possibility to choose the boundaries for the histograms

nutrimorph.py

@@ -98,9 +98,11 @@ method = None
 hist_min_length = None
 hist_step_length = None
 number_of_bins_length = None
+hist_bins_borders_length = None
 hist_min_curvature = None
 hist_step_curvature = None
 number_of_bins_curvature = None
+hist_bins_borders_curvature = None
 with_plot = None
 in_parallel = None
 
@@ -126,7 +128,7 @@ 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[:, 512:, 512:]  # 512 # 562 # Just for development
+# image = image[:, 800:, 800:]  # 512 # 562 # Just for development
 img_shape = image.shape
 
 #
@@ -405,12 +407,21 @@ elapsed_time = tm_.gmtime(tm_.time() - start_time)
 # Extract features
 print('\n--- Features Extraction\n')
 # Prms
-number_of_bins_length = int(number_of_bins_length)
-bins_length = np_.linspace(hist_min_length, hist_min_length + hist_step_length * number_of_bins_length, num=number_of_bins_length)
-bins_length[-1] = np_.inf
-number_of_bins_curvature = int(number_of_bins_curvature)
-bins_curvature = np_.linspace(hist_min_curvature, hist_min_curvature + hist_step_curvature * number_of_bins_curvature, num=number_of_bins_curvature)
-bins_curvature[-1] = np_.inf
+if hist_bins_borders_length is None:
+    number_of_bins_length = int(number_of_bins_length)
+    bins_length = np_.linspace(hist_min_length, hist_min_length + hist_step_length * number_of_bins_length, num=number_of_bins_length)
+    bins_length[-1] = np_.inf
+else:
+    bins_length = np_.array(hist_bins_borders_length)
+    bins_length[-1] = np_.inf
+
+if hist_bins_borders_curvature is None:
+    number_of_bins_curvature = int(number_of_bins_curvature)
+    bins_curvature = np_.linspace(hist_min_curvature, hist_min_curvature + hist_step_curvature * number_of_bins_curvature, num=number_of_bins_curvature)
+    bins_curvature[-1] = np_.inf
+else:
+    bins_curvature = np_.array(hist_bins_borders_curvature)
+    bins_curvature[-1] = np_.inf
 
 # DF creation
 features_df = ge_.ExtractFeaturesInDF(somas, size_voxel_in_micron, bins_length, bins_curvature, ext_scales)

parameters.ini

@@ -96,19 +96,31 @@ method                     :    c
 
 [Features Extraction]
 ; histograms of extensions lengths
-hist_min_length            :    0
+hist_min_length
+#:    0
 ; in micron
 ; by default, 0
-hist_step_length           :    6
+hist_step_length
+#:    6
 ; in micron
-number_of_bins_length      :    5
+number_of_bins_length
+#:    5
 ; by default, 5
 ; extensions generally do not exceed 30 microns
 
+; if the above parameters are set to None, you can directly use the boundaries of your choice for the histogram:
+hist_bins_borders_length   :    (0, 0.5, 1, 5, 10, 50)
+
 ; histograms of extensions curvatures
-hist_min_curvature         :    0
-hist_step_curvature        :    6
-number_of_bins_curvature   :    5
+hist_min_curvature
+#:    0
+hist_step_curvature
+#:    6
+number_of_bins_curvature
+#:    5
+
+; if the above parameters are set to None, you can directly use the boundaries of your choice for the histogram:
+hist_bins_borders_curvature :    (0, 0.05, 0.3, 1, 10, 50)
 
 
 [Program Running]

search_parameters.py

@@ -83,9 +83,11 @@ method = parameters['Frangi']['method']
 hist_min_length = IfNotFloat('Features Extraction', 'hist_min_length')
 hist_step_length = IfNotFloat('Features Extraction', 'hist_step_length')
 number_of_bins_length = IfNotFloat('Features Extraction', 'number_of_bins_length')
+hist_bins_borders_length = IfNotFloat('Features Extraction', 'hist_bins_borders_length')
 hist_min_curvature = IfNotFloat('Features Extraction', 'hist_min_curvature')
 hist_step_curvature = IfNotFloat('Features Extraction', 'hist_step_curvature')
 number_of_bins_curvature = IfNotFloat('Features Extraction', 'number_of_bins_curvature')
+hist_bins_borders_curvature = IfNotFloat('Features Extraction', 'hist_bins_borders_curvature')
 
 # [Program running]
 with_plot = parameters.getboolean('Program Running', 'with_plot')