celldetective 1.4.0__py3-none-any.whl → 1.4.1__py3-none-any.whl

celldetective/gui/generic_signal_plot.py

@@ -504,7 +504,8 @@ class GenericSignalPlotWidget(CelldetectiveWidget):
 		# Spines
 		self.ax.spines['top'].set_visible(False)
 		self.ax.spines['right'].set_visible(False)
-
+		self.ax.grid(which='major', color='black', linestyle='-', linewidth=0.8, alpha=0.2)
+		self.ax.grid(which='minor', color='lightgray', linestyle='--', linewidth=0.5, alpha=0.1)
 		# Lims
 		safe_df = self.df.dropna(subset=self.feature_selected)
 		values = safe_df[self.feature_selected].values

celldetective/gui/gui_utils.py

@@ -653,6 +653,7 @@ class FilterChoice(CelldetectiveWidget):
 			'log_filter': {'blob_size': 30},
 			'tophat_filter': {'size': 4, 'connectivity': 4},
 			'otsu_filter': None,
+			'multiotsu_filter': {'classes': 3},
 			'local_filter': {'block_size': 73, 'method': 'mean', 'offset': 0},
 			'niblack_filter': {'window_size': 15, 'k': 0.2},
 			# 'sauvola_filter': {'window_size': 15, 'k': 0.2}
@@ -1210,7 +1211,7 @@ def color_from_state(state, recently_modified=False):
 	"""
 
 	unique_values = np.unique(state)
-	color_map={}
+	color_map = {}
 	for value in unique_values:
 
 		if np.isnan(value):
@@ -1220,8 +1221,10 @@ def color_from_state(state, recently_modified=False):
 			color_map[value] = 'tab:blue'
 		elif value==1:
 			color_map[value] = 'tab:red'
+		elif value==99:
+			color_map[value] = 'k'
 		else:
-			color_map[value] = plt.cm.tab10(value)
+			color_map[value] = plt.cm.tab20(value/20.0)
 
 	return color_map
 

celldetective/gui/help/neighborhood.json

@@ -3,13 +3,13 @@
     "yes": {
       "Do you have the complete shape information for both populations?": {
         "yes": "You can calculate a mask-contact neighborhood. Define the reference and neighbor populations. Adjust the tolerance parameter to control how sensitive the analysis is to contact between reference and neighbor cells.",
-        "no": "You can use an isotropic distance threshold. Define the reference and neighbor populations. Set a radius \( r > (R_{\text{ref}} + 0.5 \times R_{\text{neigh}}) \), where \( R_{\text{ref}} \) is the average radius of reference cells and \( R_{\text{neigh}} \) is the average radius of neighbor cells."
+        "no": "You can use an isotropic distance threshold. Define the reference and neighbor populations. Set a radius ( r > (R_{\text{ref}} + 0.5 \times R_{\text{neigh}}) ), where ( R_{\text{ref}} ) is the average radius of reference cells and ( R_{\text{neigh}} ) is the average radius of neighbor cells."
       }
     },
     "no": {
       "Do you have the complete shape information for the population of interest?": {
         "yes": "You can calculate a mask-contact neighborhood. Use the same population as both the reference and neighbor. Adjust the tolerance parameter to control sensitivity to cell-cell contact.",
-        "no": "You can use an isotropic distance threshold. Use the same population as both the reference and neighbor. Set a radius \( r > 1.5 \times R \), where \( R \) is the average cell radius."
+        "no": "You can use an isotropic distance threshold. Use the same population as both the reference and neighbor. Set a radius ( r > 1.5 \times R ), where ( R ) is the average cell radius."
       }
     }
   }

celldetective/gui/layouts.py

@@ -882,7 +882,7 @@ class BackgroundFitCorrectionLayout(QGridLayout, Styles):
 		else:
 			clip = False
 
-		corrected_stack = correct_background_model(self.attr_parent.exp_dir, 
+		corrected_stack = correct_background_model(self.attr_parent.exp_dir,
 						   well_option=self.attr_parent.well_list.getSelectedIndices(), #+1 ??
 						   position_option=self.attr_parent.position_list.getSelectedIndices(), #+1??
 						   target_channel=self.channels_cb.currentText(),
@@ -897,14 +897,18 @@ class BackgroundFitCorrectionLayout(QGridLayout, Styles):
 						   show_progress_per_pos = False,
 							)
 
-		self.viewer = StackVisualizer(
-									  stack=corrected_stack[0],
-									  window_title='Corrected channel',
-									  target_channel=self.channels_cb.currentIndex(),
-									  frame_slider = True,
-									  contrast_slider = True
-									 )
-		self.viewer.show()
+		if corrected_stack:
+			self.viewer = StackVisualizer(
+										  stack=corrected_stack[0],
+										  window_title='Corrected channel',
+										  target_channel=self.channels_cb.currentIndex(),
+										  frame_slider = True,
+										  contrast_slider = True
+										 )
+			self.viewer.show()
+		else:
+			print("Corrected stack could not be generated... No stack available...")
+
 
 
 class LocalCorrectionLayout(BackgroundFitCorrectionLayout):
@@ -1330,6 +1334,8 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 		for c in self.coef_widgets:
 			c.setEnabled(False)
 
+		self.interpolate_check = QCheckBox("interpolate NaNs")
+
 	def add_to_layout(self):
 		
 		channel_layout = QHBoxLayout()
@@ -1394,10 +1400,12 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 		self.operation_layout = OperationLayout()
 		self.addLayout(self.operation_layout, 9, 0, 1, 3)
 
+		self.addWidget(self.interpolate_check, 10, 0, 1, 1)
+
 		correction_layout = QHBoxLayout()
 		correction_layout.addWidget(self.add_correction_btn, 95)
 		correction_layout.addWidget(self.corrected_stack_viewer_btn, 5)
-		self.addLayout(correction_layout, 10, 0, 1, 3)
+		self.addLayout(correction_layout, 11, 0, 1, 3)
 
 		# verticalSpacer = QSpacerItem(20, 40, QSizePolicy.Minimum, QSizePolicy.Expanding)
 		# self.addItem(verticalSpacer, 5, 0, 1, 3)
@@ -1456,7 +1464,8 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 					  "opt_coef_nbr": opt_coef_nbr,
 					  "operation": operation,
 					  "clip": clip,
-					  "offset": offset
+					  "offset": offset,
+					  "fix_nan": self.interpolate_check.isChecked(),
 					 }
 
 	def set_target_channel(self):
@@ -1532,6 +1541,7 @@ class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 						   clip = clip,
 						   export= False,
 						   return_stacks=True,
+						   fix_nan=self.interpolate_check.isChecked(),
 						   show_progress_per_well = True,
 						   show_progress_per_pos = False,
 							)

celldetective/gui/{signal_annotator2.py → pair_event_annotator.py}

@@ -26,7 +26,7 @@ from sklearn.preprocessing import MinMaxScaler
 from functools import partial
 from pandas.api.types import is_numeric_dtype
 
-class SignalAnnotator2(CelldetectiveMainWindow):
+class PairEventAnnotator(CelldetectiveMainWindow):
 
 	"""
 	UI to set tracking parameters for bTrack.
@@ -167,8 +167,10 @@ class SignalAnnotator2(CelldetectiveMainWindow):
 		self.left_panel.addLayout(neigh_hbox)
 
 		self.reference_cell_info = QLabel('')
+		self.reference_cell_info.setStyleSheet("color: #1f77b4;")
 		self.pair_info = QLabel('')
 		self.neighbor_cell_info= QLabel('')
+		self.neighbor_cell_info.setStyleSheet("color: #d62728;")
 
 		class_hbox = QHBoxLayout()
 		class_hbox.addWidget(QLabel('interaction event: '), 25)

celldetective/gui/process_block.py

@@ -7,18 +7,20 @@ import gc
 from PyQt5.QtGui import QDoubleValidator, QIntValidator
 
 from celldetective.gui.processes.compute_neighborhood import NeighborhoodProcess
-from celldetective.gui.signal_annotator import MeasureAnnotator
-from celldetective.gui.signal_annotator2 import SignalAnnotator2
+from celldetective.gui.event_annotator import MeasureAnnotator
 from celldetective.io import get_segmentation_models_list, control_segmentation_napari, get_signal_models_list, \
 	control_tracks, load_experiment_tables, get_pair_signal_models_list
 from celldetective.io import locate_segmentation_model, extract_position_name, fix_missing_labels, locate_signal_model
-from celldetective.gui import SegmentationModelLoader, ClassifierWidget, ConfigNeighborhoods, \
-	ConfigSegmentationModelTraining, ConfigTracking, SignalAnnotator, ConfigSignalModelTraining, ConfigMeasurements, \
-	ConfigSignalAnnotator, TableUI, CelldetectiveWidget
+from celldetective.gui import SegmentationModelLoader, ClassifierWidget, \
+	EventAnnotator, TableUI, CelldetectiveWidget, PairEventAnnotator
+
+from celldetective.gui.settings import SettingsSegmentation, SettingsMeasurements, SettingsTracking, \
+	SettingsSignalAnnotator, SettingsNeighborhood, SettingsSegmentationModelTraining, SettingsEventDetectionModelTraining
+
 from celldetective.gui.gui_utils import QHSeperationLine
 from celldetective.relative_measurements import rel_measure_at_position
 from celldetective.signals import analyze_signals_at_position, analyze_pair_signals_at_position
-from celldetective.utils import extract_experiment_channels
+from celldetective.utils import extract_experiment_channels, remove_file_if_exists
 import numpy as np
 from glob import glob
 from natsort import natsorted
@@ -81,13 +83,13 @@ class ProcessPanel(QFrame, Styles):
 		title_hbox = QHBoxLayout()
 		self.grid.addWidget(panel_title, 0, 0, 1, 4, alignment=Qt.AlignCenter)
 
-		self.help_pop_btn = QPushButton()
-		self.help_pop_btn.setIcon(icon(MDI6.help_circle, color=self.help_color))
-		self.help_pop_btn.setIconSize(QSize(20, 20))
-		self.help_pop_btn.clicked.connect(self.help_population)
-		self.help_pop_btn.setStyleSheet(self.button_select_all)
-		self.help_pop_btn.setToolTip("Help.")
-		self.grid.addWidget(self.help_pop_btn, 0, 0, 1, 3, alignment=Qt.AlignRight)
+		# self.help_pop_btn = QPushButton()
+		# self.help_pop_btn.setIcon(icon(MDI6.help_circle, color=self.help_color))
+		# self.help_pop_btn.setIconSize(QSize(20, 20))
+		# self.help_pop_btn.clicked.connect(self.help_population)
+		# self.help_pop_btn.setStyleSheet(self.button_select_all)
+		# self.help_pop_btn.setToolTip("Help.")
+		# self.grid.addWidget(self.help_pop_btn, 0, 0, 1, 3, alignment=Qt.AlignRight)
 
 		# self.select_all_btn = QPushButton()
 		# self.select_all_btn.setIcon(icon(MDI6.checkbox_blank_outline,color="black"))
@@ -106,7 +108,7 @@ class ProcessPanel(QFrame, Styles):
 
 		title_hbox.addWidget(QLabel(), 5) #self.select_all_btn
 		title_hbox.addWidget(QLabel(), 85, alignment=Qt.AlignCenter)
-		title_hbox.addWidget(self.help_pop_btn, 5)
+		# title_hbox.addWidget(self.help_pop_btn, 5)
 		title_hbox.addWidget(self.collapse_btn, 5)
 
 		self.grid.addLayout(title_hbox, 0, 0, 1, 4)
@@ -136,29 +138,29 @@ class ProcessPanel(QFrame, Styles):
 			self.parent_window.scroll.setMinimumHeight(min(int(930), int(0.9*self.parent_window.screen_height)))
 
 
-	def help_population(self):
+	# def help_population(self):
 
-		"""
-		Helper to choose a proper cell population structure.
-		"""
+	# 	"""
+	# 	Helper to choose a proper cell population structure.
+	# 	"""
 
-		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','cell-populations.json'])
+	# 	dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','cell-populations.json'])
 
-		with open(dict_path) as f:
-			d = json.load(f)
+	# 	with open(dict_path) as f:
+	# 		d = json.load(f)
 
-		suggestion = help_generic(d)
-		if isinstance(suggestion, str):
-			print(f"{suggestion=}")
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Information)
-			msgBox.setTextFormat(Qt.RichText)
-			msgBox.setText(suggestion)
-			msgBox.setWindowTitle("Info")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return None			
+	# 	suggestion = help_generic(d)
+	# 	if isinstance(suggestion, str):
+	# 		print(f"{suggestion=}")
+	# 		msgBox = QMessageBox()
+	# 		msgBox.setIcon(QMessageBox.Information)
+	# 		msgBox.setTextFormat(Qt.RichText)
+	# 		msgBox.setText(suggestion)
+	# 		msgBox.setWindowTitle("Info")
+	# 		msgBox.setStandardButtons(QMessageBox.Ok)
+	# 		returnValue = msgBox.exec()
+	# 		if returnValue == QMessageBox.Ok:
+	# 			return None			
 
 	def populate_contents(self):
 		self.ContentsFrame = QFrame()
@@ -284,9 +286,16 @@ class ProcessPanel(QFrame, Styles):
 		self.grid_contents.addLayout(signal_layout,6,0,1,4)
 
 	def refresh_signal_models(self):
-		signal_models = get_signal_models_list()
+		self.signal_models = get_signal_models_list()
 		self.signal_models_list.clear()
-		self.signal_models_list.addItems(signal_models)
+		
+		thresh = 35
+		models_truncated = [m[:thresh - 3]+'...' if len(m)>thresh else m for m in self.signal_models]
+		
+		self.signal_models_list.addItems(models_truncated)
+		for i in range(len(self.signal_models)):
+			self.signal_models_list.setItemData(i, self.signal_models[i], Qt.ToolTipRole)
+
 
 	def generate_tracking_options(self):
 
@@ -347,14 +356,10 @@ class ProcessPanel(QFrame, Styles):
 		if returnValue == QMessageBox.No:
 			return None
 		elif returnValue == QMessageBox.Yes:
-			if os.path.exists(os.sep.join([self.parent_window.pos, 'output', 'tables', f'trajectories_{self.mode}.csv'])):
-				os.remove(os.sep.join([self.parent_window.pos, 'output', 'tables', f'trajectories_{self.mode}.csv']))
-			if os.path.exists(os.sep.join([self.parent_window.pos, 'output', 'tables', f'trajectories_{self.mode}.pkl'])):
-				os.remove(os.sep.join([self.parent_window.pos, 'output', 'tables', f'trajectories_{self.mode}.pkl']))
-			if os.path.exists(os.sep.join([self.parent_window.pos, 'output', 'tables', f'napari_{self.mode[:-1]}_trajectories.npy'])):
-				os.remove(os.sep.join([self.parent_window.pos, 'output', 'tables', f'napari_{self.mode[:-1]}_trajectories.npy']))
-			if os.path.exists(os.sep.join([self.parent_window.pos, 'output', 'tables', f'trajectories_pairs.csv'])):
-				os.remove(os.sep.join([self.parent_window.pos, 'output', 'tables', f'trajectories_pairs.csv']))
+			remove_file_if_exists(os.sep.join([self.parent_window.pos, 'output', 'tables', f'trajectories_{self.mode}.csv']))
+			remove_file_if_exists(os.sep.join([self.parent_window.pos, 'output', 'tables', f'trajectories_{self.mode}.pkl']))
+			remove_file_if_exists(os.sep.join([self.parent_window.pos, 'output', 'tables', f'napari_{self.mode[:-1]}_trajectories.npy']))
+			remove_file_if_exists(os.sep.join([self.parent_window.pos, 'output', 'tables', f'trajectories_pairs.csv']))
 			self.parent_window.update_position_options()
 		else:
 			return None
@@ -373,13 +378,21 @@ class ProcessPanel(QFrame, Styles):
 		#self.to_disable.append(self.segment_action)
 		grid_segment.addWidget(self.segment_action, 90)
 
-		self.flip_segment_btn = QPushButton()
-		self.flip_segment_btn.setIcon(icon(MDI6.camera_flip_outline,color="black"))
-		self.flip_segment_btn.setIconSize(QSize(20, 20))
-		self.flip_segment_btn.clicked.connect(self.flip_segmentation)
-		self.flip_segment_btn.setStyleSheet(self.button_select_all)
-		self.flip_segment_btn.setToolTip("Flip the order of the frames for segmentation.")
-		grid_segment.addWidget(self.flip_segment_btn, 5)
+		# self.flip_segment_btn = QPushButton()
+		# self.flip_segment_btn.setIcon(icon(MDI6.camera_flip_outline,color="black"))
+		# self.flip_segment_btn.setIconSize(QSize(20, 20))
+		# self.flip_segment_btn.clicked.connect(self.flip_segmentation)
+		# self.flip_segment_btn.setStyleSheet(self.button_select_all)
+		# self.flip_segment_btn.setToolTip("Flip the order of the frames for segmentation.")
+		# grid_segment.addWidget(self.flip_segment_btn, 5)
+
+		self.segmentation_config_btn = QPushButton()
+		self.segmentation_config_btn.setIcon(icon(MDI6.cog_outline,color="black"))
+		self.segmentation_config_btn.setIconSize(QSize(20, 20))
+		self.segmentation_config_btn.setToolTip("Configure segmentation.")
+		self.segmentation_config_btn.setStyleSheet(self.button_select_all)
+		self.segmentation_config_btn.clicked.connect(self.open_segmentation_configuration_ui)
+		grid_segment.addWidget(self.segmentation_config_btn, 5)
 
 
 		self.check_seg_btn = QPushButton()
@@ -572,6 +585,14 @@ class ProcessPanel(QFrame, Styles):
 			print(f"Loading images and labels into napari...")
 			try:
 				control_segmentation_napari(self.parent_window.pos, prefix=self.parent_window.movie_prefix, population=self.mode,flush_memory=True)
+			except FileNotFoundError as e:
+				msgBox = QMessageBox()
+				msgBox.setIcon(QMessageBox.Warning)
+				msgBox.setText(str(e))
+				msgBox.setWindowTitle("Warning")
+				msgBox.setStandardButtons(QMessageBox.Ok)
+				_ = msgBox.exec()
+				return
 			except Exception as e:
 				print(f'Task unsuccessful... Exception {e}...')
 				msgBox = QMessageBox()
@@ -604,15 +625,15 @@ class ProcessPanel(QFrame, Styles):
 
 		test = self.parent_window.locate_selected_position()
 		if test:
-			self.SignalAnnotator = SignalAnnotator(self)
-			self.SignalAnnotator.show()
+			self.event_annotator = EventAnnotator(self)
+			self.event_annotator.show()
 
 	def check_measurements(self):
 
 		test = self.parent_window.locate_selected_position()
 		if test:
-			self.MeasureAnnotator = MeasureAnnotator(self)
-			self.MeasureAnnotator.show()
+			self.measure_annotator = MeasureAnnotator(self)
+			self.measure_annotator.show()
 
 	def enable_segmentation_model_list(self):
 		if self.segment_action.isChecked():
@@ -630,22 +651,22 @@ class ProcessPanel(QFrame, Styles):
 
 		self.seg_model_list.clear()
 		self.seg_models_specific = get_segmentation_models_list(mode=self.mode, return_path=False)
-		self.seg_models = self.seg_models_specific.copy() #get_segmentation_models_list(mode=self.mode, return_path=False)
-		thresh = 40
-		self.models_truncated = [m[:thresh - 3]+'...' if len(m)>thresh else m for m in self.seg_models]
-		#self.seg_model_list.addItems(models_truncated)
+		self.seg_models = self.seg_models_specific.copy()
+		self.n_specific_seg_models = len(self.seg_models)
 
 		self.seg_models_generic = get_segmentation_models_list(mode="generic", return_path=False)
 		self.seg_models.append('Threshold')
 		self.seg_models.extend(self.seg_models_generic)
 
-		#self.seg_models_generic.insert(0,'Threshold')
-		self.seg_model_list.addItems(self.seg_models)
+		thresh = 35
+		self.models_truncated = [m[:thresh - 3]+'...' if len(m)>thresh else m for m in self.seg_models]
+
+		self.seg_model_list.addItems(self.models_truncated)
 
 		for i in range(len(self.seg_models)):
 			self.seg_model_list.setItemData(i, self.seg_models[i], Qt.ToolTipRole)
 
-		self.seg_model_list.insertSeparator(len(self.models_truncated))
+		self.seg_model_list.insertSeparator(self.n_specific_seg_models)
 
 	# def tick_all_actions(self):
 	# 	self.switch_all_ticks_option()
@@ -671,23 +692,28 @@ class ProcessPanel(QFrame, Styles):
 
 	def open_tracking_configuration_ui(self):
 		print('Set the tracking parameters...')
-		self.ConfigTracking = ConfigTracking(self)
-		self.ConfigTracking.show()
+		self.settings_tracking = SettingsTracking(self)
+		self.settings_tracking.show()
 
 	def open_signal_model_config_ui(self):
 		print('Set the training parameters for new signal models...')
-		self.ConfigSignalTrain = ConfigSignalModelTraining(self)
-		self.ConfigSignalTrain.show()
+		self.settings_event_detection_training = SettingsEventDetectionModelTraining(self)
+		self.settings_event_detection_training.show()
 
 	def open_segmentation_model_config_ui(self):
 		print('Set the training parameters for a new segmentation model...')
-		self.ConfigSegmentationTrain = ConfigSegmentationModelTraining(self)
-		self.ConfigSegmentationTrain.show()
+		self.settings_segmentation_training = SettingsSegmentationModelTraining(self)
+		self.settings_segmentation_training.show()
 
 	def open_measurement_configuration_ui(self):
 		print('Set the measurements to be performed...')
-		self.ConfigMeasurements = ConfigMeasurements(self)
-		self.ConfigMeasurements.show()
+		self.settings_measurements = SettingsMeasurements(self)
+		self.settings_measurements.show()
+		
+	def open_segmentation_configuration_ui(self):
+		print('Set the segmentation settings to be performed...')
+		self.settings_segmentation = SettingsSegmentation(self)
+		self.settings_segmentation.show()
 
 	def open_classifier_ui(self):
 
@@ -709,8 +735,8 @@ class ProcessPanel(QFrame, Styles):
 			self.ClassifierWidget.show()
 
 	def open_signal_annotator_configuration_ui(self):
-		self.ConfigSignalAnnotator = ConfigSignalAnnotator(self)
-		self.ConfigSignalAnnotator.show()
+		self.settings_signal_annotator = SettingsSignalAnnotator(self)
+		self.settings_signal_annotator.show()
 
 	def reset_generalist_setup(self, index):
 		self.cellpose_calibrated = False
@@ -766,10 +792,11 @@ class ProcessPanel(QFrame, Styles):
 				#tabs += [pos+os.sep.join(['output', 'tables', f'trajectories_pairs.csv']) for pos in self.df_pos_info['pos_path'].unique()]
 				tabs += [pos+os.sep.join(['output', 'tables', f'napari_{self.mode}_trajectories.npy']) for pos in self.df_pos_info['pos_path'].unique()]
 				for t in tabs:
-					if os.path.exists(t.replace('.csv','.pkl')):
-						os.remove(t.replace('.csv','.pkl'))
-					os.remove(t)				
-
+					remove_file_if_exists(t.replace('.csv','.pkl'))
+					try:
+						os.remove(t)
+					except:
+						pass
 		loop_iter=0
 
 		if self.parent_window.position_list.isMultipleSelection():
@@ -782,7 +809,7 @@ class ProcessPanel(QFrame, Styles):
 			if returnValue == QMessageBox.No:
 				return None
 
-		if self.seg_model_list.currentIndex() > len(self.models_truncated):
+		if self.seg_model_list.currentIndex() > self.n_specific_seg_models:
 			self.model_name = self.seg_models[self.seg_model_list.currentIndex()-1]
 		else:
 			self.model_name = self.seg_models[self.seg_model_list.currentIndex()]
@@ -806,7 +833,8 @@ class ProcessPanel(QFrame, Styles):
 			return None
 
 		if self.signal_analysis_action.isChecked() and not self.signalChannelsSet:
-			self.signalChannelWidget = SignalModelParamsWidget(self, model_name = self.signal_models_list.currentText())
+			self.signal_model_name = self.signal_models[self.signal_models_list.currentIndex()]
+			self.signalChannelWidget = SignalModelParamsWidget(self, model_name = self.signal_model_name)
 			self.signalChannelWidget.show()
 			return None
 
@@ -856,7 +884,7 @@ class ProcessPanel(QFrame, Styles):
 								return None
 						else:
 							print(f"Segmentation from threshold config: {self.threshold_config}")
-							process_args = {"pos": self.pos, "mode": self.mode, "n_threads": self.n_threads, "threshold_instructions": self.threshold_config, "use_gpu": self.use_gpu, 'flip': self.flipSeg}
+							process_args = {"pos": self.pos, "mode": self.mode, "n_threads": self.n_threads, "threshold_instructions": self.threshold_config, "use_gpu": self.use_gpu}
 							self.job = ProgressWindow(SegmentCellThresholdProcess, parent_window=self, title="Segment", process_args = process_args)
 							result = self.job.exec_()
 							if result == QDialog.Accepted:
@@ -871,7 +899,7 @@ class ProcessPanel(QFrame, Styles):
 						# 	process = {"output_dir": self.output_dir, "file": self.model_name}
 						# 	self.download_model_job = ProgressWindow(DownloadProcess, parent_window=self, title="Download", process_args = args)
 
-						process_args = {"pos": self.pos, "mode": self.mode, "n_threads": self.n_threads, "model_name": self.model_name, "use_gpu": self.use_gpu, 'flip': self.flipSeg}
+						process_args = {"pos": self.pos, "mode": self.mode, "n_threads": self.n_threads, "model_name": self.model_name, "use_gpu": self.use_gpu}
 						self.job = ProgressWindow(SegmentCellDLProcess, parent_window=self, title="Segment", process_args = process_args)
 						result = self.job.exec_()
 						if result == QDialog.Accepted:
@@ -926,7 +954,8 @@ class ProcessPanel(QFrame, Styles):
 								returnValue = msgBox.exec()
 								if returnValue == QMessageBox.No:
 									return None
-					analyze_signals_at_position(self.pos, self.signal_models_list.currentText(), self.mode)
+					self.signal_model_name = self.signal_models[self.signal_models_list.currentIndex()]
+					analyze_signals_at_position(self.pos, self.signal_model_name, self.mode)
 
 
 			# self.stack = None
@@ -940,7 +969,16 @@ class ProcessPanel(QFrame, Styles):
 
 	def open_napari_tracking(self):
 		print(f'View the tracks before post-processing for position {self.parent_window.pos} in napari...')
-		control_tracks(self.parent_window.pos, prefix=self.parent_window.movie_prefix, population=self.mode, threads=self.parent_window.parent_window.n_threads)
+		try:
+			control_tracks(self.parent_window.pos, prefix=self.parent_window.movie_prefix, population=self.mode, threads=self.parent_window.parent_window.n_threads)
+		except FileNotFoundError as e:
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Warning)
+			msgBox.setText(str(e))
+			msgBox.setWindowTitle("Warning")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			_ = msgBox.exec()
+			return
 
 	def view_table_ui(self):
 
@@ -1045,8 +1083,8 @@ class ProcessPanel(QFrame, Styles):
 		self.process_population()
 
 	def set_selected_signals_for_event_detection(self):
-
-		model_complete_path = locate_signal_model(self.signal_models_list.currentText())
+		self.signal_model_name = self.signal_models[self.signal_models_list.currentIndex()]
+		model_complete_path = locate_signal_model(self.signal_model_name)
 		input_config_path = model_complete_path+"config_input.json"
 		new_channels = [self.signalChannelWidget.channel_cbs[i].currentText() for i in range(len(self.signalChannelWidget.channel_cbs))]
 		with open(input_config_path) as config_file:
@@ -1441,12 +1479,12 @@ class NeighPanel(QFrame, Styles):
 
 	def open_signal_annotator_configuration_ui(self):
 		self.mode = 'pairs'
-		self.ConfigSignalAnnotator = ConfigSignalAnnotator(self)
-		self.ConfigSignalAnnotator.show()
+		self.config_signal_annotator = SettingsSignalAnnotator(self)
+		self.config_signal_annotator.show()
 
 	def open_signal_model_config_ui(self):
-		self.ConfigSignalTrain = ConfigSignalModelTraining(self, signal_mode='pairs')
-		self.ConfigSignalTrain.show()
+		self.settings_pair_event_detection_training = SettingsEventDetectionModelTraining(self, signal_mode='pairs')
+		self.settings_pair_event_detection_training.show()
 		
 	def remove_protocol_from_list(self):
 
@@ -1457,7 +1495,7 @@ class NeighPanel(QFrame, Styles):
 
 	def open_config_distance_threshold_neighborhood(self):
 
-		self.ConfigNeigh = ConfigNeighborhoods(parent_window=self,
+		self.ConfigNeigh = SettingsNeighborhood(parent_window=self,
 											   neighborhood_type='distance_threshold',
 											   neighborhood_parameter_name='threshold distance',
 											   )
@@ -1465,7 +1503,7 @@ class NeighPanel(QFrame, Styles):
 
 	def open_config_contact_neighborhood(self):
 
-		self.ConfigNeigh = ConfigNeighborhoods(parent_window=self,
+		self.ConfigNeigh = SettingsNeighborhood(parent_window=self,
 											   neighborhood_type='mask_contact',
 											   neighborhood_parameter_name='tolerance contact distance',
 											   )
@@ -1548,8 +1586,8 @@ class NeighPanel(QFrame, Styles):
 
 		test = self.parent_window.locate_selected_position()
 		if test:
-			self.SignalAnnotator2 = SignalAnnotator2(self)
-			self.SignalAnnotator2.show()
+			self.pair_event_annotator = PairEventAnnotator(self)
+			self.pair_event_annotator.show()
 
 
 class PreprocessingPanel(QFrame, Styles):

celldetective/gui/processes/downloader.py

@@ -43,41 +43,44 @@ class DownloadProcess(Process):
 		self.t0 = time.time()
 
 	def download_url_to_file(self, url, dst):
-
-		file_size = None
-		ssl._create_default_https_context = ssl._create_unverified_context
-		u = urlopen(url)
-		meta = u.info()
-		if hasattr(meta, 'getheaders'):
-			content_length = meta.getheaders("Content-Length")
-		else:
-			content_length = meta.get_all("Content-Length")
-		if content_length is not None and len(content_length) > 0:
-			file_size = int(content_length[0])
-		# We deliberately save it in a temp file and move it after
-		dst = os.path.expanduser(dst)
-		dst_dir = os.path.dirname(dst)
-		f = tempfile.NamedTemporaryFile(delete=False, dir=dst_dir)
-
 		try:
-			with tqdm(total=file_size, disable=not self.progress,
-					  unit='B', unit_scale=True, unit_divisor=1024) as pbar:
-				while True:
-					buffer = u.read(8192) #8192
-					if len(buffer) == 0:
-						break
-					f.write(buffer)
-					pbar.update(len(buffer))
-					self.sum_done+=len(buffer) / file_size * 100
-					mean_exec_per_step = (time.time() - self.t0) / (self.sum_done*file_size / 100 + 1)
-					pred_time = (file_size - (self.sum_done*file_size / 100 + 1)) * mean_exec_per_step
-					self.queue.put([self.sum_done, pred_time])
-			f.close()
-			shutil.move(f.name, dst)
-		finally:
-			f.close()
-			if os.path.exists(f.name):
-				os.remove(f.name)
+			file_size = None
+			ssl._create_default_https_context = ssl._create_unverified_context
+			u = urlopen(url)
+			meta = u.info()
+			if hasattr(meta, 'getheaders'):
+				content_length = meta.getheaders("Content-Length")
+			else:
+				content_length = meta.get_all("Content-Length")
+			if content_length is not None and len(content_length) > 0:
+				file_size = int(content_length[0])
+			# We deliberately save it in a temp file and move it after
+			dst = os.path.expanduser(dst)
+			dst_dir = os.path.dirname(dst)
+			f = tempfile.NamedTemporaryFile(delete=False, dir=dst_dir)
+
+			try:
+				with tqdm(total=file_size, disable=not self.progress,
+						  unit='B', unit_scale=True, unit_divisor=1024) as pbar:
+					while True:
+						buffer = u.read(8192) #8192
+						if len(buffer) == 0:
+							break
+						f.write(buffer)
+						pbar.update(len(buffer))
+						self.sum_done+=len(buffer) / file_size * 100
+						mean_exec_per_step = (time.time() - self.t0) / (self.sum_done*file_size / 100 + 1)
+						pred_time = (file_size - (self.sum_done*file_size / 100 + 1)) * mean_exec_per_step
+						self.queue.put([self.sum_done, pred_time])
+				f.close()
+				shutil.move(f.name, dst)
+			finally:
+				f.close()
+				if os.path.exists(f.name):
+					os.remove(f.name)
+		except Exception as e:
+			print("No internet connection: ", e)
+			return None
 
 	def run(self):