celldetective 1.1.1.post3__py3-none-any.whl → 1.2.0__py3-none-any.whl

celldetective/gui/process_block.py

@@ -7,14 +7,17 @@ import gc
 from PyQt5.QtGui import QIcon, QDoubleValidator, QIntValidator
 
 from celldetective.gui.signal_annotator import MeasureAnnotator
-from celldetective.io import get_segmentation_models_list, control_segmentation_napari, get_signal_models_list, control_tracking_btrack, load_experiment_tables
-from celldetective.io import locate_segmentation_model, auto_load_number_of_frames, load_frames
+from celldetective.gui.signal_annotator2 import SignalAnnotator2
+from celldetective.io import get_segmentation_models_list, control_segmentation_napari, get_signal_models_list, \
+	control_tracking_btrack, load_experiment_tables, get_pair_signal_models_list, get_position_pickle, get_position_table
+from celldetective.io import locate_segmentation_model, auto_load_number_of_frames, load_frames, locate_signal_model
 from celldetective.gui import SegmentationModelLoader, ClassifierWidget, ConfigNeighborhoods, ConfigSegmentationModelTraining, ConfigTracking, SignalAnnotator, ConfigSignalModelTraining, ConfigMeasurements, ConfigSignalAnnotator, TableUI
 from celldetective.gui.gui_utils import QHSeperationLine
+from celldetective.relative_measurements import rel_measure_at_position
 from celldetective.segmentation import segment_at_position, segment_from_threshold_at_position
 from celldetective.tracking import track_at_position
 from celldetective.measure import measure_at_position
-from celldetective.signals import analyze_signals_at_position
+from celldetective.signals import analyze_signals_at_position, analyze_pair_signals, analyze_pair_signals_at_position
 from celldetective.utils import extract_experiment_channels
 import numpy as np
 from glob import glob
@@ -42,7 +45,7 @@ from celldetective.gui import Styles
 class ProcessPanel(QFrame, Styles):
 	def __init__(self, parent_window, mode):
 
-		super().__init__()		
+		super().__init__()
 		self.parent_window = parent_window
 		self.mode = mode
 		self.exp_channels = self.parent_window.exp_channels
@@ -59,7 +62,7 @@ class ProcessPanel(QFrame, Styles):
 		self.grid = QGridLayout(self)
 		self.grid.setContentsMargins(5,5,5,5)
 		self.generate_header()
-	
+
 	def generate_header(self):
 
 		"""
@@ -83,7 +86,7 @@ class ProcessPanel(QFrame, Styles):
 		self.select_all_btn.setStyleSheet(self.button_select_all)
 		self.grid.addWidget(self.select_all_btn, 0, 0, 1, 4, alignment=Qt.AlignLeft)
 		#self.to_disable.append(self.all_tc_actions)
-		
+
 		self.collapse_btn = QPushButton()
 		self.collapse_btn.setIcon(icon(MDI6.chevron_down,color="black"))
 		self.collapse_btn.setIconSize(QSize(25, 25))
@@ -110,7 +113,7 @@ class ProcessPanel(QFrame, Styles):
 			self.collapse_btn.setIconSize(QSize(20, 20))
 			#self.parent.w.adjustSize()
 			#self.parent.adjustSize()
-			self.parent_window.scroll.setMinimumHeight(min(int(880), int(0.8*self.parent_window.screen_height)))
+			self.parent_window.scroll.setMinimumHeight(min(int(930), int(0.9*self.parent_window.screen_height)))
 			self.parent_window.scroll.setMinimumWidth(425)
 
 			#self.parent.scroll.adjustSize()
@@ -142,7 +145,7 @@ class ProcessPanel(QFrame, Styles):
 		self.grid_contents.addWidget(self.submit_btn, 11, 0, 1, 4)
 
 	def generate_measure_options(self):
-		
+
 		measure_layout = QHBoxLayout()
 
 		self.measure_action = QCheckBox("MEASURE")
@@ -221,7 +224,7 @@ class ProcessPanel(QFrame, Styles):
 
 		signal_model_vbox = QVBoxLayout()
 		signal_model_vbox.setContentsMargins(25,0,25,0)
-		
+
 		model_zoo_layout = QHBoxLayout()
 		model_zoo_layout.addWidget(QLabel("Model zoo:"),90)
 
@@ -233,11 +236,11 @@ class ProcessPanel(QFrame, Styles):
 		self.train_signal_model_btn = QPushButton("TRAIN")
 		self.train_signal_model_btn.setToolTip("Open a dialog box to create a new target segmentation model.")
 		self.train_signal_model_btn.setIcon(icon(MDI6.redo_variant,color='black'))
-		self.train_signal_model_btn.setIconSize(QSize(20, 20)) 
+		self.train_signal_model_btn.setIconSize(QSize(20, 20))
 		self.train_signal_model_btn.setStyleSheet(self.button_style_sheet_3)
 		model_zoo_layout.addWidget(self.train_signal_model_btn, 5)
 		self.train_signal_model_btn.clicked.connect(self.open_signal_model_config_ui)
-		
+
 		signal_model_vbox.addLayout(model_zoo_layout)
 		signal_model_vbox.addWidget(self.signal_models_list)
 
@@ -274,6 +277,16 @@ class ProcessPanel(QFrame, Styles):
 		# self.show_track_table_btn.setEnabled(False)
 		# grid_track.addWidget(self.show_track_table_btn, 6)  #4,3,1,1, alignment=Qt.AlignLeft
 
+		self.delete_tracks_btn = QPushButton()
+		self.delete_tracks_btn.setIcon(icon(MDI6.trash_can,color="black"))
+		self.delete_tracks_btn.setIconSize(QSize(20, 20))
+		self.delete_tracks_btn.setToolTip("Delete existing tracks.")
+		self.delete_tracks_btn.setStyleSheet(self.button_select_all)
+		self.delete_tracks_btn.clicked.connect(self.delete_tracks)
+		self.delete_tracks_btn.setEnabled(True)
+		self.delete_tracks_btn.hide()
+		grid_track.addWidget(self.delete_tracks_btn, 6)  #4,3,1,1, alignment=Qt.AlignLeft
+
 		self.check_tracking_result_btn = QPushButton()
 		self.check_tracking_result_btn.setIcon(icon(MDI6.eye_check_outline,color="black"))
 		self.check_tracking_result_btn.setIconSize(QSize(20, 20))
@@ -293,6 +306,28 @@ class ProcessPanel(QFrame, Styles):
 
 		self.grid_contents.addLayout(grid_track, 4, 0, 1,4)
 
+	def delete_tracks(self):
+
+		msgBox = QMessageBox()
+		msgBox.setIcon(QMessageBox.Question)
+		msgBox.setText("Do you want to erase the tracks? All subsequent annotations will be erased...")
+		msgBox.setWindowTitle("Info")
+		msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
+		returnValue = msgBox.exec()
+		if returnValue == QMessageBox.No:
+			return None
+		elif returnValue == QMessageBox.Yes:
+			if os.path.exists(os.sep.join([self.parent_window.pos,'output','tables',f'trajectories_{self.mode}.csv'])):
+				os.remove(os.sep.join([self.parent_window.pos,'output','tables',f'trajectories_{self.mode}.csv']))
+			if os.path.exists(os.sep.join([self.parent_window.pos,'output','tables',f'trajectories_{self.mode}.pkl'])):
+				os.remove(os.sep.join([self.parent_window.pos,'output','tables',f'trajectories_{self.mode}.pkl']))
+			if os.path.exists(os.sep.join([self.parent_window.pos,'output','tables',f'napari_{self.mode[:-1]}_trajectories.npy'])):
+				os.remove(os.sep.join([self.parent_window.pos,'output','tables',f'napari_{self.mode[:-1]}_trajectories.npy']))
+			if os.path.exists(os.sep.join([self.parent_window.pos,'output','tables',f'trajectories_pairs.csv'])):
+				os.remove(os.sep.join([self.parent_window.pos,'output','tables',f'trajectories_pairs.csv']))
+			self.parent_window.update_position_options()
+		else:
+			return None
 
 	def generate_segmentation_options(self):
 
@@ -310,7 +345,7 @@ class ProcessPanel(QFrame, Styles):
 		self.segment_action.toggled.connect(self.enable_segmentation_model_list)
 		#self.to_disable.append(self.segment_action)
 		grid_segment.addWidget(self.segment_action, 90)
-		
+
 		self.check_seg_btn = QPushButton()
 		self.check_seg_btn.setIcon(icon(MDI6.eye_check_outline,color="black"))
 		self.check_seg_btn.setIconSize(QSize(20, 20))
@@ -321,7 +356,7 @@ class ProcessPanel(QFrame, Styles):
 		#self.to_disable.append(self.control_target_seg)
 		grid_segment.addWidget(self.check_seg_btn, 10)
 		self.grid_contents.addLayout(grid_segment, 0,0,1,4)
-		
+
 		seg_option_vbox = QVBoxLayout()
 		seg_option_vbox.setContentsMargins(25,0,25,0)
 		model_zoo_layout = QHBoxLayout()
@@ -394,7 +429,7 @@ class ProcessPanel(QFrame, Styles):
 		test = self.parent_window.locate_selected_position()
 		if test:
 			self.SignalAnnotator = SignalAnnotator(self)
-			self.SignalAnnotator.show()		
+			self.SignalAnnotator.show()
 
 	def check_measurements(self):
 
@@ -413,8 +448,8 @@ class ProcessPanel(QFrame, Styles):
 		if self.signal_analysis_action.isChecked():
 			self.signal_models_list.setEnabled(True)
 		else:
-			self.signal_models_list.setEnabled(False)			
-	
+			self.signal_models_list.setEnabled(False)
+
 	def init_seg_model_list(self):
 
 		self.seg_model_list.clear()
@@ -428,14 +463,14 @@ class ProcessPanel(QFrame, Styles):
 		self.seg_models.extend(self.seg_models_generic)
 
 		#self.seg_models_generic.insert(0,'Threshold')
-		self.seg_model_list.addItems(self.seg_models)		
+		self.seg_model_list.addItems(self.seg_models)
 
 		for i in range(len(self.seg_models)):
 			self.seg_model_list.setItemData(i, self.seg_models[i], Qt.ToolTipRole)
 
 		self.seg_model_list.insertSeparator(len(self.models_truncated))
 
-		
+
 		#if ("live_nuclei_channel" in self.exp_channels)*("dead_nuclei_channel" in self.exp_channels):
 		# 	print("both channels found")
 		# 	index = self.tc_seg_model_list.findText("MCF7_Hoescht_PI_w_primary_NK", Qt.MatchFixedString)
@@ -508,10 +543,10 @@ class ProcessPanel(QFrame, Styles):
 			msgBox.setStandardButtons(QMessageBox.Ok)
 			returnValue = msgBox.exec()
 			if returnValue == QMessageBox.Ok:
-				return None	
+				return None
 			else:
 				return None
-		else:	
+		else:
 			self.ClassifierWidget = ClassifierWidget(self)
 			self.ClassifierWidget.show()
 
@@ -520,7 +555,7 @@ class ProcessPanel(QFrame, Styles):
 		self.ConfigSignalAnnotator.show()
 
 	def process_population(self):
-		
+
 		if self.parent_window.well_list.currentText()=="*":
 			self.well_index = np.linspace(0,len(self.wells)-1,len(self.wells),dtype=int)
 		else:
@@ -534,7 +569,28 @@ class ProcessPanel(QFrame, Styles):
 			self.threshold_config = self.threshold_config_targets
 		elif self.mode=="effectors":
 			self.threshold_config = self.threshold_config_effectors
-		
+
+		self.load_available_tables()
+
+		if self.df is not None and self.segment_action.isChecked():
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Question)
+			msgBox.setText("Measurement tables have been found... Re-segmenting may create mismatches between the cell labels and the associated measurements. Do you want to erase the tables post-segmentation?")
+			msgBox.setWindowTitle("Info")
+			msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No | QMessageBox.Cancel)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.No:
+				pass
+			elif returnValue == QMessageBox.Cancel:
+				return None
+			else:
+				print('erase tabs!')
+				tabs = [pos+os.sep.join(['output', 'tables', f'trajectories_{self.mode}.csv']) for pos in self.df_pos_info['pos_path'].unique()]
+				for t in tabs:
+					if os.path.exists(t.replace('.csv','.pkl')):
+						os.remove(t.replace('.csv','.pkl'))
+					os.remove(t)				
+
 		loop_iter=0
 
 		if self.parent_window.position_list.currentText()=="*":
@@ -546,7 +602,7 @@ class ProcessPanel(QFrame, Styles):
 			returnValue = msgBox.exec()
 			if returnValue == QMessageBox.No:
 				return None
-		
+
 		if self.seg_model_list.currentIndex() > len(self.models_truncated):
 			self.model_name = self.seg_models[self.seg_model_list.currentIndex()-1]
 		else:
@@ -557,7 +613,7 @@ class ProcessPanel(QFrame, Styles):
 
 			self.diamWidget = QWidget()
 			self.diamWidget.setWindowTitle('Estimate diameter')
-			
+
 			layout = QVBoxLayout()
 			self.diamWidget.setLayout(layout)
 
@@ -583,12 +639,12 @@ class ProcessPanel(QFrame, Styles):
 				if k==1:
 					self.cellpose_channel_cb[k].addItems(list(self.exp_channels)+['None'])
 				else:
-					self.cellpose_channel_cb[k].addItems(list(self.exp_channels))					
+					self.cellpose_channel_cb[k].addItems(list(self.exp_channels))
 				idx = self.cellpose_channel_cb[k].findText(self.cellpose_channel_template[k])
 				if idx>0:
 					self.cellpose_channel_cb[k].setCurrentIndex(idx)
 				else:
-					self.cellpose_channel_cb[k].setCurrentIndex(0)			
+					self.cellpose_channel_cb[k].setCurrentIndex(0)
 
 				if k==1:
 					idx = self.cellpose_channel_cb[k].findText('None')
@@ -610,7 +666,7 @@ class ProcessPanel(QFrame, Styles):
 			hbox = QHBoxLayout()
 			hbox.addWidget(QLabel('flow threshold: '), 33)
 			hbox.addWidget(self.flow_slider, 66)
-			layout.addLayout(hbox)	
+			layout.addLayout(hbox)
 
 			self.cellprob_slider = QLabeledDoubleSlider()
 			self.cellprob_slider.setOrientation(1)
@@ -620,7 +676,7 @@ class ProcessPanel(QFrame, Styles):
 			hbox = QHBoxLayout()
 			hbox.addWidget(QLabel('cellprob threshold: '), 33)
 			hbox.addWidget(self.cellprob_slider, 66)
-			layout.addLayout(hbox)			
+			layout.addLayout(hbox)
 
 			self.set_cellpose_scale_btn = QPushButton('set')
 			self.set_cellpose_scale_btn.clicked.connect(self.set_cellpose_scale)
@@ -635,7 +691,7 @@ class ProcessPanel(QFrame, Styles):
 
 			self.diamWidget = QWidget()
 			self.diamWidget.setWindowTitle('Channels')
-			
+
 			layout = QVBoxLayout()
 			self.diamWidget.setLayout(layout)
 
@@ -654,7 +710,7 @@ class ProcessPanel(QFrame, Styles):
 				if k==1:
 					self.stardist_channel_cb[k].addItems(list(self.exp_channels)+['None'])
 				else:
-					self.stardist_channel_cb[k].addItems(list(self.exp_channels))					
+					self.stardist_channel_cb[k].addItems(list(self.exp_channels))
 				idx = self.stardist_channel_cb[k].findText(self.stardist_channel_template[k])
 				if idx>0:
 					self.stardist_channel_cb[k].setCurrentIndex(idx)
@@ -685,7 +741,7 @@ class ProcessPanel(QFrame, Styles):
 			well = self.parent_window.wells[w_idx]
 
 			for pos_idx in pos_indices:
-				
+
 				self.pos = natsorted(glob(well+f"{os.path.split(well)[-1].replace('W','').replace(os.sep,'')}*/"))[pos_idx]
 				print(f"Position {self.pos}...\nLoading stack movie...")
 
@@ -695,7 +751,7 @@ class ProcessPanel(QFrame, Styles):
 					os.mkdir(self.pos + 'output/tables/')
 
 				if self.segment_action.isChecked():
-					
+
 					if len(glob(os.sep.join([self.pos, f'labels_{self.mode}','*.tif'])))>0 and self.parent_window.position_list.currentText()!="*":
 						msgBox = QMessageBox()
 						msgBox.setIcon(QMessageBox.Question)
@@ -715,7 +771,7 @@ class ProcessPanel(QFrame, Styles):
 							msgBox.setStandardButtons(QMessageBox.Ok)
 							returnValue = msgBox.exec()
 							if returnValue == QMessageBox.Ok:
-								return None					
+								return None
 						else:
 							print(f"Segmentation from threshold config: {self.threshold_config}")
 							segment_from_threshold_at_position(self.pos, self.mode, self.threshold_config, threads=self.parent_window.parent_window.n_threads)
@@ -768,12 +824,12 @@ class ProcessPanel(QFrame, Styles):
 		# self.unfreeze()
 
 	def view_current_stack_with_scale_bar(self):
-		
+
 		self.parent_window.locate_image()
 		if self.parent_window.current_stack is not None:
 			self.viewer = CellSizeViewer(
-										  initial_diameter = float(self.diameter_le.text().replace(',','.')),
-										  parent_le = self.diameter_le,
+										  initial_diameter = float(self.diameter_le.text().replace(',', '.')),
+				parent_le = self.diameter_le,
 										  stack_path=self.parent_window.current_stack,
 										  window_title=f'Position {self.parent_window.position_list.currentText()}',
 										  frame_slider = True,
@@ -791,7 +847,7 @@ class ProcessPanel(QFrame, Styles):
 		control_tracking_btrack(self.parent_window.pos, prefix=self.parent_window.movie_prefix, population=self.mode, threads=self.parent_window.parent_window.n_threads)
 
 	def view_table_ui(self):
-		
+
 		print('Load table...')
 		self.load_available_tables()
 
@@ -813,13 +869,13 @@ class ProcessPanel(QFrame, Styles):
 				return None
 
 	# def interpret_pos_location(self):
-		
+
 	# 	"""
 	# 	Read the well/position selection from the control panel to decide which data to load
 	# 	Set position_indices to None if all positions must be taken
 
 	# 	"""
-		
+
 	# 	if self.well_option==len(self.wells):
 	# 		self.well_indices = np.arange(len(self.wells))
 	# 	else:
@@ -865,7 +921,7 @@ class ProcessPanel(QFrame, Styles):
 		print(new_channels)
 		with open(input_config_path) as config_file:
 			input_config = json.load(config_file)
-		
+
 		input_config['spatial_calibration'] = scale
 		input_config['channels'] = new_channels
 		input_config['flow_threshold'] = flow_thresh
@@ -890,7 +946,7 @@ class ProcessPanel(QFrame, Styles):
 		new_channels = [self.stardist_channel_cb[i].currentText() for i in range(len(self.stardist_channel_cb))]
 		with open(input_config_path) as config_file:
 			input_config = json.load(config_file)
-		
+
 		# input_config['spatial_calibration'] = scale
 		input_config['channels'] = new_channels
 		# input_config['flow_threshold'] = flow_thresh
@@ -906,17 +962,18 @@ class ProcessPanel(QFrame, Styles):
 class NeighPanel(QFrame, Styles):
 	def __init__(self, parent_window):
 
-		super().__init__()		
+		super().__init__()
 		self.parent_window = parent_window
 		self.exp_channels = self.parent_window.exp_channels
 		self.exp_dir = self.parent_window.exp_dir
 		self.wells = np.array(self.parent_window.wells,dtype=str)
 		self.protocols = []
+		self.mode='neighborhood'
 
 		self.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.grid = QGridLayout(self)
 		self.generate_header()
-	
+
 	def generate_header(self):
 
 		"""
@@ -924,7 +981,7 @@ class NeighPanel(QFrame, Styles):
 
 		"""
 
-		panel_title = QLabel(f"NEIGHBORHOOD")
+		panel_title = QLabel(f"INTERACTIONS")
 		panel_title.setStyleSheet(self.block_title)
 
 		self.grid.addWidget(panel_title, 0, 0, 1, 4, alignment=Qt.AlignCenter)
@@ -935,7 +992,7 @@ class NeighPanel(QFrame, Styles):
 		# self.all_ticked = False
 		# self.select_all_btn.setStyleSheet(self.button_select_all)
 		# self.grid.addWidget(self.select_all_btn, 0, 0, 1, 4, alignment=Qt.AlignLeft)
-		
+
 		self.collapse_btn = QPushButton()
 		self.collapse_btn.setIcon(icon(MDI6.chevron_down,color="black"))
 		self.collapse_btn.setIconSize(QSize(25, 25))
@@ -943,7 +1000,7 @@ class NeighPanel(QFrame, Styles):
 		self.grid.addWidget(self.collapse_btn, 0, 0, 1, 4, alignment=Qt.AlignRight)
 
 		self.populate_contents()
-		
+
 		self.grid.addWidget(self.ContentsFrame, 1, 0, 1, 4, alignment=Qt.AlignTop)
 		self.collapse_btn.clicked.connect(lambda: self.ContentsFrame.setHidden(not self.ContentsFrame.isHidden()))
 		self.collapse_btn.clicked.connect(self.collapse_advanced)
@@ -962,7 +1019,7 @@ class NeighPanel(QFrame, Styles):
 			self.collapse_btn.setIconSize(QSize(20, 20))
 			#self.parent.w.adjustSize()
 			#self.parent.adjustSize()
-			self.parent_window.scroll.setMinimumHeight(min(int(750), int(0.8*self.parent_window.screen_height)))
+			self.parent_window.scroll.setMinimumHeight(min(int(1000), int(0.9*self.parent_window.screen_height)))
 			self.parent_window.scroll.setMinimumWidth(425)
 
 
@@ -971,8 +1028,26 @@ class NeighPanel(QFrame, Styles):
 		self.ContentsFrame = QFrame()
 		self.grid_contents = QGridLayout(self.ContentsFrame)
 		self.grid_contents.setContentsMargins(0,0,0,0)
-		self.grid_contents.setSpacing(0)
-
+		self.grid_contents.setSpacing(3)
+
+		# Button to compute the neighborhoods
+		neigh_option_hbox = QHBoxLayout()
+		self.neigh_action = QCheckBox('NEIGHBORHOODS')
+		self.neigh_action.setStyleSheet("""
+					font-size: 10px;
+					padding-left: 10px;
+					padding-top: 5px;
+					""")
+		#self.neigh_action.setIcon(icon(MDI6.eyedropper, color="black"))
+		#self.neigh_action.setIconSize(QSize(20, 20))
+		self.neigh_action.setToolTip(
+			"Compute neighborhoods in list below.")
+		neigh_option_hbox.addWidget(self.neigh_action,90)
+		self.grid_contents.addLayout(neigh_option_hbox, 1,0,1,4)
+
+		neigh_options_layout = QVBoxLayout()
+
+		neigh_options_vbox = QVBoxLayout()
 
 		# DISTANCE NEIGHBORHOOD
 		dist_neigh_hbox = QHBoxLayout()
@@ -982,10 +1057,11 @@ class NeighPanel(QFrame, Styles):
 		self.dist_neigh_action = QLabel("ISOTROPIC DISTANCE THRESHOLD")
 		self.dist_neigh_action.setStyleSheet(self.action_lbl_style_sheet)
 		#self.dist_neigh_action.setIcon(icon(MDI6.circle_expand, color='black'))
+		self.dist_neigh_action.setToolTip("")
 		self.dist_neigh_action.setToolTip("Define an isotropic neighborhood between the center of mass\nof the cells, within a threshold distance.")
 		#self.segment_action.toggled.connect(self.enable_segmentation_model_list)
 		#self.to_disable.append(self.segment_action)
-		
+
 		self.config_distance_neigh_btn = QPushButton()
 		self.config_distance_neigh_btn.setIcon(icon(MDI6.plus,color="black"))
 		self.config_distance_neigh_btn.setIconSize(QSize(20, 20))
@@ -994,10 +1070,9 @@ class NeighPanel(QFrame, Styles):
 		self.config_distance_neigh_btn.clicked.connect(self.open_config_distance_threshold_neighborhood)
 		dist_neigh_hbox.addWidget(self.config_distance_neigh_btn,5)
 		dist_neigh_hbox.addWidget(self.dist_neigh_action, 95)
+		neigh_options_vbox.addLayout(dist_neigh_hbox)
 
-		self.grid_contents.addLayout(dist_neigh_hbox, 0,0,1,4)
-
-		# DISTANCE NEIGHBORHOOD
+		# CONTACT NEIGHBORHOOD
 		contact_neighborhood_layout = QHBoxLayout()
 		contact_neighborhood_layout.setContentsMargins(0,0,0,0)
 		contact_neighborhood_layout.setSpacing(0)
@@ -1006,7 +1081,8 @@ class NeighPanel(QFrame, Styles):
 		self.contact_neigh_action.setToolTip("Identify touching cell masks, within a threshold edge distance.")
 		self.contact_neigh_action.setStyleSheet(self.action_lbl_style_sheet)
 		#self.contact_neigh_action.setIcon(icon(MDI6.transition_masked, color='black'))
-		
+		self.contact_neigh_action.setToolTip("")
+
 		self.config_contact_neigh_btn = QPushButton()
 		self.config_contact_neigh_btn.setIcon(icon(MDI6.plus,color="black"))
 		self.config_contact_neigh_btn.setIconSize(QSize(20, 20))
@@ -1015,10 +1091,10 @@ class NeighPanel(QFrame, Styles):
 		self.config_contact_neigh_btn.clicked.connect(self.open_config_contact_neighborhood)
 		contact_neighborhood_layout.addWidget(self.config_contact_neigh_btn,5)
 		contact_neighborhood_layout.addWidget(self.contact_neigh_action, 95)
+		neigh_options_vbox.addLayout(contact_neighborhood_layout)
+		#self.grid_contents.addLayout(neigh_options_vbox, 2,0,1,4)
 
-		self.grid_contents.addLayout(contact_neighborhood_layout, 1,0,1,4)
-
-		self.grid_contents.addWidget(QHSeperationLine(), 2, 0, 1, 4)
+		#self.grid_contents.addWidget(QHSeperationLine(), 3, 0, 1, 4)
 
 		self.delete_protocol_btn = QPushButton('')
 		self.delete_protocol_btn.setStyleSheet(self.button_select_all)
@@ -1034,15 +1110,205 @@ class NeighPanel(QFrame, Styles):
 		list_header_layout = QHBoxLayout()
 		list_header_layout.addWidget(self.protocol_list_lbl)
 		list_header_layout.addWidget(self.delete_protocol_btn, alignment=Qt.AlignRight)
-		self.grid_contents.addLayout(list_header_layout, 3, 0, 1, 4)
-		self.grid_contents.addWidget(self.protocol_list, 4, 0, 1, 4)
+		#self.grid_contents.addLayout(list_header_layout, 4, 0, 1, 4)
+		#self.grid_contents.addWidget(self.protocol_list, 5, 0, 1, 4)
+
+		neigh_options_layout.addLayout(neigh_options_vbox)
+		neigh_options_layout.addWidget(QHSeperationLine())
+		neigh_options_layout.addLayout(list_header_layout)
+		neigh_options_layout.addWidget(self.protocol_list)
+
+		neigh_options_layout.setContentsMargins(30,5,30,5)
+		neigh_options_layout.setSpacing(1)
+		self.grid_contents.addLayout(neigh_options_layout, 5, 0, 1, 4)
+
+
+		rel_layout = QHBoxLayout()
+		self.measure_pairs_action = QCheckBox("MEASURE PAIRS")
+		self.measure_pairs_action.setStyleSheet("""
+					font-size: 10px;
+					padding-left: 10px;
+					padding-top: 5px;
+					""")
+		self.measure_pairs_action.setIcon(icon(MDI6.eyedropper, color="black"))
+		self.measure_pairs_action.setIconSize(QSize(20, 20))
+		self.measure_pairs_action.setToolTip("Measure the relative quantities defined for the cell pairs, for all neighborhoods.")
+		rel_layout.addWidget(self.measure_pairs_action, 90)
+
+		# self.visu_btn = QPushButton()
+		# self.visu_btn.setIcon(icon(MDI6.eye_check_outline,color="black"))
+		# self.visu_btn.setIconSize(QSize(20, 20))
+		# self.visu_btn.clicked.connect(self.check_measurements2)
+		# self.visu_btn.setToolTip("Open measurement annotator for two populations.")
+		# self.visu_btn.setStyleSheet(self.button_select_all)
+		# self.grid_contents.addWidget(self.visu_btn, 1,1,1,1,alignment=Qt.AlignRight)
+		# rel_layout.addWidget(self.visu_btn, 6)
+
+		# self.config_rel_annotator_btn = QPushButton()
+		# self.config_rel_annotator_btn.setIcon(icon(MDI6.cog_outline, color="black"))
+		# self.config_rel_annotator_btn.setIconSize(QSize(20, 20))
+		# self.config_rel_annotator_btn.setToolTip("Configure the animation of the annotation tool.")
+		# self.config_rel_annotator_btn.setStyleSheet(self.button_select_all)
+		# self.config_rel_annotator_btn.clicked.connect(self.open_signal_annotator_configuration_ui)
+		# # self.grid_contents.addWidget(self.config_rel_annotator_btn, 1,2,1,1, alignment=Qt.AlignRight)
+		# rel_layout.addWidget(self.config_rel_annotator_btn, 6)
+		self.grid_contents.addLayout(rel_layout, 6, 0, 1, 4)
+
+		signal_layout = QVBoxLayout()
+		signal_hlayout = QHBoxLayout()
+		self.signal_analysis_action = QCheckBox("PAIR SIGNAL ANALYSIS")
+		self.signal_analysis_action.setStyleSheet("""
+		font-size: 10px;
+		padding-left: 10px;
+		padding-top: 5px;""")
+
+		self.signal_analysis_action.setIcon(icon(MDI6.chart_bell_curve_cumulative, color="black"))
+		self.signal_analysis_action.setIconSize(QSize(20, 20))
+		self.signal_analysis_action.setToolTip("Detect cell pair events using a DL model.")
+		self.signal_analysis_action.toggled.connect(self.enable_signal_model_list)
+		signal_hlayout.addWidget(self.signal_analysis_action, 90)
+
+		self.check_signals_btn = QPushButton()
+		self.check_signals_btn.setIcon(icon(MDI6.eye_check_outline, color="black"))
+		self.check_signals_btn.setIconSize(QSize(20, 20))
+		self.check_signals_btn.clicked.connect(self.check_signals2)
+		self.check_signals_btn.setToolTip("Annotate dynamic cell pairs.")
+		self.check_signals_btn.setStyleSheet(self.button_select_all)
+		signal_hlayout.addWidget(self.check_signals_btn, 6)
+
+		self.config_signal_annotator_btn = QPushButton()
+		self.config_signal_annotator_btn.setIcon(icon(MDI6.cog_outline, color="black"))
+		self.config_signal_annotator_btn.setIconSize(QSize(20, 20))
+		self.config_signal_annotator_btn.setToolTip("Configure the animation of the annotation tool.")
+		self.config_signal_annotator_btn.setStyleSheet(self.button_select_all)
+		self.config_signal_annotator_btn.clicked.connect(self.open_signal_annotator_configuration_ui)
+		signal_hlayout.addWidget(self.config_signal_annotator_btn, 6)
+		signal_layout.addLayout(signal_hlayout)
+		# self.to_disable.append(self.measure_action_tc)
+		pair_signal_model_vbox = QVBoxLayout()
+		pair_signal_model_vbox.setContentsMargins(25, 0, 25, 0)
+
+		pair_model_zoo_layout = QHBoxLayout()
+		pair_model_zoo_layout.addWidget(QLabel("Model zoo:"), 90)
+
+		self.pair_signal_models_list = QComboBox()
+		self.pair_signal_models_list.setEnabled(False)
+		self.refresh_signal_models()
+		# self.to_disable.append(self.cell_models_list)
+
+		self.pair_train_signal_model_btn = QPushButton("TRAIN")
+		self.pair_train_signal_model_btn.setToolTip("Train a cell pair event detection model.")
+		self.pair_train_signal_model_btn.setIcon(icon(MDI6.redo_variant, color='black'))
+		self.pair_train_signal_model_btn.setIconSize(QSize(20, 20))
+		self.pair_train_signal_model_btn.setStyleSheet(self.button_style_sheet_3)
+		pair_model_zoo_layout.addWidget(self.pair_train_signal_model_btn, 5)
+		self.pair_train_signal_model_btn.clicked.connect(self.open_signal_model_config_ui)
+
+		pair_signal_model_vbox.addLayout(pair_model_zoo_layout)
+		pair_signal_model_vbox.addWidget(self.pair_signal_models_list)
+
+		signal_layout.addLayout(pair_signal_model_vbox)
+		self.grid_contents.addLayout(signal_layout, 7, 0, 1, 4)
+		self.grid_contents.addWidget(QHSeperationLine(), 11, 0, 1, 4)
+
+		self.view_tab_btn = QPushButton("View table")
+		self.view_tab_btn.setStyleSheet(self.button_style_sheet_2)
+		self.view_tab_btn.clicked.connect(self.view_table_ui)
+		self.view_tab_btn.setToolTip('View table')
+		self.view_tab_btn.setIcon(icon(MDI6.table,color="#1565c0"))
+		self.view_tab_btn.setIconSize(QSize(20, 20))
+		#self.view_tab_btn.setEnabled(False)
+		self.grid_contents.addWidget(self.view_tab_btn, 12, 0, 1, 4)
+
+		#self.grid_contents.addWidget(QLabel(''), 12, 0, 1, 4)
 
 		self.submit_btn = QPushButton("Submit")
 		self.submit_btn.setStyleSheet(self.button_style_sheet_2)
 		self.submit_btn.setToolTip("Compute the neighborhoods of the selected positions.")
 		self.submit_btn.clicked.connect(self.process_neighborhood)
-		self.grid_contents.addWidget(self.submit_btn, 5, 0, 1, 4)
+		self.grid_contents.addWidget(self.submit_btn, 14, 0, 1, 4)
+
+		self.neigh_action.toggled.connect(self.activate_neigh_options)
+		self.neigh_action.setChecked(True)
+		self.neigh_action.setChecked(False)
+
+
+	def load_available_tables(self):
+
+		"""
+		Load the tables of the selected wells/positions from the control Panel for the population of interest
+
+		"""
+
+		self.well_option = self.parent_window.well_list.currentIndex()
+		if self.well_option==len(self.wells):
+			wo = '*'
+		else:
+			wo = self.well_option
+		self.position_option = self.parent_window.position_list.currentIndex()
+		if self.position_option==0:
+			po = '*'
+		else:
+			po = self.position_option - 1
+
+		self.df, self.df_pos_info = load_experiment_tables(self.exp_dir, well_option=wo, position_option=po, population="pairs", return_pos_info=True)
+		if self.df is None:
+			print('No table could be found...')
+
+
+	def view_table_ui(self):
+
+		print('Load table...')
+		self.load_available_tables()
+
+		if self.df is not None:
+			plot_mode = 'static'
+			self.tab_ui = TableUI(self.df, f"Well {self.parent_window.well_list.currentText()}; Position {self.parent_window.position_list.currentText()}", population='pairs', plot_mode=plot_mode)
+			self.tab_ui.show()
+		else:
+			print('Table could not be loaded...')
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Warning)
+			msgBox.setText("No table could be loaded...")
+			msgBox.setWindowTitle("Info")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None
+
+
+	def activate_neigh_options(self):
+
+		if self.neigh_action.isChecked():
+			self.dist_neigh_action.setEnabled(True)
+			self.contact_neigh_action.setEnabled(True)
+			self.config_distance_neigh_btn.setEnabled(True)
+			self.config_contact_neigh_btn.setEnabled(True)
+			self.protocol_list_lbl.setEnabled(True)
+			self.protocol_list.setEnabled(True)
+			self.delete_protocol_btn.setEnabled(True)
+		else:
+			self.dist_neigh_action.setEnabled(False)
+			self.contact_neigh_action.setEnabled(False)
+			self.config_distance_neigh_btn.setEnabled(False)
+			self.config_contact_neigh_btn.setEnabled(False)
+			self.protocol_list_lbl.setEnabled(False)
+			self.protocol_list.setEnabled(False)
+			self.delete_protocol_btn.setEnabled(False)
+
+	def refresh_signal_models(self):
+		signal_models = get_pair_signal_models_list()
+		self.pair_signal_models_list.clear()
+		self.pair_signal_models_list.addItems(signal_models)
+
+	def open_signal_annotator_configuration_ui(self):
+		self.ConfigSignalAnnotator = ConfigSignalAnnotator(self)
+		self.ConfigSignalAnnotator.show()
 
+	def open_signal_model_config_ui(self):
+		self.ConfigSignalTrain = ConfigSignalModelTraining(self, signal_mode='pairs')
+		self.ConfigSignalTrain.show()
+		
 	def remove_protocol_from_list(self):
 
 		current_item = self.protocol_list.currentRow()
@@ -1066,9 +1332,14 @@ class NeighPanel(QFrame, Styles):
 											   )
 		self.ConfigNeigh.show()
 
+	def enable_signal_model_list(self):
+		if self.signal_analysis_action.isChecked():
+			self.pair_signal_models_list.setEnabled(True)
+		else:
+			self.pair_signal_models_list.setEnabled(False)
 
 	def process_neighborhood(self):
-		
+
 		if self.parent_window.well_list.currentText()=="*":
 			self.well_index = np.linspace(0,len(self.wells)-1,len(self.wells),dtype=int)
 		else:
@@ -1089,7 +1360,7 @@ class NeighPanel(QFrame, Styles):
 			returnValue = msgBox.exec()
 			if returnValue == QMessageBox.No:
 				return None
-		
+
 		for w_idx in self.well_index:
 
 			pos = self.parent_window.positions[w_idx]
@@ -1103,7 +1374,7 @@ class NeighPanel(QFrame, Styles):
 			well = self.parent_window.wells[w_idx]
 
 			for pos_idx in pos_indices:
-				
+
 				self.pos = natsorted(glob(well+f"{os.path.split(well)[-1].replace('W','').replace(os.sep,'')}*{os.sep}"))[pos_idx]
 				print(f"Position {self.pos}...\nLoading stack movie...")
 
@@ -1112,41 +1383,88 @@ class NeighPanel(QFrame, Styles):
 				if not os.path.exists(self.pos + os.sep.join(['output','tables'])+os.sep):
 					os.mkdir(self.pos + os.sep.join(['output','tables'])+os.sep)
 
-				for protocol in self.protocols:
-
-					if protocol['neighborhood_type']=='distance_threshold':
-						
-						compute_neighborhood_at_position(self.pos, 
-														protocol['distance'], 
-														population=protocol['population'], 
-														theta_dist=None, 
-														img_shape=(self.parent_window.shape_x,self.parent_window.shape_y), 
+				if self.neigh_action.isChecked():
+					for protocol in self.protocols:
+
+						if protocol['neighborhood_type']=='distance_threshold':
+
+							compute_neighborhood_at_position(self.pos,
+															protocol['distance'],
+															population=protocol['population'],
+															theta_dist=None,
+															img_shape=(self.parent_window.shape_x,self.parent_window.shape_y),
+															return_tables=False,
+															clear_neigh=protocol['clear_neigh'],
+															event_time_col=protocol['event_time_col'],
+															neighborhood_kwargs=protocol['neighborhood_kwargs'],
+															)
+
+						elif protocol['neighborhood_type']=='mask_contact':
+
+							compute_contact_neighborhood_at_position(self.pos,
+														protocol['distance'],
+														population=protocol['population'],
+														theta_dist=None,
+														img_shape=(self.parent_window.shape_x,self.parent_window.shape_y),
 														return_tables=False,
 														clear_neigh=protocol['clear_neigh'],
 														event_time_col=protocol['event_time_col'],
 														neighborhood_kwargs=protocol['neighborhood_kwargs'],
 														)
+				if self.measure_pairs_action.isChecked():
+					rel_measure_at_position(self.pos)
 
-					elif protocol['neighborhood_type']=='mask_contact':
-
-						compute_contact_neighborhood_at_position(self.pos, 
-														protocol['distance'], 
-														population=protocol['population'], 
-														theta_dist=None, 
-														img_shape=(self.parent_window.shape_x,self.parent_window.shape_y), 
-														return_tables=False,
-														clear_neigh=protocol['clear_neigh'],
-														event_time_col=protocol['event_time_col'],
-														neighborhood_kwargs=protocol['neighborhood_kwargs'],
-														)
+				if self.signal_analysis_action.isChecked():
+					
+					# df_targets = get_position_pickle(self.pos, population='targets')
+					# df_effectors = get_position_pickle(self.pos, population='effectors')
+					# self.dataframes = {
+					# 	'targets': df_targets,
+					# 	'effectors': df_effectors,
+					# }
+
+					# df_pairs = get_position_table(self.pos, population='pairs')
+
+					# # Need to identify expected reference / neighbor tables
+					# model_path = locate_signal_model(self.pair_signal_models_list.currentText(), pairs=True)
+					# print(f'Looking for model in {model_path}...')
+					# complete_path = model_path
+					# complete_path = rf"{complete_path}"
+					# model_config_path = os.sep.join([complete_path, 'config_input.json'])
+					# model_config_path = rf"{model_config_path}"
+					# f = open(model_config_path)
+					# model_config_path = json.load(f)
+
+					# reference_population = model_config_path['reference_population']
+					# neighbor_population = model_config_path['neighbor_population']
+
+					# analyze_pair_signals(df_pairs, self.dataframes[reference_population], self.dataframes[neighbor_population], model=self.pair_signal_models_list.currentText())
+					analyze_pair_signals_at_position(self.pos, self.pair_signal_models_list.currentText(), use_gpu=self.parent_window.parent_window.use_gpu)
+		self.parent_window.update_position_options()
 		print('Done.')
 
 
+	def check_signals2(self):
+
+		test = self.parent_window.locate_selected_position()
+		if test:
+			self.SignalAnnotator2 = SignalAnnotator2(self)
+			self.SignalAnnotator2.show()
+
+	def check_measurements2(self):
+
+		test = self.parent_window.locate_selected_position()
+		if test:
+			self.MeasurementAnnotator2 = MeasureAnnotator2(self)
+			self.MeasurementAnnotator2.show()
+
+
+
 class PreprocessingPanel(QFrame, Styles):
-	
+
 	def __init__(self, parent_window):
 
-		super().__init__()		
+		super().__init__()
 		self.parent_window = parent_window
 		self.exp_channels = self.parent_window.exp_channels
 		self.exp_dir = self.parent_window.exp_dir
@@ -1157,12 +1475,12 @@ class PreprocessingPanel(QFrame, Styles):
 		self.background_correction = []
 		self.onlyFloat = QDoubleValidator()
 		self.onlyInt = QIntValidator()
-		
+
 		self.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.grid = QGridLayout(self)
 
 		self.generate_header()
-	
+
 	def generate_header(self):
 
 		"""
@@ -1186,7 +1504,7 @@ class PreprocessingPanel(QFrame, Styles):
 		self.select_all_btn.setStyleSheet(self.button_select_all)
 		self.grid.addWidget(self.select_all_btn, 0, 0, 1, 4, alignment=Qt.AlignLeft)
 		#self.to_disable.append(self.all_tc_actions)
-		
+
 		self.collapse_btn = QPushButton()
 		self.collapse_btn.setIcon(icon(MDI6.chevron_down,color="black"))
 		self.collapse_btn.setIconSize(QSize(25, 25))
@@ -1194,7 +1512,7 @@ class PreprocessingPanel(QFrame, Styles):
 		self.grid.addWidget(self.collapse_btn, 0, 0, 1, 4, alignment=Qt.AlignRight)
 
 		self.populate_contents()
-		
+
 		self.grid.addWidget(self.ContentsFrame, 1, 0, 1, 4, alignment=Qt.AlignTop)
 		self.collapse_btn.clicked.connect(lambda: self.ContentsFrame.setHidden(not self.ContentsFrame.isHidden()))
 		self.collapse_btn.clicked.connect(self.collapse_advanced)
@@ -1213,7 +1531,7 @@ class PreprocessingPanel(QFrame, Styles):
 			self.collapse_btn.setIconSize(QSize(20, 20))
 			#self.parent.w.adjustSize()
 			#self.parent.adjustSize()
-			self.parent_window.scroll.setMinimumHeight(min(int(880), int(0.8*self.parent_window.screen_height)))
+			self.parent_window.scroll.setMinimumHeight(min(int(930), int(0.9*self.parent_window.screen_height)))
 			self.parent_window.scroll.setMinimumWidth(425)
 
 	def populate_contents(self):
@@ -1237,7 +1555,7 @@ class PreprocessingPanel(QFrame, Styles):
 
 
 	def launch_preprocessing(self):
-		
+
 		msgBox1 = QMessageBox()
 		msgBox1.setIcon(QMessageBox.Question)
 		msgBox1.setText("Do you want to apply the preprocessing\nto all wells and positions?")
@@ -1260,7 +1578,7 @@ class PreprocessingPanel(QFrame, Styles):
 				return None
 			if returnValue == QMessageBox.No:
 				return None
-		
+
 		print('Proceed with correction...')
 
 		if self.parent_window.well_list.currentText()=='*':
@@ -1275,7 +1593,7 @@ class PreprocessingPanel(QFrame, Styles):
 
 
 		for k,correction_protocol in enumerate(self.protocol_layout.protocols):
-			
+
 			movie_prefix = None
 			export_prefix = 'Corrected'
 			if k>0:
@@ -1299,7 +1617,7 @@ class PreprocessingPanel(QFrame, Styles):
 			
 			elif correction_protocol['correction_type']=='fit':
 
-				correct_background_model(self.exp_dir, 
+				correct_background_model(self.exp_dir,
 								   well_option=well_option,
 								   position_option=pos_option,
 								   export= True,