celldetective 1.3.0.post1__tar.gz → 1.3.1__tar.gz

{celldetective-1.3.0.post1 → celldetective-1.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.3.0.post1
+Version: 1.3.1
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -69,7 +69,7 @@ analysis on multimodal time lapse microscopy images.
 
 ## Overview
 
-![Pipeline](https://github.com/remyeltorro/celldetective/raw/main/docs/source/_static/celldetective-blocks.png)
+![Pipeline](https://github.com/celldetective/celldetective/raw/main/docs/source/_static/celldetective-blocks.png)
 
 
 Celldetective was designed to analyze time-lapse microscopy images in difficult situations: mixed cell populations that are only separable through multimodal information. This software provides a toolkit for the analysis of cell population interactions. 
@@ -88,7 +88,7 @@ Instead of reinventing the wheel and out of respect for the amazing work done by
 
 **Target Audience**: The software is targeted to scientists who are interested in quantifying dynamically (or not) cell populations from microscopy images. Experimental scientists who produce such images can also analyze their data, thanks to the graphical interface, that completely removes the need for coding, and the many helper functions that guide the user in the analysis steps. Finally, the modular structure of Celldetective welcomes users with a partial need. 
 
-![Signal analysis](https://github.com/remyeltorro/celldetective/raw/main/docs/source/_static/signal-annotator.gif)
+![Signal analysis](https://github.com/celldetective/celldetective/raw/main/docs/source/_static/signal-annotator.gif)
 
 
 # System requirements

{celldetective-1.3.0.post1 → celldetective-1.3.1}/README.md

@@ -25,7 +25,7 @@ analysis on multimodal time lapse microscopy images.
 
 ## Overview
 
-![Pipeline](https://github.com/remyeltorro/celldetective/raw/main/docs/source/_static/celldetective-blocks.png)
+![Pipeline](https://github.com/celldetective/celldetective/raw/main/docs/source/_static/celldetective-blocks.png)
 
 
 Celldetective was designed to analyze time-lapse microscopy images in difficult situations: mixed cell populations that are only separable through multimodal information. This software provides a toolkit for the analysis of cell population interactions. 
@@ -44,7 +44,7 @@ Instead of reinventing the wheel and out of respect for the amazing work done by
 
 **Target Audience**: The software is targeted to scientists who are interested in quantifying dynamically (or not) cell populations from microscopy images. Experimental scientists who produce such images can also analyze their data, thanks to the graphical interface, that completely removes the need for coding, and the many helper functions that guide the user in the analysis steps. Finally, the modular structure of Celldetective welcomes users with a partial need. 
 
-![Signal analysis](https://github.com/remyeltorro/celldetective/raw/main/docs/source/_static/signal-annotator.gif)
+![Signal analysis](https://github.com/celldetective/celldetective/raw/main/docs/source/_static/signal-annotator.gif)
 
 
 # System requirements

celldetective-1.3.1/celldetective/_version.py

@@ -0,0 +1 @@
+__version__ = "1.3.1"

{celldetective-1.3.0.post1 → celldetective-1.3.1}/celldetective/events.py

@@ -1,7 +1,7 @@
 import numpy as np
 from lifelines import KaplanMeierFitter
 
-def switch_to_events(classes, event_times, max_times, origin_times=None, left_censored=True, FrameToMin=None):
+def switch_to_events(classes, event_times, max_times, origin_times=None, left_censored=True, FrameToMin=None, cut_observation_time=None):
 	
 
 	"""
@@ -29,6 +29,8 @@ def switch_to_events(classes, event_times, max_times, origin_times=None, left_ce
 	FrameToMin : float, optional
 		A conversion factor to transform survival times from frames (or any other unit) to minutes. If None, no conversion 
 		is applied (default is None).
+	cut_observation_time : float or None, optional
+		A cutoff time to artificially reduce the observation window and exclude late events. If None, uses all available data (default is None).
 
 	Returns
 	-------
@@ -70,13 +72,36 @@ def switch_to_events(classes, event_times, max_times, origin_times=None, left_ce
 			if ot>=0. and ot==ot:
 				# origin time is larger than zero, no censorship
 				if c==0 and t>0:
+					
 					delta_t = t - ot
-					if delta_t>0:
-						events.append(1)
-						survival_times.append(delta_t)
-					else:
-						# negative delta t, invalid cell
-						pass
+
+					# Special case: observation cut at arbitrary time
+					if cut_observation_time is not None:
+						if t>=cut_observation_time:
+							# event time larger than cut, becomes no event
+							delta_t = cut_observation_time - ot # new time
+							if delta_t > 0:
+								events.append(0)
+								survival_times.append(delta_t)
+							else:
+								# negative delta t, invalid cell
+								pass
+						else:
+							# still event
+							if delta_t > 0:
+								events.append(1)
+								survival_times.append(delta_t)	
+							else:
+								# negative delta t, invalid cell
+								pass				
+					else: 
+						# standard mode
+						if delta_t>0:
+							events.append(1)
+							survival_times.append(delta_t)
+						else:
+							# negative delta t, invalid cell
+							pass
 				elif c==1:
 					delta_t = mt - ot
 					if delta_t>0:
@@ -93,10 +118,20 @@ def switch_to_events(classes, event_times, max_times, origin_times=None, left_ce
 
 		else:
 			if c==0 and t>0:
-				events.append(1)
-				survival_times.append(t - ot)
+				if cut_observation_time is not None:
+					if t>cut_observation_time:
+						events.append(0)
+						survival_times.append(cut_observation_time - ot)
+					else:
+						events.append(1)
+						survival_times.append(t - ot)						
+				else:				
+					events.append(1)
+					survival_times.append(t - ot)
 			elif c==1:
 				events.append(0)
+				if cut_observation_time is not None:
+					mt = cut_observation_time
 				survival_times.append(mt - ot)
 			else:
 				pass
@@ -106,7 +141,47 @@ def switch_to_events(classes, event_times, max_times, origin_times=None, left_ce
 		survival_times = [s*FrameToMin for s in survival_times]
 	return events, survival_times
 
-def compute_survival(df, class_of_interest, t_event, t_reference=None, FrameToMin=1):
+def compute_survival(df, class_of_interest, t_event, t_reference=None, FrameToMin=1, cut_observation_time=None):
+
+	"""
+	Computes survival analysis for a specific class of interest within a dataset, returning a fitted Kaplan-Meier 
+	survival curve based on event and reference times.
+
+	Parameters
+	----------
+	df : pandas.DataFrame
+		The dataset containing tracking data, event times, and other relevant columns for survival analysis.
+	class_of_interest : str
+		The name of the column that specifies the class for which survival analysis is to be computed.
+	t_event : str
+		The column indicating the time of the event of interest (e.g., cell death or migration stop).
+	t_reference : str or None, optional
+		The reference column indicating the start or origin time for each track (e.g., detection time). If None, 
+		events are not left-censored (default is None).
+	FrameToMin : float, optional
+		Conversion factor to scale the frame time to minutes (default is 1, assuming no scaling).
+	cut_observation_time : float or None, optional
+		A cutoff time to artificially reduce the observation window and exclude late events. If None, uses all available data (default is None).
+	Returns
+	-------
+	ks : lifelines.KaplanMeierFitter or None
+		A fitted Kaplan-Meier estimator object. If there are no events, returns None.
+
+	Notes
+	-----
+	- The function groups the data by 'position' and 'TRACK_ID', extracting the minimum `class_of_interest` and `t_event` 
+	  values for each track.
+	- If `t_reference` is provided, the analysis assumes left-censoring and will use `t_reference` as the origin time for 
+	  each track.
+	- The function calls `switch_to_events` to determine the event occurrences and their associated survival times.
+	- A Kaplan-Meier estimator (`KaplanMeierFitter`) is fitted to the data to compute the survival curve.
+
+	Example
+	-------
+	>>> ks = compute_survival(df, class_of_interest="class_custom", t_event="time_custom", t_reference="t_firstdetection")
+	>>> ks.plot_survival_function()
+	
+	"""
 
 	cols = list(df.columns)
 	assert class_of_interest in cols,"The requested class cannot be found in the dataframe..."
@@ -127,7 +202,7 @@ def compute_survival(df, class_of_interest, t_event, t_reference=None, FrameToMi
 		assert t_reference in cols,"The reference time cannot be found in the dataframe..."
 		first_detections = df.groupby(['position','TRACK_ID'])[t_reference].max().values
 	
-	events, survival_times = switch_to_events(classes, event_times, max_times, origin_times=first_detections, left_censored=left_censored, FrameToMin=FrameToMin)
+	events, survival_times = switch_to_events(classes, event_times, max_times, origin_times=first_detections, left_censored=left_censored, FrameToMin=FrameToMin, cut_observation_time=cut_observation_time)
 	ks = KaplanMeierFitter()
 	if len(events)>0:
 		ks.fit(survival_times, event_observed=events)

{celldetective-1.3.0.post1 → celldetective-1.3.1}/celldetective/extra_properties.py

@@ -57,7 +57,11 @@ def intensity_median(regionmask, intensity_image):
 	return np.nanmedian(intensity_image[regionmask])
 
 def intensity_nanmean(regionmask, intensity_image):
-	return np.nanmean(intensity_image[regionmask])
+	
+	if np.all(intensity_image==0):
+		return np.nan
+	else:
+		return np.nanmean(intensity_image[regionmask])
 
 def intensity_centre_of_mass_displacement(regionmask, intensity_image):
 

{celldetective-1.3.0.post1 → celldetective-1.3.1}/celldetective/gui/InitWindow.py

@@ -1,5 +1,5 @@
 from PyQt5.QtWidgets import QApplication, QMainWindow
-from celldetective.utils import get_software_location
+from celldetective.utils import get_software_location, download_zenodo_file
 import os
 from PyQt5.QtWidgets import QFileDialog, QWidget, QVBoxLayout, QCheckBox, QHBoxLayout, QLabel, QLineEdit, QPushButton, QMessageBox, QMenu, QAction
 from PyQt5.QtCore import Qt, QUrl
@@ -108,6 +108,10 @@ class AppInitWindow(QMainWindow):
 			for i in range(len(self.recentFileActs)):
 				self.OpenRecentAction.addAction(self.recentFileActs[i])
 
+		fileMenu.addMenu(self.openDemo)
+		self.openDemo.addAction(self.openSpreadingAssayDemo)
+		self.openDemo.addAction(self.openCytotoxicityAssayDemo)
+
 		fileMenu.addAction(self.openModels)
 		fileMenu.addSeparator()
 		fileMenu.addAction(self.exitAction)
@@ -124,7 +128,7 @@ class AppInitWindow(QMainWindow):
 		helpMenu = QMenu("Help", self)
 		helpMenu.clear()
 		helpMenu.addAction(self.DocumentationAction)
-		helpMenu.addAction(self.SoftwareAction)
+		#helpMenu.addAction(self.SoftwareAction)
 		helpMenu.addSeparator()
 		helpMenu.addAction(self.AboutAction)
 		menuBar.addMenu(helpMenu)
@@ -137,13 +141,17 @@ class AppInitWindow(QMainWindow):
 		#self.newAction = QAction(self)
 		#self.newAction.setText("&New")
 		# Creating actions using the second constructor
-		self.openAction = QAction('Open...', self)
+		self.openAction = QAction('Open Project', self)
 		self.openAction.setShortcut("Ctrl+O")
 		self.openAction.setShortcutVisibleInContextMenu(True)
 
-		self.MemoryAndThreadsAction = QAction('Memory & Threads...')
+		self.openDemo = QMenu('Open Demo')
+		self.openSpreadingAssayDemo = QAction('Spreading Assay Demo', self)
+		self.openCytotoxicityAssayDemo = QAction('Cytotoxicity Assay Demo', self)
+
+		self.MemoryAndThreadsAction = QAction('Threads')
 
-		self.CorrectAnnotationAction = QAction('Correct a segmentation annotation...')
+		self.CorrectAnnotationAction = QAction('Correct a segmentation annotation')
 
 		self.newExpAction = QAction('New', self)
 		self.newExpAction.setShortcut("Ctrl+N")
@@ -154,14 +162,14 @@ class AppInitWindow(QMainWindow):
 		self.openModels.setShortcut("Ctrl+L")
 		self.openModels.setShortcutVisibleInContextMenu(True)
 
-		self.OpenRecentAction = QMenu('Open Recent')
+		self.OpenRecentAction = QMenu('Open Recent Project')
 		self.reload_previous_experiments()
 
 		self.DocumentationAction = QAction("Documentation", self)
 		self.DocumentationAction.setShortcut("Ctrl+D")
 		self.DocumentationAction.setShortcutVisibleInContextMenu(True)
 
-		self.SoftwareAction = QAction("Software", self) #1st arg icon(MDI6.information)
+		#self.SoftwareAction = QAction("Software", self) #1st arg icon(MDI6.information)
 		self.AboutAction = QAction("About celldetective", self)
 
 		#self.DocumentationAction.triggered.connect(self.load_previous_config)
@@ -172,9 +180,27 @@ class AppInitWindow(QMainWindow):
 		self.AboutAction.triggered.connect(self.open_about_window)
 		self.MemoryAndThreadsAction.triggered.connect(self.set_memory_and_threads)
 		self.CorrectAnnotationAction.triggered.connect(self.correct_seg_annotation)
-
 		self.DocumentationAction.triggered.connect(self.open_documentation)
 
+		self.openSpreadingAssayDemo.triggered.connect(self.download_spreading_assay_demo)
+		self.openCytotoxicityAssayDemo.triggered.connect(self.download_cytotoxicity_assay_demo)
+
+	def download_spreading_assay_demo(self):
+		
+		self.target_dir = str(QFileDialog.getExistingDirectory(self, 'Select Folder for Download'))
+		if not os.path.exists(os.sep.join([self.target_dir,'demo_ricm'])):
+			download_zenodo_file('demo_ricm', self.target_dir)
+		self.experiment_path_selection.setText(os.sep.join([self.target_dir, 'demo_ricm']))
+		self.validate_button.click()
+
+	def download_cytotoxicity_assay_demo(self):
+		
+		self.target_dir = str(QFileDialog.getExistingDirectory(self, 'Select Folder for Download'))
+		if not os.path.exists(os.sep.join([self.target_dir,'demo_adcc'])):
+			download_zenodo_file('demo_adcc', self.target_dir)
+		self.experiment_path_selection.setText(os.sep.join([self.target_dir, 'demo_adcc']))
+		self.validate_button.click()
+
 	def reload_previous_gpu_threads(self):
 
 		self.recentFileActs = []
@@ -256,7 +282,7 @@ class AppInitWindow(QMainWindow):
 
 
 	def open_experiment(self):
-		print('ok')
+		
 		self.browse_experiment_folder()
 		if self.experiment_path_selection.text()!='':
 			self.open_directory()

{celldetective-1.3.0.post1 → celldetective-1.3.1}/celldetective/gui/classifier_widget.py

@@ -120,9 +120,11 @@ class ClassifierWidget(QWidget, Styles):
 		self.property_query_le = QLineEdit()
 		self.property_query_le.setPlaceholderText('classify points using a query such as: area > 100 or eccentricity > 0.95')
 		self.property_query_le.setToolTip('Classify points using a query on measurements.\nYou can use "and" and "or" conditions to combine\nmeasurements (e.g. "area > 100 or eccentricity > 0.95").')
+		self.property_query_le.textChanged.connect(self.activate_submit_btn)
 		hbox_classify.addWidget(self.property_query_le, 70)
 		self.submit_query_btn = QPushButton('Submit...')
 		self.submit_query_btn.clicked.connect(self.apply_property_query)
+		self.submit_query_btn.setEnabled(False)
 		hbox_classify.addWidget(self.submit_query_btn, 20)
 		layout.addLayout(hbox_classify)
 
@@ -182,15 +184,24 @@ class ClassifierWidget(QWidget, Styles):
 
 		layout.addWidget(QLabel())
 
-
 		self.submit_btn = QPushButton('apply')
 		self.submit_btn.setStyleSheet(self.button_style_sheet)
 		self.submit_btn.clicked.connect(self.submit_classification)
+		self.submit_btn.setEnabled(False)
 		layout.addWidget(self.submit_btn, 30)
 
 		self.frame_slider.valueChanged.connect(self.set_frame)
 		self.alpha_slider.valueChanged.connect(self.set_transparency)
 
+	def activate_submit_btn(self):
+
+		if self.property_query_le.text()=='':
+			self.submit_query_btn.setEnabled(False)
+			self.submit_btn.setEnabled(False)
+		else:
+			self.submit_query_btn.setEnabled(True)
+			self.submit_btn.setEnabled(True)
+
 	def activate_r2(self):
 		if self.irreversible_event_btn.isChecked() and self.time_corr.isChecked():
 			for wg in [self.r2_slider, self.r2_label]:
@@ -250,32 +261,32 @@ class ClassifierWidget(QWidget, Styles):
 				self.scat_props.set_offsets(self.df.loc[self.df['FRAME']==self.currentFrame,[self.features_cb[1].currentText(),self.features_cb[0].currentText()]].to_numpy())
 				colors = [color_from_status(c) for c in self.df.loc[self.df['FRAME']==self.currentFrame,class_name].to_numpy()]
 				self.scat_props.set_facecolor(colors)
-				self.scat_props.set_alpha(self.currentAlpha)
-				self.ax_props.set_xlabel(self.features_cb[1].currentText())
-				self.ax_props.set_ylabel(self.features_cb[0].currentText())
 			else:
 				self.scat_props.set_offsets(self.df[[self.features_cb[1].currentText(),self.features_cb[0].currentText()]].to_numpy())
 				colors = [color_from_status(c) for c in self.df[class_name].to_numpy()]
 				self.scat_props.set_facecolor(colors)
-				self.scat_props.set_alpha(self.currentAlpha)
+			
+			self.scat_props.set_alpha(self.currentAlpha)
+
+			if feature_changed:
+	
 				self.ax_props.set_xlabel(self.features_cb[1].currentText())
 				self.ax_props.set_ylabel(self.features_cb[0].currentText())
 
-
-			feat_x = self.features_cb[1].currentText()
-			feat_y = self.features_cb[0].currentText()
-			min_x = self.df.dropna(subset=feat_x)[feat_x].min()
-			max_x = self.df.dropna(subset=feat_x)[feat_x].max()
-			min_y = self.df.dropna(subset=feat_y)[feat_y].min()
-			max_y = self.df.dropna(subset=feat_y)[feat_y].max()
-
-			if min_x==min_x and max_x==max_x:
-				self.ax_props.set_xlim(min_x, max_x)
-			if min_y==min_y and max_y==max_y:
-				self.ax_props.set_ylim(min_y, max_y)
+				feat_x = self.features_cb[1].currentText()
+				feat_y = self.features_cb[0].currentText()
+				min_x = self.df.dropna(subset=feat_x)[feat_x].min()
+				max_x = self.df.dropna(subset=feat_x)[feat_x].max()
+				min_y = self.df.dropna(subset=feat_y)[feat_y].min()
+				max_y = self.df.dropna(subset=feat_y)[feat_y].max()
+
+				if min_x==min_x and max_x==max_x:
+					self.ax_props.set_xlim(min_x, max_x)
+				if min_y==min_y and max_y==max_y:
+					self.ax_props.set_ylim(min_y, max_y)
 			
-			if feature_changed:
 				self.propscanvas.canvas.toolbar.update()
+
 			self.propscanvas.canvas.draw_idle()
 		
 		except Exception as e:
@@ -284,7 +295,20 @@ class ClassifierWidget(QWidget, Styles):
 	def apply_property_query(self):
 		
 		query = self.property_query_le.text()
-		self.df = classify_cells_from_query(self.df, self.name_le.text(), query)
+		
+		try:
+			self.df = classify_cells_from_query(self.df, self.name_le.text(), query)
+		except Exception as e:
+			msgBox = QMessageBox()
+			msgBox.setIcon(QMessageBox.Warning)
+			msgBox.setText(f"The query could not be understood. No filtering was applied. {e}")
+			msgBox.setWindowTitle("Warning")
+			msgBox.setStandardButtons(QMessageBox.Ok)
+			returnValue = msgBox.exec()
+			if returnValue == QMessageBox.Ok:
+				self.auto_close = False
+				return None
+
 		self.class_name = "status_"+self.name_le.text()
 		if self.df is None:
 			msgBox = QMessageBox()
@@ -294,8 +318,10 @@ class ClassifierWidget(QWidget, Styles):
 			msgBox.setStandardButtons(QMessageBox.Ok)
 			returnValue = msgBox.exec()
 			if returnValue == QMessageBox.Ok:
+				self.auto_close = False
 				return None
-		self.update_props_scatter()
+
+		self.update_props_scatter(feature_changed=False)
 
 	def set_frame(self, value):
 		xlim=self.ax_props.get_xlim()
@@ -329,12 +355,14 @@ class ClassifierWidget(QWidget, Styles):
 			self.project_times_btn.setIcon(icon(MDI6.math_integral_box,color="black"))
 			self.project_times_btn.setIconSize(QSize(20, 20))
 			self.frame_slider.setEnabled(False)
-		self.update_props_scatter()
+		self.update_props_scatter(feature_changed=False)
 
 	def submit_classification(self):
 		
-		print('submit')
+		self.auto_close = True
 		self.apply_property_query()
+		if not self.auto_close:
+			return None
 
 		if self.time_corr.isChecked():
 			self.class_name_user = 'class_'+self.name_le.text()

{celldetective-1.3.0.post1 → celldetective-1.3.1}/celldetective/gui/layouts.py

@@ -8,7 +8,7 @@ from superqt import QLabeledRangeSlider, QLabeledDoubleSlider, QLabeledSlider, Q
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 from celldetective.utils import _extract_channel_indices_from_config
-from celldetective.gui.viewers import ThresholdedStackVisualizer, CellEdgeVisualizer, StackVisualizer, CellSizeViewer
+from celldetective.gui.viewers import ThresholdedStackVisualizer, CellEdgeVisualizer, StackVisualizer, CellSizeViewer, ChannelOffsetViewer
 from celldetective.gui import Styles
 from celldetective.preprocessing import correct_background_model, correct_background_model_free, estimate_background_per_condition
 from functools import partial
@@ -535,7 +535,6 @@ class BackgroundFitCorrectionLayout(QGridLayout, Styles):
 		self.threshold_viewer_btn.clicked.connect(self.set_threshold_graphically)
 		self.threshold_viewer_btn.setToolTip('Set the threshold graphically.')
 
-
 		self.model_lbl = QLabel('Model: ')
 		self.model_lbl.setToolTip('2D model to fit the background with.')
 		self.models_cb = QComboBox()
@@ -560,6 +559,8 @@ class BackgroundFitCorrectionLayout(QGridLayout, Styles):
 																			   self.corrected_stack_viewer,
 																			   self.add_correction_btn
 																			   ])
+
+
 	def add_to_layout(self):
 		
 		channel_layout = QHBoxLayout()
@@ -572,6 +573,7 @@ class BackgroundFitCorrectionLayout(QGridLayout, Styles):
 		subthreshold_layout = QHBoxLayout()
 		subthreshold_layout.addWidget(self.threshold_le, 95)
 		subthreshold_layout.addWidget(self.threshold_viewer_btn, 5)
+
 		threshold_layout.addLayout(subthreshold_layout, 75)
 		self.addLayout(threshold_layout, 1, 0, 1, 3)
 
@@ -878,18 +880,26 @@ class ProtocolDesignerLayout(QVBoxLayout, Styles):
 
 	def generate_layout(self):
 
+		self.correction_layout = QVBoxLayout()
+
+		self.background_correction_layout = QVBoxLayout()
+		self.background_correction_layout.setContentsMargins(0,0,0,0)
 		self.title_layout = QHBoxLayout()
 		self.title_layout.addWidget(self.title_lbl, 100, alignment=Qt.AlignCenter)
+		self.background_correction_layout.addLayout(self.title_layout)
+		self.background_correction_layout.addWidget(self.tabs)
+		self.correction_layout.addLayout(self.background_correction_layout)
+		
+		self.addLayout(self.correction_layout)
 
-		self.addLayout(self.title_layout)
-		self.addWidget(self.tabs)
-
+		self.list_layout = QVBoxLayout()
 		list_header_layout = QHBoxLayout()
 		list_header_layout.addWidget(self.protocol_list_lbl)
 		list_header_layout.addWidget(self.delete_protocol_btn, alignment=Qt.AlignRight)
-		self.addLayout(list_header_layout)
+		self.list_layout.addLayout(list_header_layout)
+		self.list_layout.addWidget(self.protocol_list)
 
-		self.addWidget(self.protocol_list)
+		self.addLayout(self.list_layout)
 
 
 	def remove_protocol_from_list(self):
@@ -899,6 +909,117 @@ class ProtocolDesignerLayout(QVBoxLayout, Styles):
 			del self.protocols[current_item]
 			self.protocol_list.takeItem(current_item)
 
+class ChannelOffsetOptionsLayout(QVBoxLayout, Styles):
+	
+	def __init__(self, parent_window=None, *args, **kwargs):
+		
+		super().__init__(*args, **kwargs)
+
+		self.parent_window = parent_window
+		if hasattr(self.parent_window.parent_window, 'exp_config'):
+			self.attr_parent = self.parent_window.parent_window
+		else:
+			self.attr_parent = self.parent_window.parent_window.parent_window
+
+		self.channel_names = self.attr_parent.exp_channels
+
+		self.setContentsMargins(15,15,15,15)
+		self.generate_widgets()
+		self.add_to_layout()
+
+	def generate_widgets(self):
+		
+		self.channel_lbl = QLabel('Channel: ')
+		self.channels_cb = QComboBox()
+		self.channels_cb.addItems(self.channel_names)
+
+		self.shift_lbl = QLabel('Shift: ')
+		self.shift_h_lbl = QLabel('(h): ')
+		self.shift_v_lbl = QLabel('(v): ')
+
+		self.set_shift_btn = QPushButton()
+		self.set_shift_btn.setIcon(icon(MDI6.image_check, color="k"))
+		self.set_shift_btn.setStyleSheet(self.button_select_all)
+		self.set_shift_btn.setToolTip('Set the channel shift.')
+		self.set_shift_btn.clicked.connect(self.open_offset_viewer)
+		
+		self.add_correction_btn = QPushButton('Add correction')
+		self.add_correction_btn.setStyleSheet(self.button_style_sheet_2)
+		self.add_correction_btn.setIcon(icon(MDI6.plus, color="#1565c0"))
+		self.add_correction_btn.setToolTip('Add correction.')
+		self.add_correction_btn.setIconSize(QSize(25, 25))
+		self.add_correction_btn.clicked.connect(self.add_instructions_to_parent_list)
+
+		self.vertical_shift_le = ThresholdLineEdit(init_value=0, connected_buttons=[self.add_correction_btn],placeholder='vertical shift [pixels]', value_type='float')
+		self.horizontal_shift_le = ThresholdLineEdit(init_value=0, connected_buttons=[self.add_correction_btn],placeholder='vertical shift [pixels]', value_type='float')
+	
+	def add_to_layout(self):
+
+		channel_ch_hbox = QHBoxLayout()
+		channel_ch_hbox.addWidget(self.channel_lbl, 25)
+		channel_ch_hbox.addWidget(self.channels_cb, 75)
+		self.addLayout(channel_ch_hbox)
+
+		shift_hbox = QHBoxLayout()
+		shift_hbox.addWidget(self.shift_lbl, 25)
+		
+		shift_subhbox = QHBoxLayout()
+		shift_subhbox.addWidget(self.shift_h_lbl, 10)
+		shift_subhbox.addWidget(self.horizontal_shift_le, 75//2)
+		shift_subhbox.addWidget(self.shift_v_lbl, 10)
+		shift_subhbox.addWidget(self.vertical_shift_le, 75//2)	
+		shift_subhbox.addWidget(self.set_shift_btn, 5)
+
+		shift_hbox.addLayout(shift_subhbox, 75)
+		self.addLayout(shift_hbox)
+
+		btn_hbox = QHBoxLayout()
+		btn_hbox.addWidget(self.add_correction_btn, 95)
+		self.addLayout(btn_hbox)		
+
+	def add_instructions_to_parent_list(self):
+
+		self.generate_instructions()
+		self.parent_window.protocol_layout.protocols.append(self.instructions)
+		correction_description = ""
+		for index, (key, value) in enumerate(self.instructions.items()):
+			if index > 0:
+				correction_description += ", "
+			correction_description += str(key) + " : " + str(value)
+		self.parent_window.protocol_layout.protocol_list.addItem(correction_description)
+
+	def generate_instructions(self):
+
+		self.instructions = {
+					  "correction_type": "offset",
+					  "target_channel": self.channels_cb.currentText(),
+					  "correction_horizontal": self.horizontal_shift_le.get_threshold(),
+					  "correction_vertical": self.vertical_shift_le.get_threshold(),
+					 }
+
+
+	def set_target_channel(self):
+
+		channel_indices = _extract_channel_indices_from_config(self.attr_parent.exp_config, [self.channels_cb.currentText()])
+		self.target_channel = channel_indices[0]
+
+	def open_offset_viewer(self):
+		
+		self.attr_parent.locate_image()
+		self.set_target_channel()
+
+		if self.attr_parent.current_stack is not None:
+			self.viewer = ChannelOffsetViewer(
+											 parent_window = self,
+											 stack_path=self.attr_parent.current_stack,
+											 channel_names=self.attr_parent.exp_channels,
+											 n_channels=len(self.channel_names),
+											 channel_cb=True,
+											 target_channel=self.target_channel,
+											 window_title='offset viewer',
+											)
+			self.viewer.show()
+
 
 class BackgroundModelFreeCorrectionLayout(QGridLayout, Styles):
 	

{celldetective-1.3.0.post1 → celldetective-1.3.1}/celldetective/gui/measurement_options.py

@@ -154,7 +154,7 @@ class ConfigMeasurements(QMainWindow, Styles):
 
 		grid = QGridLayout(self.iso_frame)
 
-		self.iso_lbl = QLabel("ISOTROPIC MEASUREMENTS")
+		self.iso_lbl = QLabel("Position-based measurements".upper())
 		self.iso_lbl.setStyleSheet("""
 			font-weight: bold;
 			padding: 0px;
@@ -171,7 +171,7 @@ class ConfigMeasurements(QMainWindow, Styles):
 
 		grid = QGridLayout(self.features_frame)
 
-		self.feature_lbl = QLabel("FEATURES")
+		self.feature_lbl = QLabel("Mask-based measurements".upper())
 		self.feature_lbl.setStyleSheet("""
 			font-weight: bold;
 			padding: 0px;
@@ -262,7 +262,7 @@ class ConfigMeasurements(QMainWindow, Styles):
 		self.add_feature_btn.setToolTip("Add feature")
 		self.add_feature_btn.setIconSize(QSize(20, 20))
 
-		self.features_list = ListWidget(FeatureChoice, initial_features=['area', 'intensity_mean', ])
+		self.features_list = ListWidget(FeatureChoice, initial_features=['area', 'intensity_nanmean', ])
 
 		self.del_feature_btn.clicked.connect(self.features_list.removeSel)
 		self.add_feature_btn.clicked.connect(self.features_list.addItem)