fastMONAI 0.5.3__py3-none-any.whl → 0.6.0__py3-none-any.whl

fastMONAI/vision_plot.py

@@ -1,9 +1,10 @@
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/00_vision_plot.ipynb.
 
 # %% auto 0
-__all__ = ['validate_anatomical_plane', 'show_med_img', 'find_max_slice']
+__all__ = ['validate_anatomical_plane', 'show_med_img', 'find_max_slice', 'show_segmentation_comparison']
 
 # %% ../nbs/00_vision_plot.ipynb 1
+import warnings
 from fastai.data.all import *
 from torchio.visualization import rotate
 
@@ -114,3 +115,91 @@ def find_max_slice(mask_data, anatomical_plane):
     idx = np.argmax(sums)
 
     return idx
+
+# %% ../nbs/00_vision_plot.ipynb 7
+def show_segmentation_comparison(
+    image, ground_truth, prediction,
+    slice_index: int = None,
+    anatomical_plane: int = 2,
+    metric_value: float = None,
+    metric_name: str = 'DSC',
+    channel: int = 0,
+    figsize: tuple = (15, 5),
+    cmap_img: str = 'gray',
+    cmap_mask: str = 'gray',
+    voxel_size = None
+):
+    """Display 3-panel comparison: Image | Ground Truth | Prediction.
+    
+    Useful for validating segmentation results, especially after patch-based 
+    inference where results are not in standard fastai batch format.
+    
+    Args:
+        image: Input image (MedImage, MedMask, or tensor [C, H, W, D])
+        ground_truth: Ground truth mask (MedMask or tensor [C, H, W, D])
+        prediction: Predicted mask (tensor [C, H, W, D])
+        slice_index: Slice to display. If None, uses find_max_slice on ground_truth.
+        anatomical_plane: 0=sagittal, 1=coronal, 2=axial (default)
+        metric_value: Optional metric value to display in prediction title
+        metric_name: Name of metric for title (default 'DSC')
+        channel: Channel to display for multi-channel data (default 0)
+        figsize: Figure size (default (15, 5))
+        cmap_img: Colormap for image (default 'gray')
+        cmap_mask: Colormap for masks (default 'gray')
+        voxel_size: Voxel spacing for aspect ratio. If None, aspect=1.
+
+    Example::
+    
+        # After patch_inference()
+        show_segmentation_comparison(
+            image=val_img,
+            ground_truth=val_gt,
+            prediction=predictions[0],
+            metric_value=results_df.iloc[0]['DSC'],
+            anatomical_plane=2
+        )
+    """
+    validate_anatomical_plane(anatomical_plane)
+    
+    # Ensure we have tensor data
+    img_data = image.data if hasattr(image, 'data') else image
+    gt_data = ground_truth.data if hasattr(ground_truth, 'data') else ground_truth
+    pred_data = prediction.data if hasattr(prediction, 'data') else prediction
+    
+    # Move to CPU if needed
+    if hasattr(img_data, 'cpu'): img_data = img_data.cpu()
+    if hasattr(gt_data, 'cpu'): gt_data = gt_data.cpu()
+    if hasattr(pred_data, 'cpu'): pred_data = pred_data.cpu()
+    
+    # Find optimal slice if not provided
+    if slice_index is None:
+        gt_np = gt_data[channel].numpy()
+        slice_index = find_max_slice(gt_np, anatomical_plane)
+    
+    # Create figure
+    fig, axes = plt.subplots(1, 3, figsize=figsize)
+    
+    # Get slices with proper aspect ratio using existing _get_slice helper
+    img_slice, img_aspect = _get_slice(img_data, channel, slice_index, anatomical_plane, voxel_size)
+    gt_slice, gt_aspect = _get_slice(gt_data, channel, slice_index, anatomical_plane, voxel_size)
+    pred_slice, pred_aspect = _get_slice(pred_data, channel, slice_index, anatomical_plane, voxel_size)
+    
+    # Plot panels
+    axes[0].imshow(img_slice, cmap=cmap_img, aspect=img_aspect)
+    axes[0].set_title('Input Image')
+    axes[0].axis('off')
+    
+    axes[1].imshow(gt_slice, cmap=cmap_mask, aspect=gt_aspect)
+    axes[1].set_title('Ground Truth')
+    axes[1].axis('off')
+    
+    # Build prediction title
+    pred_title = 'Prediction'
+    if metric_value is not None:
+        pred_title = f'Prediction ({metric_name}: {metric_value:.4f})'
+    
+    axes[2].imshow(pred_slice, cmap=cmap_mask, aspect=pred_aspect)
+    axes[2].set_title(pred_title)
+    axes[2].axis('off')
+    
+    plt.tight_layout()

{fastmonai-0.5.3.dist-info → fastmonai-0.6.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fastMONAI
-Version: 0.5.3
+Version: 0.6.0
 Summary: fastMONAI library
 Home-page: https://github.com/MMIV-ML/fastMONAI
 Author: Satheshkumar Kaliyugarasan
@@ -120,10 +120,10 @@ https://fastmonai.no for more information.
 
 | Notebook | 1-Click Notebook |
 |:---|----|
-| [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) |
+| [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) |
+| [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) |
+| [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) |
+| [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) |
 
 # How to contribute
 

fastmonai-0.6.0.dist-info/RECORD

@@ -0,0 +1,21 @@
+fastMONAI/__init__.py,sha256=cID1jLnC_vj48GgMN6Yb1FA3JsQ95zNmCHmRYE8TFhY,22
+fastMONAI/_modidx.py,sha256=9e2FCrV3l4HYPJ-qcHUVqI_Q6ps6UVxEEdD3OBCSwhw,66249
+fastMONAI/dataset_info.py,sha256=hLNX0Jps8dPCbF6HYPO2PScZtn2qqAQBH07LtSubeFM,16306
+fastMONAI/external_data.py,sha256=Ofa6RmSKYj8LKlzWqPGfg9lu9lTjBmolJTo1zVgTe6g,12263
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+fastMONAI/utils.py,sha256=8avga5wIGK4IlJ04SrN_Ba5STkBSuEA5G06EvdDHNBs,30493
+fastMONAI/vision_all.py,sha256=L2JVYQq77X7Ko2SmzKUGAXwVjw898V_skGuQuYxjVd8,385
+fastMONAI/vision_augmentation.py,sha256=nhFA-usts59AIYdDtzX8QJ1HrGY3bcEKu2koP3HZews,20604
+fastMONAI/vision_core.py,sha256=xXGnutYD3sdWzpoMZHSfClUFmphsB7yFsDcY91Fa844,9539
+fastMONAI/vision_data.py,sha256=_SgwSlNm4ZOooFnrp5vYnA7ZAweV60a3XaOnozDKm6w,11569
+fastMONAI/vision_inference.py,sha256=fRPgIO-3XifBlCZY7qaucgymSLQQajcKvmZKWg0XfS4,7688
+fastMONAI/vision_loss.py,sha256=NrHnk1yD4EBKsp6aippppXU4l-mwmsZOqE_bsZP3ZNI,3591
+fastMONAI/vision_metrics.py,sha256=OED2ewWaZUtmkqc5CjmBWDboTVUlpsnsuFU-ZrIw4tI,18572
+fastMONAI/vision_patch.py,sha256=SkEdOc_U2nrpjIVZ3wW4qwgciKnOCuzQXixRGyK3KaA,50118
+fastMONAI/vision_plot.py,sha256=7HLkKQAwmwPvwrDxWlKP5IIHNNwWIrLkdsejqlOc27k,7282
+fastmonai-0.6.0.dist-info/licenses/LICENSE,sha256=xV8xoN4VOL0uw9X8RSs2IMuD_Ss_a9yAbtGNeBWZwnw,11337
+fastmonai-0.6.0.dist-info/METADATA,sha256=vdTSIppLb0xQtNgaAtKQfyTDKH7qqVd2sZFsv1cKgoI,7075
+fastmonai-0.6.0.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+fastmonai-0.6.0.dist-info/entry_points.txt,sha256=mVBsykSXMairzzk3hJaQ8c-UiwUZqGnn4aFZ24CpsBM,40
+fastmonai-0.6.0.dist-info/top_level.txt,sha256=o8y7SWF9odtnIT3jvYtUn9okbJRlaAMCy7oPFCeQvQ8,10
+fastmonai-0.6.0.dist-info/RECORD,,

{fastmonai-0.5.3.dist-info → fastmonai-0.6.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

fastmonai-0.5.3.dist-info/RECORD

@@ -1,20 +0,0 @@
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-fastMONAI/_modidx.py,sha256=pV36J9-oryTjfV9gL-lXJqoCH9SCQFGsa_NIRdkUlYI,39527
-fastMONAI/dataset_info.py,sha256=aJ-utYZ1OrA32RIQbF7jHxcDE8SgOZE3Vt1AojxnvZc,5026
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-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-0.5.3.dist-info/licenses/LICENSE,sha256=xV8xoN4VOL0uw9X8RSs2IMuD_Ss_a9yAbtGNeBWZwnw,11337
-fastmonai-0.5.3.dist-info/METADATA,sha256=S_ocpvWghuz7Jau4C-2YKCtDaC7pI8qG3hvCtQvkybk,7075
-fastmonai-0.5.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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