From 3ff4cecf86e9a24db75619491da27c16950805e8 Mon Sep 17 00:00:00 2001
From: monadal <morgane.nadal@inria.fr>
Date: Mon, 9 Mar 2020 17:41:56 +0100
Subject: [PATCH] changed label into relabel + max - modified Filtered Maps
---
brick/__init__.py | 0
brick/component/extension.py | 3 ++-
brick/component/soma.py | 3 ++-
nutrimorph.py | 28 +++++++++++++---------------
4 files changed, 17 insertions(+), 17 deletions(-)
delete mode 100644 brick/__init__.py
diff --git a/brick/__init__.py b/brick/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/brick/component/extension.py b/brick/component/extension.py
index 4b88e1d..dc6c556 100644
--- a/brick/component/extension.py
+++ b/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:
diff --git a/brick/component/soma.py b/brick/component/soma.py
index c081bce..43fd4ec 100644
--- a/brick/component/soma.py
+++ b/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:
diff --git a/nutrimorph.py b/nutrimorph.py
index d47cfbf..3df86f9 100644
--- a/nutrimorph.py
+++ b/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:
--
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