fixed bug in perimeter calculation

convergence_extension/perimeter_long_axis.py

@@ -2,27 +2,13 @@ import numpy as np
 import matplotlib.pyplot as plt
 import matplotlib.pyplot as plt
 import pandas as pd
 import pandas as pd
 from matplotlib.widgets import Slider
 from matplotlib.widgets import Slider
+from scipy.spatial import ConvexHull
 
 
-def perimeter(X, Y, n):
-    # Initialize perimeter
-    perimeter = 0
-
-    # Calculate distance between each pair of consecutive points
-    for j in range(n):
-
-        # Get current point
-        x1, y1 = X[j], Y[j]
-
-        # Get next point (if i is the last index, get the first point)
-        if j == n-1:
-            x2, y2 = X[0], Y[0]
-        else:
-            x2, y2 = X[j+1], Y[j+1]
-        
-        # Calculate distance between points and add to perimeter
-        perimeter += np.sqrt((x2-x1)**2 + (y2-y1)**2)
-
-    return perimeter
+def perimeter(X, Y):
+    points = np.column_stack((X, Y))
+    hull = ConvexHull(points)
+    value = sum(np.linalg.norm(points[hull.vertices[i]] - points[hull.vertices[(i+1)%len(hull.vertices)]]) for i in range(len(hull.vertices)))
+    return value
 
 
 def long_axis(x, y):
 def long_axis(x, y):
     x_diff = x[:, None] - x
     x_diff = x[:, None] - x
@@ -31,13 +17,16 @@ def long_axis(x, y):
     return np.max(distances)
     return np.max(distances)
 
 
 # NOTE: check perimeter and long_axis functions on known shapes
 # NOTE: check perimeter and long_axis functions on known shapes
-# x = np.array([0, 1, 0, -1])
-# y = np.array([2, 0, -2, 0])
-# print(x, y)
-# print(long_axis(x, y))   
+# x = np.array([1, 0, -1, 0])
+# y = np.array([0, 2, 0, -2])
+# print(long_axis(x, y))
+
+# points = np.column_stack((x, y))
+# hull = ConvexHull(points)
+# print(long_axis(x, y))
 # raise SystemExit
 # raise SystemExit
 
 
-file = np.loadtxt('xy_coordinates_movie1.txt')
+file = np.loadtxt('xy_coordinates_movie15.txt')
 number_of_pixels = file.shape[0]
 number_of_pixels = file.shape[0]
 time_points = file.shape[1]
 time_points = file.shape[1]
 time_array = np.arange(0, 5*int(time_points/2), 5)
 time_array = np.arange(0, 5*int(time_points/2), 5)
@@ -95,7 +84,7 @@ plt.show()
 perimeter_array = np.zeros(int(time_points/2))
 perimeter_array = np.zeros(int(time_points/2))
 
 
 for k in range(0,  int(time_points/2)):
 for k in range(0,  int(time_points/2)):
-    perimeter_array[k] = perimeter(x[k], y[k], number_of_pixels)   
+    perimeter_array[k] = perimeter(x[k], y[k])   
 
 
 plt.plot(time_array, perimeter_array, marker='o', linestyle='None')     
 plt.plot(time_array, perimeter_array, marker='o', linestyle='None')     
 plt.xlabel('Time')
 plt.xlabel('Time')