added basic soma validation interface

brick/interface/soma_validation.py

+import tkinter as tk
+
+import numpy as np
+from PIL import Image, ImageTk
+
+
+array_t = np.ndarray
+
+
+class soma_validation_window_t:
+    def __init__(self, lmap: array_t, mip_axis: int = -1):
+        """"""
+        self.lmap = lmap
+        self.mip = np.max(lmap, axis=mip_axis)
+        mip_shape = self.mip.shape
+
+        offset = 50
+        scaling = (255.0 - offset) / np.max(self.mip)
+        self.scaled_mip = scaling * self.mip + offset
+        self.scaled_mip[self.mip == 0] = 0
+
+        self.root = tk.Tk()
+        self.canvas = tk.Canvas(
+            self.root, width=mip_shape[1], height=mip_shape[0]
+        )
+        self.tk_image = ImageTk.PhotoImage(
+            master=self.root, image=Image.fromarray(self.scaled_mip)
+        )
+        self.canvas_image = self.canvas.create_image(
+            0, 0, anchor="nw", image=self.tk_image
+        )
+
+        self.canvas.bind("<Button-1>", self._DeleteSoma)
+
+        self.canvas.pack()
+
+    def LaunchInteraction(self) -> None:
+        """"""
+        self.root.mainloop()
+        # scikit-image.relabel(self.lmap)
+
+    def _DeleteSoma(self, event) -> None:
+        """"""
+        row = event.y
+        col = event.x
+        value = self.mip[row, col]
+
+        if value > 0:
+            self.lmap[self.lmap == value] = 0
+
+            soma_bmap = self.mip == value
+            self.mip[soma_bmap] = 0
+            self.scaled_mip[soma_bmap] = 0
+            self.tk_image = ImageTk.PhotoImage(
+                master=self.root, image=Image.fromarray(self.scaled_mip)
+            )
+            self.canvas.itemconfig(self.canvas_image, image=self.tk_image)

nutrimorph.py

@@ -65,6 +65,7 @@ import skimage.measure as ms_
 import skimage.exposure as ex_
 import pandas as pd_
 import networkx as nx_
+import brick.interface.soma_validation as smvl
 
 print(sy_.argv, sy_.argv.__len__())
 
@@ -113,6 +114,7 @@ hist_step_curvature = None
 number_of_bins_curvature = None
 hist_bins_borders_curvature = None
 with_plot = None
+interactive = None
 in_parallel = None
 
 exec(open(sy_.argv[1]).read())  # Only with search_parameters.py (stable version)
@@ -272,6 +274,10 @@ def NutriMorph(data_path: str,
 
     if with_plot:
         fb_.PlotSomas(somas, som_nfo, axes)
+    elif interactive:
+        # smvl.SomaValidation(som_nfo["lmp"], mip_axis=0)
+        window = smvl.soma_validation_window_t(som_nfo["lmp"], mip_axis=0)
+        window.LaunchInteraction()
 
     #
     # -- Extentions

parameters.ini

@@ -49,7 +49,10 @@ parameter3                  :   None
 ; then your parameter has the value string: 'None', and not None
 
 [Input]
-data_path                   :   /home/eric/Pictures/carole-rovere/CHO_1H_D_1.70_3.3_8.tif
+data_path                   :   ./data/DIO_6H_6_1.70bis_2.2_3.tif
+#/home/eric/Pictures/carole-rovere/clara-test/TO5_2_12W_pos1.tif
+#/home/eric/Pictures/carole-rovere/clara-test/ST8_1.tif
+#/home/eric/Pictures/carole-rovere/CHO_1H_D_1.70_3.3_8.tif
 #.\\data\\DIO_6H_6_1.70bis_2.2_3.tif
 ; direct data path to the image
 channel                     :   G
@@ -138,4 +141,5 @@ hist_bins_borders_curvature :    (0, 0.05, 0.3, 1, 10, 50)
 
 [Program Running]
 with_plot                  :    False
+interactive                :    True
 in_parallel                :    False

search_parameters.py

-# Copyright CNRS/Inria/UNS
-# Contributor(s): Eric Debreuve (since 2019), Morgane Nadal (2020)
-#
-# eric.debreuve@cnrs.fr
-#
-# This software is governed by the CeCILL  license under French law and
-# abiding by the rules of distribution of free software.  You can  use,
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info".
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability.
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or
-# data to be ensured and,  more generally, to use and operate it in the
-# same conditions as regards security.
-#
-# 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 configparser
-from typing import Union, Any
-
-# --Parameters from .INI file
-parameters = configparser.ConfigParser(allow_no_value=True)
-parameters.read('parameters.ini')
-
-
-def IfNotFloat(section: str, key: str) -> Union[Union[float, str], Any]:
-    if parameters.get(section, key) is not None:
-        try:
-            value = parameters.getfloat(section, key)
-            return value
-        except:
-            return eval(parameters.get(section, key))
-    else:
-        return parameters.get(section, key)
-
-
-# [Input]
-data_path = parameters['Input']['data_path']
-channel = parameters['Input']['channel']
-size_voxel_in_micron = IfNotFloat('Input', 'size_voxel_in_micron')
-dilatation_erosion = parameters.getboolean('Input', 'dilatation_erosion')
-save_images = parameters['Input']['save_images']
-save_csv = parameters['Input']['save_csv']
-save_features_analysis = parameters['Input']['save_features_analysis']
-statistical_analysis = parameters.getboolean('Input', 'statistical_analysis')
-
-# [Somas]
-soma_low_c = IfNotFloat('Somas', 'soma_low_c')
-soma_high_c = IfNotFloat('Somas', 'soma_high_c')
-soma_selem_micron_c = IfNotFloat('Somas', 'soma_selem_micron_c')
-soma_min_area_c = IfNotFloat('Somas', 'soma_min_area_c')
-soma_max_area_c = IfNotFloat('Somas', 'soma_max_area_c')
-
-# [Extensions]
-adapt_hist_equalization = parameters.getboolean('Extensions', 'adapt_hist_equalization')
-ext_low_c = IfNotFloat('Extensions', 'ext_low_c')
-ext_high_c = IfNotFloat('Extensions', 'ext_high_c')
-ext_selem_micron_c = IfNotFloat('Extensions', 'ext_selem_micron_c')
-ext_min_area_c = IfNotFloat('Extensions', 'ext_min_area_c')
-
-# [Connexions]
-max_straight_sq_dist_c = IfNotFloat('Connexions', 'max_straight_sq_dist_c')
-max_weighted_length_c = IfNotFloat('Connexions', 'max_weighted_length_c')
-
-# [Frangi]
-
-scale_range = IfNotFloat('Frangi', 'scale_range')
-scale_step = IfNotFloat('Frangi', 'scale_step')
-alpha = IfNotFloat('Frangi', 'alpha')
-beta = IfNotFloat('Frangi', 'beta')
-frangi_c = IfNotFloat('Frangi', 'frangi_c')
-diff_mode = parameters['Frangi']['diff_mode']
-bright_on_dark = parameters.getboolean('Frangi', 'bright_on_dark')
-method = parameters['Frangi']['method']
-
-# [Features Extraction]
-hist_min_length = IfNotFloat('Features Extraction', 'hist_min_length')
-hist_step_length = IfNotFloat('Features Extraction', 'hist_step_length')
-number_of_bins_length = IfNotFloat('Features Extraction', 'number_of_bins_length')
-hist_bins_borders_length = IfNotFloat('Features Extraction', 'hist_bins_borders_length')
-hist_min_curvature = IfNotFloat('Features Extraction', 'hist_min_curvature')
-hist_step_curvature = IfNotFloat('Features Extraction', 'hist_step_curvature')
-number_of_bins_curvature = IfNotFloat('Features Extraction', 'number_of_bins_curvature')
-hist_bins_borders_curvature = IfNotFloat('Features Extraction', 'hist_bins_borders_curvature')
-
-# [Program running]
-with_plot = parameters.getboolean('Program Running', 'with_plot')
-in_parallel = parameters.getboolean('Program Running', 'in_parallel')
-
-# data_path = "./data/DIO_6H_6_1.70bis_2.2_3.tif"
-# channel = 'G'
-# size_voxel_in_micron = None  # -> list [X,Y,Z]
-# with_plot = False
-#
-# soma_low_c = 0.15
-# soma_high_c = 0.7126
-# ext_low_c = 0.2 #3 #1e-7    ##0.2  # 0.02  # 0.2  # ext_low_c = 9.0e-4
-# ext_high_c = 0.6 #1e-10 #1.2e-7    ##0.6  # 0.04  # 0.6  # high_ext = 8.0e-3
-#
-# # soma_selem_c = mp_.disk(2)
-# # ext_selem_c = mp_.disk(1)
-# soma_selem_micron_c = 0.24050024 * 2
-# ext_selem_micron_c = 0.24050024 * 1
-#
-# max_straight_sq_dist_c = (30 ** 2) * 0.24050024
-# max_weighted_length_c = 20.0 * 0.24050024
-#
-# soma_min_area_c = 1000 * (0.24050024 ** 2)
-# ext_min_area_c = 100 * (0.24050024 ** 2)
-# # soma_min_area_c = 1000
-# # ext_min_area_c = 100
-#
-# in_parallel = False
+# Copyright CNRS/Inria/UNS
+# Contributor(s): Eric Debreuve (since 2019), Morgane Nadal (2020)
+#
+# eric.debreuve@cnrs.fr
+#
+# This software is governed by the CeCILL  license under French law and
+# abiding by the rules of distribution of free software.  You can  use,
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info".
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability.
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and,  more generally, to use and operate it in the
+# same conditions as regards security.
+#
+# 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 configparser
+from typing import Union, Any
+
+# --Parameters from .INI file
+parameters = configparser.ConfigParser(allow_no_value=True)
+parameters.read('parameters.ini')
+
+
+def IfNotFloat(section: str, key: str) -> Union[Union[float, str], Any]:
+    if parameters.get(section, key) is not None:
+        try:
+            value = parameters.getfloat(section, key)
+            return value
+        except:
+            return eval(parameters.get(section, key))
+    else:
+        return parameters.get(section, key)
+
+
+# [Input]
+data_path = parameters['Input']['data_path']
+channel = parameters['Input']['channel']
+size_voxel_in_micron = IfNotFloat('Input', 'size_voxel_in_micron')
+dilatation_erosion = parameters.getboolean('Input', 'dilatation_erosion')
+save_images = parameters['Input']['save_images']
+save_csv = parameters['Input']['save_csv']
+save_features_analysis = parameters['Input']['save_features_analysis']
+statistical_analysis = parameters.getboolean('Input', 'statistical_analysis')
+
+# [Somas]
+soma_low_c = IfNotFloat('Somas', 'soma_low_c')
+soma_high_c = IfNotFloat('Somas', 'soma_high_c')
+soma_selem_micron_c = IfNotFloat('Somas', 'soma_selem_micron_c')
+soma_min_area_c = IfNotFloat('Somas', 'soma_min_area_c')
+soma_max_area_c = IfNotFloat('Somas', 'soma_max_area_c')
+
+# [Extensions]
+adapt_hist_equalization = parameters.getboolean('Extensions', 'adapt_hist_equalization')
+ext_low_c = IfNotFloat('Extensions', 'ext_low_c')
+ext_high_c = IfNotFloat('Extensions', 'ext_high_c')
+ext_selem_micron_c = IfNotFloat('Extensions', 'ext_selem_micron_c')
+ext_min_area_c = IfNotFloat('Extensions', 'ext_min_area_c')
+
+# [Connexions]
+max_straight_sq_dist_c = IfNotFloat('Connexions', 'max_straight_sq_dist_c')
+max_weighted_length_c = IfNotFloat('Connexions', 'max_weighted_length_c')
+
+# [Frangi]
+
+scale_range = IfNotFloat('Frangi', 'scale_range')
+scale_step = IfNotFloat('Frangi', 'scale_step')
+alpha = IfNotFloat('Frangi', 'alpha')
+beta = IfNotFloat('Frangi', 'beta')
+frangi_c = IfNotFloat('Frangi', 'frangi_c')
+diff_mode = parameters['Frangi']['diff_mode']
+bright_on_dark = parameters.getboolean('Frangi', 'bright_on_dark')
+method = parameters['Frangi']['method']
+
+# [Features Extraction]
+hist_min_length = IfNotFloat('Features Extraction', 'hist_min_length')
+hist_step_length = IfNotFloat('Features Extraction', 'hist_step_length')
+number_of_bins_length = IfNotFloat('Features Extraction', 'number_of_bins_length')
+hist_bins_borders_length = IfNotFloat('Features Extraction', 'hist_bins_borders_length')
+hist_min_curvature = IfNotFloat('Features Extraction', 'hist_min_curvature')
+hist_step_curvature = IfNotFloat('Features Extraction', 'hist_step_curvature')
+number_of_bins_curvature = IfNotFloat('Features Extraction', 'number_of_bins_curvature')
+hist_bins_borders_curvature = IfNotFloat('Features Extraction', 'hist_bins_borders_curvature')
+
+# [Program running]
+with_plot = parameters.getboolean('Program Running', 'with_plot')
+interactive = parameters.getboolean('Program Running', 'interactive')
+in_parallel = parameters.getboolean('Program Running', 'in_parallel')
+
+# data_path = "./data/DIO_6H_6_1.70bis_2.2_3.tif"
+# channel = 'G'
+# size_voxel_in_micron = None  # -> list [X,Y,Z]
+# with_plot = False
+#
+# soma_low_c = 0.15
+# soma_high_c = 0.7126
+# ext_low_c = 0.2 #3 #1e-7    ##0.2  # 0.02  # 0.2  # ext_low_c = 9.0e-4
+# ext_high_c = 0.6 #1e-10 #1.2e-7    ##0.6  # 0.04  # 0.6  # high_ext = 8.0e-3
+#
+# # soma_selem_c = mp_.disk(2)
+# # ext_selem_c = mp_.disk(1)
+# soma_selem_micron_c = 0.24050024 * 2
+# ext_selem_micron_c = 0.24050024 * 1
+#
+# max_straight_sq_dist_c = (30 ** 2) * 0.24050024
+# max_weighted_length_c = 20.0 * 0.24050024
+#
+# soma_min_area_c = 1000 * (0.24050024 ** 2)
+# ext_min_area_c = 100 * (0.24050024 ** 2)
+# # soma_min_area_c = 1000
+# # ext_min_area_c = 100
+#
+# in_parallel = False