Merge branch 'vizualization_update' into 'main'

Vizualization update

See merge request !4

qim3d/utils/__init__.py

 from . import internal_tools
+from . import models
 from .data import Dataset
\ No newline at end of file

qim3d/utils/models.py

+""" Tools performed with trained models."""
+import torch
+
+def inference(data,model):
+    """Performs inference on input data using the specified model.
+    
+    Performs inference on the input data using the provided model. The input data should be in the form of a list,
+    where each item is a tuple containing the input image tensor and the corresponding target label tensor.
+
+    The function checks the format and validity of the input data, ensures the model is in evaluation mode,
+    and generates predictions using the model. The input images, target labels, and predicted labels are returned
+    as a tuple.
+    
+    Args:
+        data (torch.utils.data.Dataset): A Torch dataset containing input image and
+            ground truth label data.
+        model (torch.nn.Module): The trained network model used for predicting segmentations.
+
+    Returns:
+        tuple: A tuple containing the input images, target labels, and predicted labels.
+
+    Raises:
+        ValueError: If the data items are not tuples or data items do not consist of tensors.
+        ValueError: If the input image is not in (C, H, W) format.
+
+    Notes:
+        - The function does not assume the model is already in evaluation mode (model.eval()).
+
+    Example:
+        dataset = MySegmentationDataset()
+        model = MySegmentationModel()
+        inference(data,model)
+    """
+    
+    # Get device
+    device = "cuda" if torch.cuda.is_available() else "cpu"
+
+    # Check if data have the right format
+    if not isinstance(data[0], tuple):
+        raise ValueError("Data items must be tuples")
+
+    # Check if data is torch tensors
+    for element in data[0]:
+        if not isinstance(element, torch.Tensor):
+            raise ValueError("Data items must consist of tensors")
+
+    # Check if input image is (C,H,W) format
+    if data[0][0].dim() == 3 and (data[0][0].shape[0] in [1, 3]):
+        pass
+    else:
+        raise ValueError("Input image must be (C,H,W) format")
+
+    
+    model.eval()
+
+    # Make new list such that possible augmentations remain identical for all three rows
+    plot_data = [data[idx] for idx in range(len(data))]
+    
+    # Create input and target batch
+    inputs = torch.stack([item[0] for item in plot_data], dim=0).to(device)
+    targets = torch.stack([item[1] for item in plot_data], dim=0)
+
+    # Get output predictions
+    with torch.no_grad():
+        outputs = model(inputs)
+
+    # Prepare data for plotting
+    inputs = inputs.cpu().squeeze()
+    targets = targets.squeeze()
+    if outputs.shape[1] == 1:
+        preds = outputs.cpu().squeeze() > 0.5
+    else:
+        preds = outputs.cpu().argmax(axis=1)
+
+    # if there is only one image
+    if inputs.dim() == 2:
+        inputs = inputs.unsqueeze(0)
+        targets = targets.unsqueeze(0)
+        preds = preds.unsqueeze(0)
+    
+    return inputs,targets,preds
\ No newline at end of file

qim3d/viz/img.py

@@ -95,100 +95,59 @@ def grid_overview(data, num_images=7, cmap_im="gray", cmap_segm="viridis", alpha
     fig.show()
 
 
-def grid_pred(
-    data, model, num_images=7, cmap_im="gray", cmap_segm="viridis", alpha=0.5
-):
-    """Displays a grid of input images, predicted segmentations, and ground truth segmentations.
+def grid_pred(in_targ_preds, num_images=7, cmap_im="gray", cmap_segm="viridis", alpha=0.5):
+    """Displays a grid of input images, predicted segmentations, ground truth segmentations, and their comparison.
 
-    Args:
-        data (torch.utils.data.Dataset): A Torch dataset containing input image and
-            ground truth label data.
-        model (torch.nn.Module): The trained network model used for predicting segmentations.
-        num_images (int, optional): The maximum number of images to display. Defaults to 7.
-        cmap_im (str, optional): The colormap to be used for displaying input images.
-            Defaults to 'gray'.
-        cmap_segm (str, optional): The colormap to be used for displaying segmentations.
-            Defaults to 'viridis'.
-        alpha (float, optional): The transparency level of the predicted segmentation overlay.
-            Defaults to 0.5.
+    Displays a grid of subplots representing different aspects of the input images and segmentations.
+    The grid includes the following rows:
+        - Row 1: Input images
+        - Row 2: Predicted segmentations overlaying input images
+        - Row 3: Ground truth segmentations overlaying input images
+        - Row 4: Comparison between true and predicted segmentations overlaying input images
 
-    Raises:
-        ValueError: If the data items are not tuples or data items do not consist of tensors.
-        ValueError: If the input image is not in (C, H, W) format.
+    Each row consists of `num_images` subplots, where each subplot corresponds to an image from the dataset.
+    The function utilizes various color maps for visualization and applies transparency to the segmentations.
 
-    Notes:
-        - The number of displayed images is limited to the minimum between `num_images`
-            and the length of the data.
-        - The function does not assume that the model is already in evaluation mode (model.eval()).
-        - The function will execute faster on a CUDA-enabled GPU.
-        - The grid layout consists of three rows: input images, predicted segmentations,
-            and ground truth segmentations.
+    Args:
+        in_targ_preds (tuple): A tuple containing input images, target segmentations, and predicted segmentations.
+        num_images (int, optional): Number of images to display. Defaults to 7.
+        cmap_im (str, optional): Color map for input images. Defaults to "gray".
+        cmap_segm (str, optional): Color map for segmentations. Defaults to "viridis".
+        alpha (float, optional): Alpha value for transparency. Defaults to 0.5.
 
     Returns:
         None
 
+    Raises:
+        None
+
     Example:
         dataset = MySegmentationDataset()
         model = MySegmentationModel()
-        grid_pred(dataset, model, cmap_im='viridis', alpha=0.5)
+        in_targ_preds = qim3d.utils.models.inference(dataset,model)
+        grid_pred(in_targ_preds, cmap_im='viridis', alpha=0.5)        
     """
-
-    # Get device
-    device = "cuda" if torch.cuda.is_available() else "cpu"
-
-    # Check if data have the right format
-    if not isinstance(data[0], tuple):
-        raise ValueError("Data items must be tuples")
-
-    # Check if data is torch tensors
-    for element in data[0]:
-        if not isinstance(element, torch.Tensor):
-            raise ValueError("Data items must consist of tensors")
-
-    # Check if input image is (C,H,W) format
-    if data[0][0].dim() == 3 and (data[0][0].shape[0] in [1, 3]):
-        pass
-    else:
-        raise ValueError("Input image must be (C,H,W) format")
-
+    
     # Check if dataset have at least specified number of images
-    if len(data) < num_images:
+    if len(in_targ_preds[0]) < num_images:
         log.warning(
             "Not enough images in the dataset. Changing num_images=%d to num_images=%d",
             num_images,
-            len(data),
+            len(in_targ_preds[0]),
         )
-        num_images = len(data)
+        num_images = len(in_targ_preds[0])
 
+    # Take only the number of images from in_targ_preds
+    inputs,targets,preds = [items[:num_images] for items in in_targ_preds]
+    
     # Adapt segmentation cmap so that background is transparent
     colors_segm = cm.get_cmap(cmap_segm)(np.linspace(0, 1, 256))
     colors_segm[:128, 3] = 0
     custom_cmap = LinearSegmentedColormap.from_list("CustomCmap", colors_segm)
-
-    model.eval()
-
-    # Make new list such that possible augmentations remain identical for all three rows
-    plot_data = [data[idx] for idx in range(num_images)]
-
-    # Create input and target batch
-    inputs = torch.stack([item[0] for item in plot_data], dim=0).to(device)
-    targets = torch.stack([item[1] for item in plot_data], dim=0)
-
-    # Get output predictions
-    with torch.no_grad():
-        outputs = model(inputs)
-
-    # Prepare data for plotting
-    inputs = inputs.cpu().squeeze()
-    targets = targets.squeeze()
-    if outputs.shape[1] == 1:
-        preds = outputs.cpu().squeeze() > 0.5
-    else:
-        preds = outputs.cpu().argmax(axis=1)
-
-    N = len(plot_data)
-    H = plot_data[0][0].shape[-2]
-    W = plot_data[0][0].shape[-1]
+    
+    N = num_images
+    H = inputs[0].shape[-2]
+    W = inputs[0].shape[-1]
 
     comp_rgb = torch.zeros((N,4,H,W))
     comp_rgb[:,1,:,:] = targets.logical_and(preds)
@@ -223,7 +182,7 @@ def grid_pred(
             elif row == 2:  # Ground truth segmentation
                 ax.imshow(inputs[col], cmap=cmap_im)
                 ax.imshow(
-                    plot_data[col][1].cpu().squeeze(), cmap=custom_cmap, alpha=alpha
+                    targets[col], cmap=custom_cmap, alpha=alpha
                 )
                 ax.axis("off")
             else:
@@ -232,3 +191,5 @@ def grid_pred(
                 ax.axis("off")
 
     fig.show()
+
+