celldetective 1.0.2.post1__py3-none-any.whl → 1.1.1__py3-none-any.whl

celldetective/gui/layouts.py

@@ -0,0 +1,756 @@
+from PyQt5.QtWidgets import QCheckBox, QLineEdit, QWidget, QListWidget, QTabWidget, QHBoxLayout,QMessageBox, QPushButton, QVBoxLayout, QRadioButton, QLabel, QButtonGroup, QSizePolicy, QComboBox,QSpacerItem, QGridLayout
+from celldetective.gui.gui_utils import ThresholdLineEdit
+from PyQt5.QtCore import Qt, QSize
+from PyQt5.QtGui import QIntValidator
+
+from superqt import QLabeledRangeSlider, QLabeledSlider, QLabeledDoubleRangeSlider
+
+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
+from celldetective.gui import Styles
+from celldetective.gui.gui_utils import QuickSliderLayout
+from celldetective.preprocessing import correct_background_model, correct_background_model_free, estimate_background_per_condition
+
+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.currentText()=="*" or self.attr_parent.position_list.currentText()=="*":
+			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.currentIndex(), #+1 ??
+						   position_option=self.attr_parent.position_list.currentIndex()-1, #+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,
+							)
+
+		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()
+
+
+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 = QWidget()
+			print('almost there',self.channel_names)
+			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.addWidget(self.title_lbl, alignment=Qt.AlignCenter)
+		self.addWidget(self.tabs)
+
+		list_header_layout = QHBoxLayout()
+		list_header_layout.addWidget(self.protocol_list_lbl)
+		list_header_layout.addWidget(self.delete_protocol_btn, alignment=Qt.AlignRight)
+		self.addLayout(list_header_layout)
+
+		self.addWidget(self.protocol_list)
+
+
+	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 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)
+		print('here ok')
+
+		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)
+
+	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)
+
+		self.operation_layout = OperationLayout()
+		self.addLayout(self.operation_layout, 8, 0, 1, 3)
+
+		correction_layout = QHBoxLayout()
+		correction_layout.addWidget(self.add_correction_btn, 95)
+		correction_layout.addWidget(self.corrected_stack_viewer_btn, 5)
+		self.addLayout(correction_layout, 9, 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
+
+		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
+					 }
+
+	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.currentText()=="*" or self.attr_parent.position_list.currentText()=="*":
+			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.currentIndex(), #+1 ??
+						   position_option=self.attr_parent.position_list.currentIndex()-1, #+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,
+						   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
+									 )
+		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']
+
+		self.viewer = StackVisualizer(
+									  stack=[bg],
+									  window_title='Reconstructed background',
+									  frame_slider = False,
+									 )
+		self.viewer.show()