celldetective 1.4.2__py3-none-any.whl → 1.5.0b0__py3-none-any.whl

celldetective/gui/layouts.py

@@ -1,1602 +0,0 @@
-from PyQt5.QtWidgets import QCheckBox, QLineEdit, QListWidget, QTabWidget, QHBoxLayout,QMessageBox, QPushButton, QVBoxLayout, QRadioButton, QLabel, QButtonGroup, QSizePolicy, QComboBox,QSpacerItem, QGridLayout
-from celldetective.gui.gui_utils import ThresholdLineEdit, QuickSliderLayout, center_window
-from PyQt5.QtCore import Qt, QSize
-from PyQt5.QtGui import QIntValidator, QDoubleValidator
-
-from superqt import QLabeledRangeSlider, QLabeledDoubleSlider, QLabeledSlider, QLabeledDoubleRangeSlider, QSearchableComboBox
-
-from superqt.fonticon import icon
-from fonticon_mdi6 import MDI6
-from celldetective.utils import _extract_channel_indices_from_config
-from celldetective.gui.viewers import ThresholdedStackVisualizer, CellEdgeVisualizer, StackVisualizer, CellSizeViewer, ChannelOffsetViewer
-from celldetective.gui import Styles, CelldetectiveWidget
-from celldetective.preprocessing import correct_background_model, correct_background_model_free, estimate_background_per_condition
-from functools import partial
-from glob import glob
-import os
-import pandas as pd
-import numpy as np
-from celldetective.io import locate_segmentation_model, locate_signal_model
-import json
-
-
-class SignalModelParamsWidget(CelldetectiveWidget):
-	
-	def __init__(self, parent_window=None, model_name=None, *args, **kwargs):
-		
-		super().__init__(*args)
-		self.setWindowTitle('Signals')
-		self.parent_window = parent_window
-		self.model_name = model_name
-		self.locate_model_path()
-		self.required_channels = self.input_config["channels"]
-		self.onlyFloat = QDoubleValidator()
-
-		# Setting up references to parent window attributes
-		if hasattr(self.parent_window.parent_window, 'locate_image'):
-			self.attr_parent = self.parent_window.parent_window
-		elif hasattr(self.parent_window.parent_window.parent_window, 'locate_image'):
-			self.attr_parent = self.parent_window.parent_window.parent_window
-		else:
-			self.attr_parent = self.parent_window.parent_window.parent_window.parent_window
-		
-		# Set up layout and widgets
-		self.layout = QVBoxLayout()
-		self.populate_widgets()
-		self.setLayout(self.layout)
-		center_window(self)
-
-	def locate_model_path(self):
-
-		self.model_complete_path = locate_signal_model(self.model_name)
-		if self.model_complete_path is None:
-			print('Model could not be found. Abort.')
-			self.abort_process()
-		else:
-			print(f'Model path: {self.model_complete_path}...')
-		
-		if not os.path.exists(self.model_complete_path+"config_input.json"):
-			print('The configuration for the inputs to the model could not be located. Abort.')
-			self.abort_process()
-
-		with open(self.model_complete_path+"config_input.json") as config_file:
-			self.input_config = json.load(config_file)
-
-	def populate_widgets(self):
-
-		self.n_channels = len(self.required_channels)
-		self.channel_cbs = [QComboBox() for i in range(self.n_channels)]
-
-		self.parent_window.load_available_tables()
-		available_channels = list(self.parent_window.signals)+['None']
-		# Populate the comboboxes with available channels from the experiment
-		for k in range(self.n_channels):
-			hbox_channel = QHBoxLayout()
-			hbox_channel.addWidget(QLabel(f'channel {k+1}: '), 33)
-
-			ch_vbox = QVBoxLayout()
-			ch_vbox.addWidget(QLabel(f'Req: {self.required_channels[k]}'), alignment=Qt.AlignLeft)
-			ch_vbox.addWidget(self.channel_cbs[k])
-
-			self.channel_cbs[k].addItems(available_channels) #Give none option for more than one channel input
-			idx = self.channel_cbs[k].findText(self.required_channels[k])
-
-			if idx>=0:
-				self.channel_cbs[k].setCurrentIndex(idx)
-			else:
-				self.channel_cbs[k].setCurrentIndex(len(available_channels)-1)
-
-			hbox_channel.addLayout(ch_vbox, 66)
-			self.layout.addLayout(hbox_channel)
-		
-		# Button to apply the StarDist settings
-		self.set_btn = QPushButton('set')
-		self.set_btn.setStyleSheet(self.button_style_sheet)
-		self.set_btn.clicked.connect(self.parent_window.set_selected_signals_for_event_detection)
-		self.layout.addWidget(self.set_btn)
-
-
-
-class SegModelParamsWidget(CelldetectiveWidget):
-	
-	def __init__(self, parent_window=None, model_name='SD_versatile_fluo', *args, **kwargs):
-		
-		super().__init__(*args)
-		self.setWindowTitle('Channels')
-		self.parent_window = parent_window
-		self.model_name = model_name
-		self.locate_model_path()
-		self.required_channels = self.input_config["channels"]
-		self.onlyFloat = QDoubleValidator()
-
-		# Setting up references to parent window attributes
-		if hasattr(self.parent_window.parent_window, 'locate_image'):
-			self.attr_parent = self.parent_window.parent_window
-		elif hasattr(self.parent_window.parent_window.parent_window, 'locate_image'):
-			self.attr_parent = self.parent_window.parent_window.parent_window
-		else:
-			self.attr_parent = self.parent_window.parent_window.parent_window.parent_window
-		
-		# Set up layout and widgets
-		self.layout = QVBoxLayout()
-		self.populate_widgets()
-		self.setLayout(self.layout)
-		center_window(self)
-
-	def locate_model_path(self):
-
-		self.model_complete_path = locate_segmentation_model(self.model_name)
-		if self.model_complete_path is None:
-			print('Model could not be found. Abort.')
-			self.abort_process()
-		else:
-			print(f'Model path: {self.model_complete_path}...')
-		
-		if not os.path.exists(self.model_complete_path+"config_input.json"):
-			print('The configuration for the inputs to the model could not be located. Abort.')
-			self.abort_process()
-
-		with open(self.model_complete_path+"config_input.json") as config_file:
-			self.input_config = json.load(config_file)
-
-	def populate_widgets(self):
-
-		self.n_channels = len(self.required_channels)
-		self.channel_cbs = [QComboBox() for i in range(self.n_channels)]
-		
-		# Button to view the current stack with a scale bar
-		self.view_diameter_btn = QPushButton()
-		self.view_diameter_btn.setStyleSheet(self.button_select_all)
-		self.view_diameter_btn.setIcon(icon(MDI6.image_check, color="black"))
-		self.view_diameter_btn.setToolTip("View stack.")
-		self.view_diameter_btn.setIconSize(QSize(20, 20))
-		self.view_diameter_btn.clicked.connect(self.view_current_stack_with_scale_bar)
-
-		# Line edit for entering cell diameter
-		self.diameter_le = ThresholdLineEdit(init_value=40, connected_buttons=[self.view_diameter_btn],placeholder='cell diameter in µm', value_type='float')
-
-		available_channels = list(self.attr_parent.exp_channels)+['None']
-		# Populate the comboboxes with available channels from the experiment
-		for k in range(self.n_channels):
-			hbox_channel = QHBoxLayout()
-			hbox_channel.addWidget(QLabel(f'channel {k+1}: '), 33)
-
-			ch_vbox = QVBoxLayout()
-			ch_vbox.addWidget(QLabel(f'Req: {self.required_channels[k]}'), alignment=Qt.AlignLeft)
-			ch_vbox.addWidget(self.channel_cbs[k])
-
-			self.channel_cbs[k].addItems(available_channels) #Give none option for more than one channel input
-			idx = self.channel_cbs[k].findText(self.required_channels[k])
-
-			if idx>=0:
-				self.channel_cbs[k].setCurrentIndex(idx)
-			else:
-				self.channel_cbs[k].setCurrentIndex(len(available_channels)-1)
-
-			hbox_channel.addLayout(ch_vbox, 66)
-			self.layout.addLayout(hbox_channel)
-
-		if 'cell_size_um' in self.input_config:
-
-			# Layout for diameter input and button
-			hbox = QHBoxLayout()
-			hbox.addWidget(QLabel('cell size [µm]: '), 33)
-			hbox.addWidget(self.diameter_le, 61)
-			hbox.addWidget(self.view_diameter_btn)
-			self.layout.addLayout(hbox)
-
-			self.diameter_le.set_threshold(self.input_config['cell_size_um'])
-
-			# size_hbox = QHBoxLayout()
-			# size_hbox.addWidget(QLabel('cell size [µm]: '), 33)
-			# self.size_le = QLineEdit(str(self.input_config['cell_size_um']).replace('.',','))
-			# self.size_le.setValidator(self.onlyFloat)
-			# size_hbox.addWidget(self.size_le, 66)
-			# self.layout.addLayout(size_hbox)
-		
-		# Button to apply the StarDist settings
-		self.set_btn = QPushButton('set')
-		self.set_btn.setStyleSheet(self.button_style_sheet)
-		self.set_btn.clicked.connect(self.parent_window.set_selected_channels_for_segmentation)
-		self.layout.addWidget(self.set_btn)
-
-	def view_current_stack_with_scale_bar(self):
-
-		"""
-		Displays the current image stack with a scale bar, allowing users to visually estimate cell diameters.
-		"""
-
-		self.attr_parent.locate_image()
-		if self.attr_parent.current_stack is not None:
-			max_size = np.amax([self.attr_parent.shape_x, self.attr_parent.shape_y])
-			self.viewer = CellSizeViewer(
-										  initial_diameter = float(self.diameter_le.text().replace(',', '.')),
-										  parent_le = self.diameter_le,
-										  stack_path=self.attr_parent.current_stack,
-										  window_title=f'Position {self.attr_parent.position_list.currentText()}',
-										  diameter_slider_range=(0,max_size*self.attr_parent.PxToUm),
-										  frame_slider = True,
-										  contrast_slider = True,
-										  channel_cb = True,
-										  channel_names = self.attr_parent.exp_channels,
-										  n_channels = self.attr_parent.nbr_channels,
-										  PxToUm = self.attr_parent.PxToUm,
-										 )
-			self.viewer.show()
-
-
-class StarDistParamsWidget(CelldetectiveWidget):
-
-	"""
-	A widget to configure parameters for StarDist segmentation.
-
-	This widget allows the user to select specific imaging channels for segmentation and adjust 
-	parameters for StarDist, a neural network-based image segmentation tool designed to segment 
-	star-convex shapes (typically nuclei).
-
-	Parameters
-	----------
-	parent_window : QWidget, optional
-		The parent window hosting this widget (default is None).
-	model_name : str, optional
-		The name of the StarDist model being used, typically 'SD_versatile_fluo' for versatile 
-		fluorescence or 'SD_versatile_he' for H&E-stained images (default is 'SD_versatile_fluo').
-	"""
-
-	def __init__(self, parent_window=None, model_name='SD_versatile_fluo', *args, **kwargs):
-		
-		super().__init__(*args)
-		self.setWindowTitle('Channels')
-		self.parent_window = parent_window
-		self.model_name = model_name
-		
-		# Setting up references to parent window attributes
-		if hasattr(self.parent_window.parent_window, 'locate_image'):
-			self.attr_parent = self.parent_window.parent_window
-		elif hasattr(self.parent_window.parent_window.parent_window, 'locate_image'):
-			self.attr_parent = self.parent_window.parent_window.parent_window
-		else:
-			self.attr_parent = self.parent_window.parent_window.parent_window.parent_window
-		
-		# Set up layout and widgets
-		self.layout = QVBoxLayout()
-		self.populate_widgets()
-		self.setLayout(self.layout)
-		center_window(self)
-
-	def populate_widgets(self):
-
-		"""
-		Populates the widget with channel selection comboboxes and a 'set' button to configure
-		the StarDist segmentation settings. Handles different models by adjusting the number of
-		available channels.
-		"""
-		
-		# Initialize comboboxes based on the selected model
-		self.stardist_channel_cb = [QComboBox() for i in range(1)]
-		self.stardist_channel_template = ['live_nuclei_channel']
-		max_i = 1
-		
-		# If the H&E model is selected, update the combobox configuration
-		if self.model_name=="SD_versatile_he":
-			self.stardist_channel_template = ["H&E_1","H&E_2","H&E_3"]
-			self.stardist_channel_cb = [QComboBox() for i in range(3)]
-			max_i = 3
-	   
-		# Populate the comboboxes with available channels from the experiment
-		for k in range(max_i):
-			hbox_channel = QHBoxLayout()
-			hbox_channel.addWidget(QLabel(f'channel {k+1}: '))
-			hbox_channel.addWidget(self.stardist_channel_cb[k])
-			if k==1:
-				self.stardist_channel_cb[k].addItems(list(self.attr_parent.exp_channels)+['None'])
-			else:
-				self.stardist_channel_cb[k].addItems(list(self.attr_parent.exp_channels))
-			
-			# Set the default channel based on the template or fallback to the first option
-			idx = self.stardist_channel_cb[k].findText(self.stardist_channel_template[k])
-			if idx>0:
-				self.stardist_channel_cb[k].setCurrentIndex(idx)
-			else:
-				self.stardist_channel_cb[k].setCurrentIndex(0)
-
-			self.layout.addLayout(hbox_channel)
-		
-		# Button to apply the StarDist settings
-		self.set_stardist_scale_btn = QPushButton('set')
-		self.set_stardist_scale_btn.setStyleSheet(self.button_style_sheet)
-		self.set_stardist_scale_btn.clicked.connect(self.parent_window.set_stardist_scale)
-		self.layout.addWidget(self.set_stardist_scale_btn)
-
-
-class CellposeParamsWidget(CelldetectiveWidget):
-
-	"""
-	A widget to configure parameters for Cellpose segmentation, allowing users to set the cell diameter, 
-	select imaging channels, and adjust flow and cell probability thresholds for cell detection.
-
-	This widget is designed for estimating cell diameters and configuring parameters for Cellpose, 
-	a deep learning-based segmentation tool. It also provides functionality to preview the image stack with a scale bar.
-
-	Parameters
-	----------
-	parent_window : QWidget, optional
-		The parent window that hosts the widget (default is None).
-	model_name : str, optional
-		The name of the Cellpose model being used, typically 'CP_cyto2' for cytoplasm or 'CP_nuclei' for nuclei segmentation 
-		(default is 'CP_cyto2').
-
-	Notes
-	-----
-	- This widget assumes that the parent window or one of its ancestor windows has access to the experiment channels
-	  and can locate the current image stack via `locate_image()`.
-	- This class integrates sliders for flow and cell probability thresholds, as well as a channel selection for running
-	  Cellpose segmentation.
-	- The `view_current_stack_with_scale_bar()` method opens a new window where the user can visually inspect the 
-	  image stack with a superimposed scale bar, to better estimate the cell diameter.
-
-	"""
-
-
-	def __init__(self, parent_window=None, model_name='CP_cyto2', *args, **kwargs):
-		
-		super().__init__(*args)
-		self.setWindowTitle('Estimate diameter')
-		self.parent_window = parent_window
-		self.model_name = model_name
-		
-		# Setting up references to parent window attributes
-		if hasattr(self.parent_window.parent_window, 'locate_image'):
-			self.attr_parent = self.parent_window.parent_window
-		elif hasattr(self.parent_window.parent_window.parent_window, 'locate_image'):
-			self.attr_parent = self.parent_window.parent_window.parent_window
-		else:
-			self.attr_parent = self.parent_window.parent_window.parent_window.parent_window
-	   
-		# Layout and widgets setup
-		self.layout = QVBoxLayout()
-		self.populate_widgets()
-		self.setLayout(self.layout)
-		center_window(self)
-
-	def populate_widgets(self):
-
-		"""
-		Populates the widget with UI elements such as buttons, sliders, and comboboxes to allow configuration
-		of Cellpose segmentation parameters.
-		"""
-
-		# Button to view the current stack with a scale bar
-		self.view_diameter_btn = QPushButton()
-		self.view_diameter_btn.setStyleSheet(self.button_select_all)
-		self.view_diameter_btn.setIcon(icon(MDI6.image_check, color="black"))
-		self.view_diameter_btn.setToolTip("View stack.")
-		self.view_diameter_btn.setIconSize(QSize(20, 20))
-		self.view_diameter_btn.clicked.connect(self.view_current_stack_with_scale_bar)
-		
-		# Line edit for entering cell diameter
-		self.diameter_le = ThresholdLineEdit(init_value=40, connected_buttons=[self.view_diameter_btn],placeholder='cell diameter in pixels', value_type='float')
-		
-		# Comboboxes for selecting imaging channels
-		self.cellpose_channel_cb = [QComboBox() for i in range(2)]
-		self.cellpose_channel_template = ['brightfield_channel', 'live_nuclei_channel']
-		if self.model_name=="CP_nuclei":
-			self.cellpose_channel_template = ['live_nuclei_channel', 'None']
-
-		for k in range(2):
-			hbox_channel = QHBoxLayout()
-			hbox_channel.addWidget(QLabel(f'channel {k+1}: '))
-			hbox_channel.addWidget(self.cellpose_channel_cb[k])
-			if k==1:
-				self.cellpose_channel_cb[k].addItems(list(self.attr_parent.exp_channels)+['None'])
-			else:
-				self.cellpose_channel_cb[k].addItems(list(self.attr_parent.exp_channels))
-			idx = self.cellpose_channel_cb[k].findText(self.cellpose_channel_template[k])
-			if idx>0:
-				self.cellpose_channel_cb[k].setCurrentIndex(idx)
-			else:
-				self.cellpose_channel_cb[k].setCurrentIndex(0)
-
-			if k==1:
-				idx = self.cellpose_channel_cb[k].findText('None')
-				self.cellpose_channel_cb[k].setCurrentIndex(idx)
-
-			self.layout.addLayout(hbox_channel)
-		
-		# Layout for diameter input and button
-		hbox = QHBoxLayout()
-		hbox.addWidget(QLabel('diameter [px]: '), 33)
-		hbox.addWidget(self.diameter_le, 61)
-		hbox.addWidget(self.view_diameter_btn)
-		self.layout.addLayout(hbox)
-		
-		# Flow threshold slider
-		self.flow_slider = QLabeledDoubleSlider()
-		self.flow_slider.setOrientation(Qt.Horizontal)
-		self.flow_slider.setRange(-6,6)
-		self.flow_slider.setValue(0.4)
-		hbox = QHBoxLayout()
-		hbox.addWidget(QLabel('flow threshold: '), 33)
-		hbox.addWidget(self.flow_slider, 66)
-		self.layout.addLayout(hbox)
-
-		# Cell probability threshold slider
-		self.cellprob_slider = QLabeledDoubleSlider()
-		self.cellprob_slider.setOrientation(Qt.Horizontal)
-		self.cellprob_slider.setRange(-6,6)
-		self.cellprob_slider.setValue(0.)
-		hbox = QHBoxLayout()
-		hbox.addWidget(QLabel('cellprob threshold: '), 33)
-		hbox.addWidget(self.cellprob_slider, 66)
-		self.layout.addLayout(hbox)
-		
-		# Button to set the scale for Cellpose segmentation
-		self.set_cellpose_scale_btn = QPushButton('set')
-		self.set_cellpose_scale_btn.setStyleSheet(self.button_style_sheet)
-		self.set_cellpose_scale_btn.clicked.connect(self.parent_window.set_cellpose_scale)
-		self.layout.addWidget(self.set_cellpose_scale_btn)
-
-	def view_current_stack_with_scale_bar(self):
-
-		"""
-		Displays the current image stack with a scale bar, allowing users to visually estimate cell diameters.
-		"""
-
-		self.attr_parent.locate_image()
-		if self.attr_parent.current_stack is not None:
-			max_size = np.amax([self.attr_parent.shape_x, self.attr_parent.shape_y])
-			self.viewer = CellSizeViewer(
-										initial_diameter = float(self.diameter_le.text().replace(',', '.')),
-										parent_le = self.diameter_le,
-										stack_path=self.attr_parent.current_stack,
-										window_title=f'Position {self.attr_parent.position_list.currentText()}',
-										diameter_slider_range=(0, max_size),
-										frame_slider = True,
-										contrast_slider = True,
-										channel_cb = True,
-										channel_names = self.attr_parent.exp_channels,
-										n_channels = self.attr_parent.nbr_channels,
-										PxToUm = 1,
-										)
-			self.viewer.show()
-
-class ChannelNormGenerator(QVBoxLayout, Styles):
-	
-	"""Generator for list of channels"""
-	
-	def __init__(self, parent_window=None, init_n_channels=4, mode='signals', *args):
-		super().__init__(*args)
-
-		self.parent_window = parent_window
-		self.mode = mode
-		self.init_n_channels = init_n_channels
-		
-		if hasattr(self.parent_window.parent_window, 'locate_image'):
-			self.attr_parent = self.parent_window.parent_window
-		elif hasattr(self.parent_window.parent_window.parent_window, 'locate_image'):
-			self.attr_parent = self.parent_window.parent_window.parent_window
-		else:
-			self.attr_parent = self.parent_window.parent_window.parent_window.parent_window
-
-		self.channel_names = self.attr_parent.exp_channels
-		self.setContentsMargins(15,15,15,15)
-		self.generate_widgets()
-		self.add_to_layout()
-
-	def generate_widgets(self):
-		
-		self.channel_cbs = [QSearchableComboBox() for i in range(self.init_n_channels)]
-		self.channel_labels = [QLabel() for i in range(self.init_n_channels)]
-
-		self.normalization_mode_btns = [QPushButton('') for i in range(self.init_n_channels)]
-		self.normalization_mode = [True for i in range(self.init_n_channels)]
-		self.normalization_clip_btns = [QPushButton('') for i in range(self.init_n_channels)]
-		self.clip_option = [False for i in range(self.init_n_channels)]
-		
-		for i in range(self.init_n_channels):
-			self.normalization_mode_btns[i].setIcon(icon(MDI6.percent_circle,color="#1565c0"))
-			self.normalization_mode_btns[i].setIconSize(QSize(20, 20))	
-			self.normalization_mode_btns[i].setStyleSheet(self.button_select_all)	
-			self.normalization_mode_btns[i].setToolTip("Switch to absolute normalization values.")
-			self.normalization_mode_btns[i].clicked.connect(partial(self.switch_normalization_mode, i))
-
-			self.normalization_clip_btns[i].setIcon(icon(MDI6.content_cut,color="black"))
-			self.normalization_clip_btns[i].setIconSize(QSize(20, 20))	
-			self.normalization_clip_btns[i].setStyleSheet(self.button_select_all)	
-			self.normalization_clip_btns[i].clicked.connect(partial(self.switch_clipping_mode, i))
-			self.normalization_clip_btns[i].setToolTip('clip')
-
-		self.normalization_min_value_lbl = [QLabel('Min %: ') for i in range(self.init_n_channels)]
-		self.normalization_min_value_le = [QLineEdit('0.1') for i in range(self.init_n_channels)]
-		self.normalization_max_value_lbl = [QLabel('Max %: ') for i in range(self.init_n_channels)]		
-		self.normalization_max_value_le = [QLineEdit('99.99') for i in range(self.init_n_channels)]
-		
-		if self.mode=='signals':
-			tables = glob(self.parent_window.exp_dir+os.sep.join(['W*','*','output','tables',f'trajectories_{self.parent_window.mode}.csv']))
-			all_measurements = []
-			for tab in tables:
-				cols = pd.read_csv(tab, nrows=1).columns.tolist()
-				all_measurements.extend(cols)
-			all_measurements = np.unique(all_measurements)
-
-		if self.mode=='signals':
-			generic_measurements = ['brightfield_channel', 'live_nuclei_channel', 'dead_nuclei_channel', 
-								 'effector_fluo_channel', 'adhesion_channel', 'fluo_channel_1', 'fluo_channel_2',
-								 "area", "area_bbox","area_convex","area_filled","major_axis_length", 
-								 "minor_axis_length", 
-								"eccentricity",
-								"equivalent_diameter_area",
-								"euler_number",
-								"extent",
-								"feret_diameter_max",
-								"orientation", 
-								"perimeter",
-								"perimeter_crofton",
-								"solidity",
-								"angular_second_moment",
-								"contrast",
-								"correlation",
-								"sum_of_square_variance",
-								"inverse_difference_moment",
-								"sum_average",
-								"sum_variance",
-								"sum_entropy",
-								"entropy",
-								"difference_variance",
-								"difference_entropy",
-								"information_measure_of_correlation_1",
-								"information_measure_of_correlation_2",
-								"maximal_correlation_coefficient",
-								"POSITION_X",
-								"POSITION_Y",
-								]
-		elif self.mode=='channels':
-			generic_measurements = ['brightfield_channel', 'live_nuclei_channel', 'dead_nuclei_channel', 
-								 'effector_fluo_channel', 'adhesion_channel', 'fluo_channel_1', 'fluo_channel_2', 'None']
-
-		if self.mode=='channels':
-			all_measurements = []
-			exp_ch = self.attr_parent.exp_channels
-			for c in exp_ch:
-				all_measurements.append(c)
-
-		self.channel_items = np.unique(generic_measurements + list(all_measurements))
-		self.channel_items = np.insert(self.channel_items, 0, '--')
-
-		self.add_col_btn = QPushButton('Add channel')
-		self.add_col_btn.clicked.connect(self.add_channel)
-		self.add_col_btn.setStyleSheet(self.button_add)
-		self.add_col_btn.setIcon(icon(MDI6.plus,color="black"))
-
-	def add_channel(self):
-
-		self.channel_cbs.append(QSearchableComboBox())
-		self.channel_labels.append(QLabel())
-		self.channel_cbs[-1].addItems(self.channel_items)
-		self.channel_cbs[-1].currentIndexChanged.connect(self.check_valid_channels)
-		self.channel_labels[-1].setText(f'channel {len(self.channel_cbs)-1}: ')
-
-		self.normalization_mode_btns.append(QPushButton(''))
-		self.normalization_mode.append(True)
-		self.normalization_clip_btns.append(QPushButton(''))
-		self.clip_option.append(False)
-
-		self.normalization_mode_btns[-1].setIcon(icon(MDI6.percent_circle,color="#1565c0"))
-		self.normalization_mode_btns[-1].setIconSize(QSize(20, 20))	
-		self.normalization_mode_btns[-1].setStyleSheet(self.button_select_all)	
-		self.normalization_mode_btns[-1].setToolTip("Switch to absolute normalization values.")
-		self.normalization_mode_btns[-1].clicked.connect(partial(self.switch_normalization_mode, len(self.channel_cbs)-1))
-
-		self.normalization_clip_btns[-1].setIcon(icon(MDI6.content_cut,color="black"))
-		self.normalization_clip_btns[-1].setIconSize(QSize(20, 20))	
-		self.normalization_clip_btns[-1].setStyleSheet(self.button_select_all)	
-		self.normalization_clip_btns[-1].clicked.connect(partial(self.switch_clipping_mode, len(self.channel_cbs)-1))
-		self.normalization_clip_btns[-1].setToolTip('clip')
-
-		self.normalization_min_value_lbl.append(QLabel('Min %: '))
-		self.normalization_min_value_le.append(QLineEdit('0.1'))
-		self.normalization_max_value_lbl.append(QLabel('Max %: '))
-		self.normalization_max_value_le.append(QLineEdit('99.99'))
-
-		ch_layout = QHBoxLayout()
-		ch_layout.addWidget(self.channel_labels[-1], 30)
-		ch_layout.addWidget(self.channel_cbs[-1], 70)
-		self.channels_vb.addLayout(ch_layout)
-
-		channel_norm_options_layout = QHBoxLayout()
-		channel_norm_options_layout.addWidget(QLabel(''),30)
-		ch_norm_sublayout = QHBoxLayout()
-		ch_norm_sublayout.addWidget(self.normalization_min_value_lbl[-1])
-		ch_norm_sublayout.addWidget(self.normalization_min_value_le[-1])
-		ch_norm_sublayout.addWidget(self.normalization_max_value_lbl[-1])
-		ch_norm_sublayout.addWidget(self.normalization_max_value_le[-1])
-		ch_norm_sublayout.addWidget(self.normalization_clip_btns[-1])
-		ch_norm_sublayout.addWidget(self.normalization_mode_btns[-1])
-		channel_norm_options_layout.addLayout(ch_norm_sublayout, 70)
-
-		self.channels_vb.addLayout(channel_norm_options_layout)
-
-
-	def add_to_layout(self):
-
-		self.channels_vb = QVBoxLayout()
-		self.channel_option_layouts = []
-		for i in range(len(self.channel_cbs)):
-			
-			ch_layout = QHBoxLayout()
-			self.channel_labels[i].setText(f'channel {i}: ')
-			ch_layout.addWidget(self.channel_labels[i], 30)
-			self.channel_cbs[i].addItems(self.channel_items)
-			self.channel_cbs[i].currentIndexChanged.connect(self.check_valid_channels)
-			ch_layout.addWidget(self.channel_cbs[i], 70)
-			self.channels_vb.addLayout(ch_layout)
-
-			channel_norm_options_layout = QHBoxLayout()
-			#channel_norm_options_layout.setContentsMargins(130,0,0,0)
-			channel_norm_options_layout.addWidget(QLabel(''),30)
-			ch_norm_sublayout = QHBoxLayout()
-			ch_norm_sublayout.addWidget(self.normalization_min_value_lbl[i])			
-			ch_norm_sublayout.addWidget(self.normalization_min_value_le[i])
-			ch_norm_sublayout.addWidget(self.normalization_max_value_lbl[i])
-			ch_norm_sublayout.addWidget(self.normalization_max_value_le[i])
-			ch_norm_sublayout.addWidget(self.normalization_clip_btns[i])
-			ch_norm_sublayout.addWidget(self.normalization_mode_btns[i])
-			channel_norm_options_layout.addLayout(ch_norm_sublayout, 70)
-			self.channels_vb.addLayout(channel_norm_options_layout)
-
-		self.addLayout(self.channels_vb)
-
-		add_hbox = QHBoxLayout()
-		add_hbox.addWidget(QLabel(''), 66)
-		add_hbox.addWidget(self.add_col_btn, 33, alignment=Qt.AlignRight)
-		self.addLayout(add_hbox)
-
-	def switch_normalization_mode(self, index):
-
-		"""
-		Use absolute or percentile values for the normalization of each individual channel.
-		
-		"""
-
-		currentNormMode = self.normalization_mode[index]
-		self.normalization_mode[index] = not currentNormMode
-
-		if self.normalization_mode[index]:
-			self.normalization_mode_btns[index].setIcon(icon(MDI6.percent_circle,color="#1565c0"))
-			self.normalization_mode_btns[index].setIconSize(QSize(20, 20))	
-			self.normalization_mode_btns[index].setStyleSheet(self.button_select_all)	
-			self.normalization_mode_btns[index].setToolTip("Switch to absolute normalization values.")
-			self.normalization_min_value_lbl[index].setText('Min %: ')
-			self.normalization_max_value_lbl[index].setText('Max %: ')
-			self.normalization_min_value_le[index].setText('0.1')
-			self.normalization_max_value_le[index].setText('99.99')
-
-		else:
-			self.normalization_mode_btns[index].setIcon(icon(MDI6.percent_circle_outline,color="black"))
-			self.normalization_mode_btns[index].setIconSize(QSize(20, 20))	
-			self.normalization_mode_btns[index].setStyleSheet(self.button_select_all)	
-			self.normalization_mode_btns[index].setToolTip("Switch to percentile normalization values.")
-			self.normalization_min_value_lbl[index].setText('Min: ')
-			self.normalization_min_value_le[index].setText('0')
-			self.normalization_max_value_lbl[index].setText('Max: ')
-			self.normalization_max_value_le[index].setText('1000')
-	
-	def switch_clipping_mode(self, index):
-
-		currentClipMode = self.clip_option[index]
-		self.clip_option[index] = not currentClipMode
-
-		if self.clip_option[index]:
-			self.normalization_clip_btns[index].setIcon(icon(MDI6.content_cut,color="#1565c0"))
-			self.normalization_clip_btns[index].setIconSize(QSize(20, 20))
-			self.normalization_clip_btns[index].setStyleSheet(self.button_select_all)	
-
-		else:
-			self.normalization_clip_btns[index].setIcon(icon(MDI6.content_cut,color="black"))
-			self.normalization_clip_btns[index].setIconSize(QSize(20, 20))		
-			self.normalization_clip_btns[index].setStyleSheet(self.button_select_all)	
-
-	def check_valid_channels(self):
-
-		if hasattr(self.parent_window, "submit_btn"):
-			if np.all([cb.currentText()=='--' for cb in self.channel_cbs]):
-				self.parent_window.submit_btn.setEnabled(False)
-
-		if hasattr(self.parent_window, "spatial_calib_le") and hasattr(self.parent_window, "submit_btn"):
-			if self.parent_window.spatial_calib_le.text()!='--':
-				self.parent_window.submit_btn.setEnabled(True)
-		elif hasattr(self.parent_window, "submit_btn"):
-			self.parent_window.submit_btn.setEnabled(True)
-
-
-
-class BackgroundFitCorrectionLayout(QGridLayout, Styles):
-	
-	"""docstring for ClassName"""
-	
-	def __init__(self, parent_window=None, *args):
-		super().__init__(*args)
-
-		self.parent_window = parent_window
-		
-		if hasattr(self.parent_window.parent_window, 'locate_image'):
-			self.attr_parent = self.parent_window.parent_window
-		elif hasattr(self.parent_window.parent_window.parent_window, 'locate_image'):
-			self.attr_parent = self.parent_window.parent_window.parent_window
-		else:
-			self.attr_parent = self.parent_window.parent_window.parent_window.parent_window
-
-		self.channel_names = self.attr_parent.exp_channels
-		self.setContentsMargins(15,15,15,15)
-		self.generate_widgets()
-		self.add_to_layout()
-
-	def generate_widgets(self):
-
-		self.channel_lbl = QLabel('Channel: ')
-		self.channels_cb = QComboBox()
-		self.channels_cb.addItems(self.channel_names)
-		
-		self.thresh_lbl = QLabel('Threshold: ')
-		self.thresh_lbl.setToolTip('Threshold on the STD-filtered image.\nPixel values above the threshold are\nconsidered as non-background and are\nmasked prior to background estimation.')
-		self.threshold_viewer_btn = QPushButton()
-		self.threshold_viewer_btn.setIcon(icon(MDI6.image_check, color="k"))
-		self.threshold_viewer_btn.setStyleSheet(self.button_select_all)
-		self.threshold_viewer_btn.clicked.connect(self.set_threshold_graphically)
-		self.threshold_viewer_btn.setToolTip('Set the threshold graphically.')
-
-		self.model_lbl = QLabel('Model: ')
-		self.model_lbl.setToolTip('2D model to fit the background with.')
-		self.models_cb = QComboBox()
-		self.models_cb.addItems(['paraboloid', 'plane'])
-		self.models_cb.setToolTip('2D model to fit the background with.')
-
-		self.corrected_stack_viewer = QPushButton("")
-		self.corrected_stack_viewer.setStyleSheet(self.button_select_all)
-		self.corrected_stack_viewer.setIcon(icon(MDI6.eye_outline, color="black"))
-		self.corrected_stack_viewer.setToolTip("View corrected image")
-		self.corrected_stack_viewer.clicked.connect(self.preview_correction)
-		self.corrected_stack_viewer.setIconSize(QSize(20, 20))
-
-		self.add_correction_btn = QPushButton('Add correction')
-		self.add_correction_btn.setStyleSheet(self.button_style_sheet_2)
-		self.add_correction_btn.setIcon(icon(MDI6.plus, color="#1565c0"))
-		self.add_correction_btn.setToolTip('Add correction.')
-		self.add_correction_btn.setIconSize(QSize(25, 25))
-		self.add_correction_btn.clicked.connect(self.add_instructions_to_parent_list)
-
-		self.threshold_le = ThresholdLineEdit(init_value=2, connected_buttons=[self.threshold_viewer_btn,
-																			   self.corrected_stack_viewer,
-																			   self.add_correction_btn
-																			   ])
-
-
-	def add_to_layout(self):
-		
-		channel_layout = QHBoxLayout()
-		channel_layout.addWidget(self.channel_lbl, 25)
-		channel_layout.addWidget(self.channels_cb, 75)
-		self.addLayout(channel_layout, 0, 0, 1, 3)
-
-		threshold_layout = QHBoxLayout()
-		threshold_layout.addWidget(self.thresh_lbl, 25)
-		subthreshold_layout = QHBoxLayout()
-		subthreshold_layout.addWidget(self.threshold_le, 95)
-		subthreshold_layout.addWidget(self.threshold_viewer_btn, 5)
-
-		threshold_layout.addLayout(subthreshold_layout, 75)
-		self.addLayout(threshold_layout, 1, 0, 1, 3)
-
-		model_layout = QHBoxLayout()
-		model_layout.addWidget(self.model_lbl, 25)
-		model_layout.addWidget(self.models_cb, 75)
-		self.addLayout(model_layout, 2, 0, 1, 3)
-
-		self.operation_layout = OperationLayout()
-		self.addLayout(self.operation_layout, 3, 0, 1, 3)
-
-		correction_layout = QHBoxLayout()
-		correction_layout.addWidget(self.add_correction_btn, 95)
-		correction_layout.addWidget(self.corrected_stack_viewer, 5)
-		self.addLayout(correction_layout, 4, 0, 1, 3)
-
-		verticalSpacer = QSpacerItem(20, 40, QSizePolicy.Minimum, QSizePolicy.Expanding)
-		self.addItem(verticalSpacer, 5, 0, 1, 3)
-
-	def add_instructions_to_parent_list(self):
-
-		self.generate_instructions()
-		self.parent_window.protocols.append(self.instructions)
-		correction_description = ""
-		for index, (key, value) in enumerate(self.instructions.items()):
-			if index > 0:
-				correction_description += ", "
-			correction_description += str(key) + " : " + str(value)
-		self.parent_window.protocol_list.addItem(correction_description)
-
-	def generate_instructions(self):
-
-		if self.operation_layout.subtract_btn.isChecked():
-			operation = "subtract"
-		else:
-			operation = "divide"
-			clip = None
-
-		if self.operation_layout.clip_btn.isChecked() and self.operation_layout.subtract_btn.isChecked():
-			clip = True
-		else:
-			clip = False
-
-		self.instructions = {
-					  "target_channel": self.channels_cb.currentText(),
-					  "correction_type": "fit",
-					  "model": self.models_cb.currentText(),
-					  "threshold_on_std": self.threshold_le.get_threshold(),
-					  "operation": operation,
-					  "clip": clip
-					 }
-
-	def set_target_channel(self):
-
-		channel_indices = _extract_channel_indices_from_config(self.attr_parent.exp_config, [self.channels_cb.currentText()])
-		self.target_channel = channel_indices[0]
-
-	def set_threshold_graphically(self):
-
-		self.attr_parent.locate_image()
-		self.set_target_channel()
-		thresh = self.threshold_le.get_threshold()
-
-		if self.attr_parent.current_stack is not None and thresh is not None:
-			self.viewer = ThresholdedStackVisualizer(initial_threshold=thresh,
-													 parent_le = self.threshold_le,
-													 preprocessing=[['gauss',2],["std",4]],
-													 stack_path=self.attr_parent.current_stack,
-													 n_channels=len(self.channel_names),
-													 target_channel=self.target_channel,
-													 window_title='Set the exclusion threshold',
-													 )
-			self.viewer.show()
-
-	def preview_correction(self):
-
-		if self.attr_parent.well_list.isMultipleSelection() or not self.attr_parent.well_list.isAnySelected() or self.attr_parent.position_list.isMultipleSelection() or not self.attr_parent.position_list.isAnySelected():
-			
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Critical)
-			msgBox.setText("Please select a single position...")
-			msgBox.setWindowTitle("Critical")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return None
-
-		if self.operation_layout.subtract_btn.isChecked():
-			operation = "subtract"
-		else:
-			operation = "divide"
-			clip = None
-
-		if self.operation_layout.clip_btn.isChecked() and self.operation_layout.subtract_btn.isChecked():
-			clip = True
-		else:
-			clip = False
-
-		corrected_stack = correct_background_model(self.attr_parent.exp_dir,
-						   well_option=self.attr_parent.well_list.getSelectedIndices(), #+1 ??
-						   position_option=self.attr_parent.position_list.getSelectedIndices(), #+1??
-						   target_channel=self.channels_cb.currentText(),
-						   model = self.models_cb.currentText(),
-						   threshold_on_std = self.threshold_le.get_threshold(),
-						   operation = operation,
-						   clip = clip,
-						   export= False,
-						   return_stacks=True,
-						   activation_protocol=[['gauss',2],['std',4]],
-						   show_progress_per_well = True,
-						   show_progress_per_pos = False,
-							)
-
-		if corrected_stack:
-			self.viewer = StackVisualizer(
-										  stack=corrected_stack[0],
-										  window_title='Corrected channel',
-										  target_channel=self.channels_cb.currentIndex(),
-										  frame_slider = True,
-										  contrast_slider = True
-										 )
-			self.viewer.show()
-		else:
-			print("Corrected stack could not be generated... No stack available...")
-
-
-
-class LocalCorrectionLayout(BackgroundFitCorrectionLayout):
-	
-	"""docstring for ClassName"""
-	
-	def __init__(self, *args):
-		
-		super().__init__(*args)
-		
-		if hasattr(self.parent_window.parent_window, 'locate_image'):
-			self.attr_parent = self.parent_window.parent_window
-		elif hasattr(self.parent_window.parent_window.parent_window, 'locate_image'):
-			self.attr_parent = self.parent_window.parent_window.parent_window
-		else:
-			self.attr_parent = self.parent_window.parent_window.parent_window.parent_window
-
-		self.thresh_lbl.setText('Distance: ')
-		self.thresh_lbl.setToolTip('Distance from the cell mask over which to estimate local intensity.')
-		
-		self.models_cb.clear()
-		self.models_cb.addItems(['mean','median'])
-
-		self.threshold_le.set_threshold(5)
-		self.threshold_le.connected_buttons = [self.threshold_viewer_btn,self.add_correction_btn]
-		self.threshold_le.setValidator(QIntValidator())
-
-		self.threshold_viewer_btn.disconnect()
-		self.threshold_viewer_btn.clicked.connect(self.set_distance_graphically)
-
-		self.corrected_stack_viewer.hide()
-
-	def set_distance_graphically(self):
-
-		self.attr_parent.locate_image()
-		self.set_target_channel()
-		thresh = self.threshold_le.get_threshold()
-
-		if self.attr_parent.current_stack is not None and thresh is not None:
-			
-			self.viewer = CellEdgeVisualizer(cell_type=self.parent_window.parent_window.mode,
-											 stack_path=self.attr_parent.current_stack,
-											 parent_le = self.threshold_le,
-											 n_channels=len(self.channel_names),
-											 target_channel=self.channels_cb.currentIndex(),
-											 edge_range = (0,30),
-											 initial_edge=int(thresh),
-											 invert=True,
-											 window_title='Set an edge distance to estimate local intensity',
-											 channel_cb=False,
-											 PxToUm = 1,
-											 )
-			self.viewer.show()
-
-	def generate_instructions(self):
-
-		if self.operation_layout.subtract_btn.isChecked():
-			operation = "subtract"
-		else:
-			operation = "divide"
-			clip = None
-
-		if self.operation_layout.clip_btn.isChecked() and self.operation_layout.subtract_btn.isChecked():
-			clip = True
-		else:
-			clip = False
-
-		self.instructions = {
-					  "target_channel": self.channels_cb.currentText(),
-					  "correction_type": "local",
-					  "model": self.models_cb.currentText(),
-					  "distance": int(self.threshold_le.get_threshold()),
-					  "operation": operation,
-					  "clip": clip,
-					 }
-
-
-class OperationLayout(QVBoxLayout):
-	
-	"""docstring for ClassName"""
-	
-	def __init__(self, ratio=(0.25,0.75), *args):
-		
-		super().__init__(*args)
-
-		self.ratio = ratio
-		self.generate_widgets()
-		self.generate_layout()
-
-	def generate_widgets(self):
-		
-		self.operation_lbl = QLabel('Operation: ')
-		self.operation_group = QButtonGroup()
-		self.subtract_btn = QRadioButton('Subtract')
-		self.divide_btn = QRadioButton('Divide')
-		self.subtract_btn.toggled.connect(self.activate_clipping_options)
-		self.divide_btn.toggled.connect(self.activate_clipping_options)
-
-		self.operation_group.addButton(self.subtract_btn)
-		self.operation_group.addButton(self.divide_btn)
-
-		self.clip_group = QButtonGroup()
-		self.clip_btn = QRadioButton('Clip')
-		self.clip_not_btn = QRadioButton('Do not clip')
-
-		self.clip_group.addButton(self.clip_btn)
-		self.clip_group.addButton(self.clip_not_btn)
-
-	def generate_layout(self):
-		
-		operation_layout = QHBoxLayout()
-		operation_layout.addWidget(self.operation_lbl, 100*int(self.ratio[0]))
-		operation_layout.addWidget(self.subtract_btn, 100*int(self.ratio[1])//2, alignment=Qt.AlignCenter)
-		operation_layout.addWidget(self.divide_btn, 100*int(self.ratio[1])//2, alignment=Qt.AlignCenter)
-		self.addLayout(operation_layout)
-
-		clip_layout = QHBoxLayout()
-		clip_layout.addWidget(QLabel(''), 100*int(self.ratio[0]))
-		clip_layout.addWidget(self.clip_btn, 100*int(self.ratio[1])//4, alignment=Qt.AlignCenter)
-		clip_layout.addWidget(self.clip_not_btn, 100*int(self.ratio[1])//4, alignment=Qt.AlignCenter)
-		clip_layout.addWidget(QLabel(''), 100*int(self.ratio[1])//2)
-		self.addLayout(clip_layout)
-
-		self.subtract_btn.click()
-		self.clip_not_btn.click()
-
-	def activate_clipping_options(self):
-		
-		if self.subtract_btn.isChecked():
-			self.clip_btn.setEnabled(True)
-			self.clip_not_btn.setEnabled(True)
-		else:
-			self.clip_btn.setEnabled(False)
-			self.clip_not_btn.setEnabled(False)
-
-class ProtocolDesignerLayout(QVBoxLayout, Styles):
-	
-	"""Multi tabs and list widget configuration for background correction
-		in preprocessing and measurements
-	"""
-	
-	def __init__(self, parent_window=None, tab_layouts=[], tab_names=[], title='',list_title='',*args):
-		
-		super().__init__(*args)
-
-		self.title = title
-		self.parent_window = parent_window
-		self.channel_names = self.parent_window.channel_names
-		self.tab_layouts = tab_layouts
-		self.tab_names = tab_names
-		self.list_title = list_title
-		self.protocols = []
-		assert len(self.tab_layouts)==len(self.tab_names)
-
-		self.generate_widgets()
-		self.generate_layout()
-
-	def generate_widgets(self):
-
-		self.title_lbl = QLabel(self.title)
-		self.title_lbl.setStyleSheet("""
-			font-weight: bold;
-			padding: 0px;
-			""")		
-
-		self.tabs = QTabWidget()
-		self.tabs.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
-		
-		for k in range(len(self.tab_layouts)):
-			wg = CelldetectiveWidget()
-			self.tab_layouts[k].parent_window = self
-			wg.setLayout(self.tab_layouts[k])
-			self.tabs.addTab(wg, self.tab_names[k])
-		
-		self.protocol_list_lbl = QLabel(self.list_title)
-		self.protocol_list = QListWidget()
-
-		self.delete_protocol_btn = QPushButton('')
-		self.delete_protocol_btn.setStyleSheet(self.button_select_all)
-		self.delete_protocol_btn.setIcon(icon(MDI6.trash_can, color="black"))
-		self.delete_protocol_btn.setToolTip("Remove.")
-		self.delete_protocol_btn.setIconSize(QSize(20, 20))
-		self.delete_protocol_btn.clicked.connect(self.remove_protocol_from_list)
-
-	def generate_layout(self):
-
-		self.correction_layout = QVBoxLayout()
-
-		self.background_correction_layout = QVBoxLayout()
-		self.background_correction_layout.setContentsMargins(0,0,0,0)
-		self.title_layout = QHBoxLayout()
-		self.title_layout.addWidget(self.title_lbl, 100, alignment=Qt.AlignCenter)
-		self.background_correction_layout.addLayout(self.title_layout)
-		self.background_correction_layout.addWidget(self.tabs)
-		self.correction_layout.addLayout(self.background_correction_layout)
-		
-		self.addLayout(self.correction_layout)
-
-		self.list_layout = QVBoxLayout()
-		list_header_layout = QHBoxLayout()
-		list_header_layout.addWidget(self.protocol_list_lbl)
-		list_header_layout.addWidget(self.delete_protocol_btn, alignment=Qt.AlignRight)
-		self.list_layout.addLayout(list_header_layout)
-		self.list_layout.addWidget(self.protocol_list)
-
-		self.addLayout(self.list_layout)
-
-
-	def remove_protocol_from_list(self):
-
-		current_item = self.protocol_list.currentRow()
-		if current_item > -1:
-			del self.protocols[current_item]
-			self.protocol_list.takeItem(current_item)
-
-class ChannelOffsetOptionsLayout(QVBoxLayout, Styles):
-	
-	def __init__(self, parent_window=None, *args, **kwargs):
-		
-		super().__init__(*args, **kwargs)
-
-		self.parent_window = parent_window
-		if hasattr(self.parent_window.parent_window, 'exp_config'):
-			self.attr_parent = self.parent_window.parent_window
-		else:
-			self.attr_parent = self.parent_window.parent_window.parent_window
-
-		self.channel_names = self.attr_parent.exp_channels
-
-		self.setContentsMargins(15,15,15,15)
-		self.generate_widgets()
-		self.add_to_layout()
-
-	def generate_widgets(self):
-		
-		self.channel_lbl = QLabel('Channel: ')
-		self.channels_cb = QComboBox()
-		self.channels_cb.addItems(self.channel_names)
-
-		self.shift_lbl = QLabel('Shift: ')
-		self.shift_h_lbl = QLabel('(h): ')
-		self.shift_v_lbl = QLabel('(v): ')
-
-		self.set_shift_btn = QPushButton()
-		self.set_shift_btn.setIcon(icon(MDI6.image_check, color="k"))
-		self.set_shift_btn.setStyleSheet(self.button_select_all)
-		self.set_shift_btn.setToolTip('Set the channel shift.')
-		self.set_shift_btn.clicked.connect(self.open_offset_viewer)
-		
-		self.add_correction_btn = QPushButton('Add correction')
-		self.add_correction_btn.setStyleSheet(self.button_style_sheet_2)
-		self.add_correction_btn.setIcon(icon(MDI6.plus, color="#1565c0"))
-		self.add_correction_btn.setToolTip('Add correction.')
-		self.add_correction_btn.setIconSize(QSize(25, 25))
-		self.add_correction_btn.clicked.connect(self.add_instructions_to_parent_list)
-
-		self.vertical_shift_le = ThresholdLineEdit(init_value=0, connected_buttons=[self.add_correction_btn],placeholder='vertical shift [pixels]', value_type='float')
-		self.horizontal_shift_le = ThresholdLineEdit(init_value=0, connected_buttons=[self.add_correction_btn],placeholder='vertical shift [pixels]', value_type='float')
-	
-	def add_to_layout(self):
-
-		channel_ch_hbox = QHBoxLayout()
-		channel_ch_hbox.addWidget(self.channel_lbl, 25)
-		channel_ch_hbox.addWidget(self.channels_cb, 75)
-		self.addLayout(channel_ch_hbox)
-
-		shift_hbox = QHBoxLayout()
-		shift_hbox.addWidget(self.shift_lbl, 25)
-		
-		shift_subhbox = QHBoxLayout()
-		shift_subhbox.addWidget(self.shift_h_lbl, 10)
-		shift_subhbox.addWidget(self.horizontal_shift_le, 75//2)
-		shift_subhbox.addWidget(self.shift_v_lbl, 10)
-		shift_subhbox.addWidget(self.vertical_shift_le, 75//2)	
-		shift_subhbox.addWidget(self.set_shift_btn, 5)
-
-		shift_hbox.addLayout(shift_subhbox, 75)
-		self.addLayout(shift_hbox)
-
-		btn_hbox = QHBoxLayout()
-		btn_hbox.addWidget(self.add_correction_btn, 95)
-		self.addLayout(btn_hbox)		
-
-	def add_instructions_to_parent_list(self):
-
-		self.generate_instructions()
-		self.parent_window.protocol_layout.protocols.append(self.instructions)
-		correction_description = ""
-		for index, (key, value) in enumerate(self.instructions.items()):
-			if index > 0:
-				correction_description += ", "
-			correction_description += str(key) + " : " + str(value)
-		self.parent_window.protocol_layout.protocol_list.addItem(correction_description)
-
-	def generate_instructions(self):
-
-		self.instructions = {
-					  "correction_type": "offset",
-					  "target_channel": self.channels_cb.currentText(),
-					  "correction_horizontal": self.horizontal_shift_le.get_threshold(),
-					  "correction_vertical": self.vertical_shift_le.get_threshold(),
-					 }
-
-
-	def set_target_channel(self):
-
-		channel_indices = _extract_channel_indices_from_config(self.attr_parent.exp_config, [self.channels_cb.currentText()])
-		self.target_channel = channel_indices[0]
-
-	def open_offset_viewer(self):
-		
-		self.attr_parent.locate_image()
-		self.set_target_channel()
-
-		if self.attr_parent.current_stack is not None:
-			self.viewer = ChannelOffsetViewer(
-											 parent_window = self,
-											 stack_path=self.attr_parent.current_stack,
-											 channel_names=self.attr_parent.exp_channels,
-											 n_channels=len(self.channel_names),
-											 channel_cb=True,
-											 target_channel=self.target_channel,
-											 window_title='offset viewer',
-											)
-			self.viewer.show()
-
-
-class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
-	
-	"""docstring for ClassName"""
-	
-	def __init__(self, parent_window=None, *args):
-		super().__init__(*args)
-
-		self.parent_window = parent_window
-
-		if hasattr(self.parent_window.parent_window, 'exp_config'):
-			self.attr_parent = self.parent_window.parent_window
-		else:
-			self.attr_parent = self.parent_window.parent_window.parent_window
-
-		self.channel_names = self.attr_parent.exp_channels
-
-		self.setContentsMargins(15,15,15,15)
-		self.generate_widgets()
-		self.add_to_layout()
-
-	def generate_widgets(self):
-
-		self.channel_lbl = QLabel('Channel: ')
-		self.channels_cb = QComboBox()
-		self.channels_cb.addItems(self.channel_names)
-		
-		self.acquistion_lbl = QLabel('Stack mode: ')
-		self.acq_mode_group = QButtonGroup()
-		self.timeseries_rb = QRadioButton('timeseries')
-		self.timeseries_rb.setChecked(True)
-		self.tiles_rb = QRadioButton('tiles')
-		self.acq_mode_group.addButton(self.timeseries_rb, 0)
-		self.acq_mode_group.addButton(self.tiles_rb, 1)
-
-		from PyQt5.QtWidgets import QSlider
-		from superqt import QRangeSlider
-		self.frame_range_slider = QLabeledRangeSlider(parent=None)
-
-		self.timeseries_rb.toggled.connect(self.activate_time_range)
-		self.tiles_rb.toggled.connect(self.activate_time_range)
-
-		self.thresh_lbl = QLabel('Threshold: ')
-		self.thresh_lbl.setToolTip('Threshold on the STD-filtered image.\nPixel values above the threshold are\nconsidered as non-background and are\nmasked prior to background estimation.')
-		self.threshold_viewer_btn = QPushButton()
-		self.threshold_viewer_btn.setIcon(icon(MDI6.image_check, color="k"))
-		self.threshold_viewer_btn.setStyleSheet(self.button_select_all)
-		self.threshold_viewer_btn.clicked.connect(self.set_threshold_graphically)
-
-		self.background_viewer_btn = QPushButton()
-		self.background_viewer_btn.setIcon(icon(MDI6.image_check, color="k"))
-		self.background_viewer_btn.setStyleSheet(self.button_select_all)
-		self.background_viewer_btn.setToolTip('View reconstructed background.')
-
-		self.corrected_stack_viewer_btn = QPushButton("")
-		self.corrected_stack_viewer_btn.setStyleSheet(self.button_select_all)
-		self.corrected_stack_viewer_btn.setIcon(icon(MDI6.eye_outline, color="black"))
-		self.corrected_stack_viewer_btn.setToolTip("View corrected image")
-		self.corrected_stack_viewer_btn.clicked.connect(self.preview_correction)
-		self.corrected_stack_viewer_btn.setIconSize(QSize(20, 20))
-
-		self.add_correction_btn = QPushButton('Add correction')
-		self.add_correction_btn.setStyleSheet(self.button_style_sheet_2)
-		self.add_correction_btn.setIcon(icon(MDI6.plus, color="#1565c0"))
-		self.add_correction_btn.setToolTip('Add correction.')
-		self.add_correction_btn.setIconSize(QSize(25, 25))
-		self.add_correction_btn.clicked.connect(self.add_instructions_to_parent_list)
-
-		self.threshold_le = ThresholdLineEdit(init_value=2, connected_buttons=[self.threshold_viewer_btn,
-																				self.background_viewer_btn, self.corrected_stack_viewer_btn, self.add_correction_btn])
-
-		self.well_slider = QLabeledSlider(parent=None)
-
-		self.background_viewer_btn.clicked.connect(self.estimate_bg)
-
-		self.regress_cb = QCheckBox('Optimize for each frame?')
-		self.regress_cb.toggled.connect(self.activate_coef_options)
-		self.regress_cb.setChecked(False)
-
-		self.coef_range_slider = QLabeledDoubleRangeSlider(parent=None)
-		self.coef_range_layout = QuickSliderLayout(label='Coef. range: ',
-											  slider = self.coef_range_slider,
-											  slider_initial_value=(0.95,1.05),
-											  slider_range=(0.75,1.25),
-											  slider_tooltip='Coefficient range to increase or decrease the background intensity level...',
-											  )
-
-		self.nbr_coefs_lbl = QLabel("Nbr of coefs: ")
-		self.nbr_coefs_lbl.setToolTip('Number of coefficients to be tested within range.\nThe more, the slower.')
-
-		self.nbr_coef_le = QLineEdit()
-		self.nbr_coef_le.setText('100')
-		self.nbr_coef_le.setValidator(QIntValidator())
-		self.nbr_coef_le.setPlaceholderText('nbr of coefs')
-
-		self.coef_widgets = [self.coef_range_layout.qlabel, self.coef_range_slider, self.nbr_coefs_lbl, self.nbr_coef_le]
-		for c in self.coef_widgets:
-			c.setEnabled(False)
-
-		self.interpolate_check = QCheckBox("interpolate NaNs")
-
-	def add_to_layout(self):
-		
-		channel_layout = QHBoxLayout()
-		channel_layout.addWidget(self.channel_lbl, 25)
-		channel_layout.addWidget(self.channels_cb, 75)
-		self.addLayout(channel_layout, 0, 0, 1, 3)
-
-		acquisition_layout = QHBoxLayout()
-		acquisition_layout.addWidget(self.acquistion_lbl, 25)
-		acquisition_layout.addWidget(self.timeseries_rb, 75//2, alignment=Qt.AlignCenter)
-		acquisition_layout.addWidget(self.tiles_rb, 75//2, alignment=Qt.AlignCenter)
-		self.addLayout(acquisition_layout, 1, 0, 1, 3)
-
-		frame_selection_layout = QuickSliderLayout(label='Time range: ',
-												  slider = self.frame_range_slider,
-												  slider_initial_value=(0,5),
-												  slider_range=(0,self.attr_parent.len_movie),
-												  slider_tooltip='frame [#]',
-												  decimal_option = False,
-												 )
-		frame_selection_layout.qlabel.setToolTip('Frame range for which the background\nis most likely to be observed.')
-		self.time_range_options = [self.frame_range_slider, frame_selection_layout.qlabel]
-		self.addLayout(frame_selection_layout, 2, 0, 1, 3)
-
-		
-		threshold_layout = QHBoxLayout()
-		threshold_layout.addWidget(self.thresh_lbl, 25)
-		subthreshold_layout = QHBoxLayout()
-		subthreshold_layout.addWidget(self.threshold_le, 95)
-		subthreshold_layout.addWidget(self.threshold_viewer_btn, 5)
-		threshold_layout.addLayout(subthreshold_layout, 75)
-		self.addLayout(threshold_layout, 3, 0, 1, 3)
-
-		background_layout = QuickSliderLayout(label='QC for well: ',
-											  slider = self.well_slider,
-											  slider_initial_value=1,
-											  slider_range=(1,len(self.attr_parent.wells)),
-											  slider_tooltip='well [#]',
-											  decimal_option = False,
-											  layout_ratio=(0.25,0.70)
-											  )
-		background_layout.addWidget(self.background_viewer_btn, 5)
-		self.addLayout(background_layout, 4, 0, 1, 3)
-
-		self.addWidget(self.regress_cb, 5, 0, 1, 3)
-
-		self.addLayout(self.coef_range_layout, 6, 0, 1, 3)
-
-		coef_nbr_layout = QHBoxLayout()
-		coef_nbr_layout.addWidget(self.nbr_coefs_lbl, 25)
-		coef_nbr_layout.addWidget(self.nbr_coef_le, 75)
-		self.addLayout(coef_nbr_layout, 7,0,1,3)
-
-		offset_layout = QHBoxLayout()
-		offset_layout.addWidget(QLabel("Offset: "), 25)
-		self.camera_offset_le = QLineEdit("0")
-		self.camera_offset_le.setPlaceholderText('camera black level')
-		self.camera_offset_le.setValidator(QDoubleValidator())
-		offset_layout.addWidget(self.camera_offset_le, 75)
-		self.addLayout(offset_layout, 8, 0, 1, 3)
-
-		self.operation_layout = OperationLayout()
-		self.addLayout(self.operation_layout, 9, 0, 1, 3)
-
-		self.addWidget(self.interpolate_check, 10, 0, 1, 1)
-
-		correction_layout = QHBoxLayout()
-		correction_layout.addWidget(self.add_correction_btn, 95)
-		correction_layout.addWidget(self.corrected_stack_viewer_btn, 5)
-		self.addLayout(correction_layout, 11, 0, 1, 3)
-
-		# verticalSpacer = QSpacerItem(20, 40, QSizePolicy.Minimum, QSizePolicy.Expanding)
-		# self.addItem(verticalSpacer, 5, 0, 1, 3)
-
-	def add_instructions_to_parent_list(self):
-
-		self.generate_instructions()
-		self.parent_window.protocols.append(self.instructions)
-		correction_description = ""
-		for index, (key, value) in enumerate(self.instructions.items()):
-			if index > 0:
-				correction_description += ", "
-			correction_description += str(key) + " : " + str(value)
-		self.parent_window.protocol_list.addItem(correction_description)
-
-	def generate_instructions(self):
-
-		if self.timeseries_rb.isChecked():
-			mode = "timeseries"
-		elif self.tiles_rb.isChecked():
-			mode = "tiles"
-
-		if self.regress_cb.isChecked():
-			optimize_option = True
-			opt_coef_range = self.coef_range_slider.value()
-			opt_coef_nbr = int(self.nbr_coef_le.text())
-		else:
-			optimize_option = False
-			opt_coef_range = None
-			opt_coef_nbr = None
-
-		if self.operation_layout.subtract_btn.isChecked():
-			operation = "subtract"
-		else:
-			operation = "divide"
-			clip = None
-
-		if self.operation_layout.clip_btn.isChecked() and self.operation_layout.subtract_btn.isChecked():
-			clip = True
-		else:
-			clip = False
-		
-		if self.camera_offset_le.text()=="":
-			offset = None
-		else:
-			offset = float(self.camera_offset_le.text().replace(",","."))
-
-		self.instructions = {
-					  "target_channel": self.channels_cb.currentText(),
-					  "correction_type": "model-free",
-					  "threshold_on_std": self.threshold_le.get_threshold(),
-					  "frame_range": self.frame_range_slider.value(),
-					  "mode": mode,
-					  "optimize_option": optimize_option,
-					  "opt_coef_range": opt_coef_range,
-					  "opt_coef_nbr": opt_coef_nbr,
-					  "operation": operation,
-					  "clip": clip,
-					  "offset": offset,
-					  "fix_nan": self.interpolate_check.isChecked(),
-					 }
-
-	def set_target_channel(self):
-
-		channel_indices = _extract_channel_indices_from_config(self.attr_parent.exp_config, [self.channels_cb.currentText()])
-		self.target_channel = channel_indices[0]
-
-	def set_threshold_graphically(self):
-
-		self.attr_parent.locate_image()
-		self.set_target_channel()
-		thresh = self.threshold_le.get_threshold()
-
-		if self.attr_parent.current_stack is not None and thresh is not None:
-			self.viewer = ThresholdedStackVisualizer(initial_threshold=thresh,
-													 parent_le = self.threshold_le,
-													 preprocessing=[['gauss',2],["std",4]],
-													 stack_path=self.attr_parent.current_stack,
-													 n_channels=len(self.channel_names),
-													 target_channel=self.target_channel,
-													 window_title='Set the exclusion threshold',
-													 )
-			self.viewer.show()
-
-	def preview_correction(self):
-
-		if self.attr_parent.well_list.isMultipleSelection() or not self.attr_parent.well_list.isAnySelected() or self.attr_parent.position_list.isMultipleSelection() or not self.attr_parent.position_list.isAnySelected():
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText("Please select a single position...")
-			msgBox.setWindowTitle("Warning")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return None
-
-		if self.timeseries_rb.isChecked():
-			mode = "timeseries"
-		elif self.tiles_rb.isChecked():
-			mode = "tiles"
-
-		if self.regress_cb.isChecked():
-			optimize_option = True
-			opt_coef_range = self.coef_range_slider.value()
-			opt_coef_nbr = int(self.nbr_coef_le.text())
-		else:
-			optimize_option = False
-			opt_coef_range = None
-			opt_coef_nbr = None
-
-		if self.operation_layout.subtract_btn.isChecked():
-			operation = "subtract"
-		else:
-			operation = "divide"
-			clip = None
-
-		if self.operation_layout.clip_btn.isChecked() and self.operation_layout.subtract_btn.isChecked():
-			clip = True
-		else:
-			clip = False
-
-		corrected_stacks = correct_background_model_free(self.attr_parent.exp_dir, 
-						   well_option=self.attr_parent.well_list.getSelectedIndices(), #+1 ??
-						   position_option=self.attr_parent.getSelectedIndices(), #+1??
-						   target_channel=self.channels_cb.currentText(),
-						   mode = mode,
-						   threshold_on_std = self.threshold_le.get_threshold(),
-						   frame_range = self.frame_range_slider.value(),
-						   optimize_option = optimize_option,
-						   opt_coef_range = opt_coef_range,
-						   opt_coef_nbr = opt_coef_nbr,
-						   operation = operation,
-						   clip = clip,
-						   export= False,
-						   return_stacks=True,
-						   fix_nan=self.interpolate_check.isChecked(),
-						   show_progress_per_well = True,
-						   show_progress_per_pos = False,
-							)
-		
-		self.viewer = StackVisualizer(
-									  stack=corrected_stacks[0],
-									  window_title='Corrected channel',
-									  frame_slider = True,
-									  contrast_slider = True,
-									  target_channel=self.channels_cb.currentIndex(),
-									 )
-		self.viewer.show()
-	
-	def activate_time_range(self):
-
-		if self.timeseries_rb.isChecked():
-			for wg in self.time_range_options:
-				wg.setEnabled(True)
-		elif self.tiles_rb.isChecked():
-			for wg in self.time_range_options:
-				wg.setEnabled(False)
-
-	def activate_coef_options(self):
-		
-		if self.regress_cb.isChecked():
-			for c in self.coef_widgets:
-				c.setEnabled(True)
-		else:
-			for c in self.coef_widgets:
-				c.setEnabled(False)
-
-	def estimate_bg(self):
-
-		if self.timeseries_rb.isChecked():
-			mode = "timeseries"
-		elif self.tiles_rb.isChecked():
-			mode = "tiles"
-
-		bg = estimate_background_per_condition(
-											  self.attr_parent.exp_dir, 
-											  well_option = self.well_slider.value() - 1,
-											  frame_range = self.frame_range_slider.value(),
-											  target_channel = self.channels_cb.currentText(),
-											  show_progress_per_pos = True,
-											  threshold_on_std = self.threshold_le.get_threshold(),
-											  mode = mode,
-											)
-		bg = bg[0]
-		bg = bg['bg']
-		print(bg)
-		if len(bg)>0:
-
-			self.viewer = StackVisualizer(
-										  stack=[bg],
-										  window_title='Reconstructed background',
-										  frame_slider = False,
-										 )
-			self.viewer.show()