62 update preprocessing tutorials

preprocessing/.gitignore

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+output
+outputs

preprocessing/utils.py

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+from pathlib import Path
+from typing import List, Optional
+import matplotlib.pyplot as plt
+import nibabel as nib
+
+
+def visualize_data(files: List[Path], label: str, titles: Optional[List[str]] = None):
+    """Visualize the MRI modalities
+
+    Args:
+        files (List[Path]): List of paths to the MRI modalities
+        label (str): Label for the y-axis on the far left left, i.e. category of the passed images (e.g. input, output)
+        titles (Optional[List[str]], optional): Title of images. Defaults to None.
+    """
+    _, axes = plt.subplots(1, len(files), figsize=(len(files) * 4, 10))
+
+    for i, file in enumerate(files):
+        modality_np = nib.load(file).get_fdata().transpose(2, 1, 0)
+        axes[i].set_title(titles[i] if titles else file.name)
+        axes[i].imshow(modality_np[modality_np.shape[0] // 2, :, :], cmap="gray")
+    axes[0].set_ylabel(label)
+
+
+def visualize_defacing(
+    file: Path,
+):
+    """Visualize the defacing of the MRI modality
+
+    Args:
+        file (Path): Path to the MRI modality
+    """
+
+    modality_np = nib.load(file).get_fdata().transpose(2, 1, 0)
+    plt.figure(figsize=(4, 5))
+    plt.title(file.name)
+    plt.imshow(modality_np[:, ::-1, 75], cmap="gray", origin="lower")