celldetective 1.3.0.post1__py3-none-any.whl → 1.3.2__py3-none-any.whl

celldetective/gui/process_block.py

@@ -30,10 +30,10 @@ import json
 import psutil
 from celldetective.neighborhood import compute_neighborhood_at_position, compute_contact_neighborhood_at_position
 from celldetective.gui.gui_utils import FigureCanvas
-from celldetective.preprocessing import correct_background_model_free, correct_background_model
+from celldetective.preprocessing import correct_background_model_free, correct_background_model, correct_channel_offset
 from celldetective.utils import _estimate_scale_factor, _extract_channel_indices_from_config, _extract_channel_indices, ConfigSectionMap, _extract_nbr_channels_from_config, _get_img_num_per_channel, normalize_per_channel
 from celldetective.gui.gui_utils import ThresholdLineEdit, QuickSliderLayout, help_generic
-from celldetective.gui.layouts import CellposeParamsWidget, StarDistParamsWidget, BackgroundModelFreeCorrectionLayout, ProtocolDesignerLayout, BackgroundFitCorrectionLayout
+from celldetective.gui.layouts import CellposeParamsWidget, StarDistParamsWidget, BackgroundModelFreeCorrectionLayout, ProtocolDesignerLayout, BackgroundFitCorrectionLayout, ChannelOffsetOptionsLayout
 from celldetective.gui import Styles
 from celldetective.utils import get_software_location
 
@@ -166,10 +166,10 @@ class ProcessPanel(QFrame, Styles):
 		self.generate_signal_analysis_options()
 
 		self.grid_contents.addWidget(QHSeperationLine(), 9, 0, 1, 4)
-		self.view_tab_btn = QPushButton("View table")
+		self.view_tab_btn = QPushButton("Explore table")
 		self.view_tab_btn.setStyleSheet(self.button_style_sheet_2)
 		self.view_tab_btn.clicked.connect(self.view_table_ui)
-		self.view_tab_btn.setToolTip('View table')
+		self.view_tab_btn.setToolTip('Explore table')
 		self.view_tab_btn.setIcon(icon(MDI6.table,color="#1565c0"))
 		self.view_tab_btn.setIconSize(QSize(20, 20))
 		#self.view_tab_btn.setEnabled(False)
@@ -177,7 +177,7 @@ class ProcessPanel(QFrame, Styles):
 
 		self.grid_contents.addWidget(QHSeperationLine(), 9, 0, 1, 4)
 		self.submit_btn = QPushButton("Submit")
-		self.submit_btn.setStyleSheet(self.button_style_sheet_2)
+		self.submit_btn.setStyleSheet(self.button_style_sheet)
 		self.submit_btn.clicked.connect(self.process_population)
 		self.grid_contents.addWidget(self.submit_btn, 11, 0, 1, 4)
 
@@ -228,7 +228,7 @@ class ProcessPanel(QFrame, Styles):
 
 		signal_layout = QVBoxLayout()
 		signal_hlayout = QHBoxLayout()
-		self.signal_analysis_action = QCheckBox("SIGNAL ANALYSIS")
+		self.signal_analysis_action = QCheckBox("DETECT EVENTS")
 		self.signal_analysis_action.setStyleSheet("""
 			font-size: 10px;
 			padding-left: 10px;
@@ -920,7 +920,7 @@ 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...')
@@ -1207,28 +1207,19 @@ 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;
@@ -1283,10 +1274,10 @@ class NeighPanel(QFrame, Styles):
 		self.grid_contents.addLayout(signal_layout, 7, 0, 1, 4)
 		self.grid_contents.addWidget(QHSeperationLine(), 11, 0, 1, 4)
 
-		self.view_tab_btn = QPushButton("View table")
+		self.view_tab_btn = QPushButton("Explore table")
 		self.view_tab_btn.setStyleSheet(self.button_style_sheet_2)
 		self.view_tab_btn.clicked.connect(self.view_table_ui)
-		self.view_tab_btn.setToolTip('View table')
+		self.view_tab_btn.setToolTip('Explore table')
 		self.view_tab_btn.setIcon(icon(MDI6.table,color="#1565c0"))
 		self.view_tab_btn.setIconSize(QSize(20, 20))
 		#self.view_tab_btn.setEnabled(False)
@@ -1295,7 +1286,7 @@ class NeighPanel(QFrame, Styles):
 		#self.grid_contents.addWidget(QLabel(''), 12, 0, 1, 4)
 
 		self.submit_btn = QPushButton("Submit")
-		self.submit_btn.setStyleSheet(self.button_style_sheet_2)
+		self.submit_btn.setStyleSheet(self.button_style_sheet)
 		self.submit_btn.setToolTip("Compute the neighborhoods of the selected positions.")
 		self.submit_btn.clicked.connect(self.process_neighborhood)
 		self.grid_contents.addWidget(self.submit_btn, 14, 0, 1, 4)
@@ -1304,6 +1295,26 @@ 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 +1371,7 @@ 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...')
@@ -1657,12 +1668,33 @@ class PreprocessingPanel(QFrame, Styles):
 
 		self.protocol_layout.title_layout.addWidget(self.help_background_btn, 5, alignment=Qt.AlignRight)
 
+		
+		self.channel_offset_correction_layout = QVBoxLayout()
+
+		self.channel_shift_lbl = QLabel("CHANNEL OFFSET CORRECTION")
+		self.channel_shift_lbl.setStyleSheet("""
+			font-weight: bold;
+			padding: 0px;
+			""")
+		self.channel_offset_correction_layout.addWidget(self.channel_shift_lbl, alignment=Qt.AlignCenter)
+
+		self.channel_offset_options_layout = ChannelOffsetOptionsLayout(self)
+		self.channel_offset_correction_layout.addLayout(self.channel_offset_options_layout)
+		
+		self.protocol_layout.correction_layout.addWidget(QLabel(''))
+		self.protocol_layout.correction_layout.addLayout(self.channel_offset_correction_layout)
+
 		self.grid_contents.addLayout(self.protocol_layout,0,0,1,4)
+
 		self.submit_preprocessing_btn = QPushButton("Submit")
-		self.submit_preprocessing_btn.setStyleSheet(self.button_style_sheet_2)
+		self.submit_preprocessing_btn.setStyleSheet(self.button_style_sheet)
 		self.submit_preprocessing_btn.clicked.connect(self.launch_preprocessing)
+		
 		self.grid_contents.addWidget(self.submit_preprocessing_btn, 1,0,1,4)
 
+	def add_offset_instructions_to_parent_list(self):
+		print('adding instructions')
+
 
 	def launch_preprocessing(self):
 
@@ -1712,7 +1744,7 @@ class PreprocessingPanel(QFrame, Styles):
 				export_prefix = None
 
 			if correction_protocol['correction_type']=='model-free':
-
+				print(f'Model-free correction; {movie_prefix=} {export_prefix=}')
 				correct_background_model_free(self.exp_dir, 
 								   well_option=well_option,
 								   position_option=pos_option,
@@ -1726,7 +1758,7 @@ class PreprocessingPanel(QFrame, Styles):
 								)
 			
 			elif correction_protocol['correction_type']=='fit':
-
+				print(f'Fit correction; {movie_prefix=} {export_prefix=} {correction_protocol=}')
 				correct_background_model(self.exp_dir,
 								   well_option=well_option,
 								   position_option=pos_option,
@@ -1738,6 +1770,19 @@ class PreprocessingPanel(QFrame, Styles):
 								   export_prefix = export_prefix,
 								   **correction_protocol,
 								)
+			elif correction_protocol['correction_type']=='offset':
+				print(f'Offset correction; {movie_prefix=} {export_prefix=} {correction_protocol=}')
+				correct_channel_offset(self.exp_dir,
+								   well_option=well_option,
+								   position_option=pos_option,
+								   export= True,
+								   return_stacks=False,
+								   show_progress_per_well = True,
+								   show_progress_per_pos = True,
+								   movie_prefix = movie_prefix,
+								   export_prefix = export_prefix,
+								   **correction_protocol,
+								)
 		print('Done.')
 
 

celldetective/gui/retrain_segmentation_model_options.py

@@ -8,7 +8,7 @@ from superqt import QLabeledDoubleSlider,QLabeledSlider
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 from celldetective.utils import get_software_location
-from celldetective.io import get_segmentation_datasets_list, locate_segmentation_dataset
+from celldetective.io import get_segmentation_datasets_list, locate_segmentation_dataset, get_segmentation_models_list
 from celldetective.segmentation import train_segmentation_model
 from celldetective.gui.layouts import CellposeParamsWidget
 import numpy as np
@@ -85,8 +85,11 @@ class ConfigSegmentationModelTraining(QMainWindow, Styles):
 		self.submit_btn.clicked.connect(self.prep_model)
 		self.main_layout.addWidget(self.submit_btn)
 		self.submit_btn.setEnabled(False)
+		self.submit_warning = QLabel('')
+		self.main_layout.addWidget(self.submit_warning)
 
 		self.spatial_calib_le.textChanged.connect(self.activate_train_btn)
+		self.modelname_le.setText(f"Untitled_model_{datetime.today().strftime('%Y-%m-%d')}")
 
 		#self.populate_left_panel()
 		#grid.addLayout(self.left_side, 0, 0, 1, 1)
@@ -273,6 +276,7 @@ class ConfigSegmentationModelTraining(QMainWindow, Styles):
 		modelname_layout.addWidget(QLabel('Model name: '), 30)
 		self.modelname_le = QLineEdit()
 		self.modelname_le.setText(f"Untitled_model_{datetime.today().strftime('%Y-%m-%d')}")
+		self.modelname_le.textChanged.connect(self.activate_train_btn)
 		modelname_layout.addWidget(self.modelname_le, 70)
 		layout.addLayout(modelname_layout)
 
@@ -317,13 +321,21 @@ class ConfigSegmentationModelTraining(QMainWindow, Styles):
 		spatial_calib_layout.addWidget(self.spatial_calib_le, 70)
 		layout.addLayout(spatial_calib_layout)
 
-
-
 	def activate_train_btn(self):
-		if self.spatial_calib_le.text()=='':
-			self.submit_btn.setEnabled(False)
-		elif not np.all([cb.currentText()=='--' for cb in self.ch_norm.channel_cbs]):
+
+		current_name = self.modelname_le.text()
+		models = get_segmentation_models_list(mode=self.mode, return_path=False)
+		if not current_name in models and not self.spatial_calib_le.text()=='' and not np.all([cb.currentText()=='--' for cb in self.ch_norm.channel_cbs]):
 			self.submit_btn.setEnabled(True)
+			self.submit_warning.setText('')
+		else:
+			self.submit_btn.setEnabled(False)
+			if current_name in models:
+				self.submit_warning.setText('A model with this name already exists... Please pick another.')
+			elif self.spatial_calib_le.text()=='':
+				self.submit_warning.setText('Please provide a valid spatial calibration...')
+			elif np.all([cb.currentText()=='--' for cb in self.ch_norm.channel_cbs]):
+				self.submit_warning.setText('Please provide valid channels...')
 
 	def rescale_slider(self):
 		if self.stardist_model.isChecked():
@@ -336,11 +348,13 @@ class ConfigSegmentationModelTraining(QMainWindow, Styles):
 
 	def showDialog_pretrained(self):
 
-		try:
-			self.cancel_pretrained.click()
-		except:
-			pass
+		# try:
+		# 	self.cancel_pretrained.click()
+		# except Exception as e:
+		# 	print(e)
+		# 	pass
 
+		self.clear_pretrained()
 		self.pretrained_model = None
 		self.pretrained_model = QFileDialog.getExistingDirectory(
 						self, "Open Directory",

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

@@ -125,7 +125,16 @@ class ConfigSurvival(QWidget, Styles):
 		select_layout.addWidget(self.query_le, 66)
 		main_layout.addLayout(select_layout)
 
-		self.cbs[0].setCurrentIndex(0)
+		time_cut_layout = QHBoxLayout()
+		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.set_classes_and_times()
 		self.cbs[1].setCurrentText('t_firstdetection')
 
 		time_calib_layout = QHBoxLayout()
@@ -167,6 +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))
@@ -259,17 +270,27 @@ class ConfigSurvival(QWidget, Styles):
 
 	def compute_survival_functions(self):
 
+		cut_observation_time = None
+		try:
+			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		
+		except Exception as e:
+			pass
+		print(f"{cut_observation_time=}")
+
 		# Per position survival
 		for block,movie_group in self.df.groupby(['well','position']):
 
-			ks = compute_survival(movie_group, self.class_of_interest, self.cbs[2].currentText(), t_reference=self.cbs[1].currentText(), FrameToMin=self.FrameToMin)
+			ks = compute_survival(movie_group, self.class_of_interest, self.cbs[2].currentText(), t_reference=self.cbs[1].currentText(), FrameToMin=self.FrameToMin, cut_observation_time=cut_observation_time)
 			if ks is not None:
 				self.df_pos_info.loc[self.df_pos_info['pos_path']==block[1],'survival_fit'] = ks
 
 		# Per well survival
 		for well,well_group in self.df.groupby('well'):
 
-			ks = compute_survival(well_group, self.class_of_interest, self.cbs[2].currentText(), t_reference=self.cbs[1].currentText(), FrameToMin=self.FrameToMin)
+			ks = compute_survival(well_group, self.class_of_interest, self.cbs[2].currentText(), t_reference=self.cbs[1].currentText(), FrameToMin=self.FrameToMin, cut_observation_time=cut_observation_time)
 			if ks is not None:
 				self.df_well_info.loc[self.df_well_info['well_path']==well,'survival_fit'] = ks