curvature and torsion coorection + lengths of edges in micron

brick/processing/best_fit_ellipsoid.py

@@ -98,7 +98,6 @@ def polyToParams3D(ellipsoid_coef: array_t, spherical_coordinates: bool = False,
     R3S = R3 / s1
 
     (el, ec) = eig(R3S)
-    print(el, ec)
 
     # Sorting in croissant order of the eigenvalues and eigenvectors
     sorting_vec = np_.argsort(el)

brick/processing/graph_feat_extraction.py

@@ -353,7 +353,6 @@ def ExtractFeaturesInDF(somas, size_voxel_in_micron: list, number_of_bins: int,
             #
             # Curvature and Torsion
             curvatures, torsions = soma.skl_graph.curvature_and_torsion(size_voxel=size_voxel_in_micron)
-            print(curvatures, "\n", torsions)
             #
             min_curvature = min(curvatures)
             max_curvature = max(curvatures)

nutrimorph.py

@@ -405,12 +405,9 @@ print('\n--- Features Extraction\n')
 # Prms
 number_of_bins = int(number_of_bins)
 max_range = hist_step * number_of_bins - hist_min_length
-# DF creation  # TODO Delete ext_lengths from df
+# DF creation
 features_df = ge_.ExtractFeaturesInDF(somas, size_voxel_in_micron, number_of_bins, max_range, hist_min_length, ext_scales)
-features_df.to_csv("D:\\MorganeNadal\\M2 report\\feat_512_3.csv")
-
-    # TODO FRANGI: CURVATURE & TORSION EXTENSIONS
-
+features_df.to_csv("D:\\MorganeNadal\\M2 report\\feat_512_4.csv")
 
 #
 elapsed_time = tm_.gmtime(tm_.time() - start_time)

sklgraph/brick/edge.py

@@ -102,9 +102,9 @@ class edge_t:
 
         sites_as_array = np_.array(self.sites)
         segments = np_.diff(sites_as_array, axis=1)
-        # segmentsT = segments.transpose()
-        # sq_lengths = (segmentsT.dot(np_.diag(size_voxel)).dot(segments)).sum(axis=0)
-        sq_lengths = (segments ** 2).sum(axis=0)
+        segmentsT = segments.transpose()
+        sq_lengths = ((segmentsT.dot(np_.diag(size_voxel)).dot(segments))**2).sum(axis=0)
+        # sq_lengths = (segments ** 2).sum(axis=0)
         lengths = np_.sqrt(sq_lengths)
         length = lengths.sum().item()
 
@@ -187,7 +187,7 @@ class edge_t:
                 c = derivates["x2"][idx][1] * derivates["x1"][idx][0] - derivates["x1"][idx][1] * derivates["x2"][idx][0]
                 d = (derivates["x1"][idx][0]**2 + derivates["x2"][idx][0]**2 + derivates["x3"][idx][0]**2)**(3/2)
                 if d != 0:
-                    k = (np_.sqrt(a**2 + b**2 + c**2)) / d
+                    k = np_.abs((np_.sqrt(a**2 + b**2 + c**2)) / d)
                 else:
                     k = 0
 
@@ -200,7 +200,6 @@ class edge_t:
 
                 curvatures.append(k)
                 torsions.append(t)
-        # print(curvatures, "\n", torsions)
 
         return curvatures, torsions