some refactoring + added sklgraph

nutrimorph.py

@@ -42,9 +42,12 @@ import brick.component.extension as xt_
 import brick.component.soma as sm_
 import brick.general.feedback as fb_
 import brick.processing.input as in_
+import brick.processing.plot as po_
 # import brick.processing.image_verification as iv_
 # from main_prm import *
-import brick.processing.SKLGraph as sk_
+from sklgraph.skl_fgraph import skl_graph_t
+from sklgraph.skl_graph import plot_mode_e
+from sklgraph.skl_map import skl_map_t
 
 import os as os_
 import sys as sy_
@@ -54,7 +57,7 @@ import time as tm_
 import matplotlib.pyplot as pl_
 import numpy as np_
 import skimage.io as io_
-from skimage.segmentation import relabel_sequential
+# from skimage.segmentation import relabel_sequential
 import skimage.morphology as mp_
 import skimage.measure as ms_
 import networkx as nx_
@@ -110,7 +113,7 @@ image = in_.ImageVerification(image, channel)
 # iv_.image_verification(image, channel)  # -> PySide2 interface  # TODO: must return the modified image!
 # /!\ conflicts between some versions of PySide2 and Python3
 
-image = image[:, 700:, 700:]  # 512 # 562 # Just for development
+image = image[:, 512:, 512:]  # 512 # 562 # Just for development
 img_shape = image.shape
 # pl_.matshow(image[image.shape[0] // 2, :, :])
 # pl_.show()
@@ -122,13 +125,14 @@ img_shape = image.shape
 print(f"IMAGE: s.{img_shape} t.{image.dtype} m.{image.min()} M.{image.max()}")
 
 # Intensity relative normalization (between 0 and 1).
-# TODO: change Frangi to take the normalization btw 0 and 1 into account
+# TODO: change Frangi to take the normalization btw 0 and 1 into account ?
 # image_for_soma = in_.IntensityNormalizedImage(image)
 # image_for_ext = in_.IntensityNormalizedImage(image)
-# image_for_soma = in_.NormalizedImage(image)
-# image_for_ext = in_.NormalizedImage(image)
-image_for_soma = image
-image_for_ext = image
+
+# This normalization is essential for the detection of extension and the connexions to the somas!
+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
@@ -305,4 +309,79 @@ print(f"DONE: {tm_.strftime('%a, %b %d %Y @ %H:%M:%S')}")
 if with_plot:
     pl_.show()
 
-# glial_graph_3d = sk_.skl_graph_t.FromSkeleton(soma_map)  # Travailler apd squelettes (soma pas sous fore de sk)
+# Skeletonize the somas to extract the graph of the glial cells
+space_dim = 3
+array_shape = (80, 80, 50)
+threshold_fct = lambda img: 0.75 * image.max()
+struct_elm_shape = (3, 3, 3)
+
+soma_w_ext_map = som_nfo['soma_w_ext_lmp']
+skeleton = skl_map_t.FromShapeMap(soma_w_ext_map, store_widths=True)
+skel_graph = skl_graph_t.FromSkeleton(skeleton)
+
+# --- Some info about the skeleton graph
+print(
+    f"Obj map area={np_.count_nonzero(soma_w_ext_map)}\n\n"
+    f"Validity={skel_graph.is_valid}\n\n"
+    f"N nodes={skel_graph.n_nodes}\n"
+    f"N edges={skel_graph.n_edges}\n"
+    f"Highest degree={skel_graph.highest_degree}/{skel_graph.highest_degree_w_nodes}\n\n"
+    f"Length={skel_graph.length}<-{skel_graph.edge_lengths}\n"
+    f"Width=Hom.{skel_graph.reduced_width()}/Het.{skel_graph.heterogeneous_reduced_width()}<-{skel_graph.edge_reduced_widths()}\n"
+    f"Area as WxL={skel_graph.reduced_width() * skel_graph.length}\n"
+    f"Area as WW Length={skel_graph.ww_length}<-{skel_graph.edge_ww_lengths}\n")
+
+# --- Checking correctness of skeleton graph via various rebuilt maps
+rebuilt_skel = skel_graph.RebuiltSkeletonMap()
+part_map_for_check = skeleton.PartMap()
+# Keep next line before its next one
+part_map_for_check[part_map_for_check == skeleton.invalid_n_neighbors] = 0
+part_map_for_check[part_map_for_check > 3] = 3
+
+print(
+    f"Rebuilt skeleton = Original one? Part map? "
+    f"{np_.array_equal(rebuilt_skel > 0, skeleton.map)} "
+    f"{np_.array_equal(rebuilt_skel, part_map_for_check)}")
+
+if space_dim == 3:
+    rebuilt_skel = rebuilt_skel.max(axis=2)
+
+# --- Checking correctness of skeleton graph via rebuilt object map
+soma_w_ext_map = soma_w_ext_map.astype(np_.uint8)
+rebuilt_map = skel_graph.RebuiltObjectMap()
+
+if space_dim == 3:
+    soma_w_ext_map = soma_w_ext_map.max(axis=2)
+    rebuilt_map = rebuilt_map.max(axis=2)
+
+# --- Show various images and plot the skeleton graph
+# ___, axes = pl_.subplots(1, 3, figsize=(15,15))
+# axes[0].matshow(soma_w_ext_map)
+# axes[1].matshow(rebuilt_map)
+# axes[2].matshow(soma_w_ext_map - rebuilt_map)
+# axes[0].set_title("Object")
+# axes[1].set_title("Rebuilt")
+# axes[2].set_title("Object - Rebuilt")
+# for axis in axes:
+#     axis.set_axis_off()
+# pl_.tight_layout(pad=0.3)
+
+# ___, axes = pl_.subplots(1, 3)
+# axes[0].matshow(rebuilt_skel + soma_w_ext_map)
+# axes[1].matshow(rebuilt_skel + rebuilt_map)
+# axes[2].matshow(rebuilt_skel)
+# axes[0].set_title("Rebuilt Skel Over Obj")
+# axes[1].set_title("Rebuilt Skel Over Rebuilt Obj")
+# axes[2].set_title("Rebuilt Skel")
+# for axis in axes:
+#     axis.set_axis_off()
+# pl_.tight_layout(pad=0.3)
+
+# if space_dim == 2:
+#     skel_graph.Plot(mode=plot_mode_e.Networkx, should_block=False)
+#     skel_graph.Plot(mode=plot_mode_e.Graphviz, should_block=False)
+
+skel_graph.Plot(mode=plot_mode_e.SKL_Curve, w_directions=True, should_block=False)
+skel_graph.Plot(should_block=False)
+
+pl_.show()
\ No newline at end of file

sklgraph/brick/edge.py

@@ -31,8 +31,8 @@
 
 from __future__ import annotations
 
-import brick.elm_id as id_
-from skl_map import LABELIZED_MAP_fct_FOR_DIM
+import sklgraph.brick.elm_id as id_
+from sklgraph.skl_map import LABELIZED_MAP_fct_FOR_DIM
 
 import itertools as it_
 from collections import namedtuple as namedtuple_t

sklgraph/brick/edge_update.py

@@ -29,9 +29,9 @@
 # The fact that you are presently reading this means that you have had
 # knowledge of the CeCILL license and that you accept its terms.
 
-import brick.edge as dg_
-import brick.node as nd_
-import skl_map as sm_
+import sklgraph.brick.edge as dg_
+import sklgraph.brick.node as nd_
+import sklgraph.skl_map as sm_
 
 from typing import List, Tuple
 

sklgraph/brick/node.py

@@ -31,9 +31,9 @@
 
 from __future__ import annotations
 
-import brick.elm_id as id_
-import skl_map as sm_
-from skl_map import LABELIZED_MAP_fct_FOR_DIM
+import sklgraph.brick.elm_id as id_
+import sklgraph.skl_map as sm_
+from sklgraph.skl_map import LABELIZED_MAP_fct_FOR_DIM
 
 from typing import Callable, Dict, Iterable, List, Tuple
 

sklgraph/test/test-2-and-3-D.py

@@ -33,9 +33,9 @@ import matplotlib as mpl_
 
 mpl_.use('TkAgg')
 
-from brick.processing.sklgraph.skl_fgraph import skl_graph_t
-from brick.processing.sklgraph.skl_graph import plot_mode_e
-from brick.processing.sklgraph.skl_map import skl_map_t
+from sklgraph.skl_fgraph import skl_graph_t
+from sklgraph.skl_graph import plot_mode_e
+from sklgraph.skl_map import skl_map_t
 
 import pathlib as ph_
 import sys as sy_