celldetective 1.3.3.post1__py3-none-any.whl → 1.3.4.post1__py3-none-any.whl

celldetective/gui/control_panel.py

@@ -1,7 +1,7 @@
-from PyQt5.QtWidgets import QMainWindow, QComboBox, QPushButton, QHBoxLayout, QLabel, QWidget, QGridLayout, QFrame, \
+from PyQt5.QtWidgets import QMainWindow, QPushButton, QHBoxLayout, QLabel, QWidget, QGridLayout, QFrame, \
 	QTabWidget, QVBoxLayout, QMessageBox, QScrollArea, QDesktopWidget
 from PyQt5.QtCore import Qt, QSize
-from celldetective.gui.gui_utils import center_window, QHSeperationLine
+from celldetective.gui.gui_utils import center_window, QHSeperationLine, QCheckableComboBox
 from celldetective.utils import _extract_labels_from_config, ConfigSectionMap, extract_experiment_channels, extract_identity_col
 from celldetective.gui import ConfigEditor, ProcessPanel, PreprocessingPanel, AnalysisPanel, NeighPanel
 from celldetective.io import get_experiment_wells, get_config, get_spatial_calibration, get_temporal_calibration, get_experiment_concentrations, get_experiment_cell_types, get_experiment_antibodies, get_experiment_pharmaceutical_agents
@@ -18,6 +18,7 @@ from celldetective.utils import extract_experiment_channels
 from celldetective.gui import Styles
 import pandas as pd
 
+
 class ControlPanel(QMainWindow, Styles):
 
 	def __init__(self, parent_window=None, exp_dir=""):
@@ -90,7 +91,7 @@ class ControlPanel(QMainWindow, Styles):
 		self.initial_width = self.size().width()
 		self.screen_height = desktop.screenGeometry().height()
 		self.screen_width = desktop.screenGeometry().width()
-		self.scroll.setMinimumWidth(425)
+		self.scroll.setMinimumWidth(440)
 
 	def init_wells_and_positions(self):
 
@@ -138,23 +139,23 @@ class ControlPanel(QMainWindow, Styles):
 		self.edit_config_button.clicked.connect(self.open_config_editor)
 		self.edit_config_button.setStyleSheet(self.button_select_all)
 
-		self.well_list = QComboBox()
+		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]		
-		self.well_list.addItems(self.well_truncated) #self.well_labels
-		for i in range(len(self.well_labels)):
-			self.well_list.setItemData(i, self.well_labels[i], Qt.ToolTipRole)
-		self.well_list.addItems(["*"])
-		self.well_list.activated.connect(self.display_positions)
-		self.to_disable.append(self.well_list)
+		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 = QComboBox()
-		self.position_list.addItems(["*"])
+		self.position_list = QCheckableComboBox(obj='position', parent_window=self)
 		self.position_list.addItems(self.positions[0])
-		self.position_list.activated.connect(self.update_position_options)
 		self.to_disable.append(self.position_list)
 		#self.locate_selected_position()
 
+		self.well_list.activated.connect(self.display_positions)
+		self.well_list.setCurrentIndex(0)
+
+		self.position_list.activated.connect(self.update_position_options)
+		self.position_list.setCurrentIndex(0)
+
 		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"))
@@ -163,6 +164,24 @@ class ControlPanel(QMainWindow, Styles):
 		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)
 
@@ -196,20 +215,52 @@ class ControlPanel(QMainWindow, Styles):
 		# Well row
 		well_hbox = QHBoxLayout()
 		well_hbox.addWidget(well_lbl, 25, alignment=Qt.AlignVCenter)
-		well_hbox.addWidget(self.well_list, 75)
+		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, 95)
+		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):
 
 		"""
@@ -341,17 +392,30 @@ class ControlPanel(QMainWindow, Styles):
 		Show the positions as the well is changed.
 		"""
 
-		if self.well_list.currentText()=="*":
+		if self.well_list.isMultipleSelection():
+
 			self.position_list.clear()
-			self.position_list.addItems(["*"])
 			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.currentIndex()
+			pos_index = self.well_list.getSelectedIndices()[0]
 			self.position_list.clear()
-			self.position_list.addItems(["*"])
 			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):
@@ -366,7 +430,7 @@ class ControlPanel(QMainWindow, Styles):
 
 		"""
 
-		if self.well_list.currentText()=="*":
+		if self.well_list.isMultipleSelection():
 			msgBox = QMessageBox()
 			msgBox.setIcon(QMessageBox.Critical)
 			msgBox.setText("Please select a single well...")
@@ -376,12 +440,12 @@ class ControlPanel(QMainWindow, Styles):
 			if returnValue == QMessageBox.Ok:
 				return False
 		else:
-			self.well_index = [self.well_list.currentIndex()]
+			self.well_index = self.well_list.getSelectedIndices() #[self.well_list.currentIndex()]
 
 		for w_idx in self.well_index:
 
 			pos = self.positions[w_idx]
-			if self.position_list.currentText()=="*":
+			if not self.position_list.isSingleSelection():
 				msgBox = QMessageBox()
 				msgBox.setIcon(QMessageBox.Critical)
 				msgBox.setText("Please select a single position...")
@@ -391,11 +455,12 @@ class ControlPanel(QMainWindow, Styles):
 				if returnValue == QMessageBox.Ok:
 					return False
 			else:
-				pos_indices = natsorted([pos.index(self.position_list.currentText())])
+				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')
@@ -405,6 +470,7 @@ class ControlPanel(QMainWindow, Styles):
 		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)
@@ -413,7 +479,8 @@ class ControlPanel(QMainWindow, Styles):
 		
 		self.pos = self.position_list.currentText()
 		panels = [self.ProcessEffectors, self.ProcessTargets]
-		if self.position_list.currentText()=="*":
+
+		if self.position_list.isMultipleSelection() or not self.position_list.isAnySelected():
 			
 			for p in panels:
 				p.check_seg_btn.setEnabled(False)
@@ -443,7 +510,9 @@ class ControlPanel(QMainWindow, Styles):
 			self.ProcessEffectors.delete_tracks_btn.hide()
 
 			self.view_stack_btn.setEnabled(False)
-		elif self.well_list.currentText()=='*':
+
+		elif self.well_list.isMultipleSelection():
+
 			self.ProcessTargets.view_tab_btn.setEnabled(True)
 			self.ProcessEffectors.view_tab_btn.setEnabled(True)	
 			self.NeighPanel.view_tab_btn.setEnabled(True)
@@ -455,7 +524,9 @@ class ControlPanel(QMainWindow, Styles):
 			self.ProcessTargets.delete_tracks_btn.hide()
 			self.ProcessEffectors.delete_tracks_btn.hide()
 		else:
-			if not self.well_list.currentText()=="*":
+
+			if self.well_list.isAnySelected() and self.position_list.isAnySelected():
+
 				self.locate_selected_position()
 				self.view_stack_btn.setEnabled(True)
 				# if os.path.exists(os.sep.join([self.pos,'labels_effectors', os.sep])):

celldetective/gui/generic_signal_plot.py

@@ -4,12 +4,12 @@ from PyQt5.QtWidgets import QMessageBox,QGridLayout, QButtonGroup, \
 from PyQt5.QtCore import Qt, QSize
 from PyQt5.QtGui import QDoubleValidator
 
-from celldetective.gui.gui_utils import center_window, FigureCanvas, ExportPlotBtn
+from celldetective.gui.gui_utils import center_window, FigureCanvas, ExportPlotBtn, QuickSliderLayout
 from celldetective.gui.tableUI import TableUI
 from celldetective.io import collect_experiment_metadata
 
 from superqt.fonticon import icon
-from superqt import QLabeledSlider
+from superqt import QLabeledSlider, QLabeledDoubleSlider
 from fonticon_mdi6 import MDI6
 import numpy as np
 import json
@@ -81,16 +81,21 @@ class GenericSignalPlotWidget(QWidget, Styles):
 			radio_subhbox.addWidget(self.plot_options[i], 33, alignment=Qt.AlignCenter)
 
 		if self.parent_window.position_indices is not None:
+			# at least a position is selected
 			if len(self.parent_window.well_indices)>1 and len(self.parent_window.position_indices)==1:
+				# several wells but one position
 				self.plot_btn_group.buttons()[0].click()
-				for i in [1,2]:
-					self.plot_options[i].setEnabled(False)
+				# for i in [1,2]:
+				# 	self.plot_options[i].setEnabled(False)
 			elif len(self.parent_window.well_indices)>1:
 				self.plot_btn_group.buttons()[0].click()
 			elif len(self.parent_window.well_indices)==1 and len(self.parent_window.position_indices)==1:
 				self.plot_btn_group.buttons()[1].click()
 				for i in [0,2]:
 					self.plot_options[i].setEnabled(False)
+			elif len(self.parent_window.well_indices)==1 and len(self.parent_window.position_indices)>1:
+				# one well, several positions
+				self.plot_btn_group.buttons()[2].click()
 		else:
 			if len(self.parent_window.well_indices)>1:
 				self.plot_btn_group.buttons()[0].click()
@@ -212,17 +217,22 @@ class GenericSignalPlotWidget(QWidget, Styles):
 		# Rescale 
 		self.cell_lines_alpha_wdg = QWidget()
 		alpha_hbox = QHBoxLayout()
-		self.cell_lines_alpha_wdg.setLayout(alpha_hbox)
 
-		alpha_hbox.addWidget(QLabel('single-cell\nsignal alpha: '), 25)
-		self.alpha_le = QLineEdit('0,8')
-		self.alpha_le.setValidator(self.float_validator)
-		alpha_hbox.addWidget(self.alpha_le, 65)
+		self.alpha_slider = QLabeledDoubleSlider()
+		alpha_hbox = QuickSliderLayout(label='single-cell\nsignal alpha: ',
+										slider=self.alpha_slider,
+										slider_initial_value=0.8,
+										slider_range=(0,1),
+										decimal_option=True,
+										precision=1.0E-05,
+										)
+		self.alpha_slider.valueChanged.connect(self.submit_alpha)
+		self.cell_lines_alpha_wdg.setLayout(alpha_hbox)
 
-		self.submit_alpha_btn = QPushButton('submit')
-		self.submit_alpha_btn.setStyleSheet(self.button_style_sheet_2)
-		self.submit_alpha_btn.clicked.connect(self.submit_alpha)
-		alpha_hbox.addWidget(self.submit_alpha_btn, 10)
+		# self.submit_alpha_btn = QPushButton('submit')
+		# self.submit_alpha_btn.setStyleSheet(self.button_style_sheet_2)
+		# self.submit_alpha_btn.clicked.connect(self.submit_alpha)
+		# alpha_hbox.addWidget(self.submit_alpha_btn, 10)
 		self.layout.addWidget(self.cell_lines_alpha_wdg)
 
 		self.select_option = [QRadioButton() for i in range(2)]
@@ -263,9 +273,9 @@ class GenericSignalPlotWidget(QWidget, Styles):
 		self.generate_pos_selection_widget()
 		self.select_btn_group.buttons()[0].click()
 
-	def submit_alpha(self):
+	def submit_alpha(self, value):
 
-		alpha = self.alpha_le.text().replace(',','.')
+		alpha = value
 		try:
 			alpha = float(alpha)
 		except:
@@ -329,17 +339,21 @@ class GenericSignalPlotWidget(QWidget, Styles):
 				if name+':' in lbl:
 					self.usable_well_labels.append(lbl)
 
+		thresh = 20
+		self.well_name_truncated = [w[:thresh - 3]+'...' if len(w)>thresh else w for w in self.usable_well_labels]
+
 		self.line_choice_widget = QWidget()
 		self.line_check_vbox = QGridLayout()
 		self.line_choice_widget.setLayout(self.line_check_vbox)
 
 		if len(self.parent_window.well_indices)>1:
-			self.well_display_options = [QCheckBox(self.usable_well_labels[i]) for i in range(len(self.usable_well_labels))]
+			self.well_display_options = [QCheckBox(self.well_name_truncated[i]) for i in range(len(self.well_name_truncated))]
 			for i in range(len(self.well_names)):
-				self.line_check_vbox.addWidget(self.well_display_options[i], i, 0, 1, 1, alignment=Qt.AlignLeft)
+				self.line_check_vbox.addWidget(self.well_display_options[i], i%4, i//4, 1, 1, alignment=Qt.AlignCenter)
 				self.well_display_options[i].setChecked(True)
 				self.well_display_options[i].setStyleSheet("font-size: 12px;")
 				self.well_display_options[i].toggled.connect(self.select_lines)
+				self.well_display_options[i].setToolTip(self.usable_well_labels[i])
 		else:
 			self.pos_display_options = [QCheckBox(self.pos_names[i]) for i in range(len(self.pos_names))]
 			for i in range(len(self.pos_names)):
@@ -648,7 +662,10 @@ class GenericSignalPlotWidget(QWidget, Styles):
 		else:
 			self.ci_btn.setIcon(icon(MDI6.arrow_expand_horizontal,color=self.help_color))
 		self.show_ci = not self.show_ci
-		self.plot_signals(0)
+		try:
+			self.plot_signals(0)
+		except Exception as e:
+			print(f"{e=}")
 
 	def switch_cell_lines(self):
 

celldetective/gui/gui_utils.py

@@ -1,8 +1,8 @@
 import numpy as np
 from PyQt5.QtWidgets import QApplication, QMessageBox, QFrame, QSizePolicy, QWidget, QLineEdit, QListWidget, QVBoxLayout, QComboBox, \
-	QPushButton, QLabel, QHBoxLayout, QCheckBox, QFileDialog
+	QPushButton, QLabel, QHBoxLayout, QCheckBox, QFileDialog, QToolButton, QMenu, QStylePainter, QStyleOptionComboBox, QStyle
 from PyQt5.QtCore import Qt, QSize, QAbstractTableModel
-from PyQt5.QtGui import QDoubleValidator, QIntValidator
+from PyQt5.QtGui import QDoubleValidator, QIntValidator, QStandardItemModel, QPalette
 
 from celldetective.gui import Styles
 from superqt.fonticon import icon
@@ -16,6 +16,147 @@ from inspect import getmembers, isfunction
 from celldetective.filters import *
 from os import sep
 
+
+class QCheckableComboBox(QComboBox):
+
+	"""
+	adapted from https://stackoverflow.com/questions/22775095/pyqt-how-to-set-combobox-items-be-checkable
+	"""
+
+	def __init__(self, obj='', parent_window=None, *args, **kwargs):
+		
+		super().__init__(parent_window, *args, **kwargs)
+
+		self.setTitle('')
+		self.view().pressed.connect(self.handleItemPressed)
+		self.setModel(QStandardItemModel(self))
+		self.obj = obj
+		self.toolButton = QToolButton(parent_window)
+		self.toolButton.setText('')
+		self.toolMenu = QMenu(parent_window)
+		self.toolButton.setMenu(self.toolMenu)
+		self.toolButton.setPopupMode(QToolButton.InstantPopup)
+		self.anySelected = False
+
+	def clear(self):
+		
+		self.unselectAll()
+		self.toolMenu.clear()
+		super().clear()
+
+
+	def handleItemPressed(self, index):
+
+		idx = index.row()
+		actions = self.toolMenu.actions()
+
+		item = self.model().itemFromIndex(index)
+		if item.checkState() == Qt.Checked:
+			item.setCheckState(Qt.Unchecked)
+			actions[idx].setChecked(False)
+		else:
+			item.setCheckState(Qt.Checked)
+			actions[idx].setChecked(True)
+			self.anySelected = True
+
+		options_checked = np.array([a.isChecked() for a in actions])
+		if len(options_checked[options_checked]) > 1:
+			self.setTitle(f'Multiple {self.obj+"s"} selected...')
+		elif len(options_checked[options_checked])==1:
+			idx_selected = np.where(options_checked)[0][0]
+			if idx_selected!=idx:
+				item = self.model().item(idx_selected)
+			self.setTitle(item.text())
+		elif len(options_checked[options_checked])==0:
+			self.setTitle(f"No {self.obj} selected...")
+			self.anySelected = False
+
+	def setCurrentIndex(self, index):
+
+		super().setCurrentIndex(index)
+
+		item = self.model().item(index)
+		modelIndex = self.model().indexFromItem(item)
+
+		self.handleItemPressed(modelIndex)
+
+	def selectAll(self):
+
+		actions = self.toolMenu.actions()
+		for i,a in enumerate(actions):
+			if not a.isChecked():
+				self.setCurrentIndex(i)
+		self.anySelected = True
+
+	def unselectAll(self):
+		
+		actions = self.toolMenu.actions()
+		for i,a in enumerate(actions):
+			if a.isChecked():
+				self.setCurrentIndex(i)
+		self.anySelected = False
+
+	def title(self):
+		return self._title
+
+	def setTitle(self, title):
+		self._title = title
+		self.repaint()
+
+	def paintEvent(self, event):
+
+		painter = QStylePainter(self)
+		painter.setPen(self.palette().color(QPalette.Text))
+		opt = QStyleOptionComboBox()
+		self.initStyleOption(opt)
+		opt.currentText = self._title
+		painter.drawComplexControl(QStyle.CC_ComboBox, opt)
+		painter.drawControl(QStyle.CE_ComboBoxLabel, opt)
+
+	def addItem(self, item, tooltip=None):
+
+		super().addItem(item)
+		idx = self.findText(item)
+		if tooltip is not None:
+			self.setItemData(idx, tooltip, Qt.ToolTipRole)
+		item2 = self.model().item(idx, 0)
+		item2.setCheckState(Qt.Unchecked)
+		action = self.toolMenu.addAction(item)
+		action.setCheckable(True)	
+
+	def addItems(self, items):
+
+		super().addItems(items)
+
+		for item in items:
+
+			idx = self.findText(item)
+			item2 = self.model().item(idx, 0)
+			item2.setCheckState(Qt.Unchecked)
+			action = self.toolMenu.addAction(item)
+			action.setCheckable(True)
+
+	def getSelectedIndices(self):
+		
+		actions = self.toolMenu.actions()
+		options_checked = np.array([a.isChecked() for a in actions])		
+		idx_selected = np.where(options_checked)[0]
+
+		return list(idx_selected)
+
+	def currentText(self):
+		return self.title()
+
+	def isMultipleSelection(self):
+		return self.currentText().startswith('Multiple')
+
+	def isSingleSelection(self):
+		return not self.currentText().startswith('Multiple') and not self.title().startswith('No')
+
+	def isAnySelected(self):
+		return not self.title().startswith('No')
+
+
 class PandasModel(QAbstractTableModel):
 
 	"""

celldetective/gui/layouts.py

@@ -650,7 +650,8 @@ class BackgroundFitCorrectionLayout(QGridLayout, Styles):
 
 	def preview_correction(self):
 
-		if self.attr_parent.well_list.currentText()=="*" or self.attr_parent.position_list.currentText()=="*":
+		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...")
@@ -672,8 +673,8 @@ class BackgroundFitCorrectionLayout(QGridLayout, Styles):
 			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??
+						   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(),
@@ -1258,7 +1259,7 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 
 	def preview_correction(self):
 
-		if self.attr_parent.well_list.currentText()=="*" or self.attr_parent.position_list.currentText()=="*":
+		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...")
@@ -1294,8 +1295,8 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 			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??
+						   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(),

celldetective/gui/measurement_options.py

@@ -24,7 +24,6 @@ from glob import glob
 from natsort import natsorted
 from tifffile import imread
 from pathlib import Path
-import gc
 
 from celldetective.gui.viewers import CellEdgeVisualizer, SpotDetectionVisualizer
 from celldetective.gui.layouts import ProtocolDesignerLayout, BackgroundFitCorrectionLayout, LocalCorrectionLayout
@@ -726,18 +725,10 @@ class ConfigMeasurements(QMainWindow, Styles):
 		else:
 			self.current_stack = movies[0]
 			self.stack_length = auto_load_number_of_frames(self.current_stack)
-			
-			if self.stack_length is None:
-				stack = imread(self.current_stack)
-				self.stack_length = len(stack)
-				del stack
-				gc.collect()
-			
 			self.mid_time = self.stack_length // 2
-			indices = self.mid_time + np.arange(len(self.channel_names))
+			indices = len(self.channel_names) * self.mid_time + np.arange(len(self.channel_names))
 			self.test_frame = load_frames(list(indices.astype(int)),self.current_stack, normalize_input=False)
 
-
 	def control_haralick_digitalization(self):
 
 		"""
@@ -746,9 +737,10 @@ class ConfigMeasurements(QMainWindow, Styles):
 
 		"""
 
-		self.locate_image()
+		self.locate_image() # pb here
 		self.extract_haralick_options()
 		if self.test_frame is not None:
+
 			digitized_img = compute_haralick_features(self.test_frame, np.zeros(self.test_frame.shape[:2]),
 													  channels=self.channel_names, return_digit_image_only=True,
 													  **self.haralick_options

celldetective/gui/plot_measurements.py

@@ -56,8 +56,8 @@ class ConfigMeasurementsPlot(QWidget,Styles):
 
         print('Parent wells: ', self.wells)
 
-        self.well_option = self.parent_window.parent_window.well_list.currentIndex()
-        self.position_option = self.parent_window.parent_window.position_list.currentIndex()
+        self.well_option = self.parent_window.parent_window.well_list.getSelectedIndices()
+        self.position_option = self.parent_window.parent_window.position_list.getSelectedIndices()
         self.interpret_pos_location()
         # self.load_available_tables()
         # self.config_path = self.exp_dir + self.config_name
@@ -526,18 +526,10 @@ class ConfigMeasurementsPlot(QWidget,Styles):
 
         """
 
-        self.well_option = self.parent_window.parent_window.well_list.currentIndex()
-        if self.well_option == len(self.wells):
-            wo = '*'
-        else:
-            wo = self.well_option
-        self.position_option = self.parent_window.parent_window.position_list.currentIndex()
-        if self.position_option == 0:
-            po = '*'
-        else:
-            po = self.position_option - 1
+        self.well_option = self.parent_window.parent_window.well_list.getSelectedIndices()
+        self.position_option = self.parent_window.parent_window.position_list.getSelectedIndices()
 
-        self.df, self.df_pos_info = load_experiment_tables(self.exp_dir, well_option=wo, position_option=po,
+        self.df, self.df_pos_info = load_experiment_tables(self.exp_dir, well_option=self.well_option, position_option=self.position_option,
                                                            population=self.cbs[0].currentText(), return_pos_info=True)
 
         if self.df is None: