solved soma_volume/convex_hull_volume issue

brick/processing/graph_feat_extraction.py

@@ -282,7 +282,7 @@ def ExtractFeaturesInDF(name_file, somas, size_voxel_in_micron: list, bins_lengt
 
         # Axes of the best fitting ellipsoid
         # a > b > c
-        _, _, soma.axes_ellipsoid, _, spherical_coor, _, volume_convex_hull = bf_.FindBestFittingEllipsoid3D(soma)
+        _, _, soma.axes_ellipsoid, _, spherical_coor,_, volume_convex_hull = bf_.FindBestFittingEllipsoid3D(soma)
 
         # This ratios give info about the shape of the soma. ex: rather flat, rather patatoide, rather spherical...
         Coef_axes_ellips_b__a = soma.axes_ellipsoid[0] / soma.axes_ellipsoid[2]
@@ -292,15 +292,15 @@ def ExtractFeaturesInDF(name_file, somas, size_voxel_in_micron: list, bins_lengt
         spherical_angles_eva = (spherical_coor[0][1], spherical_coor[0][2])
         spherical_angles_evb = (spherical_coor[1][1], spherical_coor[1][2])
 
-        # Volume of the soma
-        soma.volume_soma_micron = in_.ToMicron(len(soma.sites[0]), size_voxel_in_micron, dimension=(0, 1, 2), decimals=3)
-        # Calculates volume of soma's convex hull
-        volume_convex_hull = in_.ToMicron(volume_convex_hull, size_voxel_in_micron, dimension=(0, 1, 2))
+        # Volume of the  in micron**3
+        soma.volume_soma_micron = in_.ToMicron(len(soma.sites[0]), size_voxel_in_micron, dimension=(0, 1, 2), decimals=2)
+        # Calculates volume of soma's convex hull in voxel volume
+        # Take into account anisotropy of the 3D space ( volume = x * y * z with z > x=y)
+        volume_convex_hull = volume_convex_hull * size_voxel_in_micron[2] / size_voxel_in_micron[0]
 
         # Volume of the soma / Volume of its convex hull gives the info about the convexity of the soma
         # If close to 0, the soma has a lot of invaginations, if close to 1, it is smooth and convex
-        Coef_V_soma__V_convex_hull = soma.volume_soma_micron / volume_convex_hull
-        # TODO Solve issue V_soma > V_convexHull
+        Coef_V_soma__V_convex_hull = len(soma.sites[0]) / round(volume_convex_hull + 0.5)
 
         # -- Extension features
         # Graph features