Script to testing the curvature metric on a circle of known radius

tests/test_curvature.py

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+from vital.utils.image.us.measure import EchoMeasure
+
+
+def main():
+    """Run the test script."""
+    import argparse
+    from math import ceil
+    from unittest.mock import patch
+
+    import numpy as np
+    from skimage.morphology import disk
+
+    parser = argparse.ArgumentParser(description="Compute the curvature of a circle of known radius.")
+    parser.add_argument("--radius", type=float, default=20, help="Radius of the circle")
+    parser.add_argument("--num_points", type=int, default=60, help="Number of points to sample along the circle")
+    parser.add_argument("--voxel_size", type=float, default=0.5, help="Voxel size (in mm)")
+    parser.add_argument("--debug_plot", action="store_true", help="Whether to plot the curvature")
+    args = parser.parse_args()
+
+    # Generate the mask for the circle (for plotting purposes)
+    # as well as sample points along the circumference of the circle
+    disk_mask = disk(radius=args.radius)
+
+    def sample_circle(radius: float, num_points: int, pixel_coords: bool = False) -> np.ndarray:
+        """Sample points along the circumference of a circle of known radius."""
+        theta = np.linspace(0, 2 * np.pi, num_points)
+        x = radius * np.cos(theta)
+        y = radius * np.sin(theta)
+        coords = np.vstack([y, x]).T
+        if pixel_coords:
+            # Convert from exact floating-point coordinates to integer coordinates
+            # + offset from origin so that the circle falls in the positive quadrant
+            coords = coords.astype(int) + ceil(radius)
+        return coords
+
+    circle_samples = sample_circle(args.radius, args.num_points, pixel_coords=args.debug_plot)
+
+    # Mock the measure object to return a known set of control points that the domain-specific code could not extract
+    # from the circle
+    with patch.object(EchoMeasure, "control_points", return_value=circle_samples):
+        # Compute the curvature of the circle
+        curvature = EchoMeasure.curvature(
+            disk_mask, None, None, None, num_control_points=60, voxelspacing=args.voxel_size, debug_plots=False
+        )
+        print(f"Computed curvature (in dm^-1): {curvature}")
+
+
+if __name__ == "__main__":
+    main()