fixed and issue which would result high negative area in triangle calculations...

fixed and issue which would result high negative area in triangle calculations when triangles were degenerate.

measure.py

 import numpy as np
 import overlap
+import logging
 
 from polygon_triangulate import polygon_triangulate, PlotTriangulation
 from tetrahedralize_triangles import tetrahedralize
 
+logging.basicConfig(filename='warnings.log', level=logging.DEBUG)
+
 def measure_volume(V_tet, T, origin, r):
 
     sphere = overlap.Sphere(origin, r)
     volume = 0.0
 
+    volumes = []
+
     for tet in T:
         vertices = V_tet[tet]
         overlap_tet = overlap.Tetrahedron(vertices)
         overlap_volume = overlap.overlap(sphere, overlap_tet)
+        volumes.append(overlap_volume)
+        if overlap_volume < 0:
+            print('Encountered negative volume overlap')
+            logging.warning('Encountered negative volume overlap')
         volume += overlap_volume
 
+    #import matplotlib.pyplot as plt
+    #plt.title(f'radius {r} total {volume}')
+    #plt.plot(np.arange(len(volumes)), volumes)
+    #plt.show()
+
     return volume
 
 def same_point(x, y):
@@ -28,6 +42,16 @@ def remove_duplicate_contour_points(P):
             return remove_duplicate_contour_points(np.delete(P, i, axis=0))
     return P
 
+def remove_line_triangles(P, F):
+    n = len(F)
+    for i in range(n-1, -1, -1):
+        PF = P[F[i]]
+        v1 = PF[0] - PF[1]
+        v2 = PF[1] - PF[2]
+        if np.isclose(np.abs(np.dot(v1/np.linalg.norm(v1),v2/np.linalg.norm(v2))),1):
+            F = np.delete(F, i, axis=0)
+    return F
+
 def measure_cumulative_volume(z, P, thickness, origin, R):
     '''
     Integration of the intersecting volume of a thick polygon and a sphere of increasing radius.
@@ -60,6 +84,13 @@ def measure_cumulative_volume(z, P, thickness, origin, R):
     z1 = z + thickness / 2
     _, V_tri, F = polygon_triangulate(P)
 
+    F = remove_line_triangles(V_tri, F)
+
+    #import matplotlib.pyplot as plt
+    #print(V_tri[:5,:])
+    #PlotTriangulation(V_tri, F)
+    #plt.show()
+
     V_tet, T = tetrahedralize(V_tri, F, z0, z1)
 
     mu = np.zeros(len(R))
@@ -123,4 +154,4 @@ def measure_cumulative_points(z, X, thickness, origin, R):
         s = h - d0
         mu[i] = np.sum(np.clip(s/thickness, 0, 1))
 
-    return mu
+    return mu
\ No newline at end of file

run.py

@@ -78,17 +78,16 @@ def write_csv(path, R, dP, dV):
         for i0,i1,a,b,c,d,e,v in zip(R[:-1], R[1:], dP, dV, Dens, intdP, intdV, intDens):
             f.write(f'{i0},{a},{b},{c},,{i0},{i1},{d},{e},{v}\n')
 
-def run(base_dir):
+def run(base_dir, output_dir):
 
     R = np.arange(0, 3001, 125)
 
-    output_dir = 'output'
+    
     os.makedirs(output_dir, exist_ok=True)
 
     for experiment in tqdm(os.listdir(base_dir), desc='experiment'):
         for reading in os.listdir(os.path.join(base_dir, experiment)):
-            #if reading != '7566':
-            #    continue
+
             data_dir = os.path.join(base_dir, experiment, reading)
             origin, thickness = parse_params(data_dir)
             
@@ -116,4 +115,5 @@ def run(base_dir):
 
 if __name__ == '__main__':
     base_dir = 'data'
-    run(base_dir)
+    output_dir = 'output'
\ No newline at end of file
+    run(base_dir, output_dir)