Merge pull request #746 from scap3yvt/scap3yvt-patch-black

Consistent black across the codebase

Author: sarthakpati

GANDLF/data/patch_miner/opm/utils.py

@@ -10,8 +10,9 @@
 from skimage.morphology import remove_small_holes
 from skimage.color.colorconv import rgb2hsv
 import cv2
-#from skimage.exposure import rescale_intensity
-#from skimage.color import rgb2hed
+
+# from skimage.exposure import rescale_intensity
+# from skimage.color import rgb2hed
 
 # import matplotlib.pyplot as plt
 import yaml
@@ -238,7 +239,8 @@ def alpha_rgb_2d_channel_check(img):
     else:
         return False
 
-#def pen_marking_check(img, intensity_thresh=225, intensity_thresh_saturation =50, intensity_thresh_b = 128):
+
+# def pen_marking_check(img, intensity_thresh=225, intensity_thresh_saturation =50, intensity_thresh_b = 128):
 #    """
 #    This function is used to curate patches from the input image. It is used to remove patches that have pen markings.
 #    Args:
@@ -259,7 +261,14 @@ def alpha_rgb_2d_channel_check(img):
 #    #Assume patch is valid
 #    return True
 
-def patch_artifact_check(img, intensity_thresh = 250, intensity_thresh_saturation = 5, intensity_thresh_b = 128, patch_size = (256,256)):
+
+def patch_artifact_check(
+    img,
+    intensity_thresh=250,
+    intensity_thresh_saturation=5,
+    intensity_thresh_b=128,
+    patch_size=(256, 256),
+):
     """
     This function is used to curate patches from the input image. It is used to remove patches that are mostly background.
     Args:
@@ -271,23 +280,36 @@ def patch_artifact_check(img, intensity_thresh = 250, intensity_thresh_saturatio
     Returns:
         bool: Whether the patch is valid (True) or not (False)
     """
-    #patch_size = config["patch_size"]
+    # patch_size = config["patch_size"]
     patch_hsv = cv2.cvtColor(img, cv2.COLOR_RGB2HSV)
     count_white_pixels = np.sum(np.logical_and.reduce(img > intensity_thresh, axis=2))
     percent_pixels = count_white_pixels / (patch_size[0] * patch_size[1])
     count_black_pixels = np.sum(np.logical_and.reduce(img < intensity_thresh_b, axis=2))
     percent_pixel_b = count_black_pixels / (patch_size[0] * patch_size[1])
-    percent_pixel_2 = np.sum(patch_hsv[...,1] < intensity_thresh_saturation) / (patch_size[0] * patch_size[1])
-    percent_pixel_3 = np.sum(patch_hsv[...,2] > intensity_thresh) / (patch_size[0] * patch_size[1])
+    percent_pixel_2 = np.sum(patch_hsv[..., 1] < intensity_thresh_saturation) / (
+        patch_size[0] * patch_size[1]
+    )
+    percent_pixel_3 = np.sum(patch_hsv[..., 2] > intensity_thresh) / (
+        patch_size[0] * patch_size[1]
+    )
 
-    if percent_pixel_2 > 0.99 or np.mean(patch_hsv[...,1]) < 5 or percent_pixel_3 > 0.99:
+    if (
+        percent_pixel_2 > 0.99
+        or np.mean(patch_hsv[..., 1]) < 5
+        or percent_pixel_3 > 0.99
+    ):
         if percent_pixel_2 < 0.1:
             return False
-    elif (percent_pixel_2 > 0.99 and percent_pixel_3 > 0.99) or percent_pixel_b > 0.99 or percent_pixels > 0.9:
+    elif (
+        (percent_pixel_2 > 0.99 and percent_pixel_3 > 0.99)
+        or percent_pixel_b > 0.99
+        or percent_pixels > 0.9
+    ):
         return False
     # assume that the patch is valid
     return True
 
+
 def parse_config(config_file):
     """
     Parse config file and return a dictionary of config values.
@@ -304,7 +326,7 @@ def parse_config(config_file):
     config["value_map"] = config.get("value_map", None)
     config["read_type"] = config.get("read_type", "random")
     config["overlap_factor"] = config.get("overlap_factor", 0.0)
-    config["patch_size"] = config.get("patch_size", [256,256])
+    config["patch_size"] = config.get("patch_size", [256, 256])
 
     return config
 

GANDLF/metrics/classification.py

@@ -64,9 +64,7 @@ def overall_stats(predictions, ground_truth, params):
             "aucroc": tm.AUROC(
                 task=task,
                 num_classes=params["model"]["num_classes"],
-                average=average_type_key
-                if average_type_key != "micro"
-                else "macro",
+                average=average_type_key if average_type_key != "micro" else "macro",
             ),
         }
         for metric_name, calculator in calculators.items():

GANDLF/metrics/generic.py

@@ -15,9 +15,7 @@
 )
 
 
-def generic_function_output_with_check(
-    predicted_classes, label, metric_function
-):
+def generic_function_output_with_check(predicted_classes, label, metric_function):
     if torch.min(predicted_classes) < 0:
         print(
             "WARNING: Negative values detected in prediction, cannot compute torchmetrics calculations."
@@ -32,16 +30,12 @@ def generic_function_output_with_check(
             max_clamp_val = metric_function.num_classes - 1
         except AttributeError:
             max_clamp_val = 1
-        predicted_new = torch.clamp(
-            predicted_classes.cpu().int(), max=max_clamp_val
-        )
+        predicted_new = torch.clamp(predicted_classes.cpu().int(), max=max_clamp_val)
         predicted_new = predicted_new.reshape(label.shape)
         return metric_function(predicted_new, label.cpu().int())
 
 
-def generic_torchmetrics_score(
-    output, label, metric_class, metric_key, params
-):
+def generic_torchmetrics_score(output, label, metric_class, metric_key, params):
     task = determine_classification_task_type(params)
     num_classes = params["model"]["num_classes"]
     predicted_classes = output
@@ -67,25 +61,19 @@ def recall_score(output, label, params):
 
 
 def precision_score(output, label, params):
-    return generic_torchmetrics_score(
-        output, label, Precision, "precision", params
-    )
+    return generic_torchmetrics_score(output, label, Precision, "precision", params)
 
 
 def f1_score(output, label, params):
     return generic_torchmetrics_score(output, label, F1Score, "f1", params)
 
 
 def accuracy(output, label, params):
-    return generic_torchmetrics_score(
-        output, label, Accuracy, "accuracy", params
-    )
+    return generic_torchmetrics_score(output, label, Accuracy, "accuracy", params)
 
 
 def specificity_score(output, label, params):
-    return generic_torchmetrics_score(
-        output, label, Specificity, "specificity", params
-    )
+    return generic_torchmetrics_score(output, label, Specificity, "specificity", params)
 
 
 def iou_score(output, label, params):

GANDLF/utils/generic.py

@@ -49,7 +49,9 @@ def checkPatchDivisibility(patch_size, number=16):
     return True
 
 
-def determine_classification_task_type(params: Dict[str, Union[Dict[str, Any], Any]]) -> str:
+def determine_classification_task_type(
+    params: Dict[str, Union[Dict[str, Any], Any]]
+) -> str:
     """Determine the task (binary or multiclass) from the model config.
     Args:
         params (dict): The parameter dictionary containing training and data information.
@@ -159,10 +161,7 @@ def checkPatchDimensions(patch_size, numlay):
         patch_size_to_check = patch_size_to_check[:-1]
 
     if all(
-        [
-            x >= 2 ** (numlay + 1) and x % 2**numlay == 0
-            for x in patch_size_to_check
-        ]
+        [x >= 2 ** (numlay + 1) and x % 2**numlay == 0 for x in patch_size_to_check]
     ):
         return numlay
     else:
@@ -198,9 +197,7 @@ def get_array_from_image_or_tensor(input_tensor_or_image):
     elif isinstance(input_tensor_or_image, np.ndarray):
         return input_tensor_or_image
     else:
-        raise ValueError(
-            "Input must be a torch.Tensor or sitk.Image or np.ndarray"
-        )
+        raise ValueError("Input must be a torch.Tensor or sitk.Image or np.ndarray")
 
 
 def set_determinism(seed=42):
@@ -270,9 +267,7 @@ def __update_metric_from_list_to_single_string(input_metrics_dict) -> dict:
     output_metrics_dict = deepcopy(cohort_level_metrics)
     for metric in metrics_dict_from_parameters:
         if isinstance(sample_level_metrics[metric], np.ndarray):
-            to_print = (
-                sample_level_metrics[metric] / length_of_dataloader
-            ).tolist()
+            to_print = (sample_level_metrics[metric] / length_of_dataloader).tolist()
         else:
             to_print = sample_level_metrics[metric] / length_of_dataloader
         output_metrics_dict[metric] = to_print
@@ -315,7 +310,5 @@ def define_multidim_average_type_key(params, metric_name) -> str:
     Returns:
         str: The average type key.
     """
-    average_type_key = params["metrics"][metric_name].get(
-        "multidim_average", "global"
-    )
+    average_type_key = params["metrics"][metric_name].get("multidim_average", "global")
     return average_type_key