celldetective 1.3.1__py3-none-any.whl → 1.3.3.post1__py3-none-any.whl

celldetective/gui/process_block.py

@@ -291,6 +291,7 @@ class ProcessPanel(QFrame, Styles):
 		self.signal_models_list.addItems(signal_models)
 
 	def generate_tracking_options(self):
+		
 		grid_track = QHBoxLayout()
 
 		self.track_action = QCheckBox("TRACK")
@@ -303,16 +304,6 @@ class ProcessPanel(QFrame, Styles):
 			padding-top: 5px;
 			""")
 		grid_track.addWidget(self.track_action, 75)
-		#self.to_disable.append(self.track_action_tc)
-
-		# self.show_track_table_btn = QPushButton()
-		# self.show_track_table_btn.setIcon(icon(MDI6.table,color="black"))
-		# self.show_track_table_btn.setIconSize(QSize(20, 20))
-		# self.show_track_table_btn.setToolTip("Show trajectories table.")
-		# self.show_track_table_btn.setStyleSheet(self.button_select_all)
-		# #self.show_track_table_btn.clicked.connect(self.display_trajectory_table)
-		# self.show_track_table_btn.setEnabled(False)
-		# grid_track.addWidget(self.show_track_table_btn, 6)  #4,3,1,1, alignment=Qt.AlignLeft
 
 		self.delete_tracks_btn = QPushButton()
 		self.delete_tracks_btn.setIcon(icon(MDI6.trash_can,color="black"))
@@ -640,25 +631,6 @@ class ProcessPanel(QFrame, Styles):
 
 		self.seg_model_list.insertSeparator(len(self.models_truncated))
 
-
-		#if ("live_nuclei_channel" in self.exp_channels)*("dead_nuclei_channel" in self.exp_channels):
-		# 	print("both channels found")
-		# 	index = self.tc_seg_model_list.findText("MCF7_Hoescht_PI_w_primary_NK", Qt.MatchFixedString)
-		# 	if index >= 0:
-		# 		self.tc_seg_model_list.setCurrentIndex(index)
-		# elif ("live_nuclei_channel" in self.exp_channels)*("dead_nuclei_channel" not in self.exp_channels):
-		# 	index = self.tc_seg_model_list.findText("MCF7_Hoescht_w_primary_NK", Qt.MatchFixedString)
-		# 	if index >= 0:
-		# 		self.tc_seg_model_list.setCurrentIndex(index)
-		# elif ("live_nuclei_channel" not in self.exp_channels)*("dead_nuclei_channel" in self.exp_channels):
-		# 	index = self.tc_seg_model_list.findText("MCF7_PI_w_primary_NK", Qt.MatchFixedString)
-		# 	if index >= 0:
-		# 		self.tc_seg_model_list.setCurrentIndex(index)
-		# elif ("live_nuclei_channel" not in self.exp_channels)*("dead_nuclei_channel" not in self.exp_channels)*("adhesion_channel" in self.exp_channels):
-		# 	index = self.tc_seg_model_list.findText("RICM", Qt.MatchFixedString)
-		# 	if index >= 0:
-		# 		self.tc_seg_model_list.setCurrentIndex(index)
-
 	def tick_all_actions(self):
 		self.switch_all_ticks_option()
 		if self.all_ticked:
@@ -884,28 +856,7 @@ class ProcessPanel(QFrame, Styles):
 		if self.segment_action.isChecked():
 			self.segment_action.setChecked(False)
 
-		# QApplication.restoreOverrideCursor()
-		# self.unfreeze()
-
-	# def view_current_stack_with_scale_bar(self):
-
-	# 	self.parent_window.locate_image()
-	# 	if self.parent_window.current_stack is not None:
-	# 		self.viewer = CellSizeViewer(
-	# 									  initial_diameter = float(self.diameter_le.text().replace(',', '.')),
-	# 			parent_le = self.diameter_le,
-	# 									  stack_path=self.parent_window.current_stack,
-	# 									  window_title=f'Position {self.parent_window.position_list.currentText()}',
-	# 									  frame_slider = True,
-	# 									  contrast_slider = True,
-	# 									  channel_cb = True,
-	# 									  channel_names = self.parent_window.exp_channels,
-	# 									  n_channels = self.parent_window.nbr_channels,
-	# 									  PxToUm = 1,
-	# 									 )
-	# 		self.viewer.show()
-
-
+		self.cellpose_calibrated = False
 
 	def open_napari_tracking(self):
 		print(f'View the tracks before post-processing for position {self.parent_window.pos} in napari...')
@@ -920,7 +871,7 @@ class ProcessPanel(QFrame, Styles):
 			plot_mode = 'plot_track_signals'
 			if 'TRACK_ID' not in list(self.df.columns):
 				plot_mode = 'static'
-			self.tab_ui = TableUI(self.df, f"Well {self.parent_window.well_list.currentText()}; Position {self.parent_window.position_list.currentText()}", population=self.mode, plot_mode=plot_mode)
+			self.tab_ui = TableUI(self.df, f"Well {self.parent_window.well_list.currentText()}; Position {self.parent_window.position_list.currentText()}", population=self.mode, plot_mode=plot_mode, save_inplace_option=True)
 			self.tab_ui.show()
 		else:
 			print('Table could not be loaded...')
@@ -933,24 +884,6 @@ class ProcessPanel(QFrame, Styles):
 			if returnValue == QMessageBox.Ok:
 				return None
 
-	# def interpret_pos_location(self):
-
-	# 	"""
-	# 	Read the well/position selection from the control panel to decide which data to load
-	# 	Set position_indices to None if all positions must be taken
-
-	# 	"""
-
-	# 	if self.well_option==len(self.wells):
-	# 		self.well_indices = np.arange(len(self.wells))
-	# 	else:
-	# 		self.well_indices = np.array([self.well_option],dtype=int)
-
-	# 	if self.position_option==0:
-	# 		self.position_indices = None
-	# 	else:
-	# 		self.position_indices = np.array([self.position_option],dtype=int)
-
 	def load_available_tables(self):
 
 		"""
@@ -1016,6 +949,7 @@ class ProcessPanel(QFrame, Styles):
 		self.process_population()
 
 
+
 class NeighPanel(QFrame, Styles):
 	def __init__(self, parent_window):
 
@@ -1207,28 +1141,19 @@ class NeighPanel(QFrame, Styles):
 		self.measure_pairs_action.setToolTip("Measure the relative quantities defined for the cell pairs, for all neighborhoods.")
 		rel_layout.addWidget(self.measure_pairs_action, 90)
 
-		# self.visu_btn = QPushButton()
-		# self.visu_btn.setIcon(icon(MDI6.eye_check_outline,color="black"))
-		# self.visu_btn.setIconSize(QSize(20, 20))
-		# self.visu_btn.clicked.connect(self.check_measurements2)
-		# self.visu_btn.setToolTip("Open measurement annotator for two populations.")
-		# self.visu_btn.setStyleSheet(self.button_select_all)
-		# self.grid_contents.addWidget(self.visu_btn, 1,1,1,1,alignment=Qt.AlignRight)
-		# rel_layout.addWidget(self.visu_btn, 6)
-
-		# self.config_rel_annotator_btn = QPushButton()
-		# self.config_rel_annotator_btn.setIcon(icon(MDI6.cog_outline, color="black"))
-		# self.config_rel_annotator_btn.setIconSize(QSize(20, 20))
-		# self.config_rel_annotator_btn.setToolTip("Configure the animation of the annotation tool.")
-		# self.config_rel_annotator_btn.setStyleSheet(self.button_select_all)
-		# self.config_rel_annotator_btn.clicked.connect(self.open_signal_annotator_configuration_ui)
-		# # self.grid_contents.addWidget(self.config_rel_annotator_btn, 1,2,1,1, alignment=Qt.AlignRight)
-		# rel_layout.addWidget(self.config_rel_annotator_btn, 6)
+		self.classify_pairs_btn = QPushButton()
+		self.classify_pairs_btn.setIcon(icon(MDI6.scatter_plot, color="black"))
+		self.classify_pairs_btn.setIconSize(QSize(20, 20))
+		self.classify_pairs_btn.setToolTip("Classify data.")
+		self.classify_pairs_btn.setStyleSheet(self.button_select_all)
+		self.classify_pairs_btn.clicked.connect(self.open_classifier_ui_pairs)
+		rel_layout.addWidget(self.classify_pairs_btn, 5) #4,2,1,1, alignment=Qt.AlignRight
+
 		self.grid_contents.addLayout(rel_layout, 6, 0, 1, 4)
 
 		signal_layout = QVBoxLayout()
 		signal_hlayout = QHBoxLayout()
-		self.signal_analysis_action = QCheckBox("PAIR SIGNAL ANALYSIS")
+		self.signal_analysis_action = QCheckBox("DETECT PAIR EVENTS")
 		self.signal_analysis_action.setStyleSheet("""
 		font-size: 10px;
 		padding-left: 10px;
@@ -1304,6 +1229,26 @@ class NeighPanel(QFrame, Styles):
 		self.neigh_action.setChecked(True)
 		self.neigh_action.setChecked(False)
 
+	def open_classifier_ui_pairs(self):
+		
+		self.mode = "pairs"
+		self.load_available_tables()
+		if self.df is None:
+
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Warning)
+			msgBox.setText("No table was found...")
+			msgBox.setWindowTitle("Warning")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				return None
+			else:
+				return None
+		else:
+			self.ClassifierWidget = ClassifierWidget(self)
+			self.ClassifierWidget.show()
+
 
 	def help_neighborhood(self):
 
@@ -1360,7 +1305,7 @@ class NeighPanel(QFrame, Styles):
 
 		if self.df is not None:
 			plot_mode = 'static'
-			self.tab_ui = TableUI(self.df, f"Well {self.parent_window.well_list.currentText()}; Position {self.parent_window.position_list.currentText()}", population='pairs', plot_mode=plot_mode)
+			self.tab_ui = TableUI(self.df, f"Well {self.parent_window.well_list.currentText()}; Position {self.parent_window.position_list.currentText()}", population='pairs', plot_mode=plot_mode, save_inplace_option=True)
 			self.tab_ui.show()
 		else:
 			print('Table could not be loaded...')
@@ -1512,35 +1457,12 @@ class NeighPanel(QFrame, Styles):
 					rel_measure_at_position(self.pos)
 
 				if self.signal_analysis_action.isChecked():
-					
-					# df_targets = get_position_pickle(self.pos, population='targets')
-					# df_effectors = get_position_pickle(self.pos, population='effectors')
-					# self.dataframes = {
-					# 	'targets': df_targets,
-					# 	'effectors': df_effectors,
-					# }
-
-					# df_pairs = get_position_table(self.pos, population='pairs')
-
-					# # Need to identify expected reference / neighbor tables
-					# model_path = locate_signal_model(self.pair_signal_models_list.currentText(), pairs=True)
-					# print(f'Looking for model in {model_path}...')
-					# complete_path = model_path
-					# complete_path = rf"{complete_path}"
-					# model_config_path = os.sep.join([complete_path, 'config_input.json'])
-					# model_config_path = rf"{model_config_path}"
-					# f = open(model_config_path)
-					# model_config_path = json.load(f)
-
-					# reference_population = model_config_path['reference_population']
-					# neighbor_population = model_config_path['neighbor_population']
-
-					# analyze_pair_signals(df_pairs, self.dataframes[reference_population], self.dataframes[neighbor_population], model=self.pair_signal_models_list.currentText())
+
 					analyze_pair_signals_at_position(self.pos, self.pair_signal_models_list.currentText(), use_gpu=self.parent_window.parent_window.use_gpu)
+
 		self.parent_window.update_position_options()
 		print('Done.')
 
-
 	def check_signals2(self):
 
 		test = self.parent_window.locate_selected_position()

celldetective/gui/retrain_segmentation_model_options.py

@@ -616,4 +616,6 @@ class ConfigSegmentationModelTraining(QMainWindow, Styles):
 		
 		train_segmentation_model(model_folder+"training_instructions.json", use_gpu=self.parent_window.parent_window.parent_window.use_gpu)
 
-		# self.parent.refresh_signal_models()
+		self.parent_window.init_seg_model_list()
+		idx = self.parent_window.seg_model_list.findText(model_name)
+		self.parent_window.seg_model_list.setCurrentIndex(idx)

celldetective/gui/signal_annotator.py

@@ -35,7 +35,10 @@ class SignalAnnotator(QMainWindow, Styles):
 	def __init__(self, parent_window=None):
 
 		super().__init__()
+		
 		center_window(self)
+		self.proceed = True
+		self.setAttribute(Qt.WA_DeleteOnClose)
 
 		self.parent_window = parent_window
 		self.setWindowTitle("Signal annotator")
@@ -65,18 +68,19 @@ class SignalAnnotator(QMainWindow, Styles):
 		self.status_name = 'status'
 
 		self.locate_stack()
-		self.load_annotator_config()
-		self.locate_tracks()
-		self.prepare_stack()
+		if not self.proceed:
+			self.close()
+		else:
+			self.load_annotator_config()
+			self.locate_tracks()
+			self.prepare_stack()
 
-		self.generate_signal_choices()
-		self.frame_lbl = QLabel('frame: ')
-		self.looped_animation()
-		self.create_cell_signal_canvas()
+			self.generate_signal_choices()
+			self.frame_lbl = QLabel('frame: ')
+			self.looped_animation()
+			self.create_cell_signal_canvas()
 
-		self.populate_widget()
-
-		self.setAttribute(Qt.WA_DeleteOnClose)
+			self.populate_widget()
 
 	def populate_widget(self):
 
@@ -645,11 +649,14 @@ class SignalAnnotator(QMainWindow, Styles):
 		if len(movies) == 0:
 			msgBox = QMessageBox()
 			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText("No movies are detected in the experiment folder. Cannot load an image to test Haralick.")
+			msgBox.setText("No movie is detected in the experiment folder.\nPlease check the stack prefix...")
 			msgBox.setWindowTitle("Warning")
 			msgBox.setStandardButtons(QMessageBox.Ok)
 			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Yes:
+			if returnValue == QMessageBox.Ok:
+				self.proceed = False
+				self.close()
+			else:
 				self.close()
 		else:
 			self.stack_path = movies[0]
@@ -977,15 +984,17 @@ class SignalAnnotator(QMainWindow, Styles):
 				self.stack[np.where(self.stack > 0.)] = np.log(self.stack[np.where(self.stack > 0.)])
 
 	def closeEvent(self, event):
-
-		self.stop()
-		# result = QMessageBox.question(self,
-		# 			  "Confirm Exit...",
-		# 			  "Are you sure you want to exit ?",
-		# 			  QMessageBox.Yes| QMessageBox.No,
-		# 			  )
-		del self.stack
-		gc.collect()
+		try:
+			self.stop()
+			# result = QMessageBox.question(self,
+			# 			  "Confirm Exit...",
+			# 			  "Are you sure you want to exit ?",
+			# 			  QMessageBox.Yes| QMessageBox.No,
+			# 			  )
+			del self.stack
+			gc.collect()
+		except:
+			pass
 
 	def looped_animation(self):
 
@@ -1118,6 +1127,7 @@ class SignalAnnotator(QMainWindow, Styles):
 		try:
 			min_values = []
 			max_values = []
+			feats = []
 			for i in range(len(self.signal_choice_cb)):
 				signal = self.signal_choice_cb[i].currentText()
 				if signal == '--':
@@ -1127,9 +1137,26 @@ class SignalAnnotator(QMainWindow, Styles):
 					minn = np.nanpercentile(self.df_tracks.loc[:, signal].to_numpy().flatten(), 1)
 					min_values.append(minn)
 					max_values.append(maxx)
+					feats.append(signal)
+
+			smallest_value = np.amin(min_values)
+			feat_smallest_value = feats[np.argmin(min_values)]
+			min_feat = self.df_tracks[feat_smallest_value].min()
+			max_feat = self.df_tracks[feat_smallest_value].max()
+			pad_small = (max_feat - min_feat) * 0.05
+			if pad_small==0:
+				pad_small = 0.05
+
+			largest_value = np.amax(max_values)
+			feat_largest_value = feats[np.argmax(max_values)]
+			min_feat = self.df_tracks[feat_largest_value].min()
+			max_feat = self.df_tracks[feat_largest_value].max()
+			pad_large = (max_feat - min_feat) * 0.05
+			if pad_large==0:
+				pad_large = 0.05
 
 			if len(min_values) > 0:
-				self.cell_ax.set_ylim(np.amin(min_values), np.amax(max_values))
+				self.cell_ax.set_ylim(smallest_value - pad_small, largest_value + pad_large)
 		except Exception as e:
 			pass
 
@@ -2305,8 +2332,8 @@ class MeasureAnnotator(SignalAnnotator):
 		else:
 			self.current_stack = self.current_stack[0]
 			if self.log_option:
-				self.current_stack[np.where(self.current_stack > 0.)] = np.log(
-					self.current_stack[np.where(self.current_stack > 0.)])
+				self.current_stack[np.where((self.current_stack > 0.)&(self.current_stack==self.current_stack))] = np.log(
+					self.current_stack[np.where((self.current_stack > 0.)&(self.current_stack==self.current_stack))])
 
 	def changed_channel(self):
 
@@ -2422,11 +2449,11 @@ class MeasureAnnotator(SignalAnnotator):
 		if len(movies) == 0:
 			msgBox = QMessageBox()
 			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText("No movies are detected in the experiment folder. Cannot load an image to test Haralick.")
+			msgBox.setText("No movie is detected in the experiment folder.\nPlease check the stack prefix...")
 			msgBox.setWindowTitle("Warning")
 			msgBox.setStandardButtons(QMessageBox.Ok)
 			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Yes:
+			if returnValue == QMessageBox.Ok:
 				self.close()
 		else:
 			self.stack_path = movies[0]

celldetective/gui/signal_annotator2.py

@@ -140,17 +140,22 @@ class SignalAnnotator2(QMainWindow,Styles):
 
 		self.button_widget = QWidget()
 		main_layout = QHBoxLayout()
+		main_layout.setSpacing(30)
+
 		self.button_widget.setLayout(main_layout)
 
 		main_layout.setContentsMargins(30,30,30,30)
 		self.left_panel = QVBoxLayout()
-		self.left_panel.setContentsMargins(30,30,30,30)
-		self.left_panel.setSpacing(10)
+		self.left_panel.setContentsMargins(5,5,5,5)
+		self.left_panel.setSpacing(5)
 
 		self.right_panel = QVBoxLayout()
+		self.right_panel.setSpacing(0)
+		self.right_panel.setContentsMargins(5,5,5,5)
 
 		#NEIGHBORHOOD
 		neigh_hbox = QHBoxLayout()
+		neigh_hbox.setContentsMargins(0,0,0,0)
 		neigh_hbox.addWidget(QLabel('neighborhood: '), 25)
 		self.neighborhood_choice_cb = QComboBox()
 		self.neighborhood_choice_cb.addItems(self.neighborhood_cols)
@@ -193,17 +198,17 @@ class SignalAnnotator2(QMainWindow,Styles):
 		self.relative_del_class_btn.clicked.connect(self.del_relative_event_class)
 		subclass_hbox.addWidget(self.relative_del_class_btn, 5)
 		class_hbox.addLayout(subclass_hbox, 75)
-
-
 		self.left_panel.addLayout(class_hbox)
 
 		self.cell_events_hbox = QHBoxLayout()
+		self.cell_events_hbox.setContentsMargins(0,0,0,0)
 		self.cell_events_hbox.addWidget(QLabel('reference event: '), 25)
 		self.reference_event_choice_cb = QComboBox()
 		self.cell_events_hbox.addWidget(self.reference_event_choice_cb, 75)
 		
 		#if 'self' not in self.neighborhood_choice_cb.currentText():
 		self.neigh_cell_events_hbox = QHBoxLayout()
+		self.neigh_cell_events_hbox.setContentsMargins(0,0,0,0)
 		self.neigh_lab=QLabel('neighbor event: ')
 		self.neigh_cell_events_hbox.addWidget(self.neigh_lab, 25)
 		self.neighbor_event_choice_cb = QComboBox()
@@ -214,7 +219,7 @@ class SignalAnnotator2(QMainWindow,Styles):
 
 		# Text information about selected cells
 		self.cell_info_hbox = QHBoxLayout()
-		self.cell_info_hbox.setContentsMargins(30,30,30,30)
+		self.cell_info_hbox.setContentsMargins(30,0,30,0)
 
 		reference_layout = QVBoxLayout()
 		reference_layout.addWidget(self.reference_cell_info)
@@ -232,7 +237,7 @@ class SignalAnnotator2(QMainWindow,Styles):
 
 		# Annotation buttons
 		options_hbox = QHBoxLayout()
-		options_hbox.setContentsMargins(150, 30, 50, 0)
+		options_hbox.setContentsMargins(150, 0, 50, 0)
 		self.event_btn = QRadioButton('event')
 		self.event_btn.setStyleSheet(self.button_style_sheet_2)
 		self.event_btn.toggled.connect(self.enable_time_of_interest)
@@ -256,7 +261,7 @@ class SignalAnnotator2(QMainWindow,Styles):
 		self.left_panel.addLayout(options_hbox)
 
 		time_option_hbox = QHBoxLayout()
-		time_option_hbox.setContentsMargins(100, 30, 100, 30)
+		time_option_hbox.setContentsMargins(100, 0, 100, 0)
 		self.time_of_interest_label = QLabel('time of interest: ')
 		time_option_hbox.addWidget(self.time_of_interest_label, 30)
 		self.time_of_interest_le = QLineEdit()
@@ -264,6 +269,7 @@ class SignalAnnotator2(QMainWindow,Styles):
 		self.left_panel.addLayout(time_option_hbox)
 
 		main_action_hbox = QHBoxLayout()
+		main_action_hbox.setContentsMargins(100, 0, 100, 0)
 		self.correct_btn = QPushButton('correct')
 		self.correct_btn.setIcon(icon(MDI6.redo_variant, color="white"))
 		self.correct_btn.setIconSize(QSize(20, 20))
@@ -320,7 +326,7 @@ class SignalAnnotator2(QMainWindow,Styles):
 		self.left_panel.addLayout(plot_buttons_hbox)
 
 		signal_choice_grid = QVBoxLayout()
-		signal_choice_grid.setContentsMargins(30,0,30,50)
+		signal_choice_grid.setContentsMargins(30,0,70,5)
 
 		header_layout = QHBoxLayout()
 		header_layout.addWidget(QLabel('reference'), 23, alignment=Qt.AlignCenter)
@@ -332,32 +338,14 @@ class SignalAnnotator2(QMainWindow,Styles):
 		for i in range(self.n_signals):
 			
 			h_layout = QHBoxLayout()
+			if i==(self.n_signals-1):
+				h_layout.setContentsMargins(0,0,0,0)
 			h_layout.addWidget(self.reference_pop_option_buttons[i], 23, alignment=Qt.AlignCenter)
 			h_layout.addWidget(self.neighbor_pop_option_buttons[i], 23, alignment=Qt.AlignCenter)
 			h_layout.addWidget(self.relative_pop_option_buttons[i], 23, alignment=Qt.AlignCenter)
 			h_layout.addWidget(self.signal_choices[i], 30)
 			signal_choice_grid.addLayout(h_layout)
 
-		# signal_choice_vbox = QVBoxLayout()
-		# signal_choice_vbox.setContentsMargins(30,0,30,50)
-		# for i in range(len(self.signal_choices)):
-		# 	signal_choice_grid.addWidget(self.signal_choices[i],i+1,3)
-		# 	# hlayout = QHBoxLayout()
-		# 	#
-		# 	# #hlayout.addLayout(self.signal_labels[i], 20)
-		# 	# #hlayout.addLayout(self.signal_choices[i], 75)
-		# 	# # if i==0:
-		# 	# #     hlayout.addWidget(self.signal_choices[i], 75,alignment=Qt.AlignBottom)
-		# 	# # else:
-		# 	# hlayout.addWidget(self.signal_choices[i], 75)
-		# 	# #hlayout.addWidget(self.log_btns[i], 5)
-		# 	# signal_choice_vbox.addLayout(hlayout)
-
-			# self.log_btns[i].setIcon(icon(MDI6.math_log,color="black"))
-			# self.log_btns[i].setStyleSheet(self.parent.parent.parent.button_select_all)
-			# self.log_btns[i].clicked.connect(lambda ch, i=i: self.switch_to_log(i))
-		#signal_choice_hbox.addLayout(signal_choice_vbox,alignment=Qt.AlignCenter)
-
 		self.left_panel.addLayout(signal_choice_grid)
 
 		btn_hbox = QHBoxLayout()
@@ -377,7 +365,6 @@ class SignalAnnotator2(QMainWindow,Styles):
 		# Animation
 		animation_buttons_box = QHBoxLayout()
 
-
 		animation_buttons_box.addWidget(self.frame_lbl, 20, alignment=Qt.AlignLeft)
 
 		self.first_frame_btn = QPushButton()
@@ -1817,7 +1804,7 @@ class SignalAnnotator2(QMainWindow,Styles):
 		else:
 			self.stack = self.stack[0]
 			if self.log_option:
-				self.stack[np.where(self.stack>0.)] = np.log(self.stack[np.where(self.stack>0.)])
+				self.stack[np.where((self.stack>0.)&(self.stack==self.stack))] = np.log(self.stack[np.where((self.stack>0.))&(self.stack==self.stack)])
 
 		print(f'Load stack of shape: {self.stack.shape}.')
 

celldetective/gui/survival_ui.py

@@ -126,13 +126,15 @@ class ConfigSurvival(QWidget, Styles):
 		main_layout.addLayout(select_layout)
 
 		time_cut_layout = QHBoxLayout()
-		time_cut_layout.addWidget(QLabel('cut observation time [min]: '), 33)
+		cut_time_lbl = QLabel('cut obs.\ntime [min]: ')
+		cut_time_lbl.setToolTip('Filter out later events from\nthe analysis (in absolute time).')
+		time_cut_layout.addWidget(cut_time_lbl, 33)
 		self.query_time_cut = QLineEdit()
 		self.query_time_cut.setValidator(self.float_validator)
 		time_cut_layout.addWidget(self.query_time_cut, 66)
 		main_layout.addLayout(time_cut_layout)
 
-		self.cbs[0].setCurrentIndex(0)
+		self.set_classes_and_times()
 		self.cbs[1].setCurrentText('t_firstdetection')
 
 		time_calib_layout = QHBoxLayout()
@@ -174,6 +176,8 @@ class ConfigSurvival(QWidget, Styles):
 			print('no column starts with t')
 			self.auto_close = True
 			return None
+		if 't0' in self.all_columns:
+			time_columns.append('t0')
 
 		self.cbs[1].clear()
 		self.cbs[1].addItems(np.unique(self.cb_options[1]+time_columns))
@@ -268,7 +272,7 @@ class ConfigSurvival(QWidget, Styles):
 
 		cut_observation_time = None
 		try:
-			cut_observation_time = float(self.query_time_cut.text()) / self.FrameToMin
+			cut_observation_time = float(self.query_time_cut.text().replace(',','.')) / self.FrameToMin
 			if not 0<cut_observation_time<=(self.df['FRAME'].max()):
 				print('Invalid cut time (larger than movie length)... Not applied.')
 				cut_observation_time = None