Update get_dataset.py

get_dataset.py

@@ -162,22 +162,22 @@ def process_landmarks_data(
                     # Assuming an image with height and width:
                     # - The data array read from bmp file is of size (height, width) -- dim1 is height, dim2 is width
                     # - The landmark coordinates are defined as the indices in width (coordinate 1) and height (coordinate 2) directions
-                    idx_dim2, idx_dim1 = map(int, line.split(","))
+                    idx_dim1, idx_dim0 = map(int, line.split(","))
 
                     # Apply transformations
                     # Note: this is definitely correct
                     # This "mismatch" indices in "idx_dim1 = img_sizes[0] - idx_dim1" is due to the way the manual landmarks are defined
                     # DO NOT SWAP the order of transformations
                     if flip_dim0:
-                        idx_dim1 = img_sizes[0] - idx_dim1
+                        idx_dim0 = img_sizes[0] - idx_dim0
                     if flip_dim1:
-                        idx_dim2 = img_sizes[1] - idx_dim2
+                        idx_dim1 = img_sizes[1] - idx_dim1
                     if swap_dim01:  # this line should be AFTER slip_x and slip_y
-                        idx_dim1, idx_dim2 = idx_dim2, idx_dim1
+                        idx_dim0, idx_dim1 = idx_dim1, idx_dim0
 
                     # Save landmark coordinates in 0-based indices
                     landmarks[f"P{i+1}"] = [
-                        coord - 1 for coord in [1, idx_dim1, idx_dim2]
+                        coord - 1 for coord in [1, idx_dim0, idx_dim1]
                     ]
 
             # This data structure is designed to be compatible with biometric data constructed from segmentation masks
@@ -229,26 +229,26 @@ def plot_sagittal_slice_with_landmarks(
     )  # the transpose is necessary only for visualization
 
     # Extract and plot landmark coordinates
-    x_coords = []
-    y_coords = []
+    coords_dim0 = []
+    coords_dim1 = []
     landmarks = landmarks_json["slice_landmarks_x"][0]["landmarks"]
     for point_id, coords in landmarks.items():
         if len(coords) == 3:  # Check for valid [1, x, y] format
             # Note: this is definitely correct, DO NOT SWAP coords[1] and coords[2]
-            x_coords.append(coords[1])
-            y_coords.append(coords[2])
+            coords_dim0.append(coords[1])
+            coords_dim1.append(coords[2])
 
     # Add landmarks and labels
     plt.scatter(
-        x_coords,
-        y_coords,
+        coords_dim0,
+        coords_dim1,
         facecolors="#18A727",
         edgecolors="black",
         marker="o",
         s=80,
         linewidth=1.5,
     )
-    for i, (x, y) in enumerate(zip(x_coords, y_coords), 1):
+    for i, (x, y) in enumerate(zip(coords_dim0, coords_dim1), 1):
         plt.annotate(
             f"$\\mathbf{{{i}}}$",
             (x, y),