celldetective 1.4.2__py3-none-any.whl → 1.5.0b1__py3-none-any.whl

celldetective/gui/control_panel.py

@@ -1,12 +1,48 @@
-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, generic_message
-from celldetective.utils import _extract_labels_from_config, config_section_to_dict, extract_identity_col
-from celldetective.gui import ConfigEditor, ProcessPanel, PreprocessingPanel, AnalysisPanel, NeighPanel
-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
+import time
+
+from PyQt5.QtWidgets import (
+    QPushButton,
+    QHBoxLayout,
+    QLabel,
+    QGridLayout,
+    QFrame,
+    QTabWidget,
+    QVBoxLayout,
+    QScrollArea,
+    QDesktopWidget,
+)
+from celldetective.gui.base.components import (
+    CelldetectiveMainWindow,
+    CelldetectiveWidget,
+    QCheckableComboBox,
+    QHSeperationLine,
+)
+
+from PyQt5.QtCore import Qt, QSize, QThread
+from celldetective.gui.base.components import generic_message
+from celldetective.utils.parsing import (
+    config_section_to_dict,
+    _extract_labels_from_config,
+)
+from celldetective.gui.process_block import ProcessPanel
+from celldetective.gui.preprocessing_block import PreprocessingPanel
+from celldetective.gui.interactions_block import NeighPanel
+from celldetective.gui.analyze_block import AnalysisPanel
+
+from celldetective.utils.experiment import (
+    get_experiment_wells,
+    extract_well_name_and_number,
+    extract_position_name,
+    extract_experiment_channels,
+    get_spatial_calibration,
+    get_temporal_calibration,
+    get_experiment_concentrations,
+    get_experiment_cell_types,
+    get_experiment_antibodies,
+    get_experiment_pharmaceutical_agents,
+    get_experiment_populations,
+    get_config,
+)
 from natsort import natsorted
 from glob import glob
 import os
@@ -15,525 +51,600 @@ from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 import gc
 import subprocess
-from celldetective.gui.viewers import StackVisualizer
-from celldetective.utils import extract_experiment_channels
-import pandas as pd
+
+import logging
+
+logger = logging.getLogger(__name__)
+
+
+class BackgroundLoader(QThread):
+     def run(self):
+         logger.info("Loading background packages...")
+         try:
+             from celldetective.gui.viewers.base_viewer import StackVisualizer
+             self.StackVisualizer = StackVisualizer
+         except Exception:
+             logger.error("Background packages not loaded...")
+         logger.info("Background packages loaded...")
 
 
 class ControlPanel(CelldetectiveMainWindow):
 
-	def __init__(self, parent_window=None, exp_dir=""):
-		
-		super().__init__()
-		
-		self.exp_dir = exp_dir
-		if not self.exp_dir.endswith(os.sep):
-			self.exp_dir = self.exp_dir+os.sep
-		self.setWindowTitle("celldetective")
-		self.parent_window = parent_window
-
-		self.init_wells_and_positions()
-		self.load_configuration()
-
-		self.w = CelldetectiveWidget()
-		self.grid = QGridLayout(self.w)
-		self.grid.setSpacing(5)
-		self.grid.setContentsMargins(10, 10, 10, 10)  # left top right bottom
-
-		self.to_disable = []
-		self.generate_header()
-		self.ProcessPopulations = [ProcessPanel(self, pop) for pop in self.populations]
-
-		self.NeighPanel = NeighPanel(self)
-		self.PreprocessingPanel = PreprocessingPanel(self)
-		
-		ProcessFrame = QFrame()
-		grid_process = QVBoxLayout(ProcessFrame)
-		grid_process.setContentsMargins(15,30,15,15)
-
-		AnalyzeFrame = QFrame()
-		grid_analyze = QVBoxLayout(AnalyzeFrame)
-		grid_analyze.setContentsMargins(15,30,15,15)
-		self.SurvivalBlock = AnalysisPanel(self,title='Survival')
-
-		grid_process.addWidget(self.PreprocessingPanel)
-		for panel in self.ProcessPopulations:
-			grid_process.addWidget(panel)
-		grid_process.addWidget(self.NeighPanel)
-
-		grid_analyze.addWidget(self.SurvivalBlock)
-
-		self.scroll=QScrollArea()
-		self.scroll.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)
-		self.scroll.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
-		self.scroll.setWidgetResizable(True)
-		desktop = QDesktopWidget()
-		self.scroll.setMinimumHeight(550)
-		#self.scroll.setMinimumHeight(int(0.4*screen_height))
-
-		tabWidget = QTabWidget()
-		tab_index_process = tabWidget.addTab(ProcessFrame, "Process")
-		tabWidget.setTabIcon(tab_index_process, icon(MDI6.cog_outline, color='black'))
-
-		tab_index_analyze = tabWidget.addTab(AnalyzeFrame, "Analyze")
-		tabWidget.setTabIcon(tab_index_analyze, icon(MDI6.poll, color='black'))
-		tabWidget.setStyleSheet(self.qtab_style)
-
-		self.grid.addWidget(tabWidget, 7,0,1,3, alignment=Qt.AlignTop)
-		self.grid.setSpacing(5)
-		self.scroll.setWidget(self.w)
-		self.setCentralWidget(self.scroll)
-		self.create_config_dir()
-		self.update_position_options()
-		#self.setMinimumHeight(int(self.sizeHint().height()))
-
-		self.initial_height = self.size().height()
-		self.initial_width = self.size().width()
-		self.screen_height = desktop.screenGeometry().height()
-		self.screen_width = desktop.screenGeometry().width()
-		self.scroll.setMinimumWidth(440)
-		
-		center_window(self)
-
-
-		self.well_list.setCurrentIndex(0)
-		#self.position_list.setCurrentIndex(0)
-
-	def init_wells_and_positions(self):
-
-		"""
-		Detect the wells in the experiment folder and the associated positions.
-		"""
-		
-		self.wells = get_experiment_wells(self.exp_dir) #natsorted(glob(self.exp_dir + "W*" + os.sep))
-		self.positions = []
-		for w in self.wells:
-			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):
-		
-		"""
-		Show the experiment name, create two QComboBox for respectively the 
-		biological condition (well) and position of interest, access the experiment config.
-		"""
-
-		condition_label = QLabel("condition: ")
-		position_label = QLabel("position: ")
-
-		name = self.exp_dir.split(os.sep)[-2]
-		experiment_label = QLabel(f"Experiment:")
-		experiment_label.setStyleSheet("""
+    def __init__(self, parent_window=None, exp_dir=""):
+
+        super().__init__()
+
+        self.exp_dir = exp_dir
+        if not self.exp_dir.endswith(os.sep):
+            self.exp_dir = self.exp_dir + os.sep
+        self.setWindowTitle("celldetective")
+        self.parent_window = parent_window
+
+        self.init_wells_and_positions()
+        self.load_configuration()
+
+        self.w = CelldetectiveWidget()
+        self.grid = QGridLayout(self.w)
+        self.grid.setSpacing(5)
+        self.grid.setContentsMargins(10, 10, 10, 10)  # left top right bottom
+
+        self.to_disable = []
+        self.generate_header()
+        self.ProcessPopulations = [ProcessPanel(self, pop) for pop in self.populations]
+
+        self.NeighPanel = NeighPanel(self)
+        self.PreprocessingPanel = PreprocessingPanel(self)
+
+        ProcessFrame = QFrame()
+        grid_process = QVBoxLayout(ProcessFrame)
+        grid_process.setContentsMargins(15, 30, 15, 15)
+
+        AnalyzeFrame = QFrame()
+        grid_analyze = QVBoxLayout(AnalyzeFrame)
+        grid_analyze.setContentsMargins(15, 30, 15, 15)
+        self.SurvivalBlock = AnalysisPanel(self, title="Survival")
+
+        grid_process.addWidget(self.PreprocessingPanel)
+        for panel in self.ProcessPopulations:
+            grid_process.addWidget(panel)
+        grid_process.addWidget(self.NeighPanel)
+
+        grid_analyze.addWidget(self.SurvivalBlock)
+
+        self.scroll = QScrollArea()
+        self.scroll.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)
+        self.scroll.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
+        self.scroll.setWidgetResizable(True)
+        desktop = QDesktopWidget()
+        self.scroll.setMinimumHeight(550)
+        # self.scroll.setMinimumHeight(int(0.4*screen_height))
+
+        tabWidget = QTabWidget()
+        tab_index_process = tabWidget.addTab(ProcessFrame, "Process")
+        tabWidget.setTabIcon(tab_index_process, icon(MDI6.cog_outline, color="black"))
+
+        tab_index_analyze = tabWidget.addTab(AnalyzeFrame, "Analyze")
+        tabWidget.setTabIcon(tab_index_analyze, icon(MDI6.poll, color="black"))
+        tabWidget.setStyleSheet(self.qtab_style)
+
+        self.grid.addWidget(tabWidget, 7, 0, 1, 3, alignment=Qt.AlignTop)
+        self.grid.setSpacing(5)
+        self.scroll.setWidget(self.w)
+        self.setCentralWidget(self.scroll)
+        self.create_config_dir()
+        self.update_position_options()
+        # self.setMinimumHeight(int(self.sizeHint().height()))
+
+        self.initial_height = self.size().height()
+        self.initial_width = self.size().width()
+        self.screen_height = desktop.screenGeometry().height()
+        self.screen_width = desktop.screenGeometry().width()
+        self.scroll.setMinimumWidth(440)
+
+        self.well_list.setCurrentIndex(0)
+        # self.position_list.setCurrentIndex(0)
+
+        t_loaded = time.time()
+        logger.info(f"Launch time: {t_loaded - self.parent_window.t_ref} s...")
+
+        self.bg_loader = BackgroundLoader()
+        self.bg_loader.start()
+
+    def init_wells_and_positions(self):
+        """
+        Detect the wells in the experiment folder and the associated positions.
+        """
+
+        self.wells = get_experiment_wells(
+            self.exp_dir
+        )  # natsorted(glob(self.exp_dir + "W*" + os.sep))
+        self.positions = []
+        self.position_paths = []
+        for w in self.wells:
+            well_name, well_nbr = extract_well_name_and_number(w)
+            positions_path = natsorted(glob(os.sep.join([w, f"{well_nbr}*", os.sep])))
+            self.position_paths.append(positions_path)
+            self.positions.append(
+                [extract_position_name(pos) for pos in positions_path]
+            )
+
+    def generate_header(self):
+        """
+        Show the experiment name, create two QComboBox for respectively the
+        biological condition (well) and position of interest, access the experiment config.
+        """
+
+        condition_label = QLabel("condition: ")
+        position_label = QLabel("position: ")
+
+        name = self.exp_dir.split(os.sep)[-2]
+        experiment_label = QLabel(f"Experiment:")
+        experiment_label.setStyleSheet("""
 			font-weight: bold;
 			""")
 
-		self.folder_exp_btn = QPushButton()
-		self.folder_exp_btn.setIcon(icon(MDI6.folder,color="black"))
-		self.folder_exp_btn.setIconSize(QSize(20, 20))
-		self.folder_exp_btn.setToolTip("Experiment folder")
-		self.folder_exp_btn.clicked.connect(self.open_experiment_folder)
-		self.folder_exp_btn.setStyleSheet(self.button_select_all)
-
-
-		self.edit_config_button = QPushButton()
-		self.edit_config_button.setIcon(icon(MDI6.cog_outline,color="black"))
-		self.edit_config_button.setIconSize(QSize(20, 20))
-		self.edit_config_button.setToolTip("Configuration file")
-		self.edit_config_button.clicked.connect(self.open_config_editor)
-		self.edit_config_button.setStyleSheet(self.button_select_all)
-
-		self.well_list = QCheckableComboBox(obj='well', parent_window=self)
-		thresh = 32
-		self.well_truncated = [w[:thresh - 3]+'...' if len(w)>thresh else w for w in self.well_labels]
-		for i in range(len(self.well_truncated)):
-			self.well_list.addItem(self.well_truncated[i], tooltip=self.well_labels[i])
-
-		self.position_list = QCheckableComboBox(obj='position', parent_window=self)
-		self.position_list.addItems(self.positions[0])
-		self.to_disable.append(self.position_list)
-		#self.locate_selected_position()
-
-		self.well_list.activated.connect(self.display_positions)
-
-		self.position_list.activated.connect(self.update_position_options)
-
-		self.view_stack_btn = QPushButton()
-		self.view_stack_btn.setStyleSheet(self.button_select_all)
-		self.view_stack_btn.setIcon(icon(MDI6.image_check, color="black"))
-		self.view_stack_btn.setToolTip("View stack.")
-		self.view_stack_btn.setIconSize(QSize(20, 20))
-		self.view_stack_btn.clicked.connect(self.view_current_stack)
-		self.view_stack_btn.setEnabled(False)
-
-		self.select_all_wells_btn = QPushButton()
-		self.select_all_wells_btn.setIcon(icon(MDI6.select_all,color="black"))
-		self.select_all_wells_btn.setIconSize(QSize(20, 20))
-		self.select_all_wells_btn.setToolTip("Select all wells.")
-		self.select_all_wells_btn.clicked.connect(self.select_all_wells)
-		self.select_all_wells_btn.setStyleSheet(self.button_select_all)
-		self.select_all_wells_option = False
-
-
-		self.select_all_pos_btn = QPushButton()
-		self.select_all_pos_btn.setIcon(icon(MDI6.select_all,color="black"))
-		self.select_all_pos_btn.setIconSize(QSize(20, 20))
-		self.select_all_pos_btn.setToolTip("Select all positions.")
-		self.select_all_pos_btn.clicked.connect(self.select_all_positions)
-		self.select_all_pos_btn.setStyleSheet(self.button_select_all)
-		self.select_all_pos_option = False
-
-
-		well_lbl = QLabel('Well: ')
-		well_lbl.setAlignment(Qt.AlignRight)
-
-		pos_lbl = QLabel('Position: ')
-		pos_lbl.setAlignment(Qt.AlignRight)
-
-		hsep = QHSeperationLine()
-
-		## LAYOUT
-
-		# Header layout
-		vbox = QVBoxLayout()
-		self.grid.addLayout(vbox, 0,0,1,3)
-
-		# Experiment row
-		exp_hbox = QHBoxLayout()
-		exp_hbox.addWidget(experiment_label, 25, alignment=Qt.AlignRight)
-		exp_subhbox = QHBoxLayout()
-		if len(name)>thresh:
-			name_cut = name[:thresh - 3]+'...'
-		else:
-			name_cut = name
-		exp_name_lbl = QLabel(name_cut)
-		exp_name_lbl.setToolTip(name)
-		exp_subhbox.addWidget(exp_name_lbl, 90, alignment=Qt.AlignLeft)
-		exp_subhbox.addWidget(self.folder_exp_btn, 5, alignment=Qt.AlignRight)
-		exp_subhbox.addWidget(self.edit_config_button, 5, alignment=Qt.AlignRight)
-		exp_hbox.addLayout(exp_subhbox, 75)
-		vbox.addLayout(exp_hbox)
-
-		# Well row
-		well_hbox = QHBoxLayout()
-		well_hbox.addWidget(well_lbl, 25, alignment=Qt.AlignVCenter)
-		well_subhbox = QHBoxLayout()
-		well_subhbox.addWidget(self.well_list, 95)
-		well_subhbox.addWidget(self.select_all_wells_btn, 5)
-		well_hbox.addLayout(well_subhbox, 75)
-		vbox.addLayout(well_hbox)
-
-		# Position row
-		position_hbox = QHBoxLayout()
-		position_hbox.addWidget(pos_lbl, 25, alignment=Qt.AlignVCenter)
-		pos_subhbox = QHBoxLayout()
-		pos_subhbox.addWidget(self.position_list, 90)
-		pos_subhbox.addWidget(self.select_all_pos_btn, 5)
-		pos_subhbox.addWidget(self.view_stack_btn, 5)
-		position_hbox.addLayout(pos_subhbox, 75)
-		vbox.addLayout(position_hbox)
-
-		vbox.addWidget(hsep)
-
-	def select_all_wells(self):
-
-		if not self.select_all_wells_option:
-			self.well_list.selectAll()
-			self.select_all_wells_option = True
-			self.select_all_wells_btn.setIcon(icon(MDI6.select_all,color=self.celldetective_blue))
-			self.select_all_wells_btn.setIconSize(QSize(20, 20))
-			self.display_positions()
-		else:
-			self.well_list.unselectAll()
-			self.select_all_wells_option = False
-			self.select_all_wells_btn.setIcon(icon(MDI6.select_all,color="black"))
-			self.select_all_wells_btn.setIconSize(QSize(20, 20))
-			self.display_positions()
-
-	def select_all_positions(self):
-
-		if not self.select_all_pos_option:
-			self.position_list.selectAll()
-			self.select_all_pos_option = True
-			self.select_all_pos_btn.setIcon(icon(MDI6.select_all,color=self.celldetective_blue))
-			self.select_all_pos_btn.setIconSize(QSize(20, 20))
-		else:
-			self.position_list.unselectAll()
-			self.select_all_pos_option = False
-			self.select_all_pos_btn.setIcon(icon(MDI6.select_all,color="black"))
-			self.select_all_pos_btn.setIconSize(QSize(20, 20))
-
-	def locate_image(self):
-
-		"""
-		Load the first frame of the first movie found in the experiment folder as a sample.
-		"""
-
-		movies = glob(self.pos + os.sep.join(['movie', f"{self.movie_prefix}*.tif"]))
-
-		if len(movies) == 0:
-			generic_message("Please select a position containing a movie...")
-			self.current_stack = None
-			return None
-		else:
-			self.current_stack = movies[0]
-
-	def view_current_stack(self):
-		
-		self.locate_image()
-		if self.current_stack is not None:
-			self.viewer = StackVisualizer(
-										  stack_path=self.current_stack,
-										  window_title=f'Position {self.position_list.currentText()}',
-										  frame_slider = True,
-										  contrast_slider = True,
-										  channel_cb = True,
-										  channel_names = self.exp_channels,
-										  n_channels = self.nbr_channels,
-										  PxToUm = self.PxToUm,
-										 )
-			self.viewer.show()
-
-	def open_experiment_folder(self):
-
-		try:
-			subprocess.Popen(f'explorer {os.path.realpath(self.exp_dir)}')
-		except:
-			try:
-				os.system('xdg-open "%s"' % self.exp_dir)
-			except:
-				return None		
-
-	def load_configuration(self):
-
-		'''
-		This methods load the configuration read in the config.ini file of the experiment.
-		'''
-
-		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(config_section_to_dict(self.exp_config, "MovieSettings")["len_movie"])
-		self.shape_x = int(config_section_to_dict(self.exp_config, "MovieSettings")["shape_x"])
-		self.shape_y = int(config_section_to_dict(self.exp_config, "MovieSettings")["shape_y"])
-		self.movie_prefix = config_section_to_dict(self.exp_config, "MovieSettings")["movie_prefix"]
-
-		# Read channels
-		self.exp_channels, channel_indices = extract_experiment_channels(self.exp_dir)
-		self.nbr_channels = len(self.exp_channels)
-
-		number_of_wells = len(self.wells)
-		self.well_labels = _extract_labels_from_config(self.exp_config,number_of_wells)
-
-		self.concentrations = get_experiment_concentrations(self.exp_dir)
-		self.cell_types = get_experiment_cell_types(self.exp_dir)
-		self.antibodies = get_experiment_antibodies(self.exp_dir)
-		self.pharmaceutical_agents = get_experiment_pharmaceutical_agents(self.exp_dir)
-
-		self.metadata = config_section_to_dict(self.exp_config, "Metadata")
-		print('Experiment configuration successfully read...')
-
-	def closeEvent(self, event):
-
-		"""
-		Close child windows if closed.
-		"""
-		
-		for process_block in self.ProcessPopulations:
-			try:
-				if process_block.SegModelLoader:
-					process_block.SegModelLoader.close()
-			except:
-				pass
-			try:
-				if process_block.ConfigTracking:
-					process_block.ConfigTracking.close()
-			except:
-				pass
-			try:
-				if process_block.ConfigSignalTrain:
-					process_block.ConfigSignalTrain.close()
-			except:
-				pass
-			try:
-				if process_block.ConfigMeasurements:
-					process_block.ConfigMeasurements.close()
-			except:
-				pass
-			try:
-				if process_block.ConfigSignalAnnotator:
-					process_block.ConfigSignalAnnotator.close()
-			except:
-				pass
-			try:
-				if process_block.tab_ui:
-					process_block.tab_ui.close()
-			except:
-				pass
-
-		try:
-			if self.cfg_editor:
-				self.cfg_editor.close()
-		except:
-			pass
-
-		gc.collect()
-
-
-	def display_positions(self):
-
-		"""
-		Show the positions as the well is changed.
-		"""
-
-		if self.well_list.isMultipleSelection():
-
-			self.position_list.clear()
-			position_linspace = np.linspace(0,len(self.positions[0])-1,len(self.positions[0]),dtype=int)
-			position_linspace = [str(s) for s in position_linspace]
-			self.position_list.addItems(position_linspace)
-			if self.select_all_pos_option:
-				self.select_all_pos_btn.click()
-			self.select_all_pos_btn.click()
-		
-		elif not self.well_list.isAnySelected():
-
-			self.position_list.unselectAll()
-			if self.select_all_pos_option:
-				self.select_all_pos_btn.click()
-
-		else:
-			pos_index = self.well_list.getSelectedIndices()[0]
-			self.position_list.clear()
-			self.position_list.addItems(self.positions[pos_index])
-			if self.select_all_pos_option:
-				self.select_all_pos_btn.click()
-			self.position_list.setCurrentIndex(0)
-		
-		self.update_position_options()
-	
-	def open_config_editor(self):
-		self.cfg_editor = ConfigEditor(self)
-		self.cfg_editor.show()
-
-	def locate_selected_position(self):
-
-		"""
-		Set the current position if the option one well, one positon is selected
-		Display error messages otherwise.
-
-		"""
-
-		if self.well_list.isMultipleSelection():
-			generic_message("Please select a single well...")
-			return False
-		else:
-			self.well_index = self.well_list.getSelectedIndices() #[self.well_list.currentIndex()]
-
-		for w_idx in self.well_index:
-
-			pos = self.positions[w_idx]
-			if not self.position_list.isSingleSelection():
-				generic_message("Please select a single position...")
-				return False
-			else:
-				pos_indices = self.position_list.getSelectedIndices()
-
-			well = self.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]
-				if not os.path.exists(self.pos + 'output'):
-					os.mkdir(self.pos + 'output')
-				if not os.path.exists(self.pos + os.sep.join(['output','tables'])):
-					os.mkdir(self.pos + os.sep.join(['output','tables']))
-
-		return True
-
-	def create_config_dir(self):
-
-		self.config_folder = self.exp_dir+'configs'+os.sep
-		if not os.path.exists(self.config_folder):
-			os.mkdir(self.config_folder)
-
-	def update_position_options(self):
-		
-		self.pos = self.position_list.currentText()
-
-		if self.position_list.isMultipleSelection() or not self.position_list.isAnySelected():
-			
-			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.NeighPanel.view_tab_btn.setEnabled(True)
-			self.NeighPanel.check_signals_btn.setEnabled(False)
-			self.view_stack_btn.setEnabled(False)
-
-		elif self.well_list.isMultipleSelection():
-
-			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)
-			if hasattr(self,'delete_tracks_btn'):
-				self.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)
-				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'])):
-						try:
-							df = pd.read_csv(os.sep.join([self.pos,'output','tables',f'trajectories_{self.populations[i]}.csv']), nrows=1)
-						except Exception as e:
-							continue
-						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:
-						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.folder_exp_btn = QPushButton()
+        self.folder_exp_btn.setIcon(icon(MDI6.folder, color="black"))
+        self.folder_exp_btn.setIconSize(QSize(20, 20))
+        self.folder_exp_btn.setToolTip("Experiment folder")
+        self.folder_exp_btn.clicked.connect(self.open_experiment_folder)
+        self.folder_exp_btn.setStyleSheet(self.button_select_all)
+
+        self.edit_config_button = QPushButton()
+        self.edit_config_button.setIcon(icon(MDI6.cog_outline, color="black"))
+        self.edit_config_button.setIconSize(QSize(20, 20))
+        self.edit_config_button.setToolTip("Configuration file")
+        self.edit_config_button.clicked.connect(self.open_config_editor)
+        self.edit_config_button.setStyleSheet(self.button_select_all)
+
+        self.well_list = QCheckableComboBox(obj="well", parent_window=self)
+        thresh = 32
+        self.well_truncated = [
+            w[: thresh - 3] + "..." if len(w) > thresh else w for w in self.well_labels
+        ]
+        for i in range(len(self.well_truncated)):
+            self.well_list.addItem(self.well_truncated[i], tooltip=self.well_labels[i])
+
+        self.position_list = QCheckableComboBox(obj="position", parent_window=self)
+        self.position_list.addItems(self.positions[0])
+        self.to_disable.append(self.position_list)
+        # self.locate_selected_position()
+
+        self.well_list.activated.connect(self.display_positions)
+
+        self.position_list.activated.connect(self.update_position_options)
+
+        self.view_stack_btn = QPushButton()
+        self.view_stack_btn.setStyleSheet(self.button_select_all)
+        self.view_stack_btn.setIcon(icon(MDI6.image_check, color="black"))
+        self.view_stack_btn.setToolTip("View stack.")
+        self.view_stack_btn.setIconSize(QSize(20, 20))
+        self.view_stack_btn.clicked.connect(self.view_current_stack)
+        self.view_stack_btn.setEnabled(False)
+
+        self.select_all_wells_btn = QPushButton()
+        self.select_all_wells_btn.setIcon(icon(MDI6.select_all, color="black"))
+        self.select_all_wells_btn.setIconSize(QSize(20, 20))
+        self.select_all_wells_btn.setToolTip("Select all wells.")
+        self.select_all_wells_btn.clicked.connect(self.select_all_wells)
+        self.select_all_wells_btn.setStyleSheet(self.button_select_all)
+        self.select_all_wells_option = False
+
+        self.select_all_pos_btn = QPushButton()
+        self.select_all_pos_btn.setIcon(icon(MDI6.select_all, color="black"))
+        self.select_all_pos_btn.setIconSize(QSize(20, 20))
+        self.select_all_pos_btn.setToolTip("Select all positions.")
+        self.select_all_pos_btn.clicked.connect(self.select_all_positions)
+        self.select_all_pos_btn.setStyleSheet(self.button_select_all)
+        self.select_all_pos_option = False
+
+        well_lbl = QLabel("Well: ")
+        well_lbl.setAlignment(Qt.AlignRight)
+
+        pos_lbl = QLabel("Position: ")
+        pos_lbl.setAlignment(Qt.AlignRight)
+
+        hsep = QHSeperationLine()
+
+        ## LAYOUT
+
+        # Header layout
+        vbox = QVBoxLayout()
+        self.grid.addLayout(vbox, 0, 0, 1, 3)
+
+        # Experiment row
+        exp_hbox = QHBoxLayout()
+        exp_hbox.addWidget(experiment_label, 25, alignment=Qt.AlignRight)
+        exp_subhbox = QHBoxLayout()
+        if len(name) > thresh:
+            name_cut = name[: thresh - 3] + "..."
+        else:
+            name_cut = name
+        exp_name_lbl = QLabel(name_cut)
+        exp_name_lbl.setToolTip(name)
+        exp_subhbox.addWidget(exp_name_lbl, 90, alignment=Qt.AlignLeft)
+        exp_subhbox.addWidget(self.folder_exp_btn, 5, alignment=Qt.AlignRight)
+        exp_subhbox.addWidget(self.edit_config_button, 5, alignment=Qt.AlignRight)
+        exp_hbox.addLayout(exp_subhbox, 75)
+        vbox.addLayout(exp_hbox)
+
+        # Well row
+        well_hbox = QHBoxLayout()
+        well_hbox.addWidget(well_lbl, 25, alignment=Qt.AlignVCenter)
+        well_subhbox = QHBoxLayout()
+        well_subhbox.addWidget(self.well_list, 95)
+        well_subhbox.addWidget(self.select_all_wells_btn, 5)
+        well_hbox.addLayout(well_subhbox, 75)
+        vbox.addLayout(well_hbox)
+
+        # Position row
+        position_hbox = QHBoxLayout()
+        position_hbox.addWidget(pos_lbl, 25, alignment=Qt.AlignVCenter)
+        pos_subhbox = QHBoxLayout()
+        pos_subhbox.addWidget(self.position_list, 90)
+        pos_subhbox.addWidget(self.select_all_pos_btn, 5)
+        pos_subhbox.addWidget(self.view_stack_btn, 5)
+        position_hbox.addLayout(pos_subhbox, 75)
+        vbox.addLayout(position_hbox)
+
+        vbox.addWidget(hsep)
+
+    def select_all_wells(self):
+
+        if not self.select_all_wells_option:
+            self.well_list.selectAll()
+            self.select_all_wells_option = True
+            self.select_all_wells_btn.setIcon(
+                icon(MDI6.select_all, color=self.celldetective_blue)
+            )
+            self.select_all_wells_btn.setIconSize(QSize(20, 20))
+            self.display_positions()
+        else:
+            self.well_list.unselectAll()
+            self.select_all_wells_option = False
+            self.select_all_wells_btn.setIcon(icon(MDI6.select_all, color="black"))
+            self.select_all_wells_btn.setIconSize(QSize(20, 20))
+            self.display_positions()
+
+    def select_all_positions(self):
+
+        if not self.select_all_pos_option:
+            self.position_list.selectAll()
+            self.select_all_pos_option = True
+            self.select_all_pos_btn.setIcon(
+                icon(MDI6.select_all, color=self.celldetective_blue)
+            )
+            self.select_all_pos_btn.setIconSize(QSize(20, 20))
+        else:
+            self.position_list.unselectAll()
+            self.select_all_pos_option = False
+            self.select_all_pos_btn.setIcon(icon(MDI6.select_all, color="black"))
+            self.select_all_pos_btn.setIconSize(QSize(20, 20))
+
+    def locate_image(self):
+        """
+        Load the first frame of the first movie found in the experiment folder as a sample.
+        """
+
+        movies = glob(self.pos + os.sep.join(["movie", f"{self.movie_prefix}*.tif"]))
+
+        if len(movies) == 0:
+            generic_message("Please select a position containing a movie...")
+            self.current_stack = None
+            return None
+        else:
+            self.current_stack = movies[0]
+
+    def view_current_stack(self):
+
+        if self.bg_loader.isFinished() and hasattr(self.bg_loader, "StackVisualizer"):
+            StackVisualizer = self.bg_loader.StackVisualizer
+        else:
+            from celldetective.gui.viewers.base_viewer import StackVisualizer
+
+        self.locate_image()
+        if self.current_stack is not None:
+            self.viewer = StackVisualizer(
+                stack_path=self.current_stack,
+                window_title=f"Position {self.position_list.currentText()}",
+                frame_slider=True,
+                contrast_slider=True,
+                channel_cb=True,
+                channel_names=self.exp_channels,
+                n_channels=self.nbr_channels,
+                PxToUm=self.PxToUm,
+            )
+
+            # Not working for some reason
+            # def post_widget(widget):
+            #     try:
+            #         widget.resize(widget.width() + 1, widget.height() + 1)
+            #         center_window(widget)
+            #     except Exception as e:
+            #         traceback.print_exc()
+
+            self.viewer.show()
+
+    def open_experiment_folder(self):
+
+        try:
+            subprocess.Popen(f"explorer {os.path.realpath(self.exp_dir)}")
+        except:
+            try:
+                os.system('xdg-open "%s"' % self.exp_dir)
+            except:
+                return None
+
+    def load_configuration(self):
+        """
+        This methods load the configuration read in the config.ini file of the experiment.
+        """
+
+        logger.info("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(
+            config_section_to_dict(self.exp_config, "MovieSettings")["len_movie"]
+        )
+        self.shape_x = int(
+            config_section_to_dict(self.exp_config, "MovieSettings")["shape_x"]
+        )
+        self.shape_y = int(
+            config_section_to_dict(self.exp_config, "MovieSettings")["shape_y"]
+        )
+        self.movie_prefix = config_section_to_dict(self.exp_config, "MovieSettings")[
+            "movie_prefix"
+        ]
+
+        # Read channels
+        self.exp_channels, channel_indices = extract_experiment_channels(self.exp_dir)
+        self.nbr_channels = len(self.exp_channels)
+
+        number_of_wells = len(self.wells)
+        self.well_labels = _extract_labels_from_config(self.exp_config, number_of_wells)
+
+        self.concentrations = get_experiment_concentrations(self.exp_dir)
+        self.cell_types = get_experiment_cell_types(self.exp_dir)
+        self.antibodies = get_experiment_antibodies(self.exp_dir)
+        self.pharmaceutical_agents = get_experiment_pharmaceutical_agents(self.exp_dir)
+
+        self.metadata = config_section_to_dict(self.exp_config, "Metadata")
+        logger.info("Experiment configuration successfully read...")
+
+    def closeEvent(self, event):
+        """
+        Close child windows if closed.
+        """
+
+        for process_block in self.ProcessPopulations:
+            try:
+                if process_block.SegModelLoader:
+                    process_block.SegModelLoader.close()
+            except:
+                pass
+            try:
+                if process_block.ConfigTracking:
+                    process_block.ConfigTracking.close()
+            except:
+                pass
+            try:
+                if process_block.ConfigSignalTrain:
+                    process_block.ConfigSignalTrain.close()
+            except:
+                pass
+            try:
+                if process_block.ConfigMeasurements:
+                    process_block.ConfigMeasurements.close()
+            except:
+                pass
+            try:
+                if process_block.ConfigSignalAnnotator:
+                    process_block.ConfigSignalAnnotator.close()
+            except:
+                pass
+            try:
+                if process_block.tab_ui:
+                    process_block.tab_ui.close()
+            except:
+                pass
+
+        try:
+            if self.cfg_editor:
+                self.cfg_editor.close()
+        except:
+            pass
+
+        gc.collect()
+
+    def display_positions(self):
+        """
+        Show the positions as the well is changed.
+        """
+
+        if self.well_list.isMultipleSelection():
+
+            self.position_list.clear()
+            position_linspace = np.linspace(
+                0, len(self.positions[0]) - 1, len(self.positions[0]), dtype=int
+            )
+            position_linspace = [str(s) for s in position_linspace]
+            self.position_list.addItems(position_linspace)
+            if self.select_all_pos_option:
+                self.select_all_pos_btn.click()
+            self.select_all_pos_btn.click()
+
+        elif not self.well_list.isAnySelected():
+
+            self.position_list.unselectAll()
+            if self.select_all_pos_option:
+                self.select_all_pos_btn.click()
+
+        else:
+            pos_index = self.well_list.getSelectedIndices()[0]
+            self.position_list.clear()
+            self.position_list.addItems(self.positions[pos_index])
+            if self.select_all_pos_option:
+                self.select_all_pos_btn.click()
+            self.position_list.setCurrentIndex(0)
+
+        self.update_position_options()
+
+    def open_config_editor(self):
+        from celldetective.gui.json_readers import ConfigEditor
+
+        self.cfg_editor = ConfigEditor(self)
+        self.cfg_editor.show()
+
+    def locate_selected_position(self):
+        """
+        Set the current position if the option one well, one positon is selected
+        Display error messages otherwise.
+
+        """
+
+        if self.well_list.isMultipleSelection():
+            generic_message("Please select a single well...")
+            return False
+        else:
+            self.well_index = (
+                self.well_list.getSelectedIndices()
+            )  # [self.well_list.currentIndex()]
+
+        for w_idx in self.well_index:
+
+            pos = self.positions[w_idx]
+            if not self.position_list.isSingleSelection():
+                generic_message("Please select a single position...")
+                return False
+            else:
+                pos_indices = self.position_list.getSelectedIndices()
+
+            well = self.wells[w_idx]
+
+            for pos_idx in pos_indices:
+
+                self.pos = self.position_paths[w_idx][pos_idx]
+                if not os.path.exists(self.pos + "output"):
+                    os.mkdir(self.pos + "output")
+                if not os.path.exists(self.pos + os.sep.join(["output", "tables"])):
+                    os.mkdir(self.pos + os.sep.join(["output", "tables"]))
+
+        return True
+
+    def create_config_dir(self):
+
+        self.config_folder = self.exp_dir + "configs" + os.sep
+        if not os.path.exists(self.config_folder):
+            os.mkdir(self.config_folder)
+
+    def update_position_options(self):
+
+        self.pos = self.position_list.currentText()
+
+        if (
+            self.position_list.isMultipleSelection()
+            or not self.position_list.isAnySelected()
+        ):
+
+            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.NeighPanel.view_tab_btn.setEnabled(True)
+            self.NeighPanel.check_signals_btn.setEnabled(False)
+            self.view_stack_btn.setEnabled(False)
+
+        elif self.well_list.isMultipleSelection():
+
+            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)
+            if hasattr(self, "delete_tracks_btn"):
+                self.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)
+                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",
+                            ]
+                        )
+                    ):
+                        try:
+                            import pandas as pd
+
+                            cols = pd.read_csv(
+                                os.sep.join(
+                                    [
+                                        self.pos,
+                                        "output",
+                                        "tables",
+                                        f"trajectories_{self.populations[i]}.csv",
+                                    ]
+                                ),
+                                nrows=0,
+                            ).columns
+                        except Exception as e:
+                            continue
+
+                        if "TRACK_ID" in cols:
+                            id_col = "TRACK_ID"
+                        elif "ID" in cols:
+                            id_col = "ID"
+                        else:
+                            id_col = None
+                        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:
+                        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)