celldetective 1.1.1.post3__tar.gz → 1.2.0__tar.gz

{celldetective-1.1.1.post3 → celldetective-1.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.1.1.post3
+Version: 1.2.0
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

celldetective-1.2.0/celldetective/__init__.py

@@ -0,0 +1,3 @@
+#from .tracking import track, clean_trajectories
+#from .measure import contour_of_instance_segmentation
+

{celldetective-1.1.1.post3 → celldetective-1.2.0}/celldetective/__main__.py

@@ -108,6 +108,10 @@ class AppInitWindow(QMainWindow):
 		OptionsMenu.addAction(self.MemoryAndThreadsAction)
 		menuBar.addMenu(OptionsMenu)
 
+		PluginsMenu = QMenu("Plugins", self)
+		PluginsMenu.addAction(self.CorrectAnnotationAction)
+		menuBar.addMenu(PluginsMenu)
+
 		helpMenu = QMenu("Help", self)
 		helpMenu.clear()
 		helpMenu.addAction(self.DocumentationAction)
@@ -130,6 +134,8 @@ class AppInitWindow(QMainWindow):
 
 		self.MemoryAndThreadsAction = QAction('Memory & Threads...')
 
+		self.CorrectAnnotationAction = QAction('Correct a segmentation annotation...')
+
 		self.newExpAction = QAction('New', self)
 		self.newExpAction.setShortcut("Ctrl+N")
 		self.newExpAction.setShortcutVisibleInContextMenu(True)
@@ -156,6 +162,7 @@ class AppInitWindow(QMainWindow):
 		self.openModels.triggered.connect(self.open_models_folder)
 		self.AboutAction.triggered.connect(self.open_about_window)
 		self.MemoryAndThreadsAction.triggered.connect(self.set_memory_and_threads)
+		self.CorrectAnnotationAction.triggered.connect(self.correct_seg_annotation)
 
 		self.DocumentationAction.triggered.connect(self.open_documentation)
 
@@ -186,6 +193,15 @@ class AppInitWindow(QMainWindow):
 			for r in self.recentFileActs:
 				r.triggered.connect(lambda checked, item=r: self.load_recent_exp(item.text()))
 
+	def correct_seg_annotation(self):
+		
+		self.filename,_ = QFileDialog.getOpenFileName(self,"Open Image", "/home/", "TIF Files (*.tif)")
+		if self.filename!='':
+			print('Opening ',self.filename,' in napari...')
+			correct_annotation(self.filename)
+		else:
+			return None
+
 	def set_memory_and_threads(self):
 		
 		print('setting memory and threads')
@@ -405,6 +421,7 @@ if __name__ == "__main__":
 	import subprocess
 	import os
 	from celldetective.gui.about import AboutWidget
+	from celldetective.io import correct_annotation
 	import psutil
 	import subprocess
 	import json

{celldetective-1.1.1.post3 → celldetective-1.2.0}/celldetective/extra_properties.py

@@ -1,15 +1,31 @@
 """
-Add extra properties to directly to regionprops
-Functions must take regionmask as first argument and optionally intensity_image as second argument
-If intensity is in function name, it will be replaced by the name of the channel. These measurements are applied automatically to all channels
+Copyright © 2022 Laboratoire Adhesion et Inflammation, Authored by Remy Torro, 
+Ksenija Dervanova.
+
+Add extra properties to measure using regionprops (measure_features). 
+The functions must take "regionmask" as the first argument, corresponding
+to the binary mask of each cell of interest generated by regionprops 
+and an optional "intensity_image" second argument, i.e. the associated 
+multichannel image crop. The measurement will be named after the function
+name. If a function function() has several outputs (e.g. due to a multichannel image),
+they will be labelled with an index as function-0, function-1... A routine 
+automatically replacements keywords "intensity-0", "intensity-1" and so on,
+with the actual name of the intensity channel (e.g. "intensity-0" -> 
+"brightfield_channel"). Due to this indexing behavior, avoid using digits 
+in the function names and prefer text instead: "intensity-99()" --> 
+"intensity-ninety-nine()".
+
+New functions appear automatically in the ConfigMeasurements widget of the
+GUI.
 
 """
+
 import warnings
 
 import numpy as np
 from scipy.ndimage import distance_transform_edt, center_of_mass
 from scipy.spatial.distance import euclidean
-
+from celldetective.utils import interpolate_nan, contour_of_instance_segmentation
 
 # Percentiles
 
@@ -44,6 +60,9 @@ def intensity_nanmean(regionmask, intensity_image):
 	return np.nanmean(intensity_image[regionmask])
 
 def intensity_centre_of_mass_displacement(regionmask, intensity_image):
+
+	intensity_image = interpolate_nan(intensity_image.copy())
+
 	y, x = np.mgrid[:regionmask.shape[0], :regionmask.shape[1]]
 	xtemp = x.copy()
 	ytemp = y.copy()
@@ -51,60 +70,69 @@ def intensity_centre_of_mass_displacement(regionmask, intensity_image):
 	centroid_x = intensity_weighted_center[1]
 	centroid_y = intensity_weighted_center[0]
 
+	#centroid_x = np.sum(xtemp * intensity_image) / np.sum(intensity_image)
 	geometric_centroid_x = np.sum(xtemp * regionmask) / np.sum(regionmask)
 	geometric_centroid_y = np.sum(ytemp * regionmask) / np.sum(regionmask)
-	distance = euclidean(np.array((geometric_centroid_y, geometric_centroid_x)), np.array((centroid_y, centroid_x)))
+	try:
+		distance = euclidean(np.array((geometric_centroid_y, geometric_centroid_x)), np.array((centroid_y, centroid_x)))
+	except:
+		distance = np.nan
+
 	delta_x = geometric_centroid_x - centroid_x
 	delta_y = geometric_centroid_y - centroid_y
 	direction_arctan = np.arctan2(delta_y, delta_x) * 180 / np.pi
 	if direction_arctan < 0:
 		direction_arctan += 360
-	return distance, direction_arctan
+
+	return distance, direction_arctan, centroid_x - geometric_centroid_x, centroid_y - geometric_centroid_y
 
 def intensity_radial_gradient(regionmask, intensity_image):
-	warnings.filterwarnings('ignore', message="Polyfit may be poorly conditioned")
-	cell_mask = regionmask.copy()
-	intensity = intensity_image.copy()
-	y = intensity[cell_mask].flatten()
-	x = distance_transform_edt(cell_mask)
-	x = x[cell_mask].flatten()
-	params = np.polyfit(x, y, 1)
-	line = np.poly1d(params)
 
-	return line.coefficients[0], line.coefficients[1]
+	try:
+		warnings.filterwarnings('ignore', message="Polyfit may be poorly conditioned")
+		cell_mask = regionmask.copy()
+		intensity = intensity_image.copy()
+		y = intensity[cell_mask].flatten()
+		x = distance_transform_edt(cell_mask)
+		x = x[cell_mask].flatten()
+		params = np.polyfit(x, y, 1)
+		line = np.poly1d(params)
+
+		return line.coefficients[0], line.coefficients[1]
+	except Exception as e:
+		print(e)
+		return np.nan, np.nan
 
 
 def intensity_centre_of_mass_displacement_edge(regionmask, intensity_image):
-	edt = distance_transform_edt(regionmask)
-	min_distance = 0
-	max_distance = 0.1*edt.max()
-	thresholded = (edt <= max_distance) * (edt > min_distance)
-	edge_mask = np.copy(regionmask)
-	edge_mask[np.where(thresholded == 0)] = 0
-	y, x = np.mgrid[:edge_mask.shape[0], :edge_mask.shape[1]]
-	xtemp = x.copy()
-	ytemp = y.copy()
-	intensity_edge = intensity_image.copy()
-	intensity_edge[np.where(edge_mask == 0)] = 0.
-	sum_intensity_edge = np.sum(intensity_edge)
-	sum_regionmask = np.sum(regionmask)
+	
+	intensity_image = interpolate_nan(intensity_image.copy())
+	edge_mask = contour_of_instance_segmentation(regionmask, 3)
 
-	if sum_intensity_edge != 0 and sum_regionmask != 0:
-		y, x = np.mgrid[:regionmask.shape[0], :regionmask.shape[1]]
+	if np.sum(edge_mask)>0:
+		
+		y, x = np.mgrid[:edge_mask.shape[0], :edge_mask.shape[1]]
 		xtemp = x.copy()
 		ytemp = y.copy()
-		intensity_weighted_center = center_of_mass(intensity_image, regionmask)
+		intensity_weighted_center = center_of_mass(intensity_image, edge_mask)
 		centroid_x = intensity_weighted_center[1]
 		centroid_y = intensity_weighted_center[0]
 
+		#centroid_x = np.sum(xtemp * intensity_image) / np.sum(intensity_image)
 		geometric_centroid_x = np.sum(xtemp * regionmask) / np.sum(regionmask)
 		geometric_centroid_y = np.sum(ytemp * regionmask) / np.sum(regionmask)
-		distance = euclidean(np.array((geometric_centroid_y, geometric_centroid_x)), np.array((centroid_y, centroid_x)))
+		
+		try:
+			distance = euclidean(np.array((geometric_centroid_y, geometric_centroid_x)), np.array((centroid_y, centroid_x)))
+		except:
+			distance = np.nan
+
 		delta_x = geometric_centroid_x - centroid_x
 		delta_y = geometric_centroid_y - centroid_y
 		direction_arctan = np.arctan2(delta_y, delta_x) * 180 / np.pi
 		if direction_arctan < 0:
 			direction_arctan += 360
-		return distance, direction_arctan
+
+		return distance, direction_arctan, centroid_x - geometric_centroid_x, centroid_y - geometric_centroid_y
 	else:
-		return np.nan, np.nan
+		return np.nan, np.nan, np.nan, np.nan

{celldetective-1.1.1.post3 → celldetective-1.2.0}/celldetective/gui/__init__.py

@@ -9,6 +9,7 @@ from .survival_ui import ConfigSurvival
 from .plot_signals_ui import ConfigSignalPlot
 from .signal_annotator_options import ConfigSignalAnnotator
 from .signal_annotator import SignalAnnotator
+from .signal_annotator2 import SignalAnnotator2
 from .retrain_signal_model_options import ConfigSignalModelTraining
 from .retrain_segmentation_model_options import ConfigSegmentationModelTraining
 from .thresholds_gui import ThresholdConfigWizard

{celldetective-1.1.1.post3 → celldetective-1.2.0}/celldetective/gui/analyze_block.py

@@ -1,4 +1,5 @@
-from PyQt5.QtWidgets import QFrame, QGridLayout, QComboBox, QSizePolicy, QSpacerItem, QLabel, QPushButton, QVBoxLayout, QHBoxLayout, QCheckBox, QMessageBox
+from PyQt5.QtWidgets import QFrame, QGridLayout, QComboBox, QLabel, QPushButton, QVBoxLayout, QHBoxLayout, QCheckBox, \
+    QMessageBox, QSpacerItem, QSizePolicy
 from PyQt5.QtCore import Qt, QSize
 from PyQt5.QtGui import QIcon
 

{celldetective-1.1.1.post3 → celldetective-1.2.0}/celldetective/gui/classifier_widget.py

@@ -12,6 +12,7 @@ from sklearn.metrics import r2_score
 from scipy.optimize import curve_fit
 from celldetective.gui import Styles
 from math import ceil
+from celldetective.utils import extract_cols_from_query
 
 def step_function(t, t_shift, dt):
 	return 1/(1+np.exp(-(t-t_shift)/dt))
@@ -263,17 +264,23 @@ class ClassifierWidget(QWidget, Styles):
 		self.propscanvas.canvas.draw_idle()
 
 	def apply_property_query(self):
+
 		query = self.property_query_le.text()
 		self.df[self.class_name] = 1
 
-		print(query, self.class_name)
+		cols = extract_cols_from_query(query) 
+		print(cols)
+		cols_in_df = np.all([c in list(self.df.columns) for c in cols], axis=0)
+		print(f'Testing if columns from query are in the dataframe: {cols_in_df}...')
 
 		if query=='':
 			print('empty query')
 		else:
 			try:
-				self.selection = self.df.query(query).index
-				print(self.selection)
+				if cols_in_df:
+					self.selection = self.df.dropna(subset=cols).query(query).index
+				else:
+					self.selection = self.df.query(query).index
 				self.df.loc[self.selection, self.class_name] = 0
 			except Exception as e:
 				print(e)
@@ -368,13 +375,14 @@ class ClassifierWidget(QWidget, Styles):
 						frames = track['FRAME'].to_numpy()
 						t_first = track['t_firstdetection'].to_numpy()[0]
 						median_status = np.nanmedian(status_values[frames>=t_first])
-						c = ceil(median_status)
-						if c==0:
-							self.df.loc[indices, self.class_name_user] = 1
-							self.df.loc[indices, self.class_name_user.replace('class','t')] = -1
-						elif c==1:
-							self.df.loc[indices, self.class_name_user] = 2
-							self.df.loc[indices, self.class_name_user.replace('class','t')] = -1
+						if median_status==median_status:
+							c = ceil(median_status)
+							if c==0:
+								self.df.loc[indices, self.class_name_user] = 1
+								self.df.loc[indices, self.class_name_user.replace('class','t')] = -1
+							elif c==1:
+								self.df.loc[indices, self.class_name_user] = 2
+								self.df.loc[indices, self.class_name_user.replace('class','t')] = -1
 				if self.irreversible_event_btn.isChecked():
 					self.estimate_time()
 		else:

{celldetective-1.1.1.post3 → celldetective-1.2.0}/celldetective/gui/control_panel.py

@@ -3,7 +3,7 @@ from PyQt5.QtWidgets import QMainWindow, QComboBox, QPushButton, QHBoxLayout, QL
 from PyQt5.QtCore import Qt, QSize
 from PyQt5.QtGui import QIcon
 from celldetective.gui.gui_utils import center_window, QHSeperationLine
-from celldetective.utils import _extract_labels_from_config, ConfigSectionMap, extract_experiment_channels
+from celldetective.utils import _extract_labels_from_config, ConfigSectionMap, extract_experiment_channels, extract_identity_col
 from celldetective.gui import ConfigEditor, ProcessPanel, PreprocessingPanel, AnalysisPanel, NeighPanel
 from natsort import natsorted
 from glob import glob
@@ -16,6 +16,7 @@ import subprocess
 from celldetective.gui.viewers import StackVisualizer
 from celldetective.utils import extract_experiment_channels
 from celldetective.gui import Styles
+import pandas as pd
 
 class ControlPanel(QMainWindow, Styles):
 
@@ -413,26 +414,46 @@ class ControlPanel(QMainWindow, Styles):
 		self.pos = self.position_list.currentText()
 		panels = [self.ProcessEffectors, self.ProcessTargets]
 		if self.position_list.currentText()=="*":
+			
 			for p in panels:
 				p.check_seg_btn.setEnabled(False)
 				p.check_tracking_result_btn.setEnabled(False)
+
 			self.ProcessTargets.view_tab_btn.setEnabled(True)
 			self.ProcessEffectors.view_tab_btn.setEnabled(True)
+			self.NeighPanel.view_tab_btn.setEnabled(True)
+			self.ProcessEffectors.signal_analysis_action.setEnabled(True)
+			self.ProcessTargets.signal_analysis_action.setEnabled(True)
+
 			self.ProcessTargets.check_seg_btn.setEnabled(False)
 			self.ProcessEffectors.check_seg_btn.setEnabled(False)
+
 			self.ProcessTargets.check_tracking_result_btn.setEnabled(False)
 			self.ProcessEffectors.check_tracking_result_btn.setEnabled(False)
+
 			self.ProcessEffectors.check_measurements_btn.setEnabled(False)
 			self.ProcessTargets.check_measurements_btn.setEnabled(False)
 			#self.ProcessTargets.signal_analysis_action.setEnabled(False)
 			#self.ProcessEffectors.signal_analysis_action.setEnabled(False)
+
 			self.ProcessTargets.check_signals_btn.setEnabled(False)
 			self.ProcessEffectors.check_signals_btn.setEnabled(False)
+			self.NeighPanel.check_signals_btn.setEnabled(False)
+			self.ProcessTargets.delete_tracks_btn.hide()
+			self.ProcessEffectors.delete_tracks_btn.hide()
+
 			self.view_stack_btn.setEnabled(False)
 		elif self.well_list.currentText()=='*':
 			self.ProcessTargets.view_tab_btn.setEnabled(True)
 			self.ProcessEffectors.view_tab_btn.setEnabled(True)	
-			self.view_stack_btn.setEnabled(False)	
+			self.NeighPanel.view_tab_btn.setEnabled(True)
+			self.view_stack_btn.setEnabled(False)
+			self.ProcessEffectors.signal_analysis_action.setEnabled(True)
+			self.ProcessTargets.signal_analysis_action.setEnabled(True)
+
+			self.delete_tracks_btn.hide()
+			self.ProcessTargets.delete_tracks_btn.hide()
+			self.ProcessEffectors.delete_tracks_btn.hide()
 		else:
 			if not self.well_list.currentText()=="*":
 				self.locate_selected_position()
@@ -452,26 +473,56 @@ class ControlPanel(QMainWindow, Styles):
 					self.ProcessEffectors.check_tracking_result_btn.setEnabled(False)
 
 				if os.path.exists(os.sep.join([self.pos,'output','tables','trajectories_effectors.csv'])):
+					df = pd.read_csv(os.sep.join([self.pos,'output','tables','trajectories_effectors.csv']), nrows=1)
+					id_col = extract_identity_col(df)
 					self.ProcessEffectors.check_measurements_btn.setEnabled(True)
-					self.ProcessEffectors.check_signals_btn.setEnabled(True)
+					if id_col=='TRACK_ID':
+						self.ProcessEffectors.check_signals_btn.setEnabled(True)
+						self.ProcessEffectors.delete_tracks_btn.show()
+						self.ProcessEffectors.signal_analysis_action.setEnabled(True)
+					else:
+						self.ProcessEffectors.signal_analysis_action.setEnabled(False)						
+
 					#self.ProcessEffectors.signal_analysis_action.setEnabled(True)
 					self.ProcessEffectors.view_tab_btn.setEnabled(True)
-
+					self.ProcessEffectors.classify_btn.setEnabled(True)
 				else:
 					self.ProcessEffectors.check_measurements_btn.setEnabled(False)
 					self.ProcessEffectors.check_signals_btn.setEnabled(False)
 					#self.ProcessEffectors.signal_analysis_action.setEnabled(False)
 					self.ProcessEffectors.view_tab_btn.setEnabled(False)
+					self.ProcessEffectors.classify_btn.setEnabled(False)
+					self.ProcessEffectors.delete_tracks_btn.hide()
+					self.ProcessEffectors.signal_analysis_action.setEnabled(False)
 
 				if os.path.exists(os.sep.join([self.pos,'output','tables','trajectories_targets.csv'])):
+					df = pd.read_csv(os.sep.join([self.pos,'output','tables','trajectories_targets.csv']), nrows=1)
+					id_col = extract_identity_col(df)
 					self.ProcessTargets.check_measurements_btn.setEnabled(True)
-					self.ProcessTargets.check_signals_btn.setEnabled(True)
+					if id_col=='TRACK_ID':
+						self.ProcessTargets.check_signals_btn.setEnabled(True)
+						self.ProcessTargets.signal_analysis_action.setEnabled(True)
+						self.ProcessTargets.delete_tracks_btn.show()
+					else:
+						self.ProcessTargets.signal_analysis_action.setEnabled(False)						
 					#self.ProcessTargets.signal_analysis_action.setEnabled(True)
 					self.ProcessTargets.view_tab_btn.setEnabled(True)
-
+					self.ProcessTargets.classify_btn.setEnabled(True)
 				else:
 					self.ProcessTargets.check_measurements_btn.setEnabled(False)
 					self.ProcessTargets.check_signals_btn.setEnabled(False)
 					#self.ProcessTargets.signal_analysis_action.setEnabled(False)
 					self.ProcessTargets.view_tab_btn.setEnabled(False)
+					self.ProcessTargets.classify_btn.setEnabled(False)
+					self.ProcessTargets.signal_analysis_action.setEnabled(False)				
+					self.ProcessTargets.delete_tracks_btn.hide()
+					self.ProcessTargets.signal_analysis_action.setEnabled(False)
+
+				if os.path.exists(os.sep.join([self.pos,'output','tables','trajectories_pairs.csv'])):
+					self.NeighPanel.view_tab_btn.setEnabled(True)
+					self.NeighPanel.check_signals_btn.setEnabled(True)
+				else:
+					self.NeighPanel.view_tab_btn.setEnabled(False)
+					self.NeighPanel.check_signals_btn.setEnabled(False)
+
 

{celldetective-1.1.1.post3 → celldetective-1.2.0}/celldetective/gui/layouts.py

@@ -73,7 +73,7 @@ class ChannelNormGenerator(QVBoxLayout, Styles):
 			for tab in tables:
 				cols = pd.read_csv(tab, nrows=1).columns.tolist()
 				all_measurements.extend(cols)
-			all_measurements = np.unique(all_measurements)		
+			all_measurements = np.unique(all_measurements)
 
 		if self.mode=='signals':
 			generic_measurements = ['brightfield_channel', 'live_nuclei_channel', 'dead_nuclei_channel', 
@@ -245,13 +245,14 @@ class ChannelNormGenerator(QVBoxLayout, Styles):
 
 	def check_valid_channels(self):
 
-		if np.all([cb.currentText()=='--' for cb in self.channel_cbs]):
-			self.parent_window.submit_btn.setEnabled(False)
+		if hasattr(self.parent_window, "submit_btn"):
+			if np.all([cb.currentText()=='--' for cb in self.channel_cbs]):
+				self.parent_window.submit_btn.setEnabled(False)
 
 		if hasattr(self.parent_window, "spatial_calib_le"):
 			if self.parent_window.spatial_calib_le.text()!='--':
 				self.parent_window.submit_btn.setEnabled(True)
-		else:
+		elif hasattr(self.parent_window, "submit_btn"):
 			self.parent_window.submit_btn.setEnabled(True)
 
 
@@ -990,10 +991,12 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 											)
 		bg = bg[0]
 		bg = bg['bg']
-
-		self.viewer = StackVisualizer(
-									  stack=[bg],
-									  window_title='Reconstructed background',
-									  frame_slider = False,
-									 )
-		self.viewer.show()
+		print(bg)
+		if len(bg)>0:
+
+			self.viewer = StackVisualizer(
+										  stack=[bg],
+										  window_title='Reconstructed background',
+										  frame_slider = False,
+										 )
+			self.viewer.show()

{celldetective-1.1.1.post3 → celldetective-1.2.0}/celldetective/gui/neighborhood_options.py

@@ -90,6 +90,8 @@ class ConfigNeighborhoods(QWidget, Styles):
 
 		self.clear_previous_btn = QCheckBox('clear previous neighborhoods')
 		self.clear_previous_btn.setToolTip('Clear all previous neighborhood measurements.')
+		self.clear_previous_btn.setIcon(icon(MDI6.broom, color='black'))
+
 		main_layout.addWidget(self.clear_previous_btn, alignment=Qt.AlignRight)
 
 		main_layout.addWidget(QLabel(''))
@@ -305,11 +307,13 @@ class ConfigNeighborhoods(QWidget, Styles):
 
 		self.cumulated_presence_btn = QCheckBox('cumulated presence')
 		self.cumulated_presence_btn.setToolTip("Compute the cumulated presence time of each neighbor around a reference cell.")
+		self.cumulated_presence_btn.setIcon(icon(MDI6.timer_outline, color='black'))
+
 		layout.addWidget(self.cumulated_presence_btn)
 
-		self.symmetrize_btn = QCheckBox('symmetrize')
-		self.symmetrize_btn.setToolTip("Write the neighborhood of the neighbor cells with respect to the reference cells.")
-		layout.addWidget(self.symmetrize_btn)
+		# self.symmetrize_btn = QCheckBox('symmetrize')
+		# self.symmetrize_btn.setToolTip("Write the neighborhood of the neighbor cells with respect to the reference cells.")
+		# layout.addWidget(self.symmetrize_btn)
 		
 		self.fill_cbs_of_neighbor_population()
 		self.neighbor_population_cb.currentIndexChanged.connect(self.fill_cbs_of_neighbor_population)
@@ -319,16 +323,16 @@ class ConfigNeighborhoods(QWidget, Styles):
 	def fill_cbs_of_neighbor_population(self):
 
 		population = self.neighbor_population_cb.currentText()
-		class_cols, status_cols, time_cols = self.locate_population_specific_columns(population)
+		class_cols, status_cols, group_cols, time_cols = self.locate_population_specific_columns(population)
 		self.neighbor_population_status_cb.clear()
-		self.neighbor_population_status_cb.addItems(['--','class', 'status']+class_cols+status_cols)
+		self.neighbor_population_status_cb.addItems(['--','class', 'status']+class_cols+status_cols+group_cols)
 
 	def fill_cbs_of_reference_population(self):
 
 		population = self.reference_population_cb.currentText()
-		class_cols, status_cols, time_cols = self.locate_population_specific_columns(population)
+		class_cols, status_cols, group_cols, time_cols = self.locate_population_specific_columns(population)
 		self.reference_population_status_cb.clear()
-		self.reference_population_status_cb.addItems(['--','class', 'status']+class_cols+status_cols)
+		self.reference_population_status_cb.addItems(['--','class', 'status']+class_cols+status_cols+group_cols)
 		self.event_time_cb.addItems(['--', 't0']+time_cols)
 
 	def switch_not_reference(self):
@@ -364,6 +368,7 @@ class ConfigNeighborhoods(QWidget, Styles):
 
 		class_idx = np.array([s.startswith('class_') for s in self.all_columns])
 		status_idx = np.array([s.startswith('status_') for s in self.all_columns])
+		group_idx = np.array([s.startswith('group_') for s in self.all_columns])		
 		time_idx = np.array([s.startswith('t_') for s in self.all_columns])
 
 		if len(class_idx)>0:
@@ -379,12 +384,17 @@ class ConfigNeighborhoods(QWidget, Styles):
 		else:
 			status_columns = []
 
+		if len(group_idx)>0:
+			group_columns = list(self.all_columns[group_idx])
+		else:
+			group_columns = []
+
 		if len(time_idx)>0:
 			time_columns = list(self.all_columns[time_idx])
 		else:
 			time_columns = []
 
-		return class_columns, status_columns, time_columns
+		return class_columns, status_columns, group_columns, time_columns
 
 	def write_instructions(self):
 
@@ -418,7 +428,7 @@ class ConfigNeighborhoods(QWidget, Styles):
 		neighborhood_options.update({'event_time_col': event_time_col})		
 
 		neighborhood_kwargs = {'mode': mode, 'status': status_options, 'not_status_option': [self.not_status_reference, self.not_status_neighbor], 
-							  'compute_cum_sum': self.cumulated_presence_btn.isChecked(), 'attention_weight': True, 'symmetrize': self.symmetrize_btn.isChecked(),
+							  'compute_cum_sum': self.cumulated_presence_btn.isChecked(), 'attention_weight': True, 'symmetrize': False,
 							  'include_dead_weight': True}
 
 		neighborhood_options.update({'neighborhood_kwargs': neighborhood_kwargs})
@@ -487,8 +497,6 @@ class ConfigNeighborhoods(QWidget, Styles):
 						neighborhood_kwargs = neigh_instructions['neighborhood_kwargs']
 						if 'compute_cum_sum' in neighborhood_kwargs:
 							self.cumulated_presence_btn.setChecked(neighborhood_kwargs['compute_cum_sum'])
-						if 'symmetrize' in neighborhood_kwargs:
-							self.symmetrize_btn.setChecked(neighborhood_kwargs['symmetrize'])
 						if 'status' in neighborhood_kwargs:
 							status_options = neighborhood_kwargs['status']
 							status_options = ['--' if s is None else s for s in status_options]
@@ -499,6 +507,6 @@ class ConfigNeighborhoods(QWidget, Styles):
 						if 'not_status_option' in neighborhood_kwargs:
 							not_status_option = neighborhood_kwargs['not_status_option']
 							if not_status_option[0]:
-								self.switch_not_reference.click()
+								self.reference_switch_status_btn.click()
 							if not_status_option[1]:
-								self.switch_not_neigh.click()
+								self.neighbor_switch_status_btn.click()