tests frangi time and memory usage + frangi prms

brick/processing/frangi3.py

@@ -38,6 +38,8 @@ import multiprocessing as pl_
 import os.path as ph_  # Pathlib not necessary
 import warnings as wn_
 from os import name as os_name_c
+import os as os_
+import psutil as mu_
 from typing import Callable, Optional, Tuple
 
 # import itk as ik_

nutrimorph.py

@@ -53,6 +53,7 @@ import brick.processing.graph_extraction as ge_
 import os as os_
 import sys as sy_
 import time as tm_
+import psutil as mu_
 
 import matplotlib.pyplot as pl_
 import numpy as np_
@@ -118,7 +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
 
 #
@@ -186,6 +187,7 @@ beta = in_.ToPixel(beta, size_voxel_in_micron, decimals=1)
 frangi_c = in_.ToPixel(frangi_c, size_voxel_in_micron)
 
 # Perform frangi feature enhancement (via python or c - faster - implementation)
+
 enhanced_ext, ext_scales = extension_t.EnhancedForDetection(
     image_for_ext,
     scale_range,
@@ -198,7 +200,7 @@ enhanced_ext, ext_scales = extension_t.EnhancedForDetection(
     in_parallel=in_parallel)
 
 elapsed_time = tm_.gmtime(tm_.time() - start_time)
-print(f"\nElapsed Time={tm_.strftime('%Hh %Mm %Ss', elapsed_time)}")
+print(f"Elapsed Time={tm_.strftime('%Hh %Mm %Ss', elapsed_time)}\n")
 
 # Creation of the enhanced maps
 ext_nfo["coarse_map"] = extension_t.CoarseMap(enhanced_ext, ext_low_c, ext_high_c, ext_selem_pixel_c)

parameters.ini

@@ -80,9 +80,8 @@ max_straight_sq_dist_c     :    0.24050024 * (30 ** 2)
 max_weighted_length_c      :    0.24050024 * 20.0
 
 [Frangi]
-scale_range                :    0.024,1,466
-#0.745
-# 0.1,3.1
+scale_range                :    0.024,1.466
+# 0.1,6.1 for the entire image. stop at 3.1 for smaller images
 ; write min,max scale range
 scale_step                 :    0.24
 #  1.0
@@ -90,10 +89,7 @@ alpha                      :    0.19
 # 0.8
 beta                       :    0.12
 # 0.5
-frangi_c                   :    0.5
-; For an image ranging from 0 to 65280 : frangi_c btw 0 and 1.
-; For an image from 200 to 65280 : frangi_c btw 1 and 10
-; highly depends on the size of the extensions in the image and on their intensity
+frangi_c                   :    3
 # 60.12506 # 500.0
 bright_on_dark             :    True
 method                     :    c