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

celldetective/gui/layouts.py

@@ -1,7 +1,7 @@
-from PyQt5.QtWidgets import QCheckBox, QLineEdit, QWidget, QListWidget, QTabWidget, QHBoxLayout,QMessageBox, QPushButton, QVBoxLayout, QRadioButton, QLabel, QButtonGroup, QSizePolicy, QComboBox,QSpacerItem, QGridLayout
+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
+from PyQt5.QtGui import QIntValidator, QDoubleValidator
 
 from superqt import QLabeledRangeSlider, QLabeledDoubleSlider, QLabeledSlider, QLabeledDoubleRangeSlider, QSearchableComboBox
 
@@ -9,15 +9,223 @@ 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
+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 StarDistParamsWidget(QWidget, Styles):
+
+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.
@@ -101,7 +309,7 @@ class StarDistParamsWidget(QWidget, Styles):
 		self.layout.addWidget(self.set_stardist_scale_btn)
 
 
-class CellposeParamsWidget(QWidget, Styles):
+class CellposeParamsWidget(CelldetectiveWidget):
 
 	"""
 	A widget to configure parameters for Cellpose segmentation, allowing users to set the cell diameter, 
@@ -204,7 +412,7 @@ class CellposeParamsWidget(QWidget, Styles):
 		
 		# Flow threshold slider
 		self.flow_slider = QLabeledDoubleSlider()
-		self.flow_slider.setOrientation(1)
+		self.flow_slider.setOrientation(Qt.Horizontal)
 		self.flow_slider.setRange(-6,6)
 		self.flow_slider.setValue(0.4)
 		hbox = QHBoxLayout()
@@ -214,7 +422,7 @@ class CellposeParamsWidget(QWidget, Styles):
 
 		# Cell probability threshold slider
 		self.cellprob_slider = QLabeledDoubleSlider()
-		self.cellprob_slider.setOrientation(1)
+		self.cellprob_slider.setOrientation(Qt.Horizontal)
 		self.cellprob_slider.setRange(-6,6)
 		self.cellprob_slider.setValue(0.)
 		hbox = QHBoxLayout()
@@ -236,18 +444,20 @@ class CellposeParamsWidget(QWidget, Styles):
 
 		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()}',
-										  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,
-										 )
+										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):
@@ -864,7 +1074,7 @@ class ProtocolDesignerLayout(QVBoxLayout, Styles):
 		self.tabs.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
 		
 		for k in range(len(self.tab_layouts)):
-			wg = QWidget()
+			wg = CelldetectiveWidget()
 			self.tab_layouts[k].parent_window = self
 			wg.setLayout(self.tab_layouts[k])
 			self.tabs.addTab(wg, self.tab_names[k])
@@ -1173,13 +1383,21 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 		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, 8, 0, 1, 3)
+		self.addLayout(self.operation_layout, 9, 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)
+		self.addLayout(correction_layout, 10, 0, 1, 3)
 
 		# verticalSpacer = QSpacerItem(20, 40, QSizePolicy.Minimum, QSizePolicy.Expanding)
 		# self.addItem(verticalSpacer, 5, 0, 1, 3)
@@ -1221,6 +1439,11 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 			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(),
@@ -1232,7 +1455,8 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 					  "opt_coef_range": opt_coef_range,
 					  "opt_coef_nbr": opt_coef_nbr,
 					  "operation": operation,
-					  "clip": clip
+					  "clip": clip,
+					  "offset": offset
 					 }
 
 	def set_target_channel(self):

celldetective/gui/measurement_options.py

@@ -1,8 +1,9 @@
+from subprocess import Popen
 
-from PyQt5.QtWidgets import QMainWindow, QApplication, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, \
-	QGridLayout, QLineEdit, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton
+from PyQt5.QtWidgets import QApplication, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, \
+	QGridLayout, QLineEdit, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
 from PyQt5.QtCore import Qt, QSize
-from PyQt5.QtGui import QIcon, QDoubleValidator, QIntValidator
+from PyQt5.QtGui import QDoubleValidator, QIntValidator
 
 from celldetective.gui.gui_utils import center_window, FeatureChoice, ListWidget, QHSeperationLine, FigureCanvas, \
 	GeometryChoice, OperationChoice
@@ -10,12 +11,10 @@ from superqt import QLabeledDoubleSlider
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 
-#from celldetective.gui.thresholds_gui import ThresholdSpot
 from celldetective.utils import extract_experiment_channels, get_software_location
 from celldetective.io import load_frames, auto_load_number_of_frames
 from celldetective.measure import compute_haralick_features
 import numpy as np
-from tifffile import imread
 import json
 import os
 import matplotlib.pyplot as plt
@@ -27,11 +26,11 @@ from pathlib import Path
 
 from celldetective.gui.viewers import CellEdgeVisualizer, SpotDetectionVisualizer
 from celldetective.gui.layouts import ProtocolDesignerLayout, BackgroundFitCorrectionLayout, LocalCorrectionLayout
-from celldetective.gui.gui_utils import ThresholdLineEdit, PreprocessingLayout2
-from celldetective.gui import Styles
+from celldetective.gui.gui_utils import PreprocessingLayout2
+from celldetective.gui import CelldetectiveMainWindow, CelldetectiveWidget
 
 
-class ConfigMeasurements(QMainWindow, Styles):
+class ConfigMeasurements(CelldetectiveMainWindow):
 	"""
 	UI to set measurement instructions.
 
@@ -43,16 +42,11 @@ class ConfigMeasurements(QMainWindow, Styles):
 
 		self.parent_window = parent_window
 		self.setWindowTitle("Configure measurements")
-		self.setWindowIcon(QIcon(os.sep.join(['celldetective', 'icons', 'mexican-hat.png'])))
 		self.mode = self.parent_window.mode
 		self.exp_dir = self.parent_window.exp_dir
 		self.background_correction = []
-		if self.mode == "targets":
-			self.config_name = "btrack_config_targets.json"
-			self.measure_instructions_path = self.parent_window.exp_dir + "configs/measurement_instructions_targets.json"
-		elif self.mode == "effectors":
-			self.config_name = "btrack_config_effectors.json"
-			self.measure_instructions_path = self.parent_window.exp_dir + "configs/measurement_instructions_effectors.json"
+		self.config_name = f"btrack_config_{self.mode}.json"
+		self.measure_instructions_path = self.parent_window.exp_dir + f"configs/measurement_instructions_{self.mode}.json"
 		self.soft_path = get_software_location()
 		self.clear_previous = False
 
@@ -83,7 +77,7 @@ class ConfigMeasurements(QMainWindow, Styles):
 
 		# Create button widget and layout
 		self.scroll_area = QScrollArea(self)
-		self.button_widget = QWidget()
+		self.button_widget = CelldetectiveWidget()
 		main_layout = QVBoxLayout()
 		self.button_widget.setLayout(main_layout)
 		main_layout.setContentsMargins(30, 30, 30, 30)
@@ -264,12 +258,21 @@ class ConfigMeasurements(QMainWindow, Styles):
 
 		self.features_list = ListWidget(FeatureChoice, initial_features=['area', 'intensity_mean', ])
 
+		self.create_feature_btn = QPushButton("")
+		self.create_feature_btn.setStyleSheet(self.button_select_all)
+		self.create_feature_btn.setIcon(icon(MDI6.file_cog, color="black"))
+		self.create_feature_btn.setToolTip("Create new feature")
+		self.create_feature_btn.setIconSize(QSize(20, 20))
+
 		self.del_feature_btn.clicked.connect(self.features_list.removeSel)
 		self.add_feature_btn.clicked.connect(self.features_list.addItem)
+		self.create_feature_btn.clicked.connect(self.go_to_extraprops)
 
 		feature_layout.addWidget(self.feature_lbl, 90)
 		feature_layout.addWidget(self.del_feature_btn, 5)
 		feature_layout.addWidget(self.add_feature_btn, 5)
+		feature_layout.addWidget(self.create_feature_btn, 5)
+
 		layout.addLayout(feature_layout)
 		layout.addWidget(self.features_list)
 
@@ -334,7 +337,7 @@ class ConfigMeasurements(QMainWindow, Styles):
 		self.haralick_scale_slider.setSingleStep(0.05)
 		self.haralick_scale_slider.setTickInterval(0.05)
 		self.haralick_scale_slider.setSingleStep(1)
-		self.haralick_scale_slider.setOrientation(1)
+		self.haralick_scale_slider.setOrientation(Qt.Horizontal)
 		self.haralick_scale_slider.setRange(0, 1)
 		self.haralick_scale_slider.setValue(0.5)
 		self.haralick_scale_lbl = QLabel('Scale: ')
@@ -426,6 +429,18 @@ class ConfigMeasurements(QMainWindow, Styles):
 		self.haralick_normalization_mode_btn.clicked.connect(self.switch_to_absolute_normalization_mode)
 		layout.addLayout(self.haralick_layout)
 
+	def go_to_extraprops(self):
+		
+		path = os.sep.join([self.soft_path,'celldetective',os.sep,'extra_properties.py'])
+		try:
+			Popen(f'explorer {os.path.realpath(path)}')
+		except:
+
+			try:
+				os.system('xdg-open "%s"' % path)
+			except:
+				return None		
+
 	def switch_to_absolute_normalization_mode(self):
 
 		if self.percentile_mode:

celldetective/gui/neighborhood_options.py

@@ -1,6 +1,5 @@
-from PyQt5.QtWidgets import QApplication, QComboBox, QFrame, QCheckBox, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton
+from PyQt5.QtWidgets import QApplication, QComboBox, QFrame, QCheckBox, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
 from PyQt5.QtCore import Qt, QSize
-from PyQt5.QtGui import QIcon
 from celldetective.gui.gui_utils import center_window, ListWidget, DistanceChoice
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
@@ -10,9 +9,10 @@ import os
 from glob import glob
 import pandas as pd
 from celldetective.gui.viewers import CellSizeViewer, CellEdgeVisualizer
-from celldetective.gui import Styles
+from celldetective.gui import CelldetectiveWidget
 
-class ConfigNeighborhoods(QWidget, Styles):
+
+class ConfigNeighborhoods(CelldetectiveWidget):
 	
 	"""
 	Widget to configure neighborhood measurements.
@@ -24,7 +24,6 @@ class ConfigNeighborhoods(QWidget, Styles):
 		super().__init__(*args, **kwargs)
 		self.parent_window = parent_window
 		self.attr_parent = self.parent_window.parent_window
-		self.setWindowIcon(QIcon(os.sep.join(['celldetective','icons','logo.png'])))
 
 		self.neighborhood_type = neighborhood_type
 		self.neighborhood_parameter_name = neighborhood_parameter_name
@@ -43,7 +42,6 @@ class ConfigNeighborhoods(QWidget, Styles):
 		self.generate_main_layout()
 		self.load_previous_neighborhood_instructions()
 		center_window(self)
-		self.setAttribute(Qt.WA_DeleteOnClose)
 
 	def generate_main_layout(self):
 
@@ -140,7 +138,7 @@ class ConfigNeighborhoods(QWidget, Styles):
 
 		layout.addLayout(list_header_layout)
 
-		self.measurements_list = ListWidget(DistanceChoice, initial_features=["60"], dtype=int)
+		self.measurements_list = ListWidget(DistanceChoice, initial_features=[], dtype=int)
 		self.measurements_list.setToolTip('Neighborhoods to compute.')
 		layout.addWidget(self.measurements_list)
 
@@ -211,7 +209,7 @@ class ConfigNeighborhoods(QWidget, Styles):
 		population_layout = QHBoxLayout()
 		population_layout.addWidget(QLabel('population: '),30)
 		self.reference_population_cb = QComboBox()
-		self.reference_population_cb.addItems(['targets','effectors'])
+		self.reference_population_cb.addItems(self.parent_window.parent_window.populations)
 		self.reference_population_cb.setToolTip('Select a reference population.')
 		population_layout.addWidget(self.reference_population_cb,70)
 		layout.addLayout(population_layout)
@@ -271,7 +269,7 @@ class ConfigNeighborhoods(QWidget, Styles):
 		population_layout = QHBoxLayout()
 		population_layout.addWidget(QLabel('population: '),30)
 		self.neighbor_population_cb = QComboBox()
-		self.neighbor_population_cb.addItems(['targets','effectors'])
+		self.neighbor_population_cb.addItems(self.parent_window.parent_window.populations)
 		self.neighbor_population_cb.setToolTip('Select a neighbor population.')
 		population_layout.addWidget(self.neighbor_population_cb,70)
 		layout.addLayout(population_layout)
@@ -315,15 +313,14 @@ class ConfigNeighborhoods(QWidget, Styles):
 		population = self.neighbor_population_cb.currentText()
 		class_cols, status_cols, group_cols, time_cols = self.locate_population_specific_columns(population)
 		self.neighbor_population_status_cb.clear()
-		self.neighbor_population_status_cb.addItems(['--','class', 'status']+class_cols+status_cols+group_cols)
+		self.neighbor_population_status_cb.addItems(list(np.unique(['--','class', 'status']+class_cols+status_cols+group_cols)))
 
 	def fill_cbs_of_reference_population(self):
 
 		population = self.reference_population_cb.currentText()
 		class_cols, status_cols, group_cols, time_cols = self.locate_population_specific_columns(population)
-		self.reference_population_status_cb.clear()
-		self.reference_population_status_cb.addItems(['--','class', 'status']+class_cols+status_cols+group_cols)
-		self.event_time_cb.addItems(['--', 't0']+time_cols)
+		self.event_time_cb.clear()
+		self.event_time_cb.addItems(list(np.unique(['--', 't0']+time_cols)))
 
 	def switch_not_reference(self):
 		

celldetective/gui/plot_measurements.py

@@ -1,10 +1,10 @@
 from PyQt5.QtWidgets import QMessageBox, QScrollArea, QButtonGroup, QComboBox, \
-    QCheckBox, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton, \
+    QCheckBox, QVBoxLayout, QLabel, QHBoxLayout, QPushButton, \
     QRadioButton, QSizePolicy
 from PyQt5.QtCore import Qt, QRect
-from PyQt5.QtGui import QIcon, QDoubleValidator
+from PyQt5.QtGui import QDoubleValidator
 
-from celldetective.gui import Styles
+from celldetective.gui import CelldetectiveWidget
 from celldetective.gui.gui_utils import center_window, FigureCanvas
 
 from superqt.fonticon import icon
@@ -12,7 +12,6 @@ from fonticon_mdi6 import MDI6
 from celldetective.utils import get_software_location, _extract_labels_from_config
 from celldetective.io import load_experiment_tables, get_experiment_antibodies, get_experiment_cell_types, get_experiment_concentrations, \
     get_positions_in_well, get_experiment_wells
-from celldetective.signals import mean_signal
 import numpy as np
 import json
 import os
@@ -26,7 +25,7 @@ import math
 import seaborn as sns
 
 
-class ConfigMeasurementsPlot(QWidget,Styles):
+class ConfigMeasurementsPlot(CelldetectiveWidget):
     """
     UI to set survival instructions.
 
@@ -37,7 +36,6 @@ class ConfigMeasurementsPlot(QWidget,Styles):
         super().__init__()
         self.parent_window = parent_window
         self.setWindowTitle("Configure signal plot")
-        self.setWindowIcon(QIcon(os.sep.join(['celldetective', 'icons', 'mexican-hat.png'])))
         self.exp_dir = self.parent_window.exp_dir
         self.soft_path = get_software_location()
         self.exp_config = self.exp_dir + "config.ini"
@@ -109,7 +107,7 @@ class ConfigMeasurementsPlot(QWidget,Styles):
         main_layout.addWidget(panel_title, alignment=Qt.AlignCenter)
 
         labels = [QLabel('population: '), QLabel('class: '), QLabel('group: ')]  # , QLabel('time of\ninterest: ')]
-        self.cb_options = [['targets', 'effectors'], ['class'], ['group']]  # , ['t0','first detection']]
+        self.cb_options = [self.parent_window.parent_window.populations, ['class'], ['group']]  # , ['t0','first detection']]
         self.cbs = [QComboBox() for i in range(len(labels))]
         self.cbs[0].currentIndexChanged.connect(self.set_classes_and_times)
 
@@ -145,7 +143,7 @@ class ConfigMeasurementsPlot(QWidget,Styles):
         # self.abs_time_checkbox = QCheckBox('absolute time')
         # self.frame_slider = QLabeledSlider()
         # self.frame_slider.setSingleStep(1)
-        # self.frame_slider.setOrientation(1)
+        # self.frame_slider.setOrientation(Qt.Horizontal)
         # self.frame_slider.setRange(0,self.parent.parent.len_movie)
         # self.frame_slider.setValue(0)
         # self.frame_slider.setEnabled(False)
@@ -202,14 +200,20 @@ class ConfigMeasurementsPlot(QWidget,Styles):
         class_idx = np.array([s.startswith('class_') for s in self.all_columns])
         group_idx = np.array([s.startswith('group_') for s in self.all_columns])
 
+        print(f'{class_idx=} {group_idx=} {self.all_columns=}')
         # time_idx = np.array([s.startswith('t_') for s in self.all_columns])
-
         try:
-            class_columns = list(self.all_columns[class_idx])
-            group_columns = list(self.all_columns[group_idx])
+            if len(class_idx)>0:
+                class_columns = list(self.all_columns[class_idx])
+            else:
+                class_columns = []
+            if len(group_idx)>0:
+                group_columns = list(self.all_columns[group_idx])
+            else:
+                group_columns = []
         # time_columns = list(self.all_columns[time_idx])
-        except:
-            print('columns not found')
+        except Exception as e:
+            print(f'L210 columns not found {e}')
             self.auto_close = True
             return None
 
@@ -227,7 +231,7 @@ class ConfigMeasurementsPlot(QWidget,Styles):
         is_number = np.vectorize(lambda x: np.issubdtype(x, np.number))
         feats = cols[is_number(self.df.dtypes)]
 
-        self.feature_choice_widget = QWidget()
+        self.feature_choice_widget = CelldetectiveWidget()
         self.feature_choice_widget.setWindowTitle("Select numeric feature")
         layout = QVBoxLayout()
         self.feature_choice_widget.setLayout(layout)
@@ -250,7 +254,7 @@ class ConfigMeasurementsPlot(QWidget,Styles):
         is_number = np.vectorize(lambda x: np.issubdtype(x, np.number))
         feats = cols[is_number(self.df.dtypes)]
 
-        self.feature_choice_widget = QWidget()
+        self.feature_choice_widget = CelldetectiveWidget()
         self.feature_choice_widget.setWindowTitle("Select numeric feature")
         layout = QVBoxLayout()
         self.feature_choice_widget.setLayout(layout)
@@ -299,7 +303,7 @@ class ConfigMeasurementsPlot(QWidget,Styles):
             # prepare survival
 
             # plot survival
-            self.survivalWidget = QWidget()
+            self.survivalWidget = CelldetectiveWidget()
             self.scroll = QScrollArea()
             self.survivalWidget.setMinimumHeight(int(0.8 * self.screen_height))
             self.survivalWidget.setWindowTitle('signals')
@@ -500,7 +504,7 @@ class ConfigMeasurementsPlot(QWidget,Styles):
                 if name + ':' in lbl:
                     self.usable_well_labels.append(lbl)
 
-        self.line_choice_widget = QWidget()
+        self.line_choice_widget = CelldetectiveWidget()
         self.line_check_vbox = QVBoxLayout()
         self.line_choice_widget.setLayout(self.line_check_vbox)
         if len(self.well_indices) > 1: