celldetective 1.3.9.post4__py3-none-any.whl → 1.4.0__py3-none-any.whl

celldetective/gui/process_block.py

@@ -1,22 +1,22 @@
 from PyQt5.QtWidgets import QDialog, QFrame, QGridLayout, QComboBox, QListWidget, QLabel, QPushButton, QVBoxLayout, QHBoxLayout, QCheckBox, \
-	QMessageBox, QWidget
+	QMessageBox
 from PyQt5.QtCore import Qt, QSize
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 import gc
 from PyQt5.QtGui import QDoubleValidator, QIntValidator
 
+from celldetective.gui.processes.compute_neighborhood import NeighborhoodProcess
 from celldetective.gui.signal_annotator import MeasureAnnotator
 from celldetective.gui.signal_annotator2 import SignalAnnotator2
 from celldetective.io import get_segmentation_models_list, control_segmentation_napari, get_signal_models_list, \
 	control_tracks, load_experiment_tables, get_pair_signal_models_list
-from celldetective.io import locate_segmentation_model, extract_position_name, fix_missing_labels, 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.io import locate_segmentation_model, extract_position_name, fix_missing_labels, locate_signal_model
+from celldetective.gui import SegmentationModelLoader, ClassifierWidget, ConfigNeighborhoods, \
+	ConfigSegmentationModelTraining, ConfigTracking, SignalAnnotator, ConfigSignalModelTraining, ConfigMeasurements, \
+	ConfigSignalAnnotator, TableUI, CelldetectiveWidget
 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, analyze_pair_signals_at_position
 from celldetective.utils import extract_experiment_channels
 import numpy as np
@@ -27,13 +27,9 @@ import pandas as pd
 from celldetective.gui.gui_utils import center_window
 from tifffile import imwrite
 import json
-import psutil
-from celldetective.neighborhood import compute_neighborhood_at_position, compute_contact_neighborhood_at_position
-from celldetective.gui.gui_utils import FigureCanvas
 from celldetective.preprocessing import correct_background_model_free, correct_background_model, correct_channel_offset
-from celldetective.utils import _estimate_scale_factor, _extract_channel_indices_from_config, _extract_channel_indices, ConfigSectionMap, _extract_nbr_channels_from_config, _get_img_num_per_channel, normalize_per_channel
-from celldetective.gui.gui_utils import ThresholdLineEdit, QuickSliderLayout, help_generic
-from celldetective.gui.layouts import CellposeParamsWidget, StarDistParamsWidget, BackgroundModelFreeCorrectionLayout, ProtocolDesignerLayout, BackgroundFitCorrectionLayout, ChannelOffsetOptionsLayout
+from celldetective.gui.gui_utils import help_generic
+from celldetective.gui.layouts import SignalModelParamsWidget, SegModelParamsWidget, CellposeParamsWidget, StarDistParamsWidget, BackgroundModelFreeCorrectionLayout, ProtocolDesignerLayout, BackgroundFitCorrectionLayout, ChannelOffsetOptionsLayout
 from celldetective.gui import Styles
 from celldetective.utils import get_software_location
 
@@ -42,10 +38,8 @@ from celldetective.gui.processes.segment_cells import SegmentCellThresholdProces
 from celldetective.gui.processes.track_cells import TrackingProcess
 from celldetective.gui.processes.measure_cells import MeasurementProcess
 
-import time
-import asyncio
-
 class ProcessPanel(QFrame, Styles):
+	
 	def __init__(self, parent_window, mode):
 
 		super().__init__()
@@ -55,17 +49,20 @@ class ProcessPanel(QFrame, Styles):
 		self.exp_dir = self.parent_window.exp_dir
 		self.exp_config = self.parent_window.exp_config
 		self.movie_prefix = self.parent_window.movie_prefix
-		self.threshold_config_targets = None
-		self.threshold_config_effectors = None
-		self.wells = np.array(self.parent_window.wells,dtype=str)
+		self.threshold_configs = [None for _ in range(len(self.parent_window.populations))]
+		self.wells = np.array(self.parent_window.wells, dtype=str)
 		self.cellpose_calibrated = False
 		self.stardist_calibrated = False
+		self.segChannelsSet = False
+		self.signalChannelsSet = False
+		self.flipSeg = False
+
 		self.use_gpu = self.parent_window.parent_window.use_gpu
 		self.n_threads = self.parent_window.parent_window.n_threads
 
 		self.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
 		self.grid = QGridLayout(self)
-		self.grid.setContentsMargins(5,5,5,5)
+		self.grid.setContentsMargins(5, 5, 5, 5)
 		self.generate_header()
 
 	def generate_header(self):
@@ -85,35 +82,34 @@ class ProcessPanel(QFrame, Styles):
 		self.grid.addWidget(panel_title, 0, 0, 1, 4, alignment=Qt.AlignCenter)
 
 		self.help_pop_btn = QPushButton()
-		self.help_pop_btn.setIcon(icon(MDI6.help_circle,color=self.help_color))
+		self.help_pop_btn.setIcon(icon(MDI6.help_circle, color=self.help_color))
 		self.help_pop_btn.setIconSize(QSize(20, 20))
 		self.help_pop_btn.clicked.connect(self.help_population)
 		self.help_pop_btn.setStyleSheet(self.button_select_all)
 		self.help_pop_btn.setToolTip("Help.")
-		#self.grid.addWidget(self.help_pop_btn, 0, 0, 1, 3, alignment=Qt.AlignRight)
+		self.grid.addWidget(self.help_pop_btn, 0, 0, 1, 3, alignment=Qt.AlignRight)
 
-
-		self.select_all_btn = QPushButton()
-		self.select_all_btn.setIcon(icon(MDI6.checkbox_blank_outline,color="black"))
-		self.select_all_btn.setIconSize(QSize(20, 20))
-		self.all_ticked = False
-		self.select_all_btn.clicked.connect(self.tick_all_actions)
-		self.select_all_btn.setStyleSheet(self.button_select_all)
+		# self.select_all_btn = QPushButton()
+		# self.select_all_btn.setIcon(icon(MDI6.checkbox_blank_outline,color="black"))
+		# self.select_all_btn.setIconSize(QSize(20, 20))
+		# self.all_ticked = False
+		# self.select_all_btn.clicked.connect(self.tick_all_actions)
+		# 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.setIcon(icon(MDI6.chevron_down, color="black"))
 		self.collapse_btn.setIconSize(QSize(25, 25))
 		self.collapse_btn.setStyleSheet(self.button_select_all)
 		#self.grid.addWidget(self.collapse_btn, 0, 0, 1, 4, alignment=Qt.AlignRight)
 
-		title_hbox.addWidget(self.select_all_btn, 5)
+		title_hbox.addWidget(QLabel(), 5) #self.select_all_btn
 		title_hbox.addWidget(QLabel(), 85, alignment=Qt.AlignCenter)
 		title_hbox.addWidget(self.help_pop_btn, 5)
 		title_hbox.addWidget(self.collapse_btn, 5)
 
-		self.grid.addLayout(title_hbox, 0,0,1,4)
+		self.grid.addLayout(title_hbox, 0, 0, 1, 4)
 		self.populate_contents()
 
 		self.grid.addWidget(self.ContentsFrame, 1, 0, 1, 4, alignment=Qt.AlignTop)
@@ -123,20 +119,19 @@ class ProcessPanel(QFrame, Styles):
 
 	def collapse_advanced(self):
 
-		effector_open = not self.parent_window.ProcessEffectors.ContentsFrame.isHidden()
-		targets_open = not self.parent_window.ProcessTargets.ContentsFrame.isHidden()
+		panels_open = [not p.ContentsFrame.isHidden() for p in self.parent_window.ProcessPopulations]
 		interactions_open = not self.parent_window.NeighPanel.ContentsFrame.isHidden()
 		preprocessing_open = not self.parent_window.PreprocessingPanel.ContentsFrame.isHidden()
-		is_open = np.array([effector_open, targets_open, interactions_open, preprocessing_open])
+		is_open = np.array(panels_open+[interactions_open, preprocessing_open])
 
 		if self.ContentsFrame.isHidden():
-			self.collapse_btn.setIcon(icon(MDI6.chevron_down,color="black"))
+			self.collapse_btn.setIcon(icon(MDI6.chevron_down, color="black"))
 			self.collapse_btn.setIconSize(QSize(20, 20))
 			if len(is_open[is_open])==0:
 				self.parent_window.scroll.setMinimumHeight(int(550))
 				self.parent_window.adjustSize()
 		else:
-			self.collapse_btn.setIcon(icon(MDI6.chevron_up,color="black"))
+			self.collapse_btn.setIcon(icon(MDI6.chevron_up, color="black"))
 			self.collapse_btn.setIconSize(QSize(20, 20))
 			self.parent_window.scroll.setMinimumHeight(min(int(930), int(0.9*self.parent_window.screen_height)))
 
@@ -352,14 +347,14 @@ class ProcessPanel(QFrame, Styles):
 		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']))
+			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
@@ -378,6 +373,15 @@ class ProcessPanel(QFrame, Styles):
 		#self.to_disable.append(self.segment_action)
 		grid_segment.addWidget(self.segment_action, 90)
 
+		self.flip_segment_btn = QPushButton()
+		self.flip_segment_btn.setIcon(icon(MDI6.camera_flip_outline,color="black"))
+		self.flip_segment_btn.setIconSize(QSize(20, 20))
+		self.flip_segment_btn.clicked.connect(self.flip_segmentation)
+		self.flip_segment_btn.setStyleSheet(self.button_select_all)
+		self.flip_segment_btn.setToolTip("Flip the order of the frames for segmentation.")
+		grid_segment.addWidget(self.flip_segment_btn, 5)
+
+
 		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))
@@ -430,13 +434,25 @@ class ProcessPanel(QFrame, Styles):
 		self.seg_model_list.setEnabled(False)
 		self.grid_contents.addLayout(seg_option_vbox, 2, 0, 1, 4)
 
+	def flip_segmentation(self):
+		if not self.flipSeg:
+			self.flipSeg = True
+			self.flip_segment_btn.setIcon(icon(MDI6.camera_flip,color=self.celldetective_blue))
+			self.flip_segment_btn.setIconSize(QSize(20, 20))
+			self.flip_segment_btn.setToolTip("Unflip the order of the frames for segmentation.")
+		else:
+			self.flipSeg = False
+			self.flip_segment_btn.setIcon(icon(MDI6.camera_flip_outline,color='black'))
+			self.flip_segment_btn.setIconSize(QSize(20, 20))
+			self.flip_segment_btn.setToolTip("Flip the order of the frames for segmentation.")
+
 	def help_segmentation(self):
 
 		"""
 		Widget with different decision helper decision trees.
 		"""
 
-		self.help_w = QWidget()
+		self.help_w = CelldetectiveWidget()
 		self.help_w.setWindowTitle('Helper')
 		layout = QVBoxLayout()
 		seg_strategy_btn = QPushButton('A guide to choose a segmentation strategy.')
@@ -552,16 +568,18 @@ class ProcessPanel(QFrame, Styles):
 		#QApplication.setOverrideCursor(Qt.WaitCursor)
 		test = self.parent_window.locate_selected_position()
 		if test:
-			print('Memory use: ', dict(psutil.virtual_memory()._asdict()))
+			#print('Memory use: ', dict(psutil.virtual_memory()._asdict()))
+			print(f"Loading images and labels into napari...")
 			try:
 				control_segmentation_napari(self.parent_window.pos, prefix=self.parent_window.movie_prefix, population=self.mode,flush_memory=True)
 			except Exception as e:
+				print(f'Task unsuccessful... Exception {e}...')
 				msgBox = QMessageBox()
 				msgBox.setIcon(QMessageBox.Warning)
 				msgBox.setText(str(e))
 				msgBox.setWindowTitle("Warning")
 				msgBox.setStandardButtons(QMessageBox.Ok)
-				returnValue = msgBox.exec()
+				_ = msgBox.exec()
 
 				msgBox = QMessageBox()
 				msgBox.setIcon(QMessageBox.Question)
@@ -611,7 +629,8 @@ class ProcessPanel(QFrame, Styles):
 	def init_seg_model_list(self):
 
 		self.seg_model_list.clear()
-		self.seg_models = get_segmentation_models_list(mode=self.mode, return_path=False)
+		self.seg_models_specific = get_segmentation_models_list(mode=self.mode, return_path=False)
+		self.seg_models = self.seg_models_specific.copy() #get_segmentation_models_list(mode=self.mode, return_path=False)
 		thresh = 40
 		self.models_truncated = [m[:thresh - 3]+'...' if len(m)>thresh else m for m in self.seg_models]
 		#self.seg_model_list.addItems(models_truncated)
@@ -628,22 +647,22 @@ class ProcessPanel(QFrame, Styles):
 
 		self.seg_model_list.insertSeparator(len(self.models_truncated))
 
-	def tick_all_actions(self):
-		self.switch_all_ticks_option()
-		if self.all_ticked:
-			self.select_all_btn.setIcon(icon(MDI6.checkbox_outline,color="black"))
-			self.select_all_btn.setIconSize(QSize(20, 20))
-			self.segment_action.setChecked(True)
-		else:
-			self.select_all_btn.setIcon(icon(MDI6.checkbox_blank_outline,color="black"))
-			self.select_all_btn.setIconSize(QSize(20, 20))
-			self.segment_action.setChecked(False)
-
-	def switch_all_ticks_option(self):
-		if self.all_ticked == True:
-			self.all_ticked = False
-		else:
-			self.all_ticked = True
+	# def tick_all_actions(self):
+	# 	self.switch_all_ticks_option()
+	# 	if self.all_ticked:
+	# 		self.select_all_btn.setIcon(icon(MDI6.checkbox_outline,color="black"))
+	# 		self.select_all_btn.setIconSize(QSize(20, 20))
+	# 		self.segment_action.setChecked(True)
+	# 	else:
+	# 		self.select_all_btn.setIcon(icon(MDI6.checkbox_blank_outline,color="black"))
+	# 		self.select_all_btn.setIconSize(QSize(20, 20))
+	# 		self.segment_action.setChecked(False)
+
+	# def switch_all_ticks_option(self):
+	# 	if self.all_ticked == True:
+	# 		self.all_ticked = False
+	# 	else:
+	# 		self.all_ticked = True
 
 	def upload_segmentation_model(self):
 		print('Load a segmentation model or pipeline...')
@@ -696,6 +715,10 @@ class ProcessPanel(QFrame, Styles):
 	def reset_generalist_setup(self, index):
 		self.cellpose_calibrated = False
 		self.stardist_calibrated = False
+		self.segChannelsSet = False
+
+	def reset_signals(self):
+		self.signalChannelsSet = False
 
 	def process_population(self):
 
@@ -721,10 +744,8 @@ class ProcessPanel(QFrame, Styles):
 		# self.freeze()
 		# QApplication.setOverrideCursor(Qt.WaitCursor)
 
-		if self.mode=="targets":
-			self.threshold_config = self.threshold_config_targets
-		elif self.mode=="effectors":
-			self.threshold_config = self.threshold_config_effectors
+		idx = self.parent_window.populations.index(self.mode)
+		self.threshold_config = self.threshold_configs[idx]
 
 		self.load_available_tables()
 
@@ -742,6 +763,8 @@ class ProcessPanel(QFrame, Styles):
 			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()]
+				#tabs += [pos+os.sep.join(['output', 'tables', f'trajectories_pairs.csv']) for pos in self.df_pos_info['pos_path'].unique()]
+				tabs += [pos+os.sep.join(['output', 'tables', f'napari_{self.mode}_trajectories.npy']) 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'))
@@ -763,7 +786,6 @@ class ProcessPanel(QFrame, Styles):
 			self.model_name = self.seg_models[self.seg_model_list.currentIndex()-1]
 		else:
 			self.model_name = self.seg_models[self.seg_model_list.currentIndex()]
-		print(self.model_name, self.seg_model_list.currentIndex())
 
 		if self.segment_action.isChecked() and self.model_name.startswith('CP') and self.model_name in self.seg_models_generic and not self.cellpose_calibrated:
 
@@ -771,12 +793,24 @@ class ProcessPanel(QFrame, Styles):
 			self.diamWidget.show()
 			return None
 
-		if self.segment_action.isChecked() and self.model_name.startswith('SD') and self.model_name in self.seg_models_generic and not self.stardist_calibrated:
+		elif self.segment_action.isChecked() and self.model_name.startswith('SD') and self.model_name in self.seg_models_generic and not self.stardist_calibrated:
 
 			self.diamWidget = StarDistParamsWidget(self, model_name = self.model_name)
 			self.diamWidget.show()
 			return None
 
+		elif self.segment_action.isChecked() and self.model_name in self.seg_models_specific and not self.segChannelsSet:
+
+			self.segChannelWidget = SegModelParamsWidget(self, model_name = self.model_name)
+			self.segChannelWidget.show()
+			return None
+
+		if self.signal_analysis_action.isChecked() and not self.signalChannelsSet:
+			self.signalChannelWidget = SignalModelParamsWidget(self, model_name = self.signal_models_list.currentText())
+			self.signalChannelWidget.show()
+			return None
+
+
 		self.movie_prefix = self.parent_window.movie_prefix
 
 		for w_idx in self.well_index:
@@ -822,12 +856,13 @@ class ProcessPanel(QFrame, Styles):
 								return None
 						else:
 							print(f"Segmentation from threshold config: {self.threshold_config}")
-							process_args = {"pos": self.pos, "mode": self.mode, "n_threads": self.n_threads, "threshold_instructions": self.threshold_config, "use_gpu": self.use_gpu}
+							process_args = {"pos": self.pos, "mode": self.mode, "n_threads": self.n_threads, "threshold_instructions": self.threshold_config, "use_gpu": self.use_gpu, 'flip': self.flipSeg}
 							self.job = ProgressWindow(SegmentCellThresholdProcess, parent_window=self, title="Segment", process_args = process_args)
 							result = self.job.exec_()
 							if result == QDialog.Accepted:
 								pass
 							elif result == QDialog.Rejected:
+								self.reset_generalist_setup(0)
 								return None
 							#segment_from_threshold_at_position(self.pos, self.mode, self.threshold_config, threads=self.parent_window.parent_window.n_threads)
 					else:
@@ -836,12 +871,13 @@ class ProcessPanel(QFrame, Styles):
 						# 	process = {"output_dir": self.output_dir, "file": self.model_name}
 						# 	self.download_model_job = ProgressWindow(DownloadProcess, parent_window=self, title="Download", process_args = args)
 
-						process_args = {"pos": self.pos, "mode": self.mode, "n_threads": self.n_threads, "model_name": self.model_name, "use_gpu": self.use_gpu}
+						process_args = {"pos": self.pos, "mode": self.mode, "n_threads": self.n_threads, "model_name": self.model_name, "use_gpu": self.use_gpu, 'flip': self.flipSeg}
 						self.job = ProgressWindow(SegmentCellDLProcess, parent_window=self, title="Segment", process_args = process_args)
 						result = self.job.exec_()
 						if result == QDialog.Accepted:
 							pass
 						elif result == QDialog.Rejected:
+							self.reset_generalist_setup(0)
 							return None
 
 				if self.track_action.isChecked():
@@ -900,6 +936,7 @@ class ProcessPanel(QFrame, Styles):
 				action.setChecked(False)
 
 		self.reset_generalist_setup(0)
+		self.reset_signals()
 
 	def open_napari_tracking(self):
 		print(f'View the tracks before post-processing for position {self.parent_window.pos} in napari...')
@@ -938,8 +975,11 @@ class ProcessPanel(QFrame, Styles):
 		self.position_option = self.parent_window.position_list.getSelectedIndices()
 
 		self.df, self.df_pos_info = load_experiment_tables(self.exp_dir, well_option=self.well_option, position_option=self.position_option, population=self.mode, return_pos_info=True)
+		self.signals = []
+		if self.df is not None:
+			self.signals = list(self.df.columns)
 		if self.df is None:
-			print('No table could be found...')
+			print('No table could be found for the selected position(s)...')
 
 	def set_cellpose_scale(self):
 
@@ -951,7 +991,6 @@ class ProcessPanel(QFrame, Styles):
 		model_complete_path = locate_segmentation_model(self.model_name)
 		input_config_path = model_complete_path+"config_input.json"
 		new_channels = [self.diamWidget.cellpose_channel_cb[i].currentText() for i in range(2)]
-		print(new_channels)
 		with open(input_config_path) as config_file:
 			input_config = json.load(config_file)
 
@@ -983,6 +1022,46 @@ class ProcessPanel(QFrame, Styles):
 		self.diamWidget.close()
 		self.process_population()
 
+	def set_selected_channels_for_segmentation(self):
+
+		model_complete_path = locate_segmentation_model(self.model_name)
+		input_config_path = model_complete_path+"config_input.json"
+		new_channels = [self.segChannelWidget.channel_cbs[i].currentText() for i in range(len(self.segChannelWidget.channel_cbs))]
+		target_cell_size = None
+		if hasattr(self.segChannelWidget, "diameter_le"):
+			target_cell_size = float(self.segChannelWidget.diameter_le.get_threshold())
+
+		with open(input_config_path) as config_file:
+			input_config = json.load(config_file)
+
+		input_config.update({'selected_channels': new_channels, 'target_cell_size_um': target_cell_size})
+
+		#input_config['channels'] = new_channels
+		with open(input_config_path, 'w') as f:
+			json.dump(input_config, f, indent=4)
+
+		self.segChannelsSet = True
+		self.segChannelWidget.close()
+		self.process_population()
+
+	def set_selected_signals_for_event_detection(self):
+
+		model_complete_path = locate_signal_model(self.signal_models_list.currentText())
+		input_config_path = model_complete_path+"config_input.json"
+		new_channels = [self.signalChannelWidget.channel_cbs[i].currentText() for i in range(len(self.signalChannelWidget.channel_cbs))]
+		with open(input_config_path) as config_file:
+			input_config = json.load(config_file)
+
+		input_config.update({'selected_channels': new_channels})
+
+		#input_config['channels'] = new_channels
+		with open(input_config_path, 'w') as f:
+			json.dump(input_config, f, indent=4)
+
+		self.signalChannelsSet = True
+		self.signalChannelWidget.close()
+		self.process_population()
+
 
 
 class NeighPanel(QFrame, Styles):
@@ -1034,11 +1113,10 @@ class NeighPanel(QFrame, Styles):
 
 	def collapse_advanced(self):
 
-		effector_open = not self.parent_window.ProcessEffectors.ContentsFrame.isHidden()
-		targets_open = not self.parent_window.ProcessTargets.ContentsFrame.isHidden()
+		panels_open = [not p.ContentsFrame.isHidden() for p in self.parent_window.ProcessPopulations]
 		interactions_open = not self.parent_window.NeighPanel.ContentsFrame.isHidden()
 		preprocessing_open = not self.parent_window.PreprocessingPanel.ContentsFrame.isHidden()
-		is_open = np.array([effector_open, targets_open, interactions_open, preprocessing_open])
+		is_open = np.array(panels_open+[interactions_open, preprocessing_open])
 
 		if self.ContentsFrame.isHidden():
 			self.collapse_btn.setIcon(icon(MDI6.chevron_down,color="black"))
@@ -1432,6 +1510,7 @@ class NeighPanel(QFrame, Styles):
 			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]
+				self.pos_name = extract_position_name(self.pos)
 				print(f"Position {self.pos}...\nLoading stack movie...")
 
 				if not os.path.exists(self.pos + 'output' + os.sep):
@@ -1442,39 +1521,27 @@ class NeighPanel(QFrame, Styles):
 				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'],
-														)
+						process_args = {"pos": self.pos, "pos_name": self.pos_name,"protocol": protocol,"img_shape": (self.parent_window.shape_x,self.parent_window.shape_y)} #"n_threads": self.n_threads
+						self.job = ProgressWindow(NeighborhoodProcess, parent_window=self, title="Neighborhood",
+												  process_args=process_args)
+						result = self.job.exec_()
+						if result == QDialog.Accepted:
+							pass
+						elif result == QDialog.Rejected:
+							return None
+
 				if self.measure_pairs_action.isChecked():
 					rel_measure_at_position(self.pos)
 
 				if self.signal_analysis_action.isChecked():
 
-					analyze_pair_signals_at_position(self.pos, self.pair_signal_models_list.currentText(), use_gpu=self.parent_window.parent_window.use_gpu)
+					analyze_pair_signals_at_position(self.pos, self.pair_signal_models_list.currentText(), use_gpu=self.parent_window.parent_window.use_gpu, populations=self.parent_window.populations)
 
 		self.parent_window.update_position_options()
+		for action in [self.neigh_action, self.measure_pairs_action, self.signal_analysis_action]:
+			if action.isChecked():
+				action.setChecked(False)
+
 		print('Done.')
 
 	def check_signals2(self):
@@ -1484,14 +1551,6 @@ class NeighPanel(QFrame, Styles):
 			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):
 
@@ -1529,13 +1588,13 @@ class PreprocessingPanel(QFrame, Styles):
 
 		self.grid.addWidget(panel_title, 0, 0, 1, 4, alignment=Qt.AlignCenter)
 
-		self.select_all_btn = QPushButton()
-		self.select_all_btn.setIcon(icon(MDI6.checkbox_blank_outline,color="black"))
-		self.select_all_btn.setIconSize(QSize(20, 20))
-		self.all_ticked = False
-		#self.select_all_btn.clicked.connect(self.tick_all_actions)
-		self.select_all_btn.setStyleSheet(self.button_select_all)
-		self.grid.addWidget(self.select_all_btn, 0, 0, 1, 4, alignment=Qt.AlignLeft)
+		# self.select_all_btn = QPushButton()
+		# self.select_all_btn.setIcon(icon(MDI6.checkbox_blank_outline,color="black"))
+		# self.select_all_btn.setIconSize(QSize(20, 20))
+		# self.all_ticked = False
+		# #self.select_all_btn.clicked.connect(self.tick_all_actions)
+		# 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()
@@ -1553,12 +1612,11 @@ class PreprocessingPanel(QFrame, Styles):
 
 	def collapse_advanced(self):
 
-		effector_open = not self.parent_window.ProcessEffectors.ContentsFrame.isHidden()
-		targets_open = not self.parent_window.ProcessTargets.ContentsFrame.isHidden()
+		panels_open = [not p.ContentsFrame.isHidden() for p in self.parent_window.ProcessPopulations]
 		interactions_open = not self.parent_window.NeighPanel.ContentsFrame.isHidden()
 		preprocessing_open = not self.parent_window.PreprocessingPanel.ContentsFrame.isHidden()
-		is_open = np.array([effector_open, targets_open, interactions_open, preprocessing_open])
-
+		is_open = np.array(panels_open+[interactions_open, preprocessing_open])
+		
 		if self.ContentsFrame.isHidden():
 			self.collapse_btn.setIcon(icon(MDI6.chevron_down,color="black"))
 			self.collapse_btn.setIconSize(QSize(20, 20))
@@ -1592,7 +1650,6 @@ class PreprocessingPanel(QFrame, Styles):
 		self.help_background_btn.setToolTip("Help.")
 
 		self.protocol_layout.title_layout.addWidget(self.help_background_btn, 5, alignment=Qt.AlignRight)
-
 		
 		self.channel_offset_correction_layout = QVBoxLayout()