Ensure synthesis metrics have an option to take voided image

.spelling/.spelling/expect.txt

@@ -1,4 +1,4 @@
 Abhishek
 Abousamra
 acdfbac
 acsconv
@@ -487,6 +487,7 @@
 rgbtorgba
 rigourous
 Ritesh
+rmse
 rmsprop
 rocm
 rocmdocs
@@ -561,7 +562,6 @@
 thresholding
 Thu
 tiatoolbox
-tiffslide
 timepoints
 timm
 tio
@@ -597,8 +597,6 @@
 unitwise
 unsqueeze
 upenn
-Uploaing
-Uploded
 upsample
 upsampled
 upsampling
@@ -725,7 +723,6 @@
 zwezggl
 zzokqk
 thirdparty
-adopy
 Shohei
 crcrpar
 lrs

GANDLF/cli/generate_metrics.py

@@ -15,13 +15,11 @@
     overall_stats,
     structural_similarity_index,
     mean_squared_error,
+    root_mean_squared_error,
     peak_signal_noise_ratio,
     mean_squared_log_error,
     mean_absolute_error,
-    ncc_mean,
-    ncc_std,
-    ncc_max,
-    ncc_min,
+    ncc_metrics,
 )
 from GANDLF.losses.segmentation import dice
 from GANDLF.metrics.segmentation import (
@@ -302,21 +300,22 @@ def __percentile_clip(
             reference_tensor = (
                 input_tensor if reference_tensor is None else reference_tensor
             )
-            v_min, v_max = np.percentile(
-                reference_tensor, [p_min, p_max]
-            )  # get p_min percentile and p_max percentile
-
+            # get p_min percentile and p_max percentile
+            v_min, v_max = np.percentile(reference_tensor, [p_min, p_max])
             # set lower bound to be 0 if strictlyPositive is enabled
             v_min = max(v_min, 0.0) if strictlyPositive else v_min
-            output_tensor = np.clip(
-                input_tensor, v_min, v_max
-            )  # clip values to percentiles from reference_tensor
-            output_tensor = (output_tensor - v_min) / (
-                v_max - v_min
-            )  # normalizes values to [0;1]
+            # clip values to percentiles from reference_tensor
+            output_tensor = np.clip(input_tensor, v_min, v_max)
+            # normalizes values to [0;1]
+            output_tensor = (output_tensor - v_min) / (v_max - v_min)
             return output_tensor
 
-        input_df = __update_header_location_case_insensitive(input_df, "Mask", False)
+        # these are additional columns that could be present for synthesis tasks
+        for column_to_make_case_insensitive in ["Mask", "VoidImage"]:
+            input_df = __update_header_location_case_insensitive(
+                input_df, column_to_make_case_insensitive, False
+            )
+
         for _, row in tqdm(input_df.iterrows(), total=input_df.shape[0]):
             current_subject_id = row["SubjectID"]
             overall_stats_dict[current_subject_id] = {}
@@ -332,16 +331,26 @@ def __percentile_clip(
                 )
             ).byte()
 
+            void_image_present = True if "VoidImage" in row else False
+            void_image = (
+                __fix_2d_tensor(torchio.ScalarImage(row["VoidImage"]).data)
+                if "VoidImage" in row
+                else torch.from_numpy(
+                    np.ones(target_image.numpy().shape, dtype=np.uint8)
+                )
+            )
+
             # Get Infill region (we really are only interested in the infill region)
             output_infill = (pred_image * mask).float()
             gt_image_infill = (target_image * mask).float()
 
             # Normalize to [0;1] based on GT (otherwise MSE will depend on the image intensity range)
             normalize = parameters.get("normalize", True)
             if normalize:
+                # use all the tissue that is not masked for normalization
                 reference_tensor = (
-                    target_image * ~mask
-                )  # use all the tissue that is not masked for normalization
+                    target_image * ~mask if not void_image_present else void_image
+                )
                 gt_image_infill = __percentile_clip(
                     gt_image_infill,
                     reference_tensor=reference_tensor,
@@ -364,18 +373,10 @@ def __percentile_clip(
             # ncc metrics
             compute_ncc = parameters.get("compute_ncc", True)
             if compute_ncc:
-                overall_stats_dict[current_subject_id]["ncc_mean"] = ncc_mean(
-                    output_infill, gt_image_infill
-                )
-                overall_stats_dict[current_subject_id]["ncc_std"] = ncc_std(
-                    output_infill, gt_image_infill
-                )
-                overall_stats_dict[current_subject_id]["ncc_max"] = ncc_max(
-                    output_infill, gt_image_infill
-                )
-                overall_stats_dict[current_subject_id]["ncc_min"] = ncc_min(
-                    output_infill, gt_image_infill
-                )
+                calculated_ncc_metrics = ncc_metrics(output_infill, gt_image_infill)
+                for key, value in calculated_ncc_metrics.items():
+                    # we don't need the ".item()" here, since the values are already scalars
+                    overall_stats_dict[current_subject_id][key] = value
 
             # only voxels that are to be inferred (-> flat array)
             # these are required for mse, psnr, etc.
@@ -386,6 +387,10 @@ def __percentile_clip(
                 output_infill, gt_image_infill
             ).item()
 
+            overall_stats_dict[current_subject_id]["rmse"] = root_mean_squared_error(
+                output_infill, gt_image_infill
+            ).item()
+
             overall_stats_dict[current_subject_id]["msle"] = mean_squared_log_error(
                 output_infill, gt_image_infill
             ).item()

GANDLF/entrypoints/hf_hub_integration.py

@@ -96,7 +96,7 @@
 @click.option(
     "--hf-template",
     "-hft",
-    help="Adding the template path for the model card it is Required during Uploaing a model",
+    help="Adding the template path for the model card: it is required during model upload",
     default=huggingface_file_path,
     type=click.Path(exists=True, file_okay=True, dir_okay=False),
 )

GANDLF/metrics/__init__.py

@@ -32,13 +32,11 @@
 from .synthesis import (
     structural_similarity_index,
     mean_squared_error,
+    root_mean_squared_error,
     peak_signal_noise_ratio,
     mean_squared_log_error,
     mean_absolute_error,
-    ncc_mean,
-    ncc_std,
-    ncc_max,
-    ncc_min,
+    ncc_metrics,
 )
 import GANDLF.metrics.classification as classification
 import GANDLF.metrics.regression as regression

GANDLF/metrics/synthesis.py

@@ -46,8 +46,28 @@ def mean_squared_error(prediction: torch.Tensor, target: torch.Tensor) -> torch.
     Args:
         prediction (torch.Tensor): The prediction tensor.
         target (torch.Tensor): The target tensor.
+
+    Returns:
+        torch.Tensor: The mean squared error or its square root.
     """
-    mse = MeanSquaredError()
+    mse = MeanSquaredError(squared=True)
+    return mse(preds=prediction, target=target)
+
+
+def root_mean_squared_error(
+    prediction: torch.Tensor, target: torch.Tensor
+) -> torch.Tensor:
+    """
+    Computes the mean squared error between the target and prediction.
+
+    Args:
+        prediction (torch.Tensor): The prediction tensor.
+        target (torch.Tensor): The target tensor.
+
+    Returns:
+        torch.Tensor: The mean squared error or its square root.
+    """
+    mse = MeanSquaredError(squared=False)
     return mse(preds=prediction, target=target)
 
 
@@ -78,10 +98,9 @@ def peak_signal_noise_ratio(
         return psnr(preds=prediction, target=target)
     else:  # implementation of PSNR that does not give 'inf'/'nan' when 'mse==0'
         mse = mean_squared_error(target, prediction)
-        if data_range == None:  # compute data_range like torchmetrics if not given
-            min_v = (
-                0 if torch.min(target) > 0 else torch.min(target)
-            )  # look at this line
+        if data_range is None:  # compute data_range like torchmetrics if not given
+            # put the min value to 0 if all values are positive
+            min_v = 0 if torch.min(target) > 0 else torch.min(target)
             max_v = torch.max(target)
         else:
             min_v, max_v = data_range
@@ -158,69 +177,27 @@ def __convert_to_grayscale(image: sitk.Image) -> sitk.Image:
     return correlation_filter.Execute(target_image, pred_image)
 
 
-def ncc_mean(prediction: torch.Tensor, target: torch.Tensor) -> float:
-    """
-    Computes normalized cross correlation mean between target and prediction.
-
-    Args:
-        prediction (torch.Tensor): The prediction tensor.
-        target (torch.Tensor): The target tensor.
-
-    Returns:
-        float: The normalized cross correlation mean.
-    """
-    stats_filter = sitk.StatisticsImageFilter()
-    corr_image = _get_ncc_image(target, prediction)
-    stats_filter.Execute(corr_image)
-    return stats_filter.GetMean()
-
-
-def ncc_std(prediction: torch.Tensor, target: torch.Tensor) -> float:
-    """
-    Computes normalized cross correlation standard deviation between target and prediction.
-
-    Args:
-        prediction (torch.Tensor): The prediction tensor.
-        target (torch.Tensor): The target tensor.
-
-    Returns:
-        float: The normalized cross correlation standard deviation.
-    """
-    stats_filter = sitk.StatisticsImageFilter()
-    corr_image = _get_ncc_image(target, prediction)
-    stats_filter.Execute(corr_image)
-    return stats_filter.GetSigma()
-
-
-def ncc_max(prediction: torch.Tensor, target: torch.Tensor) -> float:
-    """
-    Computes normalized cross correlation maximum between target and prediction.
-
-    Args:
-        prediction (torch.Tensor): The prediction tensor.
-        target (torch.Tensor): The target tensor.
-
-    Returns:
-        float: The normalized cross correlation maximum.
-    """
-    stats_filter = sitk.StatisticsImageFilter()
-    corr_image = _get_ncc_image(target, prediction)
-    stats_filter.Execute(corr_image)
-    return stats_filter.GetMaximum()
-
-
-def ncc_min(prediction: torch.Tensor, target: torch.Tensor) -> float:
+def ncc_metrics(prediction: torch.Tensor, target: torch.Tensor) -> dict:
     """
-    Computes normalized cross correlation minimum between target and prediction.
+    Computes normalized cross correlation metrics between target and prediction.
 
     Args:
         prediction (torch.Tensor): The prediction tensor.
         target (torch.Tensor): The target tensor.
 
     Returns:
-        float: The normalized cross correlation minimum.
+        dict: The normalized cross correlation metrics.
     """
-    stats_filter = sitk.StatisticsImageFilter()
     corr_image = _get_ncc_image(target, prediction)
-    stats_filter.Execute(corr_image)
-    return stats_filter.GetMinimum()
+    stats_filter = sitk.LabelStatisticsImageFilter()
+    stats_filter.UseHistogramsOn()
+    # ensure that we are not considering zeros
+    onesImage = corr_image == corr_image
+    stats_filter.Execute(corr_image, onesImage)
+    return {
+        "ncc_mean": stats_filter.GetMean(1),
+        "ncc_std": stats_filter.GetSigma(1),
+        "ncc_max": stats_filter.GetMaximum(1),
+        "ncc_min": stats_filter.GetMinimum(1),
+        "ncc_median": stats_filter.GetMedian(1),
+    }