44 feature request ereg tutorial

eReg/README.md

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+
+# eReg tutorial
+This folder contains tutorials for the [eReg](https://github.com/BrainLesion/eReg) package for image registration.
+Please have a look at the Jupyter notebooks.

eReg/temporary_directory/.gitignore

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+*
+!.gitignore

eReg/utils.py

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+import os
+import matplotlib.pyplot as plt
+import nibabel as nib
+from pathlib import Path
+
+
+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
+
+    Args:
+        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)]
+    ):
+
+        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
+        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
+
+    Args:
+        data_folder (str, optional): Path to the folder containing the t1, t1c, t2 & flair file. Defaults to DATA_FOLDER.
+        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))
+
+    modalities = ["t1", "t1c", "t2", "flair"]
+    for i, mod in enumerate(modalities):
+        modality_file = os.path.join(data_folder, f"{mod}.nii.gz")
+        modality_np = nib.load(modality_file).get_fdata().transpose(2, 1, 0)
+        axes[i].set_title(mod)
+        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):
+    """Visualize the MRI modality and the segmentation
+
+    Args:
+        modality_file (str): Path to the desired modality file
+        segmentation_file (str): Path to the segmentation file
+    """
+    modality_np = nib.load(modality_file).get_fdata().transpose(2, 1, 0)
+    seg_np = nib.load(segmentation_file).get_fdata().transpose(2, 1, 0)
+    _, ax = plt.subplots(1, 2, figsize=(8, 4))
+
+    slice_index = int(modality_np.shape[0] * slice_p)  # You can choose any slice here
+    ax[0].imshow(modality_np[slice_index, :, :], cmap="gray")
+    ax[1].imshow(modality_np[slice_index, :, :], cmap="gray")
+    ax[1].imshow(seg_np[slice_index, :, :], cmap="plasma", alpha=0.5)
+    for ax in ax:
+        ax.axis("off")
+    plt.tight_layout()