72 feature update brats tutorial

BraTS/utils.py

@@ -1,19 +1,22 @@
 from pathlib import Path
+from typing import Union
+
 import matplotlib.pyplot as plt
 import nibabel as nib
+import numpy as np
 
-DATA_FOLDER = "data"
+DATA_FOLDER = Path("data")
 
 
 def visualize_segmentation_data(
-    data_folder: str = DATA_FOLDER,
+    data_folder: Union[str, Path] = DATA_FOLDER,
     subject_id: str = "BraTS-GLI-00001-000",
     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.
+        data_folder (Union[str, Path]): 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))
@@ -29,14 +32,14 @@ def visualize_segmentation_data(
 
 
 def visualize_inpainting_data(
-    data_folder: str = DATA_FOLDER,
+    data_folder: Union[str, Path] = DATA_FOLDER,
     subject_id: str = "BraTS-GLI-00001-000",
     slice_index: int = 75,
 ):
     """Visualize the MRI modalities for a given slice index
 
     Args:
-        data_folder (str, optional): Path to the folder containing the t1n and mask files. Defaults to DATA_FOLDER.
+        data_folder (Union[str, Path]): Path to the folder containing the t1n and mask files. 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, 2, figsize=(6, 10))
@@ -51,32 +54,39 @@ def visualize_inpainting_data(
         axes[i].axis("off")
 
 
-def visualize_segmentation(modality_file: str, segmentation_file: str):
+def visualize_segmentation(
+    modality_file: Union[str, Path], segmentation_file: Union[str, Path]
+):
     """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_file (Union[str, Path]): Path to the desired modality file
+        segmentation_file (Union[str, Path]): 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 = modality_np.shape[0] // 2  # You can choose any slice here
+
+    # Mask out background (0) in the segmentation
+    seg_slice = seg_np[slice_index, :, :]
     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=0.3)
+    ax[1].imshow(seg_slice, cmap="plasma", alpha=np.where(seg_slice > 0, 0.3, 0))
+
     for ax in ax:
         ax.axis("off")
     plt.tight_layout()
 
 
-def visualize_inpainting(t1n_voided: str, prediction: str):
+def visualize_inpainting(t1n_voided: Union[str, Path], prediction: Union[str, Path]):
     """Visualize the inpainting results
 
     Args:
-        t1n_voided (str): Voided T1 modality file
-        prediction (str): Inpainting prediction file
+        t1n_voided (Union[str, Path]): Voided T1 modality file
+        prediction (Union[str, Path]): Inpainting prediction file
     """
     voided_np = nib.load(t1n_voided).get_fdata().transpose(2, 1, 0)
     inpainting_np = nib.load(prediction).get_fdata().transpose(2, 1, 0)
@@ -91,15 +101,17 @@ def visualize_inpainting(t1n_voided: str, prediction: str):
 
 
 def visualize_missing_mri_t2w(
-    synthesized_t2w: str,
-    data_folder: str = DATA_FOLDER,
+    synthesized_t2w: Union[str, Path],
+    data_folder: Union[str, Path] = DATA_FOLDER,
     subject_id: str = "BraTS-GLI-00001-000",
     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.
+        synthesized_t2w (Union[str, Path]): Path to the synthesized T2w file
+        data_folder (Union[str, Path], optional): Path to the folder containing the t1, t1c, t2 & flair file. Defaults to DATA_FOLDER.
+        subject_id (str, optional): Subject ID to visualize. Defaults to "BraTS-GLI-00001-000".
         slice_index (int, optional): Slice to be visualized (first index in data of shape (155, 240, 240)). Defaults to 75.
     """
     _, axes = plt.subplots(1, 5, figsize=(12, 10))