celldetective 1.3.7.post2__tar.gz → 1.3.8__tar.gz

{celldetective-1.3.7.post2 → celldetective-1.3.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: celldetective
-Version: 1.3.7.post2
+Version: 1.3.8
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

celldetective-1.3.8/celldetective/_version.py

@@ -0,0 +1 @@
+__version__ = "1.3.8"

{celldetective-1.3.7.post2 → celldetective-1.3.8}/celldetective/gui/btrack_options.py

@@ -379,15 +379,15 @@ class ConfigTracking(QMainWindow, Styles):
 		clean_traj_sublayout.addWidget(self.extrapolate_post_checkbox)
 		clean_traj_sublayout.addWidget(self.extrapolate_pre_checkbox)
 
-		self.interpolate_na_features_checkbox = QCheckBox('Interpolate features of missed detections')
-		self.interpolate_na_features_checkbox.setIcon(icon(MDI6.format_color_fill,color="k"))
+		# self.interpolate_na_features_checkbox = QCheckBox('Interpolate features of missed detections')
+		# self.interpolate_na_features_checkbox.setIcon(icon(MDI6.format_color_fill,color="k"))
 
-		clean_traj_sublayout.addWidget(self.interpolate_na_features_checkbox)
+		# clean_traj_sublayout.addWidget(self.interpolate_na_features_checkbox)
 		clean_traj_sublayout.addStretch()
 
 		self.post_proc_options_to_disable = [self.post_proc_lbl, self.min_tracklength_slider, self.remove_not_in_first_checkbox,
 											self.remove_not_in_last_checkbox, self.interpolate_gaps_checkbox, self.extrapolate_post_checkbox,
-											self.extrapolate_pre_checkbox, self.interpolate_na_features_checkbox]
+											self.extrapolate_pre_checkbox] #, self.interpolate_na_features_checkbox
 
 		layout.addLayout(clean_traj_sublayout)
 
@@ -898,7 +898,7 @@ class ConfigTracking(QMainWindow, Styles):
 									   "interpolate_position_gaps": self.interpolate_gaps_checkbox.isChecked(), 
 									   "extrapolate_tracks_pre": self.extrapolate_pre_checkbox.isChecked(),
 									   "extrapolate_tracks_post": self.extrapolate_post_checkbox.isChecked(),
-									   'interpolate_na': self.interpolate_na_features_checkbox.isChecked()
+									   'interpolate_na': False, #self.interpolate_na_features_checkbox.isChecked()
 									   }
 		else:
 
@@ -1044,7 +1044,7 @@ class ConfigTracking(QMainWindow, Styles):
 					self.uncheck_post_proc()
 					self.ContentsPostProc.hide()
 					for element in [self.remove_not_in_last_checkbox, self.remove_not_in_first_checkbox, self.interpolate_gaps_checkbox, 
-									self.extrapolate_post_checkbox, self.extrapolate_pre_checkbox, self.interpolate_na_features_checkbox]:
+									self.extrapolate_post_checkbox, self.extrapolate_pre_checkbox]: #self.interpolate_na_features_checkbox
 						element.setChecked(False)
 					self.min_tracklength_slider.setValue(0)
 
@@ -1063,8 +1063,8 @@ class ConfigTracking(QMainWindow, Styles):
 						self.extrapolate_pre_checkbox.setChecked(post_processing_options["extrapolate_tracks_pre"])
 					if "extrapolate_tracks_post" in post_processing_options:
 						self.extrapolate_post_checkbox.setChecked(post_processing_options["extrapolate_tracks_post"])
-					if "interpolate_na" in post_processing_options:
-						self.interpolate_na_features_checkbox.setChecked(post_processing_options["interpolate_na"])
+					# if "interpolate_na" in post_processing_options:
+					# 	self.interpolate_na_features_checkbox.setChecked(post_processing_options["interpolate_na"])
 
 	def locate_image(self):
 		

{celldetective-1.3.7.post2 → celldetective-1.3.8}/celldetective/gui/classifier_widget.py

@@ -212,6 +212,8 @@ class ClassifierWidget(QWidget, Styles):
 		self.frame_slider.valueChanged.connect(self.set_frame)
 		self.alpha_slider.valueChanged.connect(self.set_transparency)
 
+		self.setAttribute(Qt.WA_DeleteOnClose)
+
 	def activate_prereq_cb(self):
 		if self.prereq_event_check.isChecked():
 			self.prereq_event_cb.setEnabled(True)
@@ -276,6 +278,12 @@ class ClassifierWidget(QWidget, Styles):
 		self.propscanvas.canvas.draw_idle()
 		self.propscanvas.canvas.setMinimumHeight(self.screen_height//5)
 
+	def closeEvent(self, event):
+		self.ax_props.cla()
+		self.fig_props.clf()
+		plt.close(self.fig_props)
+		super().closeEvent(event) 
+
 	def update_props_scatter(self, feature_changed=True):
 
 		try:

{celldetective-1.3.7.post2 → celldetective-1.3.8}/celldetective/gui/configure_new_exp.py

@@ -429,7 +429,7 @@ class ConfigNewExperiment(QMainWindow, Styles):
 		Write all user input parameters to a configuration file associated to an experiment.
 		"""
 
-		config = ConfigParser()
+		config = ConfigParser(interpolation=None)
 
 		# add a new section and some values
 		config.add_section('MovieSettings')

{celldetective-1.3.7.post2 → celldetective-1.3.8}/celldetective/gui/json_readers.py

@@ -49,7 +49,7 @@ class ConfigEditor(QWidget, Styles):
         file_name = self.config_path
         #self.file_edit.setText(file_name)
 
-        config = configparser.ConfigParser()
+        config = configparser.ConfigParser(interpolation=None)
         config.read(file_name)
 
         # Create a layout for each section of the config file
@@ -93,12 +93,10 @@ class ConfigEditor(QWidget, Styles):
         # Save the configuration to the file
         file_name = self.config_path
             
-        config = configparser.ConfigParser()
+        config = configparser.ConfigParser(interpolation=None)
 
         # Update the values in the config object
 
-
-
         for key, (section, edit_box) in self.sections.items():
             if not config.has_section(section):
                 config.add_section(section)

{celldetective-1.3.7.post2 → celldetective-1.3.8}/celldetective/gui/plot_signals_ui.py

@@ -117,7 +117,10 @@ class ConfigSignalPlot(QWidget, Styles):
 		all_cms = list(colormaps)
 		for cm in all_cms:
 			if hasattr(matplotlib.cm, str(cm).lower()):
-				self.cbs[-1].addColormap(cm.lower())
+				try:
+					self.cbs[-1].addColormap(cm.lower())
+				except:
+					pass
 
 		self.cbs[0].setCurrentIndex(1)
 		self.cbs[0].setCurrentIndex(0)
@@ -138,13 +141,14 @@ class ConfigSignalPlot(QWidget, Styles):
 		self.abs_time_checkbox.stateChanged.connect(self.switch_ref_time_mode)
 
 		select_layout = QHBoxLayout()
+		select_layout.setContentsMargins(20,3,20,3)
 		select_layout.addWidget(QLabel('select cells\nwith query: '), 33)
 		self.query_le = QLineEdit()
 		select_layout.addWidget(self.query_le, 66)
 		main_layout.addLayout(select_layout)
 
 		time_calib_layout = QHBoxLayout()
-		time_calib_layout.setContentsMargins(20,20,20,20)
+		time_calib_layout.setContentsMargins(20,3,20,3)
 		time_calib_layout.addWidget(QLabel('time calibration\n(frame to min)'), 33)
 		self.time_calibration_le = QLineEdit(str(self.FrameToMin).replace('.',','))
 		self.time_calibration_le.setValidator(self.float_validator)
@@ -152,6 +156,14 @@ class ConfigSignalPlot(QWidget, Styles):
 		#time_calib_layout.addWidget(QLabel(' min'))
 		main_layout.addLayout(time_calib_layout)
 
+		pool_layout = QHBoxLayout()
+		pool_layout.setContentsMargins(20,3,20,3)
+		self.pool_option_cb = QComboBox()
+		self.pool_option_cb.addItems(['mean','median'])
+		pool_layout.addWidget(QLabel('pool\nprojection:'), 33)
+		pool_layout.addWidget(self.pool_option_cb, 66)
+		main_layout.addLayout(pool_layout)
+
 		self.submit_btn = QPushButton('Submit')
 		self.submit_btn.setStyleSheet(self.button_style_sheet)
 		self.submit_btn.clicked.connect(self.process_signal)
@@ -271,9 +283,10 @@ class ConfigSignalPlot(QWidget, Styles):
 			self.feature_selected = self.feature_cb.currentText()
 			self.feature_choice_widget.close()
 			self.compute_signal_functions()
-			self.interpret_pos_location()
-			self.plot_window = GenericSignalPlotWidget(parent_window=self, df=self.df, df_pos_info = self.df_pos_info, df_well_info = self.df_well_info, feature_selected=self.feature_selected, title='plot signals')
-			self.plot_window.show()
+			if self.open_widget:
+				self.interpret_pos_location()
+				self.plot_window = GenericSignalPlotWidget(parent_window=self, df=self.df, df_pos_info = self.df_pos_info, df_well_info = self.df_well_info, feature_selected=self.feature_selected, title='plot signals')
+				self.plot_window.show()
 
 	def process_signal(self):
 
@@ -335,7 +348,19 @@ class ConfigSignalPlot(QWidget, Styles):
 
 	def compute_signal_functions(self):
 
-		# REPLACE EVRYTHING WITH MEAN_SIGNAL FUNCTION
+		# Check to move at the beginning
+		self.open_widget = True
+		if len(self.time_columns)==0:
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Warning)
+			msgBox.setText("No synchronizing time is available...")
+			msgBox.setWindowTitle("Warning")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				pass
+			self.open_widget = False
+			return None
 
 		# Per position signal
 		max_time = int(self.df.FRAME.max()) + 1
@@ -346,9 +371,9 @@ class ConfigSignalPlot(QWidget, Styles):
 
 		for block,movie_group in self.df.groupby(['well','position']):
 
-			well_signal_mean, well_std_mean, timeline_all, matrix_all = mean_signal(movie_group, self.feature_selected, class_col, time_col=time_col, class_value=None, return_matrix=True, forced_max_duration=max_time)
-			well_signal_event, well_std_event, timeline_event, matrix_event = mean_signal(movie_group, self.feature_selected, class_col, time_col=time_col, class_value=[0], return_matrix=True, forced_max_duration=max_time)		
-			well_signal_no_event, well_std_no_event, timeline_no_event, matrix_no_event = mean_signal(movie_group, self.feature_selected, class_col, time_col=time_col, class_value=[1], return_matrix=True, forced_max_duration=max_time)
+			well_signal_mean, well_std_mean, timeline_all, matrix_all = mean_signal(movie_group, self.feature_selected, class_col, time_col=time_col, class_value=None, return_matrix=True, forced_max_duration=max_time, projection=self.pool_option_cb.currentText())
+			well_signal_event, well_std_event, timeline_event, matrix_event = mean_signal(movie_group, self.feature_selected, class_col, time_col=time_col, class_value=[0], return_matrix=True, forced_max_duration=max_time, projection=self.pool_option_cb.currentText())		
+			well_signal_no_event, well_std_no_event, timeline_no_event, matrix_no_event = mean_signal(movie_group, self.feature_selected, class_col, time_col=time_col, class_value=[1], return_matrix=True, forced_max_duration=max_time, projection=self.pool_option_cb.currentText())
 			self.mean_plots_timeline = timeline_all
 
 			self.df_pos_info.loc[self.df_pos_info['pos_path'] == block[1], 'signal'] = [
@@ -361,9 +386,9 @@ class ConfigSignalPlot(QWidget, Styles):
 		# Per well
 		for well,well_group in self.df.groupby('well'):
 
-			well_signal_mean, well_std_mean, timeline_all, matrix_all = mean_signal(well_group, self.feature_selected, class_col, time_col=time_col, class_value=None, return_matrix=True, forced_max_duration=max_time)
-			well_signal_event, well_std_event, timeline_event, matrix_event = mean_signal(well_group, self.feature_selected, class_col, time_col=time_col, class_value=[0], return_matrix=True, forced_max_duration=max_time)			
-			well_signal_no_event, well_std_no_event, timeline_no_event, matrix_no_event = mean_signal(well_group, self.feature_selected, class_col, time_col=time_col, class_value=[1], return_matrix=True, forced_max_duration=max_time)
+			well_signal_mean, well_std_mean, timeline_all, matrix_all = mean_signal(well_group, self.feature_selected, class_col, time_col=time_col, class_value=None, return_matrix=True, forced_max_duration=max_time, projection=self.pool_option_cb.currentText())
+			well_signal_event, well_std_event, timeline_event, matrix_event = mean_signal(well_group, self.feature_selected, class_col, time_col=time_col, class_value=[0], return_matrix=True, forced_max_duration=max_time, projection=self.pool_option_cb.currentText())			
+			well_signal_no_event, well_std_no_event, timeline_no_event, matrix_no_event = mean_signal(well_group, self.feature_selected, class_col, time_col=time_col, class_value=[1], return_matrix=True, forced_max_duration=max_time, projection=self.pool_option_cb.currentText())
 			
 			self.df_well_info.loc[self.df_well_info['well_path']==well,'signal'] = [{'mean_all': well_signal_mean, 'std_all': well_std_mean,'matrix_all': matrix_all,'mean_event': well_signal_event, 'std_event': well_std_event,
 																					'matrix_event': matrix_event,'mean_no_event': well_signal_no_event, 'std_no_event': well_std_no_event, 'matrix_no_event': matrix_no_event, 'timeline':  self.mean_plots_timeline}]
@@ -418,23 +443,7 @@ class ConfigSignalPlot(QWidget, Styles):
 					cid+=1
 				except:
 					pass
-		return matrix		
-
-	def col_mean(self, matrix):
-
-		mean_line = np.zeros(matrix.shape[1])
-		mean_line[:] = np.nan
-		std_line = np.copy(mean_line)
-
-		for k in range(matrix.shape[1]):
-			values = matrix[:,k]
-			#values = values[values!=0]
-			if len(values[values==values])>2:
-				mean_line[k] = np.nanmean(values)
-				std_line[k] = np.nanstd(values)
-
-		return mean_line, std_line
-
+		return matrix
 
 	def switch_ref_time_mode(self):
 		if self.abs_time_checkbox.isChecked():

{celldetective-1.3.7.post2 → celldetective-1.3.8}/celldetective/gui/process_block.py

@@ -1362,6 +1362,7 @@ class NeighPanel(QFrame, Styles):
 		self.pair_signal_models_list.addItems(signal_models)
 
 	def open_signal_annotator_configuration_ui(self):
+		self.mode = 'pairs'
 		self.ConfigSignalAnnotator = ConfigSignalAnnotator(self)
 		self.ConfigSignalAnnotator.show()
 

{celldetective-1.3.7.post2 → celldetective-1.3.8}/celldetective/gui/processes/segment_cells.py

@@ -3,15 +3,17 @@ import time
 import datetime
 import os
 import json
+import numpy as np
 from celldetective.io import extract_position_name, locate_segmentation_model, auto_load_number_of_frames, load_frames, _check_label_dims, _load_frames_to_segment
 from celldetective.utils import _rescale_labels, _segment_image_with_stardist_model, _segment_image_with_cellpose_model, _prep_stardist_model, _prep_cellpose_model, _get_normalize_kwargs_from_config, extract_experiment_channels, _estimate_scale_factor, _extract_channel_indices_from_config, ConfigSectionMap, _extract_nbr_channels_from_config, _get_img_num_per_channel
+
 from pathlib import Path, PurePath
 from glob import glob
 from shutil import rmtree
 from tqdm import tqdm
 import numpy as np
 from csbdeep.io import save_tiff_imagej_compatible
-from celldetective.segmentation import segment_frame_from_thresholds
+from celldetective.segmentation import segment_frame_from_thresholds, merge_instance_segmentation
 import gc
 from art import tprint
 
@@ -232,6 +234,7 @@ class SegmentCellThresholdProcess(BaseSegmentProcess):
 		self.equalize = False
 
 		# Model
+
 		self.load_threshold_config()
 		self.extract_threshold_parameters()
 		self.detect_channels()
@@ -244,28 +247,41 @@ class SegmentCellThresholdProcess(BaseSegmentProcess):
 
 	def prepare_equalize(self):
 
-		if self.equalize:
-			f_reference = load_frames(self.img_num_channels[:,self.equalize_time], self.file, scale=None, normalize_input=False)
-			f_reference = f_reference[:,:,self.threshold_instructions['target_channel']]
-		else:
-			f_reference = None
+		for i in range(len(self.instructions)):
 
-		self.threshold_instructions.update({'equalize_reference': f_reference})
+			if self.equalize[i]:
+				f_reference = load_frames(self.img_num_channels[:,self.equalize_time[i]], self.file, scale=None, normalize_input=False)
+				f_reference = f_reference[:,:,self.instructions[i]['target_channel']]
+			else:
+				f_reference = None
+
+			self.instructions[i].update({'equalize_reference': f_reference})
 
 	def load_threshold_config(self):
-		
-		if os.path.exists(self.threshold_instructions):
-			with open(self.threshold_instructions, 'r') as f:
-				self.threshold_instructions = json.load(f)
-		else:
-			print('The configuration path is not valid. Abort.')
-			self.abort_process()
+
+		self.instructions = []
+		for inst in self.threshold_instructions:
+			if os.path.exists(inst):
+				with open(inst, 'r') as f:
+					self.instructions.append(json.load(f))
+			else:
+				print('The configuration path is not valid. Abort.')
+				self.abort_process()
 
 	def extract_threshold_parameters(self):
 		
-		self.required_channels = [self.threshold_instructions['target_channel']]
-		if 'equalize_reference' in self.threshold_instructions:
-			self.equalize, self.equalize_time = self.threshold_instructions['equalize_reference']		
+		self.required_channels = []
+		self.equalize = []
+		self.equalize_time = []
+
+		for i in range(len(self.instructions)):
+			ch = [self.instructions[i]['target_channel']]
+			self.required_channels.append(ch)
+
+			if 'equalize_reference' in self.instructions[i]:
+				equalize, equalize_time = self.instructions[i]['equalize_reference']	
+				self.equalize.append(equalize)
+				self.equalize_time.append(equalize_time)
 
 	def write_log(self):
 
@@ -276,12 +292,14 @@ class SegmentCellThresholdProcess(BaseSegmentProcess):
 
 	def detect_channels(self):
 
-		self.channel_indices = _extract_channel_indices_from_config(self.config, self.required_channels)
-		print(f'Required channels: {self.required_channels} located at channel indices {self.channel_indices}.')
+		for i in range(len(self.instructions)):
+			
+			self.channel_indices = _extract_channel_indices_from_config(self.config, self.required_channels[i])
+			print(f'Required channels: {self.required_channels[i]} located at channel indices {self.channel_indices}.')
+			self.instructions[i].update({'target_channel': self.channel_indices[0]})
+			self.instructions[i].update({'channel_names': self.channel_names})
 		
 		self.img_num_channels = _get_img_num_per_channel(np.arange(self.nbr_channels), self.len_movie, self.nbr_channels)
-		self.threshold_instructions.update({'target_channel': self.channel_indices[0]})
-		self.threshold_instructions.update({'channel_names': self.channel_names})
 
 	def parallel_job(self, indices):
 
@@ -290,8 +308,16 @@ class SegmentCellThresholdProcess(BaseSegmentProcess):
 			for t in tqdm(indices,desc="frame"): #for t in tqdm(range(self.len_movie),desc="frame"):
 				
 				# Load channels at time t
-				f = load_frames(self.img_num_channels[:,t], self.file, scale=None, normalize_input=False)
-				mask = segment_frame_from_thresholds(f, **self.threshold_instructions)
+				masks = []
+				for i in range(len(self.instructions)):
+					f = load_frames(self.img_num_channels[:,t], self.file, scale=None, normalize_input=False)
+					mask = segment_frame_from_thresholds(f, **self.instructions[i])
+					#print(f'Frame {t}; segment with {self.instructions[i]=}...')
+					masks.append(mask)
+
+				if len(self.instructions)>1:
+					mask = merge_instance_segmentation(masks, mode='OR')
+
 				save_tiff_imagej_compatible(os.sep.join([self.pos, self.label_folder, f"{str(t).zfill(4)}.tif"]), mask.astype(np.uint16), axes='YX')
 
 				del f;
@@ -308,6 +334,7 @@ class SegmentCellThresholdProcess(BaseSegmentProcess):
 			print(e)
 
 		return
+			
 
 	def run(self):
 

{celldetective-1.3.7.post2 → celldetective-1.3.8}/celldetective/gui/seg_model_loader.py

@@ -1,4 +1,4 @@
-from PyQt5.QtWidgets import QWidget, QGridLayout, QVBoxLayout, QLabel, QLineEdit, QHBoxLayout, QRadioButton, QFileDialog, QPushButton, QMessageBox
+from PyQt5.QtWidgets import QWidget, QGridLayout, QComboBox, QVBoxLayout, QLabel, QLineEdit, QHBoxLayout, QRadioButton, QFileDialog, QPushButton, QMessageBox
 from PyQt5.QtCore import Qt, QSize
 from celldetective.gui.gui_utils import center_window
 from celldetective.gui.layouts import ChannelNormGenerator
@@ -79,13 +79,24 @@ class SegmentationModelLoader(QWidget, Styles):
 		self.layout.addWidget(self.open_dialog_button, 9, 0, 1, 1)
 		self.layout.addWidget(self.file_label, 9, 1, 1, 1)
 
+
+		self.merge_lbl = QLabel('Merging option: ')
+		self.merge_cb = QComboBox()
+		self.merge_cb.addItems(['OR'])
+		merge_hbox = QHBoxLayout()
+		merge_hbox.addWidget(self.merge_lbl, 33)
+		merge_hbox.addWidget(self.merge_cb, 66)
+		self.layout.addLayout(merge_hbox, 10, 0, 1, 2)
+		self.merge_lbl.hide()
+		self.merge_cb.hide()
+
 		self.upload_button = QPushButton("Upload")
 		self.upload_button.clicked.connect(self.upload_model)
 		self.upload_button.setIcon(icon(MDI6.upload,color="white"))
 		self.upload_button.setIconSize(QSize(25, 25))
 		self.upload_button.setStyleSheet(self.button_style_sheet)
 		self.upload_button.setEnabled(False)
-		self.layout.addWidget(self.upload_button, 10, 0, 1, 1)
+		self.layout.addWidget(self.upload_button, 11, 0, 1, 1)
 		
 		self.base_block_options = [self.calibration_label, self.spatial_calib_le,*self.channel_layout.channel_cbs,*self.channel_layout.channel_labels,*self.channel_layout.normalization_mode_btns, *self.channel_layout.normalization_clip_btns, *self.channel_layout.normalization_min_value_lbl,
 								   *self.channel_layout.normalization_min_value_le, *self.channel_layout.normalization_max_value_lbl,*self.channel_layout.normalization_max_value_le,
@@ -207,41 +218,73 @@ class SegmentationModelLoader(QWidget, Styles):
 			self.file_dialog.setFileMode(QFileDialog.ExistingFile)
 
 		# If accepted check validity of data
-		if self.file_dialog.exec_() == QFileDialog.Accepted:
-			self.filename = self.file_dialog.selectedFiles()[0]
-			if self.seg_mode=="stardist":
-				subfiles = glob(self.filename+"/*")
-				subfiles = [s.replace('\\','/') for s in subfiles]
-				if self.filename+"/thresholds.json" in subfiles:
+		if self.seg_mode!='threshold':
+			if self.file_dialog.exec_() == QFileDialog.Accepted:
+				self.filename = self.file_dialog.selectedFiles()[0]
+				if self.seg_mode=="stardist":
+					subfiles = glob(self.filename+"/*")
+					subfiles = [s.replace('\\','/') for s in subfiles]
+					if self.filename+"/thresholds.json" in subfiles:
+						self.file_label.setText(self.filename.split("/")[-1])
+						self.modelname = self.filename.split("/")[-1]
+						self.destination = os.path.split(os.path.dirname(os.path.realpath(__file__)))[0]+f"/models/{self.target_folder}/"+self.modelname
+						self.folder_dest = self.destination
+					else:
+						msgBox = QMessageBox()
+						msgBox.setIcon(QMessageBox.Warning)
+						msgBox.setText("StarDist model not recognized... Please ensure that it contains a thresholds.json file or that it is a valid StarDist model...")
+						msgBox.setWindowTitle("Warning")
+						msgBox.setStandardButtons(QMessageBox.Ok)
+						returnValue = msgBox.exec()
+						if returnValue == QMessageBox.Ok:
+							return None					
+				
+				if self.seg_mode=="cellpose":
 					self.file_label.setText(self.filename.split("/")[-1])
 					self.modelname = self.filename.split("/")[-1]
-					self.destination = os.path.split(os.path.dirname(os.path.realpath(__file__)))[0]+f"/models/{self.target_folder}/"+self.modelname
-					self.folder_dest = self.destination
+					print(f"Transferring Cellpose model {self.filename}...")
+					self.folder_dest = os.path.split(os.path.dirname(os.path.realpath(__file__)))[0]+f"/models/{self.target_folder}/"+self.modelname
+					self.destination = self.folder_dest+f"/{self.modelname}"
+
+		else:
+			self.filename, _ = QFileDialog.getOpenFileNames(
+														None,
+														"Load threshold configuration(s)...",
+														"",
+														"Json Configs (*.json)",
+														)
+			if self.filename:
+				n_files = len(self.filename)
+				print(f'You loaded {n_files} threshold configuration files...')
+				for i,filename in enumerate(self.filename):
+					print(f"Config {i}: ",filename,"...")
+
+				if n_files==1:
+					self.merge_cb.hide()
+					self.merge_lbl.hide()
+					self.file_label.setText(self.filename[0].split("/")[-1])
 				else:
 					msgBox = QMessageBox()
 					msgBox.setIcon(QMessageBox.Warning)
-					msgBox.setText("StarDist model not recognized... Please ensure that it contains a thresholds.json file or that it is a valid StarDist model...")
+					msgBox.setText("You selected more than one pipeline. Please set a merging procedure for the resulting masks...")
 					msgBox.setWindowTitle("Warning")
 					msgBox.setStandardButtons(QMessageBox.Ok)
 					returnValue = msgBox.exec()
 					if returnValue == QMessageBox.Ok:
-						return None					
-			
-			if self.seg_mode=="cellpose":
-				self.file_label.setText(self.filename.split("/")[-1])
-				self.modelname = self.filename.split("/")[-1]
-				print(f"Transferring Cellpose model {self.filename}...")
-				self.folder_dest = os.path.split(os.path.dirname(os.path.realpath(__file__)))[0]+f"/models/{self.target_folder}/"+self.modelname
-				self.destination = self.folder_dest+f"/{self.modelname}"
+						pass
 
-			if self.seg_mode=="threshold":
-				self.file_label.setText(self.filename.split("/")[-1])
+					self.merge_cb.show()
+					self.merge_lbl.show()
+					self.file_label.setText(f"{n_files} configs loaded...")
 
 	def show_seg_options(self):
 
 		"""
 		Show the relevant widgets, mask the others.
 		"""
+
+		self.filename = None
+		self.file_label.setText('No file chosen')
 		self.base_block_options = [self.calibration_label, self.spatial_calib_le,*self.channel_layout.channel_cbs,*self.channel_layout.channel_labels,*self.channel_layout.normalization_mode_btns, *self.channel_layout.normalization_clip_btns, *self.channel_layout.normalization_min_value_lbl,
 								   *self.channel_layout.normalization_min_value_le, *self.channel_layout.normalization_max_value_lbl,*self.channel_layout.normalization_max_value_le,
 								   self.channel_layout.add_col_btn]
@@ -250,7 +293,7 @@ class SegmentationModelLoader(QWidget, Styles):
 			self.spatial_calib_le.setToolTip('Cellpose rescales the images such that the cells are 30.0 pixels. You can compute the scale from the training data as\n(pixel calibration [µm] in training images)*(cell diameter [px] in training images)/(30 [px]).\nIf you pass images with a different calibration to the model, they will be rescaled automatically.\nThe rescaling is ignored if you pass a diameter different from 30 px below.')
 			self.channel_layout.channel_labels[0].setText('cyto: ')
 			self.channel_layout.channel_labels[1].setText('nuclei: ')
-			for c in [self.threshold_config_button]:
+			for c in [self.threshold_config_button, self.merge_lbl, self.merge_cb]:
 				c.hide()
 			for c in self.cellpose_options+self.base_block_options:
 				c.show()
@@ -261,7 +304,7 @@ class SegmentationModelLoader(QWidget, Styles):
 			self.channel_layout.channel_labels[1].setText('channel 2: ')
 			for c in self.base_block_options:
 				c.show()
-			for c in self.cellpose_options+[self.threshold_config_button]:
+			for c in self.cellpose_options+[self.threshold_config_button, self.merge_lbl, self.merge_cb]:
 				c.hide()
 			self.unlock_upload()
 		else:
@@ -346,7 +389,10 @@ class SegmentationModelLoader(QWidget, Styles):
 			self.parent_window.init_seg_model_list()
 			self.close()
 		else:
-			if self.mode=="targets":	
+			if not isinstance(self.filename, list):
+				if not self.filename is None:
+					self.filename = [self.filename]
+			if self.mode=="targets":
 				self.parent_window.threshold_config_targets = self.filename
 				self.parent_window.seg_model_list.setCurrentText('Threshold')
 				print('Path to the traditional segmentation pipeline successfully set in celldetective...')
@@ -355,7 +401,7 @@ class SegmentationModelLoader(QWidget, Styles):
 				self.parent_window.threshold_config_effectors = self.filename
 				self.parent_window.seg_model_list.setCurrentText('Threshold')
 				print('Path to the traditional segmentation pipeline successfully set in celldetective...')
-				self.close()	
+				self.close()
 
 	def generate_input_config(self):
 

{celldetective-1.3.7.post2 → celldetective-1.3.8}/celldetective/gui/signal_annotator2.py

@@ -1577,13 +1577,16 @@ class SignalAnnotator2(QMainWindow,Styles):
 					self.cell_ax.set_ylim(self.value_magnitude, self.non_log_ymax)					
 
 		if self.reference_track_of_interest is not None and self.neighbor_track_of_interest is not None:
-			t0 = self.df_relative.loc[(self.df_relative['REFERENCE_ID'] == self.reference_track_of_interest)&(self.df_relative['NEIGHBOR_ID'] == self.neighbor_track_of_interest)&(self.df_relative['reference_population'] == self.reference_population)&(self.df_relative['neighbor_population'] == self.neighbor_population), self.pair_time_name].dropna().to_numpy()
-			if t0!=[]:
-				t0=t0[0]
-				ymin,ymax = self.cell_ax.get_ylim()
-				self.line_dt.set_xdata([t0, t0])
-				self.line_dt.set_ydata([ymin,ymax])
-
+			t0 = self.df_relative.loc[(self.df_relative['REFERENCE_ID'] == self.reference_track_of_interest)&(self.df_relative['NEIGHBOR_ID'] == self.neighbor_track_of_interest)&(self.df_relative['reference_population'] == self.reference_population)&(self.df_relative['neighbor_population'] == self.neighbor_population), self.pair_time_name].dropna().values
+			try:
+				if t0!=[]:
+					t0=t0[0]
+					ymin,ymax = self.cell_ax.get_ylim()
+					self.line_dt.set_xdata([t0, t0])
+					self.line_dt.set_ydata([ymin,ymax])
+			except Exception as e:
+				print(e)
+			
 		self.cell_ax.legend()
 		self.cell_fcanvas.canvas.draw()
 

{celldetective-1.3.7.post2 → celldetective-1.3.8}/celldetective/gui/signal_annotator_options.py

@@ -34,7 +34,7 @@ class ConfigSignalAnnotator(QMainWindow, Styles):
 			self.instructions_path = self.parent_window.exp_dir + "configs/signal_annotator_config_targets.json"
 		elif self.mode=="effectors":
 			self.instructions_path = self.parent_window.exp_dir + "configs/signal_annotator_config_effectors.json"
-		elif self.mode == "neighborhood":
+		elif self.mode == "pairs":
 			self.instructions_path = self.parent_window.exp_dir + "configs/signal_annotator_config_neighborhood.json"
 
 		exp_config = self.exp_dir +"config.ini"