From 1ab352218c9c98eab0af95675bbf982a6f1013f7 Mon Sep 17 00:00:00 2001
From: DEBREUVE Eric <eric.debreuve@inria.fr>
Date: Thu, 19 Sep 2019 16:00:17 +0200
Subject: [PATCH] reorg+somas to img w or wo ext
---
connection.py | 2 +
extension.py | 5 ++
main.py | 186 +++++++++++++++++++++-----------------------------
main_prm.py | 17 +++++
soma.py | 19 +++---
5 files changed, 113 insertions(+), 116 deletions(-)
create mode 100644 main_prm.py
diff --git a/connection.py b/connection.py
index 0f8794c..ee0d89b 100644
--- a/connection.py
+++ b/connection.py
@@ -18,6 +18,8 @@ def CandidateConnections(
) -> list:
#
candidate_conn_nfo = [] # conn=connection
+
+ extensions = filter(lambda ext: ext.is_unconnected, extensions)
for soma, extension in it_.product(somas, extensions):
new_candidates = extension.EndPointsForSoma(soma.uid, influence_map)
candidate_conn_nfo.extend(
diff --git a/extension.py b/extension.py
index 8633e4b..66db159 100644
--- a/extension.py
+++ b/extension.py
@@ -51,6 +51,11 @@ class extension_t(glial_cmp_t):
return instance
+ @property
+ def is_unconnected(self) -> bool:
+ #
+ return self.soma_uid is None
+
@property
def end_points_as_array(self) -> array_t:
#
diff --git a/main.py b/main.py
index b289d5d..435f5ac 100644
--- a/main.py
+++ b/main.py
@@ -1,6 +1,7 @@
import connection as cn_
import extension as xt_
import feedback as fb_
+from main_prm import *
import soma as sm_
import time as tm_
@@ -10,33 +11,14 @@ import numpy as np_
import skimage.color as cl_
import skimage.io as io_
import skimage.measure as ms_
-import skimage.morphology as mp_
-
-
-print(f"STARTED: {tm_.strftime('%a, %b %d %Y @ %H:%M:%S')}")
-start_time = tm_.time()
soma_t = sm_.soma_t
extension_t = xt_.extension_t
-# --- Parameters
-data_path = "./DIO_6H_6_1.70bis_2.2_3.tif"
-run = ("soma", "extension", "som-ext", "ext-ext")
-with_plot = False
-
-soma_low_c = 0.15
-soma_high_c = 0.7126
-ext_low_c = 0.2 # 0.02 # 0.2 # ext_low_c = 9.0e-4
-ext_high_c = 0.6 # 0.04 # 0.6 # high_ext = 8.0e-3
-
-soma_selem_c = mp_.disk(2)
-
-max_straight_sq_dist_c = 30 ** 2
-max_weighted_length_c = 20.0
-
-min_area_c = 1000
+print(f"STARTED: {tm_.strftime('%a, %b %d %Y @ %H:%M:%S')}")
+start_time = tm_.time()
# --- Images
@@ -50,79 +32,73 @@ costs = 1.0 / (image + 1.0)
# --- Initialization
-n_somas = 0
som_nfo = {} # som=soma, nfo=info
-somas = None # Tuple of soma objects
-
-n_extensions = 0
ext_nfo = {} # ext=extension, nfo=info
-extensions = None # Tuple of extension objects
-
axes = {}
+# n_somas = 0
+# n_extensions = 0
+# somas = None # Tuple of soma objects
+# extensions = None # Tuple of extension objects
+
# --- Somas
-if "soma" in run:
- print("\n--- Soma Detection")
+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)
- som_nfo["lmp"], n_somas = ms_.label(som_nfo["map"], return_num=True)
- som_nfo["dist_to_closest"], som_nfo["influence_map"] = soma_t.InfluenceMaps(
- som_nfo["lmp"]
- )
+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)
+som_nfo["lmp"], n_somas = ms_.label(som_nfo["map"], return_num=True)
+som_nfo["dist_to_closest"], som_nfo["influence_map"] = soma_t.InfluenceMaps(
+ som_nfo["lmp"]
+)
- somas = tuple(
- soma_t().FromMap(som_nfo["lmp"], uid) for uid in range(1, n_somas + 1)
- )
+somas = tuple(
+ soma_t().FromMap(som_nfo["lmp"], uid) for uid in range(1, n_somas + 1)
+)
- print(f" n = {n_somas}")
- if with_plot:
- fb_.PlotSomas(somas, som_nfo, axes)
+print(f" n = {n_somas}")
+if with_plot:
+ fb_.PlotSomas(somas, som_nfo, axes)
# -- Extentions
-if "extension" in run:
- print("\n--- Extension Detection")
-
- enhanced_ext, ext_scales = extension_t.EnhancedForDetection(image_for_ext)
- 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["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)
-
- extensions = tuple(
- extension_t().FromMap(ext_nfo["lmp"], ext_scales, uid)
- for uid in range(1, n_extensions + 1)
- )
+print("\n--- Extension Detection")
- print(f" n = {n_extensions}")
- if with_plot:
- fb_.PlotExtensions(extensions, ext_nfo, img_shape)
+enhanced_ext, ext_scales = extension_t.EnhancedForDetection(image_for_ext)
+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["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)
+extensions = tuple(
+ extension_t().FromMap(ext_nfo["lmp"], ext_scales, uid)
+ for uid in range(1, n_extensions + 1)
+)
-# -- Soma-Extention
-if "som-ext" in run:
- print("\n--- Soma <-> Extension")
-
- # TODO: Ideally, the extension part should be dilated
- # but in ext-ext connections, there must not be dilation around the current ext
- # (current ext plays the role of a soma in soma-ext step)
- costs[np_.logical_or(som_nfo["map"] > 0, ext_nfo["map"] > 0)] = np_.inf
-
- candidate_conn_nfo = cn_.CandidateConnections(
- somas,
- som_nfo["influence_map"],
- som_nfo["dist_to_closest"],
- extensions,
- max_straight_sq_dist_c,
- )
+print(f" n = {n_extensions}")
+if with_plot:
+ fb_.PlotExtensions(extensions, ext_nfo, img_shape)
- for ep_idx, soma, extension, end_point in candidate_conn_nfo:
- if extension.soma_uid is not None:
- continue
+# -- Soma-Extention
+print("\n--- Soma <-> Extension")
+
+# TODO: Ideally, the extension part should be dilated
+# but in ext-ext connections, there must not be dilation around the current ext
+# (current ext plays the role of a soma in soma-ext step)
+costs[np_.logical_or(som_nfo["map"] > 0, ext_nfo["map"] > 0)] = np_.inf
+
+candidate_conn_nfo = cn_.CandidateConnections(
+ somas,
+ som_nfo["influence_map"],
+ som_nfo["dist_to_closest"],
+ extensions,
+ max_straight_sq_dist_c,
+)
+
+for ep_idx, soma, extension, end_point in candidate_conn_nfo:
+ if extension.is_unconnected:
print(f" Soma.{soma.uid} <-?-> Ext.{extension.uid}({ep_idx})", end="")
path, length = cn_.ShortestPathTo(
end_point,
@@ -136,41 +112,35 @@ if "som-ext" in run:
else:
print("")
- # for soma in somas:
- # soma.Extend(extensions, som_nfo["dist_to_closest"], costs)
+# for soma in somas:
+# soma.Extend(extensions, som_nfo["dist_to_closest"], costs)
- fb_.PrintConnectedExtensions(extensions)
- if with_plot:
- fb_.PlotSomasWithExtensions(somas, som_nfo, "all")
+fb_.PrintConnectedExtensions(extensions)
+if with_plot:
+ fb_.PlotSomasWithExtensions(somas, som_nfo, "all")
# -- Extention-Extention
-if "ext-ext" in run:
- print("\n--- Extension <-> Extension")
-
- should_look_for_connections = True
- while should_look_for_connections:
- som_nfo["soma_w_ext_lmp"] = soma_t.SomasWithExtensionsLMap(somas)
- som_nfo["dist_to_closest"], som_nfo["influence_map"] = soma_t.InfluenceMaps(
- som_nfo["soma_w_ext_lmp"]
- )
- unconnected_extensions = list(
- filter(lambda ext: ext.soma_uid is None, extensions)
- )
+print("\n--- Extension <-> Extension")
- candidate_conn_nfo = cn_.CandidateConnections(
- somas,
- som_nfo["influence_map"],
- som_nfo["dist_to_closest"],
- unconnected_extensions,
- max_straight_sq_dist_c,
- )
+should_look_for_connections = True
+while should_look_for_connections:
+ som_nfo["soma_w_ext_lmp"] = soma_t.SomasWithExtensionsLMap(somas)
+ som_nfo["dist_to_closest"], som_nfo["influence_map"] = soma_t.InfluenceMaps(
+ som_nfo["soma_w_ext_lmp"]
+ )
- should_look_for_connections = False
- for ep_idx, soma, extension, end_point in candidate_conn_nfo:
- if extension.soma_uid is not None:
- continue
+ candidate_conn_nfo = cn_.CandidateConnections(
+ somas,
+ som_nfo["influence_map"],
+ som_nfo["dist_to_closest"],
+ extensions,
+ max_straight_sq_dist_c,
+ )
+ should_look_for_connections = False
+ for ep_idx, soma, extension, end_point in candidate_conn_nfo:
+ if extension.is_unconnected:
print(f" Soma.{soma.uid} <-?-> Ext.{extension.uid}({ep_idx})", end="")
path, length = cn_.ShortestPathTo(
end_point,
@@ -186,9 +156,9 @@ if "ext-ext" in run:
else:
print("")
- fb_.PrintConnectedExtensions(extensions)
- if with_plot:
- fb_.PlotSomasWithExtensions(somas, som_nfo, "with_ext_of_ext")
+fb_.PrintConnectedExtensions(extensions)
+if with_plot:
+ fb_.PlotSomasWithExtensions(somas, som_nfo, "with_ext_of_ext")
# -- Summary
diff --git a/main_prm.py b/main_prm.py
new file mode 100644
index 0000000..80c03a0
--- /dev/null
+++ b/main_prm.py
@@ -0,0 +1,17 @@
+import skimage.morphology as mp_
+
+
+data_path = "./DIO_6H_6_1.70bis_2.2_3.tif"
+with_plot = False
+
+soma_low_c = 0.15
+soma_high_c = 0.7126
+ext_low_c = 0.2 # 0.02 # 0.2 # ext_low_c = 9.0e-4
+ext_high_c = 0.6 # 0.04 # 0.6 # high_ext = 8.0e-3
+
+soma_selem_c = mp_.disk(2)
+
+max_straight_sq_dist_c = 30 ** 2
+max_weighted_length_c = 20.0
+
+min_area_c = 1000
diff --git a/soma.py b/soma.py
index af24ece..7b81978 100644
--- a/soma.py
+++ b/soma.py
@@ -158,6 +158,7 @@ class soma_t(glial_cmp_t):
return (
f"Soma.{self.uid}, "
+ f"area={self.sites[0].__len__()}, "
f"contour points={self.contour_points.__len__()}, "
f"extensions={n_extensions}"
)
@@ -227,7 +228,7 @@ class soma_t(glial_cmp_t):
return dist_map, np_.array(map_[tuple(idx_map)])
@staticmethod
- def SomasWithExtensionsLMap(somas: Sequence[soma_t]) -> array_t:
+ def SomasLMap(somas: Sequence[soma_t], with_extensions: bool = True) -> array_t:
#
shape = somas[0].img_shape
result = np_.zeros(shape, dtype=np_.int64)
@@ -235,16 +236,18 @@ class soma_t(glial_cmp_t):
for soma in somas:
result[soma.sites] = soma.uid
- for connection_path in filter(
- lambda path: path is not None, soma.connection_path.values()
- ):
- result[connection_path] = soma.uid
- for extension in soma.Extensions():
+ if with_extensions:
for connection_path in filter(
- lambda path: path is not None, extension.connection_path.values()
+ lambda path: path is not None, soma.connection_path.values()
):
result[connection_path] = soma.uid
- result[extension.sites] = soma.uid
+ for extension in soma.Extensions():
+ for connection_path in filter(
+ lambda path: path is not None,
+ extension.connection_path.values(),
+ ):
+ result[connection_path] = soma.uid
+ result[extension.sites] = soma.uid
return result
--
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