Diff of /Extracting_Planes.py [000000] .. [b52eda]

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--- a
+++ b/Extracting_Planes.py
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+from nibabel import load
+from numpy import ndarray, array, int32, uint8
+from time import time
+
+def Convert_To_Graph(image: ndarray, label: ndarray) -> tuple[ndarray, ndarray]:
+    r"""
+        Arguments:
+            image (numpy.ndarray): Source coronary-CT image.
+            label (numpy.ndarray): Ground truth segmentation.
+        
+        Returns:
+            out (tuple[numpy.ndarray, numpy.ndarray]): Source coronary-CT image and ground truth segmentation as graphs.
+    """
+    # start = time()
+    img = array(image, dtype = int32)
+    lab = array(label, dtype = uint8)
+    img[1::2, :] = image[1::2, ::-1]
+    lab[1::2, :] = label[1::2, ::-1]
+    
+    img = img.flatten()
+    img = img.reshape((img.shape[0], 1))
+
+    lab[lab > 7] = 0
+    lab = lab.flatten()
+    # print('Convert_To_Graph time: ', time() - start)
+    return (img, lab)
+
+def Extract_And_Convert(path_to_image: str, path_to_label: str,
+                        plane_type: str, plane_index: int) \
+                        -> tuple[ndarray, ndarray]:
+    r"""
+        Arguments:
+            path_to_image (str): Full path to the coronary-CT .nii.gz file.
+            path_to_label (str): Full path to the segmentation label .nii.gz file.
+            plane_type (str): One-character string with a value of 'A', 'C', or 'S'.
+            plane_index (int): Index of plane to be extracted from the image and label.
+        
+        Returns:
+            out (tuple[numpy.ndarray, numpy.ndarray]): Source coronary-CT image and ground truth segmentation as graphs.
+    """
+    # start = time()
+    match plane_type:
+        case 'A': # Axial plane
+            image = load(path_to_image).dataobj[:, :, plane_index]
+            label = load(path_to_label).dataobj[:, :, plane_index]
+        case 'C': # Coronal plane
+            image = load(path_to_image).dataobj[:, plane_index, :]
+            label = load(path_to_label).dataobj[:, plane_index, :]
+        case 'S': # Sagittal plane
+            image = load(path_to_image).dataobj[plane_index, :, :]
+            label = load(path_to_label).dataobj[plane_index, :, :]
+    # print('Nibabel loading time: ', time() - start)
+    return Convert_To_Graph(image, label)
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