: (int, list), anatomical_plane: int, voxel_size: (int, list)):
-    """
-    A private method to get a 2D tensor and aspect ratio for plotting.
+    """A private method to get a 2D tensor and aspect ratio for plotting.
     This is modified code from the torchio function `plot_volume`.
 
     Args:
@@ -53,11 +52,9 @@ def _get_slice(image, channel: int, indices: (int, list), anatomical_plane: int,
 
 # %% ../nbs/00_vision_plot.ipynb 4
 @delegates(plt.Axes.imshow, keep=True, but=['shape', 'imlim'])
-def show_med_img(
-    im, ctx, channel: int, indices: (int, list), anatomical_plane: int,
-    voxel_size: (int, list), ax=None, figsize=None, title=None, **kwargs):
-    """
-    Show an image on `ax`. This is a modified code from the fastai function `show_image`.
+def show_med_img(im, ctx, channel: int, indices: (int, list), anatomical_plane: int,
+                 voxel_size: (int, list), ax=None, figsize=None, title=None, **kwargs):
+    """Show an image on `ax`. This is a modified code from the fastai function `show_image`.
 
     Args:
         im: The input image.
@@ -74,18 +71,23 @@ def show_med_img(
     Returns:
         Axis with the plot.
     """
-    if hasattrs(im, ('data', 'cpu', 'permute')):
+    if hasattrs(im, ('data', 'cpu', 'permute')): # Check if `im` has the necessary attributes
         im = im.data.cpu()
         im, aspect = _get_slice(
-            im, channel=channel, anatomical_plane=anatomical_plane,
-            voxel_size=voxel_size, indices=indices
+            im, 
+            channel=channel, 
+            anatomical_plane=anatomical_plane,
+            voxel_size=voxel_size, 
+            indices=indices
         )
 
-    ax = ifnone(ax, ctx)
-    if ax is None:
-        _, ax = plt.subplots(figsize=figsize)  # ax is only None when .show() is used.
+    ax = ax if ax is not None else ctx 
+
+    if ax is None: # ax is only None when .show() is used.
+        _, ax = plt.subplots(figsize=figsize)
 
     ax.imshow(im, aspect=aspect, **kwargs)
+
     if title is not None:
         ax.set_title(title)
 

{fastMONAI-0.3.1.dist-info → fastMONAI-0.3.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fastMONAI
-Version: 0.3.1
+Version: 0.3.3
 Summary: fastMONAI library
 Home-page: https://github.com/MMIV-ML/fastMONAI
 Author: Satheshkumar Kaliyugarasan

fastMONAI-0.3.3.dist-info/RECORD

@@ -0,0 +1,20 @@
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+fastMONAI/_modidx.py,sha256=AGOW75o_d2Vd7CBku-4zz53OzUqkp4QqTEqsucyU7jg,27510
+fastMONAI/dataset_info.py,sha256=w5LKGmEzFtlqhxqzhFLWUfyVkUL0EYypZQCH9Ay6jgg,4948
+fastMONAI/external_data.py,sha256=Hq4GPEWsBi9-fyk9r3WlBdUZjfNzeaKe5uqTwFD8qfU,11016
+fastMONAI/research_utils.py,sha256=LZu62g8BQAVYS4dD7qDsKHJXZnDd1uLkJ6LoaMDhUhk,590
+fastMONAI/utils.py,sha256=9I5nl6Sb0NbTxhr6FDnW4dapDhzPtmxGcJeXkkY4v3E,1406
+fastMONAI/vision_all.py,sha256=qAsncBCDTx3Ae8Hw44TK4E5wflO-8JbRWBu0CRLLGnY,360
+fastMONAI/vision_augmentation.py,sha256=lAlrLm8jbXRmk9a6e8_o_CNTS6Pyp-KKNXwjpelUUJc,9070
+fastMONAI/vision_core.py,sha256=KDoLS9UYNsh5nPIYc2JiDjWBLy1IRSpjH9cqEHjk4Vw,7428
+fastMONAI/vision_data.py,sha256=QZqHK35L9sU9BiQ2nIqGzOEBAGHfuke7YloyZrPkYto,10491
+fastMONAI/vision_inference.py,sha256=k-rGKhVtdrZT9GvQEglEa0sZ283ue16mEPTZ-ZSKc5Q,3744
+fastMONAI/vision_loss.py,sha256=NrHnk1yD4EBKsp6aippppXU4l-mwmsZOqE_bsZP3ZNI,3591
+fastMONAI/vision_metrics.py,sha256=CVxdOBPaMJT6Mo5jF3WoQj6a3C-_FsnBicMAU_ZrFS8,3549
+fastMONAI/vision_plot.py,sha256=S2_yE0VcAwECgvXHb1YMJbTZq4iREh-VIgPShLcUma0,3095
+fastMONAI-0.3.3.dist-info/LICENSE,sha256=xV8xoN4VOL0uw9X8RSs2IMuD_Ss_a9yAbtGNeBWZwnw,11337
+fastMONAI-0.3.3.dist-info/METADATA,sha256=xVkZtZdie9sgwLhpKNl8yZaA7YKFDDFLYB-PDo5yOeA,5770
+fastMONAI-0.3.3.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
+fastMONAI-0.3.3.dist-info/entry_points.txt,sha256=mVBsykSXMairzzk3hJaQ8c-UiwUZqGnn4aFZ24CpsBM,40
+fastMONAI-0.3.3.dist-info/top_level.txt,sha256=o8y7SWF9odtnIT3jvYtUn9okbJRlaAMCy7oPFCeQvQ8,10
+fastMONAI-0.3.3.dist-info/RECORD,,

fastMONAI-0.3.1.dist-info/RECORD

@@ -1,20 +0,0 @@
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-fastMONAI/_modidx.py,sha256=Tp9TjFPpgC4R8zVx0avHRoGX-H-aGKJukuvUhvu-FwU,29361
-fastMONAI/dataset_info.py,sha256=ZCqha0HcuhGcRxCG5TAsGua0gam3C2ZnyjjpG47gcHo,4795
-fastMONAI/external_data.py,sha256=_HU5mTJs5xSS8y0be51mrfQ93HJUidq6PGm9n6rfOW4,8357
-fastMONAI/research_utils.py,sha256=LZu62g8BQAVYS4dD7qDsKHJXZnDd1uLkJ6LoaMDhUhk,590
-fastMONAI/utils.py,sha256=oPEfBEJDlUzNu5KTuwFW5bjuieI7SqdOlbcy7eiTazA,1431
-fastMONAI/vision_all.py,sha256=qAsncBCDTx3Ae8Hw44TK4E5wflO-8JbRWBu0CRLLGnY,360
-fastMONAI/vision_augmentation.py,sha256=9O7pafQz9PP_bqA0drjeVVg6_uqKUT-L-lGtW2k7fjw,9887
-fastMONAI/vision_core.py,sha256=dLsl3IRkssQ-iXljwcsixP3hU0IzLfhvHhyKNUtMFCk,6553
-fastMONAI/vision_data.py,sha256=99BL-yrXoXHNjWYbtI49t0E1lEXiY5FFHy_TSgXBjEI,9193
-fastMONAI/vision_inference.py,sha256=Q5Dd-kCK639QF7qkgnbniQPcCM0oHvYt5xEn07YuIxU,3352
-fastMONAI/vision_loss.py,sha256=_Rf8rpsNb2cru8R3NGU1WNxuR0pWN7acX6qjNT-lPcE,3674
-fastMONAI/vision_metrics.py,sha256=mY3Nw6hN7qh-zrpT-kXjJj6J3bd5DFAfmpxVMVHFdfU,3035
-fastMONAI/vision_plot.py,sha256=vot916053eK8xTVnK2fOGJ6mfruzKZsS-Qae3-4m5Vw,2997
-fastMONAI-0.3.1.dist-info/LICENSE,sha256=xV8xoN4VOL0uw9X8RSs2IMuD_Ss_a9yAbtGNeBWZwnw,11337
-fastMONAI-0.3.1.dist-info/METADATA,sha256=1pdeHnOQBY2z9uaCrVoNxU-6TsMCYAadovuF6m-Z5Ao,5770
-fastMONAI-0.3.1.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
-fastMONAI-0.3.1.dist-info/entry_points.txt,sha256=mVBsykSXMairzzk3hJaQ8c-UiwUZqGnn4aFZ24CpsBM,40
-fastMONAI-0.3.1.dist-info/top_level.txt,sha256=o8y7SWF9odtnIT3jvYtUn9okbJRlaAMCy7oPFCeQvQ8,10
-fastMONAI-0.3.1.dist-info/RECORD,,