changed label into relabel + max - modified Filtered Maps

brick/component/extension.py

@@ -191,8 +191,9 @@ class extension_t(glial_cmp_t):
             if region.area <= min_area_c:
                 region_sites = (lmp == region.label).nonzero()
                 result[region_sites] = 0
+                lmp[region_sites] = 0
 
-        return result
+        return result, lmp
 
     @staticmethod
     def FineMapFromCoarseMap(coarse_map: array_t) -> array_t:

brick/component/soma.py

@@ -169,8 +169,9 @@ class soma_t(glial_cmp_t):
             if region.area <= min_area:
                 region_sites = (lmp == region.label).nonzero()
                 result[region_sites] = 0
+                lmp[region_sites] = 0
 
-        return result
+        return result, lmp
 
     @staticmethod
     def ContourMap(map_: array_t) -> array_t:

nutrimorph.py

@@ -53,6 +53,7 @@ import matplotlib.pyplot as pl_
 import numpy as np_
 import skimage.io as io_
 import skimage.measure as ms_
+from skimage.segmentation import relabel_sequential
 
 print(sy_.argv, sy_.argv.__len__())
 
@@ -81,7 +82,6 @@ exec(open(sy_.argv[1]).read())
 soma_t = sm_.soma_t
 extension_t = xt_.extension_t
 
-
 print(f"STARTED: {tm_.strftime('%a, %b %d %Y @ %H:%M:%S')}")
 start_time = tm_.time()
 
@@ -93,12 +93,12 @@ image = io_.imread(data_path)
 
 # Image size verification - simple version without user interface
 image = in_.ImageVerification(image, channel)
-# TODO make a user friendly interface (PySide2) BUT bug with the importation of Shiboken2 on Windows8.1
+# TODO make a user friendly interface (PySide2) BUT bug with the importation of Shiboken2 on Windows8.1.
 
 image = image[:, 512:, 512:]  # 562
 img_shape = image.shape
-pl_.matshow(image[image.shape[0] // 2,:,:])
-pl_.show()
+# pl_.matshow(image[image.shape[0] // 2, :, :])
+# pl_.show()
 #
 # max_img = image.max()
 # image.fill(image.min())
@@ -110,7 +110,6 @@ image_for_soma = in_.NormalizedImage(image)
 image_for_ext = in_.NormalizedImage(image)
 print(f"NRM-IMG: t.{image_for_soma.dtype} m.{image_for_soma.min():.2f} M.{image_for_soma.max():.2f}")
 
-
 # --- Initialization
 som_nfo = {}
 ext_nfo = {}
@@ -126,9 +125,11 @@ axes = {}
 print("\n--- Soma Detection")
 
 som_nfo["map"] = soma_t.Map(image_for_soma, soma_low_c, soma_high_c, soma_selem_c)
-som_nfo["map"] = soma_t.FilteredMap(som_nfo["map"], min_area_c)
-#TODO: change label into relabel + max
-som_nfo["lmp"], n_somas = ms_.label(som_nfo["map"], return_num=True)
+som_nfo["map"], som_lmp = soma_t.FilteredMap(som_nfo["map"], min_area_c)
+# som_nfo["lmp"], n_somas= ms_.label(som_nfo["map"], return_num=True)
+som_nfo["lmp"] = relabel_sequential(som_lmp)[0]  # Use relabel instead of label to optimize the algorithm.
+n_somas = som_nfo["lmp"].max()
+
 som_nfo["dist_to_closest"], som_nfo["influence_map"] = soma_t.InfluenceMaps(
     som_nfo["lmp"]
 )
@@ -143,16 +144,17 @@ print(f"\nElapsed Time={tm_.strftime('%Hh %Mm %Ss', elapsed_time)}")
 if with_plot:
     fb_.PlotSomas(somas, som_nfo, axes)
 
-
 # -- Extentions
 print("\n--- Extension Detection")
 
 enhanced_ext, ext_scales = extension_t.EnhancedForDetection(image_for_ext, in_parallel=in_parallel)
 ext_nfo["coarse_map"] = extension_t.CoarseMap(enhanced_ext, ext_low_c, ext_high_c)
-ext_nfo["coarse_map"] = extension_t.FilteredCoarseMap(ext_nfo["coarse_map"])
+ext_nfo["coarse_map"], ext_lmp = extension_t.FilteredCoarseMap(ext_nfo["coarse_map"])
 ext_nfo["map"] = extension_t.FineMapFromCoarseMap(ext_nfo["coarse_map"])
 ext_nfo["map"][som_nfo["map"] > 0] = 0
-ext_nfo["lmp"], n_extensions = ms_.label(ext_nfo["map"], return_num=True)
+# ext_nfo["lmp"], n_extensions = ms_.label(ext_nfo["map"], return_num=True)
+ext_nfo["lmp"] = relabel_sequential(ext_lmp)[0]  # Use relabel instead of label to optimize the algorithm.
+n_extensions = ext_nfo["lmp"].max()
 
 extensions = tuple(
     extension_t().FromMap(ext_nfo["lmp"], ext_scales, uid)
@@ -165,11 +167,9 @@ print(f"\nElapsed Time={tm_.strftime('%Hh %Mm %Ss', elapsed_time)}")
 if with_plot:
     fb_.PlotExtensions(extensions, ext_nfo, img_shape)
 
-
 # -- Preparation for Connections
 dijkstra_costs = in_.DijkstraCosts(image, som_nfo["map"], ext_nfo["map"])
 
-
 # -- Soma-Extention
 print("\n--- Soma <-> Extension")
 
@@ -205,7 +205,6 @@ print(f"\nElapsed Time={tm_.strftime('%Hh %Mm %Ss', elapsed_time)}")
 if with_plot:
     fb_.PlotSomasWithExtensions(somas, som_nfo, "all")
 
-
 # -- Extention-Extention
 print("\n--- Extension <-> Extension")
 
@@ -248,7 +247,6 @@ print(f"\nElapsed Time={tm_.strftime('%Hh %Mm %Ss', elapsed_time)}")
 if with_plot:
     fb_.PlotSomasWithExtensions(somas, som_nfo, "with_ext_of_ext")
 
-
 # -- Summary
 print("\n")
 for soma in somas: