celldetective 1.3.9.post4__py3-none-any.whl → 1.4.0__py3-none-any.whl

celldetective/gui/control_panel.py

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

celldetective/gui/generic_signal_plot.py

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

celldetective/gui/gui_utils.py

@@ -1,23 +1,48 @@
-import numpy as np
-from PyQt5.QtWidgets import QGridLayout, QApplication, QMessageBox, QFrame, QSizePolicy, QWidget, QLineEdit, QListWidget, QVBoxLayout, QComboBox, \
+import os
+
+from PyQt5.QtWidgets import QGridLayout, QApplication, QMessageBox, QFrame, QSizePolicy, QLineEdit, QListWidget, QVBoxLayout, QComboBox, \
 	QPushButton, QLabel, QHBoxLayout, QCheckBox, QFileDialog, QToolButton, QMenu, QStylePainter, QStyleOptionComboBox, QStyle
 from PyQt5.QtCore import Qt, QSize, QAbstractTableModel, QEvent, pyqtSignal
 from PyQt5.QtGui import QDoubleValidator, QIntValidator, QStandardItemModel, QPalette
 
-from celldetective.gui import Styles
+from celldetective.gui import Styles, CelldetectiveWidget
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg
 from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT
 import matplotlib.pyplot as plt
-import celldetective.extra_properties as extra_properties
+
+from celldetective.utils import get_software_location
+
+try:
+	import celldetective.extra_properties as extra_properties
+	extra_props = True
+except Exception as e:
+	print(f"The module extra_properties seems corrupted: {e}... Skip...")
+	extra_props = False
+
 from inspect import getmembers, isfunction
 from celldetective.filters import *
 from os import sep
 import json
 
 
+def generic_message(message, msg_type="warning"):
+	
+	print(message)
+	message_box = QMessageBox()
+	if msg_type=="warning":
+		message_box.setIcon(QMessageBox.Warning)
+	elif msg_type=="info":
+		message_box.setIcon(QMessageBox.Information)
+	elif msg_type=="critical":
+		message_box.setIcon(QMessageBox.Critical)
+	message_box.setText(message)
+	message_box.setWindowTitle(msg_type)
+	message_box.setStandardButtons(QMessageBox.Ok)
+	_ = message_box.exec()
+
 class PreprocessingLayout(QVBoxLayout, Styles):
 
 	"""
@@ -328,7 +353,7 @@ class PandasModel(QAbstractTableModel):
 		self.dataChanged.emit(ix, ix, (Qt.BackgroundRole,))
 
 
-class GenericOpColWidget(QWidget, Styles):
+class GenericOpColWidget(CelldetectiveWidget):
 
 	def __init__(self, parent_window, column=None, title=''):
 
@@ -415,7 +440,7 @@ class QuickSliderLayout(QHBoxLayout):
 		The slider widget that allows the user to select a value.
 	"""
 
-	def __init__(self, label=None, slider=None, layout_ratio=(0.25,0.75), slider_initial_value=1, slider_range=(0,1), slider_tooltip=None, decimal_option=True, precision=1.0E-03, *args):
+	def __init__(self, label=None, slider=None, layout_ratio=(0.25,0.75), slider_initial_value=1, slider_range=(0,1), slider_tooltip=None, decimal_option=True, precision=3, *args):
 		super().__init__(*args)
 
 		if label is not None and isinstance(label,str):
@@ -423,10 +448,11 @@ class QuickSliderLayout(QHBoxLayout):
 			self.addWidget(self.qlabel, int(100*layout_ratio[0]))
 
 		self.slider = slider
-		self.slider.setOrientation(1)
+		self.slider.setOrientation(Qt.Horizontal)
 		if decimal_option:
-			self.slider.setSingleStep(precision)
-			self.slider.setTickInterval(precision)
+			self.slider.setSingleStep(1.0*(10**(-precision)))
+			self.slider.setTickInterval(1.0*(10**(-precision)))
+			self.slider.setDecimals(precision)
 		else:
 			self.slider.setSingleStep(1)
 			self.slider.setTickInterval(1)
@@ -546,7 +572,7 @@ class QHSeperationLine(QFrame):
 		self.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Minimum)
 
 
-class FeatureChoice(QWidget, Styles):
+class FeatureChoice(CelldetectiveWidget):
 
 	def __init__(self, parent_window):
 		super().__init__()
@@ -575,10 +601,11 @@ class FeatureChoice(QWidget, Styles):
 								 "intensity_min",
 								 ]
 
-		members = getmembers(extra_properties, isfunction)
-		for o in members:
-			if isfunction(o[1]) and o[1].__module__=="celldetective.extra_properties":
-				standard_measurements.append(o[0])
+		if extra_props:
+			members = getmembers(extra_properties, isfunction)
+			for o in members:
+				if isfunction(o[1]) and o[1].__module__=="celldetective.extra_properties":
+					standard_measurements.append(o[0])
 
 		self.combo_box.addItems(standard_measurements)
 
@@ -599,7 +626,7 @@ class FeatureChoice(QWidget, Styles):
 		self.close()
 
 
-class FilterChoice(QWidget, Styles):
+class FilterChoice(CelldetectiveWidget):
 
 	def __init__(self, parent_window):
 
@@ -707,7 +734,7 @@ class FilterChoice(QWidget, Styles):
 				self.arguments_labels[i].setText('')
 
 
-class OperationChoice(QWidget):
+class OperationChoice(CelldetectiveWidget):
 	"""
 	Mini window to select an operation from numpy to apply on the ROI.
 
@@ -738,7 +765,7 @@ class OperationChoice(QWidget):
 		self.close()
 
 
-class GeometryChoice(QWidget):
+class GeometryChoice(CelldetectiveWidget):
 
 	def __init__(self, parent_window):
 
@@ -802,7 +829,7 @@ class GeometryChoice(QWidget):
 		self.close()
 
 
-class DistanceChoice(QWidget):
+class DistanceChoice(CelldetectiveWidget):
 
 	def __init__(self, parent_window):
 		super().__init__()
@@ -836,7 +863,7 @@ class DistanceChoice(QWidget):
 		self.close()
 
 
-class ListWidget(QWidget):
+class ListWidget(CelldetectiveWidget):
 
 	"""
 	A customizable widget for displaying and managing a list of items, with the 
@@ -963,7 +990,7 @@ class ListWidget(QWidget):
 				del self.items[idx]
 
 
-class FigureCanvas(QWidget):
+class FigureCanvas(CelldetectiveWidget):
 	"""
 	Generic figure canvas.
 	"""
@@ -1185,6 +1212,7 @@ def color_from_state(state, recently_modified=False):
 	unique_values = np.unique(state)
 	color_map={}
 	for value in unique_values:
+
 		if np.isnan(value):
 			value = "nan"
 			color_map[value] = 'k'
@@ -1219,7 +1247,7 @@ def color_from_class(cclass, recently_modified=False):
 			return 'k'
 
 
-class ChannelChoice(QWidget):
+class ChannelChoice(CelldetectiveWidget):
 
 	def __init__(self, parent_window):
 		super().__init__()

celldetective/gui/json_readers.py

@@ -1,10 +1,11 @@
 import configparser
-from PyQt5.QtWidgets import QWidget, QVBoxLayout, QScrollArea, QLabel, QHBoxLayout, QLineEdit, QPushButton
+from PyQt5.QtWidgets import QVBoxLayout, QScrollArea, QLabel, QHBoxLayout, QLineEdit, QPushButton
 from PyQt5.QtCore import Qt
 import configparser
-from celldetective.gui import Styles
+from celldetective.gui import CelldetectiveWidget
 
-class ConfigEditor(QWidget, Styles):
+
+class ConfigEditor(CelldetectiveWidget):
     
     def __init__(self, parent_window):
 
@@ -27,7 +28,7 @@ class ConfigEditor(QWidget, Styles):
         # Create a scroll area to contain the main layout
         scroll = QScrollArea()
         scroll.setWidgetResizable(True)
-        scroll_content = QWidget()
+        scroll_content = CelldetectiveWidget()
         self.scroll_layout = QVBoxLayout(scroll_content)
         scroll_content.setLayout(self.scroll_layout)
         scroll.setWidget(scroll_content)