added extensions lengths hist

nutrimorph.py

@@ -119,7 +119,7 @@ image = in_.ImageVerification(image, channel)
 # iv_.image_verification(image, channel)  # -> PySide2 user interface  # TODO: must return the modified image!
 # /!\ conflicts between some versions of PySide2 and Python3
 
-image = image[:, 800:, 800:]  # 512 # 562 # Just for development
+image = image[:, 512:, 512:]  # 512 # 562 # Just for development
 img_shape = image.shape
 
 #
@@ -454,6 +454,12 @@ for soma in somas:
             f"  Min/Mean/Median/Max Length = {min_length} / {mean_length} / {median_length} / {max_length}\n"
             f"  Standard Deviation = {std_length} / Entropy = {entropy_length}")
 
+        pl_.hist(ext_lengths)
+        pl_.title("Histogram of all the extensions lengths")
+        pl_.xlabel("Lengths")
+        pl_.ylabel('Number of extensions')
+        pl_.show(block=True)
+
         # PRIMARY extensions
         ext_lengths_P = soma.skl_graph.primary_edge_lengths(soma)
         total_ext_length_P = sum(ext_lengths_P)
@@ -471,8 +477,14 @@ for soma in somas:
                 f"  Min/Mean/Median/Max Length = {min_length_P} / {mean_length_P} / {median_length_P} / {max_length_P}\n"
                 f"  Standard Deviation = {std_length_P} / Entropy = {entropy_length_P}")
 
+            pl_.hist(ext_lengths_P)
+            pl_.title("Histogram of Primary extensions lengths")
+            pl_.xlabel("Lengths")
+            pl_.ylabel('Number of Primary extensions')
+            pl_.show(block=True)
+
         # SECONDARY extensions
-        ext_lengths_S = soma.skl_graph.secondary_edge_lengths(soma)  # TODO secondary fct doesnt work = takes all the ext
+        ext_lengths_S = soma.skl_graph.secondary_edge_lengths(soma)
         total_ext_length_S = sum(ext_lengths_S)
         # min, mean, median, max and standard deviation of the PRIMARY extensions
         if total_ext_length_S > 0:
@@ -488,7 +500,13 @@ for soma in somas:
                 f"  Min/Mean/Median/Max Length = {min_length_S} / {mean_length_S} / {median_length_S} / {max_length_S}\n"
                 f"  Standard Deviation = {std_length_S} / Entropy = {entropy_length_S}")
 
-    # TODO HISTOGRAMS, FRANGI:WIDTH OF EXTENSIONS, CURVATURE EXTENSIONS
+            pl_.hist(ext_lengths_S)
+            pl_.title("Histogram of Secondary extensions lengths")
+            pl_.xlabel("Lengths")
+            pl_.ylabel('Number of Secondary extensions')
+            pl_.show(block=True)
+
+    # TODO FRANGI:WIDTH OF EXTENSIONS, CURVATURE EXTENSIONS
 
     # TODO = Add all the info in a csv or pandas df