black formatting

Author: evamariie

BraTS-Toolkit/glioma_segmentation_with_BraTS_Toolkit.ipynb

@@ -3,31 +3,37 @@
 import nibabel as nib
 from pathlib import Path
 
-    
-def visualize_data2(t1c, t1, t2, flair, height_p = 0.5):    #
+
+def visualize_data2(t1c, t1, t2, flair, height_p=0.5):  #
     """Visualize the MRI modalities. This function is different from "visualize_data" in the following ways:
-    	a) it expects the four file paths directly (no naming convention required)
-    	b) it does not take a slice index but a percentage height (e.g. 0.5 = 50% = middle slice) as imputs may have different dimensions
+        a) it expects the four file paths directly (no naming convention required)
+        b) it does not take a slice index but a percentage height (e.g. 0.5 = 50% = middle slice) as imputs may have different dimensions
 
     Args:
-    	height_p (float, optional): the percentage of slicing height. 0.5 means 50% means exactly in the middle of the cuboid
+        height_p (float, optional): the percentage of slicing height. 0.5 means 50% means exactly in the middle of the cuboid
         slice_index (int, optional): Slice to be visualized (first index in data of shape (155, 240, 240)). Defaults to 75.
     """
     _, axes = plt.subplots(1, 4, figsize=(12, 10))
 
-    for i, (mod, modality_file) in enumerate([("t1",t1), ("t1c",t1c), ("t2",t2), ("flair",flair)]):
-    
+    for i, (mod, modality_file) in enumerate(
+        [("t1", t1), ("t1c", t1c), ("t2", t2), ("flair", flair)]
+    ):
+
         data = nib.load(modality_file).get_fdata()
-         # Get the middle slice along the specified axis
-        slice_index = int(data.shape[2] * height_p)  # show slice that is exactly in the middle
+        # Get the middle slice along the specified axis
+        slice_index = int(
+            data.shape[2] * height_p
+        )  # show slice that is exactly in the middle
         slice_data = data[:, ::-1, slice_index].T
-        
+
         axes[i].set_title(mod)
         axes[i].imshow(slice_data, cmap="gray")
         axes[i].axis("off")
 
+
 DATA_FOLDER = "data"
 
+
 def visualize_data(data_folder: str = DATA_FOLDER, slice_index: int = 75):
     """Visualize the MRI modalities for a given slice index
 
@@ -45,7 +51,8 @@ def visualize_data(data_folder: str = DATA_FOLDER, slice_index: int = 75):
         axes[i].imshow(modality_np[slice_index, :, :], cmap="gray")
         axes[i].axis("off")
 
-def visualize_segmentation(modality_file: str, segmentation_file: str, slice_p = 0.5):
+
+def visualize_segmentation(modality_file: str, segmentation_file: str, slice_p=0.5):
     """Visualize the MRI modality and the segmentation
 
     Args:
@@ -63,5 +70,3 @@ def visualize_segmentation(modality_file: str, segmentation_file: str, slice_p =
     for ax in ax:
         ax.axis("off")
     plt.tight_layout()
-    
-