celldetective 1.3.9.post5__py3-none-any.whl → 1.4.0__py3-none-any.whl

celldetective/gui/configure_new_exp.py

@@ -1,7 +1,6 @@
-from PyQt5.QtWidgets import QMainWindow, QApplication, QMessageBox, QHBoxLayout, QFileDialog, QVBoxLayout, QScrollArea, QCheckBox, QGridLayout, QLabel, QLineEdit, QPushButton, QWidget
+from PyQt5.QtWidgets import QApplication, QMessageBox, QHBoxLayout, QFileDialog, QVBoxLayout, QScrollArea, QCheckBox, QGridLayout, QLabel, QLineEdit, QPushButton
 from PyQt5.QtGui import QIntValidator, QDoubleValidator
 from celldetective.gui.gui_utils import center_window, help_generic
-from celldetective.gui.styles import Styles
 from celldetective.utils import get_software_location
 import json
 
@@ -13,9 +12,10 @@ from configparser import ConfigParser
 import os
 from functools import partial
 import numpy as np
-from celldetective.gui import Styles
+from celldetective.gui import CelldetectiveMainWindow, CelldetectiveWidget
 
-class ConfigNewExperiment(QMainWindow, Styles):
+
+class ConfigNewExperiment(CelldetectiveMainWindow):
 
 	def __init__(self, parent_window=None):
 		
@@ -34,11 +34,11 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		
 		# Create button widget and layout
 		self.scroll_area = QScrollArea(self)
-		button_widget = QWidget()
+		button_widget = CelldetectiveWidget()
 		self.grid = QGridLayout()
 		button_widget.setLayout(self.grid)
 
-		self.grid.setContentsMargins(30,30,30,30)
+		self.grid.setContentsMargins(30, 30, 30, 30)
 		self.grid.addWidget(QLabel("Folder:"), 0, 0, 1, 3)
 		self.supFolder = QLineEdit()
 		self.supFolder.setAlignment(Qt.AlignLeft)	
@@ -64,17 +64,20 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		self.grid.addWidget(self.expName, 3, 0, 1, 3)
 
 		self.generate_movie_settings()
-		self.grid.addLayout(self.ms_grid,29,0,1,3)
+		self.grid.addLayout(self.ms_grid, 29, 0, 1, 3)
 
 		self.generate_channel_params_box()
-		self.grid.addLayout(self.channel_grid,30,0,1,3)
+		self.grid.addLayout(self.channel_grid, 30, 0, 1, 3)
+
+		self.generate_population_params_box()
+		self.grid.addLayout(self.population_grid, 31, 0, 1, 3)
 
 		self.validate_button = QPushButton("Submit")
 		self.validate_button.clicked.connect(self.create_config)
 		self.validate_button.setStyleSheet(self.button_style_sheet)
 		#self.validate_button.setIcon(QIcon_from_svg(abs_path+f"/icons/process.svg", color='white'))
 
-		self.grid.addWidget(self.validate_button, 31, 0, 1, 3, alignment = Qt.AlignBottom)		
+		self.grid.addWidget(self.validate_button, 32, 0, 1, 3, alignment = Qt.AlignBottom)		
 		button_widget.adjustSize()
 
 		self.scroll_area.setAlignment(Qt.AlignCenter)
@@ -128,10 +131,9 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		self.help_btn.setToolTip("Help.")
 		self.ms_grid.addWidget(self.help_btn, 1, 0, 1, 3, alignment=Qt.AlignRight)
 
-
 		self.SliderWells = QLabeledSlider(Qt.Horizontal, self)
 		self.SliderWells.setMinimum(1)
-		self.SliderWells.setMaximum(32)
+		self.SliderWells.setMaximum(512)
 		self.ms_grid.addWidget(self.SliderWells, 2, 0, 1, 3, alignment=Qt.AlignTop)
 
 		self.number_of_positions = QLabel("Number of positions per well:")
@@ -139,7 +141,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 
 		self.SliderPos = QLabeledSlider(Qt.Horizontal, self)
 		self.SliderPos.setMinimum(1)
-		self.SliderPos.setMaximum(50)
+		self.SliderPos.setMaximum(512)
 
 		self.ms_grid.addWidget(self.SliderPos, 4, 0, 1, 3)
 
@@ -168,7 +170,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		self.ms_grid.addWidget(self.movie_length,9, 0, 1, 3)
 		self.MovieLengthSlider = QLabeledSlider(Qt.Horizontal, self)
 		self.MovieLengthSlider.setMinimum(2)
-		self.MovieLengthSlider.setMaximum(128)
+		#self.MovieLengthSlider.setMaximum(128)
 		self.ms_grid.addWidget(self.MovieLengthSlider, 10, 0, 1, 3)
 
 		self.prefix_lbl = QLabel("Prefix for the movies:")
@@ -181,7 +183,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		self.movie_prefix_field.setText("")
 		self.ms_grid.addWidget(self.movie_prefix_field, 12, 0, 1, 3)
 
-		self.ms_grid.addWidget(QLabel("X shape in pixels:"), 13, 0, 1, 3)
+		self.ms_grid.addWidget(QLabel("Image width:"), 13, 0, 1, 3)
 		self.shape_x_field = QLineEdit()
 		self.shape_x_field.setValidator(onlyInt)
 		self.shape_x_field.setAlignment(Qt.AlignLeft)	
@@ -190,7 +192,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		self.shape_x_field.setText("2048")
 		self.ms_grid.addWidget(self.shape_x_field, 14, 0, 1, 3)
 
-		self.ms_grid.addWidget(QLabel("Y shape in pixels:"), 15, 0, 1, 3)
+		self.ms_grid.addWidget(QLabel("Image height:"), 15, 0, 1, 3)
 		self.shape_y_field = QLineEdit()
 		self.shape_y_field.setValidator(onlyInt)
 		self.shape_y_field.setAlignment(Qt.AlignLeft)	
@@ -271,7 +273,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 
 	def add_custom_channel(self):
 
-		self.CustomChannelWidget = QWidget()
+		self.CustomChannelWidget = CelldetectiveWidget()
 		self.CustomChannelWidget.setWindowTitle("Custom channel")
 		layout = QVBoxLayout()
 		self.CustomChannelWidget.setLayout(layout)
@@ -323,6 +325,83 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		else:
 			self.sliders[index].setEnabled(False)
 
+	def generate_population_params_box(self):
+
+		"""
+		Parameters related to the movie channels
+		Rewrite all of it
+
+		"""
+
+		self.population_grid = QGridLayout()
+		self.population_grid.setContentsMargins(21,30,20,30)
+
+		pop_lbl = QLabel("CELL POPULATIONS")
+		pop_lbl.setStyleSheet("""
+			font-weight: bold;
+			""")
+		self.population_grid.addWidget(pop_lbl, 0,0,1,3, alignment=Qt.AlignCenter)
+
+
+		self.populations = ['effectors','targets']
+		self.population_checkboxes = [QCheckBox() for i in range(len(self.populations))]
+
+		for i in range(len(self.populations)):
+
+			self.population_checkboxes[i].setText(self.populations[i])
+			self.population_checkboxes[i].setChecked(True)
+			self.population_grid.addWidget(self.population_checkboxes[i], i+1, 0, 1, 1)
+
+		# Add channel button
+		self.addPopBtn = QPushButton('Add a cell population')
+		self.addPopBtn.setIcon(icon(MDI6.plus,color="white"))
+		self.addPopBtn.setIconSize(QSize(25, 25))
+		self.addPopBtn.setStyleSheet(self.button_style_sheet)
+		self.addPopBtn.clicked.connect(self.add_custom_population)
+		self.population_grid.addWidget(self.addPopBtn, 1000, 0, 1, 1)
+
+
+	def add_custom_population(self):
+		self.CustomPopWidget = CelldetectiveWidget()
+		self.CustomPopWidget.setWindowTitle("Define custom population")
+		layout = QVBoxLayout()
+		self.CustomPopWidget.setLayout(layout)
+
+		self.name_le = QLineEdit()
+		self.name_le.setPlaceholderText('name')
+		self.name_le.textChanged.connect(self.check_population_name)
+		hbox = QHBoxLayout()
+		hbox.addWidget(QLabel('population name: '), 33)
+		hbox.addWidget(self.name_le, 66)
+		layout.addLayout(hbox)
+
+		self.addPopBtn = QPushButton('add')
+		self.addPopBtn.setStyleSheet(self.button_style_sheet)
+		self.addPopBtn.setEnabled(False)
+		self.addPopBtn.clicked.connect(self.write_custom_population)
+		layout.addWidget(self.addPopBtn)
+		center_window(self.CustomPopWidget)
+		self.CustomPopWidget.show()
+
+	def check_population_name(self, text):
+		# define all conditions for valid population name (like no space)
+		if len(text)>0 and ' ' not in text:
+			self.addPopBtn.setEnabled(True)
+		else:
+			self.addPopBtn.setEnabled(False)
+
+	def write_custom_population(self):
+
+		self.new_population_name = self.name_le.text()
+		name_map = self.new_population_name
+
+		self.populations.append(self.new_population_name)
+		self.population_checkboxes.append(QCheckBox())
+		self.CustomPopWidget.close()
+
+		self.population_checkboxes[-1].setText(self.populations[-1])
+		self.population_grid.addWidget(self.population_checkboxes[-1], len(self.populations)+1, 0, 1, 1)
+
 	def browse_experiment_folder(self):
 
 		"""
@@ -362,6 +441,17 @@ class ConfigNewExperiment(QMainWindow, Styles):
 			if returnValue == QMessageBox.Ok:
 				return None
 
+		populations_checked = [self.population_checkboxes[i].isChecked() for i in range(len(self.population_checkboxes))]
+		if not np.any(populations_checked):
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Warning)
+			msgBox.setText("Please set at least one cell population before proceeding...")
+			msgBox.setWindowTitle("Warning")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None
+
 		sorted_list = set(channel_indices)
 		expected_list = set(np.arange(max(sorted_list)+1))
 		print(sorted_list, expected_list, sorted_list==expected_list)
@@ -429,8 +519,13 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		Write all user input parameters to a configuration file associated to an experiment.
 		"""
 
+
 		config = ConfigParser(interpolation=None)
 
+		config.add_section('Populations')
+		pops = ','.join([self.populations[i].lower() for i in range(len(self.population_checkboxes)) if self.population_checkboxes[i].isChecked()])
+		config.set('Populations','populations', pops)
+
 		# add a new section and some values
 		config.add_section('MovieSettings')
 		config.set('MovieSettings', 'PxToUm', self.PxToUm_field.text().replace(',','.'))
@@ -456,6 +551,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		config.add_section('Metadata')
 		config.set('Metadata', 'concentration_units', self.concentration_units)
 
+
 		# save to a file
 		with open('config.ini', 'w') as configfile:
 			config.write(configfile)
@@ -464,7 +560,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		print(f'New experiment successfully configured in folder {self.directory}...')
 		self.close()
 
-class SetupConditionLabels(QWidget, Styles):
+class SetupConditionLabels(CelldetectiveWidget):
 	def __init__(self, parent_window, n_wells):
 		super().__init__()
 		self.parent_window = parent_window

celldetective/gui/control_panel.py

@@ -1,10 +1,12 @@
-from PyQt5.QtWidgets import QMainWindow, QPushButton, QHBoxLayout, QLabel, QWidget, QGridLayout, QFrame, \
-	QTabWidget, QVBoxLayout, QMessageBox, QScrollArea, QDesktopWidget
+from PyQt5.QtWidgets import QPushButton, QHBoxLayout, QLabel, QGridLayout, QFrame, \
+	QTabWidget, QVBoxLayout, QScrollArea, QDesktopWidget
+from celldetective.gui import CelldetectiveMainWindow, CelldetectiveWidget
+
 from PyQt5.QtCore import Qt, QSize
-from celldetective.gui.gui_utils import center_window, QHSeperationLine, QCheckableComboBox
-from celldetective.utils import _extract_labels_from_config, ConfigSectionMap, extract_experiment_channels, extract_identity_col
+from celldetective.gui.gui_utils import center_window, QHSeperationLine, QCheckableComboBox, generic_message
+from celldetective.utils import _extract_labels_from_config, ConfigSectionMap, extract_identity_col
 from celldetective.gui import ConfigEditor, ProcessPanel, PreprocessingPanel, AnalysisPanel, NeighPanel
-from celldetective.io import get_experiment_wells, get_config, get_spatial_calibration, get_temporal_calibration, get_experiment_concentrations, get_experiment_cell_types, get_experiment_antibodies, get_experiment_pharmaceutical_agents
+from celldetective.io import extract_position_name, get_experiment_wells, get_config, get_spatial_calibration, get_temporal_calibration, get_experiment_concentrations, get_experiment_cell_types, get_experiment_antibodies, get_experiment_pharmaceutical_agents, get_experiment_populations, extract_well_name_and_number
 from natsort import natsorted
 from glob import glob
 import os
@@ -15,11 +17,10 @@ import gc
 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):
+class ControlPanel(CelldetectiveMainWindow):
 
 	def __init__(self, parent_window=None, exp_dir=""):
 		
@@ -29,21 +30,20 @@ class ControlPanel(QMainWindow, Styles):
 		if not self.exp_dir.endswith(os.sep):
 			self.exp_dir = self.exp_dir+os.sep
 		self.setWindowTitle("celldetective")
-		self.setWindowIcon(self.celldetective_icon)
 		self.parent_window = parent_window
 
 		self.init_wells_and_positions()
 		self.load_configuration()
 
-		self.w = QWidget()
+		self.w = CelldetectiveWidget()
 		self.grid = QGridLayout(self.w)
 		self.grid.setSpacing(5)
-		self.grid.setContentsMargins(10,10,10,10) #left top right bottom
+		self.grid.setContentsMargins(10, 10, 10, 10)  # left top right bottom
 
 		self.to_disable = []
 		self.generate_header()
-		self.ProcessEffectors = ProcessPanel(self,'effectors')
-		self.ProcessTargets = ProcessPanel(self,'targets')
+		self.ProcessPopulations = [ProcessPanel(self, pop) for pop in self.populations]
+
 		self.NeighPanel = NeighPanel(self)
 		self.PreprocessingPanel = PreprocessingPanel(self)
 		
@@ -57,9 +57,10 @@ class ControlPanel(QMainWindow, Styles):
 		self.SurvivalBlock = AnalysisPanel(self,title='Survival')
 
 		grid_process.addWidget(self.PreprocessingPanel)
-		grid_process.addWidget(self.ProcessEffectors)
-		grid_process.addWidget(self.ProcessTargets)
+		for panel in self.ProcessPopulations:
+			grid_process.addWidget(panel)
 		grid_process.addWidget(self.NeighPanel)
+
 		grid_analyze.addWidget(self.SurvivalBlock)
 
 		self.scroll=QScrollArea()
@@ -92,7 +93,6 @@ class ControlPanel(QMainWindow, Styles):
 		self.screen_width = desktop.screenGeometry().width()
 		self.scroll.setMinimumWidth(440)
 		
-		self.setAttribute(Qt.WA_DeleteOnClose)
 		center_window(self)
 
 
@@ -108,11 +108,9 @@ class ControlPanel(QMainWindow, Styles):
 		self.wells = get_experiment_wells(self.exp_dir) #natsorted(glob(self.exp_dir + "W*" + os.sep))
 		self.positions = []
 		for w in self.wells:
-			w = os.path.split(w[:-1])
-			root = w[0]
-			w = w[1]
-			positions_path = natsorted(glob(os.sep.join([root, w, f"{w[1:]}*{os.sep}"])))
-			self.positions.append([os.path.split(pos[:-1])[1] for pos in positions_path])
+			well_name, well_nbr = extract_well_name_and_number(w)
+			positions_path = natsorted(glob(os.sep.join([w,f"{well_nbr}*", os.sep])))
+			self.positions.append([extract_position_name(pos) for pos in positions_path])
 
 	def generate_header(self):
 		
@@ -274,15 +272,9 @@ class ControlPanel(QMainWindow, Styles):
 		movies = glob(self.pos + os.sep.join(['movie', f"{self.movie_prefix}*.tif"]))
 
 		if len(movies) == 0:
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText("Please select a position containing a movie...")
-			msgBox.setWindowTitle("Warning")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				self.current_stack = None
-				return None
+			generic_message("Please select a position containing a movie...")
+			self.current_stack = None
+			return None
 		else:
 			self.current_stack = movies[0]
 
@@ -321,9 +313,11 @@ class ControlPanel(QMainWindow, Styles):
 		print('Reading experiment configuration...')
 		self.exp_config = get_config(self.exp_dir)
 
+		self.populations = get_experiment_populations(self.exp_dir)
 		self.PxToUm = get_spatial_calibration(self.exp_dir)
 		self.FrameToMin = get_temporal_calibration(self.exp_dir)
 
+
 		self.len_movie = int(ConfigSectionMap(self.exp_config,"MovieSettings")["len_movie"])
 		self.shape_x = int(ConfigSectionMap(self.exp_config,"MovieSettings")["shape_x"])
 		self.shape_y = int(ConfigSectionMap(self.exp_config,"MovieSettings")["shape_y"])
@@ -350,7 +344,7 @@ class ControlPanel(QMainWindow, Styles):
 		Close child windows if closed.
 		"""
 		
-		for process_block in [self.ProcessTargets, self.ProcessEffectors]:
+		for process_block in self.ProcessPopulations:
 			try:
 				if process_block.SegModelLoader:
 					process_block.SegModelLoader.close()
@@ -436,14 +430,8 @@ class ControlPanel(QMainWindow, Styles):
 		"""
 
 		if self.well_list.isMultipleSelection():
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Critical)
-			msgBox.setText("Please select a single well...")
-			msgBox.setWindowTitle("Error")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return False
+			generic_message("Please select a single well...")
+			return False
 		else:
 			self.well_index = self.well_list.getSelectedIndices() #[self.well_list.currentIndex()]
 
@@ -451,14 +439,8 @@ class ControlPanel(QMainWindow, Styles):
 
 			pos = self.positions[w_idx]
 			if not self.position_list.isSingleSelection():
-				msgBox = QMessageBox()
-				msgBox.setIcon(QMessageBox.Critical)
-				msgBox.setText("Please select a single position...")
-				msgBox.setWindowTitle("Error")
-				msgBox.setStandardButtons(QMessageBox.Ok)
-				returnValue = msgBox.exec()
-				if returnValue == QMessageBox.Ok:
-					return False
+				generic_message("Please select a single position...")
+				return False
 			else:
 				pos_indices = self.position_list.getSelectedIndices()
 
@@ -483,127 +465,72 @@ class ControlPanel(QMainWindow, Styles):
 	def update_position_options(self):
 		
 		self.pos = self.position_list.currentText()
-		panels = [self.ProcessEffectors, self.ProcessTargets]
 
 		if self.position_list.isMultipleSelection() or not self.position_list.isAnySelected():
 			
-			for p in panels:
+			for p in self.ProcessPopulations:
 				p.check_seg_btn.setEnabled(False)
 				p.check_tracking_result_btn.setEnabled(False)
+				p.view_tab_btn.setEnabled(True)
+				p.signal_analysis_action.setEnabled(True)
+				p.check_seg_btn.setEnabled(False)
+				p.check_tracking_result_btn.setEnabled(False)
+				p.check_measurements_btn.setEnabled(False)
+				p.check_signals_btn.setEnabled(False)
+				p.delete_tracks_btn.hide()
 
-			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.view_tab_btn.setEnabled(True)
 			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.isMultipleSelection():
 
-			self.ProcessTargets.view_tab_btn.setEnabled(True)
-			self.ProcessEffectors.view_tab_btn.setEnabled(True)	
+			for p in self.ProcessPopulations:
+				p.view_tab_btn.setEnabled(True)
+				p.signal_analysis_action.setEnabled(True)
+				p.delete_tracks_btn.hide()
+
+
 			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)
 			if hasattr(self,'delete_tracks_btn'):
 				self.delete_tracks_btn.hide()
-			self.ProcessTargets.delete_tracks_btn.hide()
-			self.ProcessEffectors.delete_tracks_btn.hide()
 		else:
 
 			if self.well_list.isAnySelected() and self.position_list.isAnySelected():
 
 				self.locate_selected_position()
 				self.view_stack_btn.setEnabled(True)
-				# if os.path.exists(os.sep.join([self.pos,'labels_effectors', os.sep])):
-				self.ProcessEffectors.check_seg_btn.setEnabled(True)
-				# if os.path.exists(os.sep.join([self.pos,'labels_targets', os.sep])):
-				self.ProcessTargets.check_seg_btn.setEnabled(True)
-				
-				# if os.path.exists(os.sep.join([self.pos,'output','tables','napari_target_trajectories.npy'])):
-				# 	self.ProcessTargets.check_tracking_result_btn.setEnabled(True)
-				# else:
-				# 	self.ProcessTargets.check_tracking_result_btn.setEnabled(False)
-				# if os.path.exists(os.sep.join([self.pos,'output','tables','napari_effector_trajectories.npy'])):
-				# 	self.ProcessEffectors.check_tracking_result_btn.setEnabled(True)
-				# else:
-				# 	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)
-					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)
-						self.ProcessEffectors.check_tracking_result_btn.setEnabled(True)
+				for i,p in enumerate(self.ProcessPopulations):
+					p.check_seg_btn.setEnabled(True)
+					if os.path.exists(os.sep.join([self.pos,'output','tables',f'trajectories_{self.populations[i]}.csv'])):
+						df = pd.read_csv(os.sep.join([self.pos,'output','tables',f'trajectories_{self.populations[i]}.csv']), nrows=1)
+						id_col = extract_identity_col(df)
+						p.check_measurements_btn.setEnabled(True)
+
+						if id_col=='TRACK_ID':
+							p.check_signals_btn.setEnabled(True)
+							p.delete_tracks_btn.show()
+							p.signal_analysis_action.setEnabled(True)
+							p.check_tracking_result_btn.setEnabled(True)
+						else:
+							p.signal_analysis_action.setEnabled(False)
+							p.check_tracking_result_btn.setEnabled(False)			
+
+						p.view_tab_btn.setEnabled(True)
+						p.classify_btn.setEnabled(True)
 					else:
-						self.ProcessEffectors.signal_analysis_action.setEnabled(False)
-						self.ProcessEffectors.check_tracking_result_btn.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)
-					if id_col=='TRACK_ID':
-						self.ProcessTargets.check_signals_btn.setEnabled(True)
-						self.ProcessTargets.signal_analysis_action.setEnabled(True)
-						self.ProcessTargets.check_tracking_result_btn.setEnabled(True)
-						self.ProcessTargets.delete_tracks_btn.show()
-					else:
-						self.ProcessTargets.signal_analysis_action.setEnabled(False)
-						self.ProcessTargets.check_tracking_result_btn.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)
+						p.check_measurements_btn.setEnabled(False)
+						p.check_signals_btn.setEnabled(False)
+						p.view_tab_btn.setEnabled(False)
+						p.classify_btn.setEnabled(False)
+						p.delete_tracks_btn.hide()
+						p.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)
-
-
+					self.NeighPanel.check_signals_btn.setEnabled(False)

celldetective/gui/generic_signal_plot.py

@@ -1,5 +1,5 @@
 from PyQt5.QtWidgets import QMessageBox,QGridLayout, QButtonGroup, \
-	QCheckBox, QLineEdit, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton, \
+	QCheckBox, QLineEdit, QVBoxLayout, QLabel, QHBoxLayout, QPushButton, \
 	QRadioButton
 from PyQt5.QtCore import Qt, QSize
 from PyQt5.QtGui import QDoubleValidator
@@ -18,13 +18,13 @@ import matplotlib.pyplot as plt
 plt.rcParams['svg.fonttype'] = 'none'
 from glob import glob
 from matplotlib.cm import tab10
-from celldetective.gui import Styles
+from celldetective.gui import CelldetectiveWidget
 import matplotlib.cm as mcm
 import pandas as pd
 
 from lifelines.utils import qth_survival_times
 
-class GenericSignalPlotWidget(QWidget, Styles):
+class GenericSignalPlotWidget(CelldetectiveWidget):
 
 	def __init__(self, df = None, df_pos_info = None, df_well_info = None, feature_selected = None, parent_window=None, title='plot', *args, **kwargs):
 		
@@ -33,7 +33,6 @@ class GenericSignalPlotWidget(QWidget, Styles):
 
 		self.parent_window = parent_window
 		self.setWindowTitle(title)
-		self.setWindowIcon(self.celldetective_icon)
 
 		self.show_ci = False
 		self.legend_visible = True
@@ -60,8 +59,6 @@ class GenericSignalPlotWidget(QWidget, Styles):
 
 		self.fig.tight_layout()
 		self.setLayout(self.layout)
-		self.setAttribute(Qt.WA_DeleteOnClose)
-
 
 	def populate_widget(self):
 
@@ -170,7 +167,7 @@ class GenericSignalPlotWidget(QWidget, Styles):
 		self.ci_btn.clicked.connect(self.switch_ci)
 		self.cell_lines_btn.clicked.connect(self.switch_cell_lines)
 
-		self.class_selection_widget = QWidget()
+		self.class_selection_widget = CelldetectiveWidget()
 
 		self.class_selection_lbl = QLabel('class of interest:')
 		class_hbox = QHBoxLayout()
@@ -197,7 +194,7 @@ class GenericSignalPlotWidget(QWidget, Styles):
 		self.layout.addWidget(self.class_selection_widget) #Layout(class_hbox)
 
 		# Rescale 
-		self.rescale_widget = QWidget()
+		self.rescale_widget = CelldetectiveWidget()
 
 		scale_hbox = QHBoxLayout()
 		self.rescale_widget.setLayout(scale_hbox)
@@ -216,7 +213,7 @@ class GenericSignalPlotWidget(QWidget, Styles):
 
 
 		# Rescale 
-		self.cell_lines_alpha_wdg = QWidget()
+		self.cell_lines_alpha_wdg = CelldetectiveWidget()
 		alpha_hbox = QHBoxLayout()
 
 		self.alpha_slider = QLabeledDoubleSlider()
@@ -225,7 +222,7 @@ class GenericSignalPlotWidget(QWidget, Styles):
 										slider_initial_value=self.alpha_setting,
 										slider_range=(0,1),
 										decimal_option=True,
-										precision=1.0E-05,
+										precision=5,
 										)
 		self.alpha_slider.valueChanged.connect(self.submit_alpha)
 		self.cell_lines_alpha_wdg.setLayout(alpha_hbox)
@@ -343,7 +340,7 @@ class GenericSignalPlotWidget(QWidget, Styles):
 		thresh = 20
 		self.well_name_truncated = [w[:thresh - 3]+'...' if len(w)>thresh else w for w in self.usable_well_labels]
 
-		self.line_choice_widget = QWidget()
+		self.line_choice_widget = CelldetectiveWidget()
 		self.line_check_vbox = QGridLayout()
 		self.line_choice_widget.setLayout(self.line_check_vbox)
 
@@ -828,7 +825,7 @@ class SurvivalPlotWidget(GenericSignalPlotWidget):
 
 	def set_table_options(self):
 
-		self.config_table_wg = QWidget()
+		self.config_table_wg = CelldetectiveWidget()
 		self.config_table_wg.setMinimumWidth(480)
 		self.config_table_wg.setWindowTitle('Survival data')