celldetective 1.3.4.post1__tar.gz → 1.3.5__tar.gz

{celldetective-1.3.4.post1 → celldetective-1.3.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celldetective
-Version: 1.3.4.post1
+Version: 1.3.5
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -20,7 +20,7 @@ Requires-Dist: cellpose<3
 Requires-Dist: scikit-learn
 Requires-Dist: btrack
 Requires-Dist: tensorflow~=2.15.0
-Requires-Dist: napari
+Requires-Dist: napari<0.6.0
 Requires-Dist: tqdm
 Requires-Dist: mahotas
 Requires-Dist: fonticon-materialdesignicons6

celldetective-1.3.5/celldetective/_version.py

@@ -0,0 +1 @@
+__version__ = "1.3.5"

{celldetective-1.3.4.post1 → celldetective-1.3.5}/celldetective/events.py

@@ -143,7 +143,7 @@ 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, cut_observation_time=None):
+def compute_survival(df, class_of_interest, t_event, t_reference=None, FrameToMin=1, cut_observation_time=None, pairs=False):
 
 	"""
 	Computes survival analysis for a specific class of interest within a dataset, returning a fitted Kaplan-Meier 
@@ -190,9 +190,14 @@ def compute_survival(df, class_of_interest, t_event, t_reference=None, FrameToMi
 	assert t_event in cols,"The event time cannot be found in the dataframe..."
 	left_censored = False
 
-	classes = df.groupby(['position','TRACK_ID'])[class_of_interest].min().values
-	event_times = df.groupby(['position','TRACK_ID'])[t_event].min().values
-	max_times = df.groupby(['position','TRACK_ID'])['FRAME'].max().values
+	if not pairs:
+		groupby_cols = ['position','TRACK_ID']
+	else:
+		groupby_cols = ['position','REFERENCE_ID','NEIGHBOR_ID']
+
+	classes = df.groupby(groupby_cols)[class_of_interest].min().values
+	event_times = df.groupby(groupby_cols)[t_event].min().values
+	max_times = df.groupby(groupby_cols)['FRAME'].max().values
 
 	if t_reference=="0" or t_reference==0:
 		t_reference = None
@@ -202,7 +207,7 @@ def compute_survival(df, class_of_interest, t_event, t_reference=None, FrameToMi
 	if t_reference is not None:
 		left_censored = True
 		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
+		first_detections = df.groupby(groupby_cols)[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, cut_observation_time=cut_observation_time)
 	ks = KaplanMeierFitter()

{celldetective-1.3.4.post1 → celldetective-1.3.5}/celldetective/gui/classifier_widget.py

@@ -1,5 +1,5 @@
 from PyQt5.QtWidgets import QWidget, QLineEdit, QMessageBox, QHBoxLayout, QVBoxLayout, QPushButton, QLabel, \
-	QCheckBox, QRadioButton, QButtonGroup
+	QCheckBox, QRadioButton, QButtonGroup, QComboBox
 from PyQt5.QtCore import Qt, QSize
 from superqt import QLabeledSlider,QLabeledDoubleSlider, QSearchableComboBox
 from superqt.fonticon import icon
@@ -163,6 +163,20 @@ class ClassifierWidget(QWidget, Styles):
 		time_corr_layout.addWidget(self.irreversible_event_btn, 50,alignment=Qt.AlignCenter)
 		layout.addLayout(time_corr_layout)
 
+		self.prereq_event_check = QCheckBox('prerequisite event:')
+		self.prereq_event_check.toggled.connect(self.activate_prereq_cb)
+		self.prereq_event_cb = QComboBox()
+		event_cols = ['--'] + [c.replace('t_','') for c in self.cols if c.startswith('t_')]
+		self.prereq_event_cb.addItems(event_cols)
+		self.prereq_event_check.setEnabled(False)
+		self.prereq_event_cb.setEnabled(False)
+
+		prereq_layout = QHBoxLayout()
+		prereq_layout.addWidget(QLabel(''), 50)
+		prereq_layout.addWidget(self.prereq_event_check, 15)
+		prereq_layout.addWidget(self.prereq_event_cb, 35)
+		layout.addLayout(prereq_layout)
+
 		self.r2_slider = QLabeledDoubleSlider()
 		self.r2_slider.setValue(0.75)
 		self.r2_slider.setRange(0,1)
@@ -170,6 +184,7 @@ class ClassifierWidget(QWidget, Styles):
 		self.r2_slider.setOrientation(1)
 		self.r2_label = QLabel('R2 tolerance:')
 		self.r2_label.setToolTip('Minimum R2 between the fit sigmoid and the binary response to the filters to accept the event.')
+
 		r2_threshold_layout = QHBoxLayout()
 		r2_threshold_layout.addWidget(QLabel(''), 50)
 		r2_threshold_layout.addWidget(self.r2_label, 15)
@@ -193,6 +208,12 @@ class ClassifierWidget(QWidget, Styles):
 		self.frame_slider.valueChanged.connect(self.set_frame)
 		self.alpha_slider.valueChanged.connect(self.set_transparency)
 
+	def activate_prereq_cb(self):
+		if self.prereq_event_check.isChecked():
+			self.prereq_event_cb.setEnabled(True)
+		else:
+			self.prereq_event_cb.setEnabled(False)
+
 	def activate_submit_btn(self):
 
 		if self.property_query_le.text()=='':
@@ -204,10 +225,10 @@ class ClassifierWidget(QWidget, Styles):
 
 	def activate_r2(self):
 		if self.irreversible_event_btn.isChecked() and self.time_corr.isChecked():
-			for wg in [self.r2_slider, self.r2_label]:
+			for wg in [self.r2_slider, self.r2_label, self.prereq_event_check]:
 				wg.setEnabled(True)
 		else:
-			for wg in [self.r2_slider, self.r2_label]:
+			for wg in [self.r2_slider, self.r2_label, self.prereq_event_check]:
 				wg.setEnabled(False)				
 
 	def activate_time_corr_options(self):
@@ -416,7 +437,11 @@ class ClassifierWidget(QWidget, Styles):
 			self.df = self.df.drop(list(set(name_map.values()) & set(self.df.columns)), axis=1).rename(columns=name_map)
 			self.df.reset_index(inplace=True, drop=True)
 
-			self.df = interpret_track_classification(self.df, self.class_name_user, irreversible_event=self.irreversible_event_btn.isChecked(), unique_state=self.unique_state_btn.isChecked(), r2_threshold=self.r2_slider.value())
+			pre_event = None
+			if self.prereq_event_check.isChecked() and "t_"+self.prereq_event_cb.currentText() in self.cols:
+				pre_event = self.prereq_event_cb.currentText()
+
+			self.df = interpret_track_classification(self.df, self.class_name_user, irreversible_event=self.irreversible_event_btn.isChecked(), unique_state=self.unique_state_btn.isChecked(), r2_threshold=self.r2_slider.value(), pre_event=pre_event)
 		
 		else:
 			self.group_name_user = 'group_' + self.name_le.text()

{celldetective-1.3.4.post1 → celldetective-1.3.5}/celldetective/gui/control_panel.py

@@ -93,6 +93,9 @@ class ControlPanel(QMainWindow, Styles):
 		self.screen_width = desktop.screenGeometry().width()
 		self.scroll.setMinimumWidth(440)
 
+		self.well_list.setCurrentIndex(0)
+		#self.position_list.setCurrentIndex(0)
+
 	def init_wells_and_positions(self):
 
 		"""
@@ -151,10 +154,8 @@ class ControlPanel(QMainWindow, Styles):
 		#self.locate_selected_position()
 
 		self.well_list.activated.connect(self.display_positions)
-		self.well_list.setCurrentIndex(0)
 
 		self.position_list.activated.connect(self.update_position_options)
-		self.position_list.setCurrentIndex(0)
 
 		self.view_stack_btn = QPushButton()
 		self.view_stack_btn.setStyleSheet(self.button_select_all)

{celldetective-1.3.4.post1 → celldetective-1.3.5}/celldetective/gui/generic_signal_plot.py

@@ -62,6 +62,7 @@ class GenericSignalPlotWidget(QWidget, Styles):
 		self.setLayout(self.layout)
 		self.setAttribute(Qt.WA_DeleteOnClose)
 
+
 	def populate_widget(self):
 
 		self.plot_options = [QRadioButton() for i in range(3)]
@@ -221,18 +222,13 @@ class GenericSignalPlotWidget(QWidget, Styles):
 		self.alpha_slider = QLabeledDoubleSlider()
 		alpha_hbox = QuickSliderLayout(label='single-cell\nsignal alpha: ',
 										slider=self.alpha_slider,
-										slider_initial_value=0.8,
+										slider_initial_value=self.alpha_setting,
 										slider_range=(0,1),
 										decimal_option=True,
 										precision=1.0E-05,
 										)
 		self.alpha_slider.valueChanged.connect(self.submit_alpha)
 		self.cell_lines_alpha_wdg.setLayout(alpha_hbox)
-
-		# self.submit_alpha_btn = QPushButton('submit')
-		# self.submit_alpha_btn.setStyleSheet(self.button_style_sheet_2)
-		# self.submit_alpha_btn.clicked.connect(self.submit_alpha)
-		# alpha_hbox.addWidget(self.submit_alpha_btn, 10)
 		self.layout.addWidget(self.cell_lines_alpha_wdg)
 
 		self.select_option = [QRadioButton() for i in range(2)]

{celldetective-1.3.4.post1 → celldetective-1.3.5}/celldetective/gui/gui_utils.py

@@ -1,7 +1,7 @@
 import numpy as np
 from PyQt5.QtWidgets import QApplication, QMessageBox, QFrame, QSizePolicy, QWidget, QLineEdit, QListWidget, QVBoxLayout, QComboBox, \
 	QPushButton, QLabel, QHBoxLayout, QCheckBox, QFileDialog, QToolButton, QMenu, QStylePainter, QStyleOptionComboBox, QStyle
-from PyQt5.QtCore import Qt, QSize, QAbstractTableModel
+from PyQt5.QtCore import Qt, QSize, QAbstractTableModel, QEvent, pyqtSignal
 from PyQt5.QtGui import QDoubleValidator, QIntValidator, QStandardItemModel, QPalette
 
 from celldetective.gui import Styles
@@ -23,12 +23,13 @@ class QCheckableComboBox(QComboBox):
 	adapted from https://stackoverflow.com/questions/22775095/pyqt-how-to-set-combobox-items-be-checkable
 	"""
 
+	activated = pyqtSignal(str)
+
 	def __init__(self, obj='', parent_window=None, *args, **kwargs):
 		
 		super().__init__(parent_window, *args, **kwargs)
 
 		self.setTitle('')
-		self.view().pressed.connect(self.handleItemPressed)
 		self.setModel(QStandardItemModel(self))
 		self.obj = obj
 		self.toolButton = QToolButton(parent_window)
@@ -38,6 +39,9 @@ class QCheckableComboBox(QComboBox):
 		self.toolButton.setPopupMode(QToolButton.InstantPopup)
 		self.anySelected = False
 
+		self.view().viewport().installEventFilter(self)		
+		self.view().pressed.connect(self.handleItemPressed)
+
 	def clear(self):
 		
 		self.unselectAll()
@@ -70,6 +74,8 @@ class QCheckableComboBox(QComboBox):
 		elif len(options_checked[options_checked])==0:
 			self.setTitle(f"No {self.obj} selected...")
 			self.anySelected = False
+		
+		self.activated.emit(self.title())
 
 	def setCurrentIndex(self, index):
 
@@ -101,6 +107,7 @@ class QCheckableComboBox(QComboBox):
 
 	def setTitle(self, title):
 		self._title = title
+		self.update()
 		self.repaint()
 
 	def paintEvent(self, event):
@@ -155,7 +162,12 @@ class QCheckableComboBox(QComboBox):
 
 	def isAnySelected(self):
 		return not self.title().startswith('No')
-
+	
+	def eventFilter(self, source, event):
+		if source is self.view().viewport():
+			if event.type() == QEvent.MouseButtonRelease:
+				return True  # Prevent the popup from closing
+		return super().eventFilter(source, event)
 
 class PandasModel(QAbstractTableModel):
 
@@ -503,7 +515,11 @@ class FilterChoice(QWidget):
 		self.combo_box.currentTextChanged.connect(self.update_arguments)
 		layout.addWidget(self.combo_box)
 
+		self.floatValidator = QDoubleValidator()
 		self.arguments_le = [QLineEdit() for i in range(3)]
+		for i in range(3):
+			self.arguments_le[i].setValidator(self.floatValidator)
+
 		self.arguments_labels = [QLabel('') for i in range(3)]
 		for i in range(2):
 			hbox = QHBoxLayout()
@@ -525,8 +541,10 @@ class FilterChoice(QWidget):
 
 		filter_instructions = [filtername.split('_')[0]]
 		for a in self.arguments_le:
-			arg = a.text()
+			
+			arg = a.text().replace(',','.')
 			arg_num = arg
+
 			if (arg != '') and arg_num.replace('.', '').replace(',', '').isnumeric():
 				num = float(arg)
 				if num.is_integer():
@@ -666,12 +684,14 @@ class DistanceChoice(QWidget):
 		super().__init__()
 		self.parent_window = parent_window
 		self.setWindowTitle("Set distances")
+		self.floatValidator = QDoubleValidator()
 		center_window(self)
 
 		# Create the QComboBox and add some items
 
 		self.dist_label = QLabel('Distance [px]: ')
 		self.dist_le = QLineEdit('10')
+		self.dist_le.setValidator(self.floatValidator)
 
 		self.add_btn = QPushButton("Add")
 		self.add_btn.clicked.connect(self.add_current_feature)
@@ -686,7 +706,7 @@ class DistanceChoice(QWidget):
 		layout.addWidget(self.add_btn)
 
 	def add_current_feature(self):
-		value = self.dist_le.text()
+		value = self.dist_le.text().replace(',','.')
 		values = [value]
 		self.parent_window.list_widget.addItems(values)
 		self.close()
@@ -827,13 +847,21 @@ class FigureCanvas(QWidget):
 		if interactive:
 			self.toolbar = NavigationToolbar2QT(self.canvas)
 		self.layout = QVBoxLayout(self)
-		self.layout.addWidget(self.canvas)
+		self.layout.addWidget(self.canvas,90)
 		if interactive:
 			self.layout.addWidget(self.toolbar)
 
 		center_window(self)
 		self.setAttribute(Qt.WA_DeleteOnClose)
 
+	def resizeEvent(self, event):
+		
+		super().resizeEvent(event)
+		try:
+			self.fig.tight_layout()
+		except:
+			pass
+
 	def draw(self):
 		self.canvas.draw()
 

{celldetective-1.3.4.post1 → celldetective-1.3.5}/celldetective/gui/measurement_options.py

@@ -261,7 +261,7 @@ 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_nanmean', ])
+		self.features_list = ListWidget(FeatureChoice, initial_features=['area', 'intensity_mean', ])
 
 		self.del_feature_btn.clicked.connect(self.features_list.removeSel)
 		self.add_feature_btn.clicked.connect(self.features_list.addItem)
@@ -313,25 +313,6 @@ class ConfigMeasurements(QMainWindow, Styles):
 
 		self.feat_sep3 = QHSeperationLine()
 		layout.addWidget(self.feat_sep3)
-		# self.radial_intensity_btn = QCheckBox('Measure radial intensity distribution')
-		# layout.addWidget(self.radial_intensity_btn)
-		# self.radial_intensity_btn.clicked.connect(self.enable_step_size)
-		# self.channel_chechkboxes=[]
-		# for channel in self.channel_names:
-		#     channel_checkbox=QCheckBox(channel)
-		#     self.channel_chechkboxes.append(channel_checkbox)
-		#     layout.addWidget(channel_checkbox)
-		#     channel_checkbox.setEnabled(False)
-		# step_box=QHBoxLayout()
-		# self.step_lbl=QLabel("Step size (in px)")
-		# self.step_size=QLineEdit()
-		# self.step_lbl.setEnabled(False)
-		# self.step_size.setEnabled(False)
-		# step_box.addWidget(self.step_lbl)
-		# step_box.addWidget(self.step_size)
-		# layout.addLayout(step_box)
-		# self.feat_sep4 = QHSeperationLine()
-		# layout.addWidget(self.feat_sep4)
 
 		# Haralick features parameters
 		self.activate_haralick_btn = QCheckBox('Measure Haralick texture features')
@@ -511,16 +492,6 @@ class ConfigMeasurements(QMainWindow, Styles):
 		if not border_distances:
 			border_distances = None
 		measurement_options.update({'border_distances': border_distances})
-		# radial_intensity = {}
-		# radial_step = int(self.step_size.text())
-		# radial_channels = []
-		# for checkbox in self.channel_chechkboxes:
-		#     if checkbox.isChecked():
-		#         radial_channels.append(checkbox.text())
-		# radial_intensity={'radial_step': radial_step, 'radial_channels': radial_channels}
-		# if not self.radial_intensity_btn.isChecked():
-		#     radial_intensity = None
-		# measurement_options.update({'radial_intensity' : radial_intensity})
 
 		self.extract_haralick_options()
 		measurement_options.update({'haralick_options': self.haralick_options})

{celldetective-1.3.4.post1 → celldetective-1.3.5}/celldetective/gui/neighborhood_options.py

@@ -174,7 +174,7 @@ class ConfigNeighborhoods(QWidget, Styles):
 		self.attr_parent.locate_image()
 		if self.attr_parent.current_stack is not None:
 			self.viewer = CellEdgeVisualizer(
-										  cell_type='effectors',
+										  cell_type=self.reference_population_cb.currentText(),
 										  edge_range=(1,30),
 										  invert=True,
 										  initial_edge=3,

{celldetective-1.3.4.post1 → celldetective-1.3.5}/celldetective/gui/plot_signals_ui.py

@@ -19,6 +19,7 @@ import pandas as pd
 import math
 from celldetective.gui import Styles
 from matplotlib import colormaps
+import matplotlib.cm
 
 
 class ConfigSignalPlot(QWidget, Styles):
@@ -110,10 +111,8 @@ class ConfigSignalPlot(QWidget, Styles):
 		
 		all_cms = list(colormaps)
 		for cm in all_cms:
-			try:
-				self.cbs[-1].addColormap(cm)
-			except:
-				pass
+			if hasattr(matplotlib.cm, str(cm).lower()):
+				self.cbs[-1].addColormap(cm.lower())
 
 		self.cbs[0].setCurrentIndex(1)
 		self.cbs[0].setCurrentIndex(0)

{celldetective-1.3.4.post1 → celldetective-1.3.5}/celldetective/gui/process_block.py

@@ -9,7 +9,7 @@ from PyQt5.QtGui import QDoubleValidator, QIntValidator
 from celldetective.gui.signal_annotator import MeasureAnnotator
 from celldetective.gui.signal_annotator2 import SignalAnnotator2
 from celldetective.io import get_segmentation_models_list, control_segmentation_napari, get_signal_models_list, \
-	control_tracking_btrack, load_experiment_tables, get_pair_signal_models_list
+	control_tracks, load_experiment_tables, get_pair_signal_models_list
 from celldetective.io import locate_segmentation_model, fix_missing_labels, auto_load_number_of_frames, load_frames, locate_signal_model
 from celldetective.gui import SegmentationModelLoader, ClassifierWidget, ConfigNeighborhoods, ConfigSegmentationModelTraining, ConfigTracking, SignalAnnotator, ConfigSignalModelTraining, ConfigMeasurements, ConfigSignalAnnotator, TableUI
 from celldetective.gui.gui_utils import QHSeperationLine
@@ -291,7 +291,7 @@ class ProcessPanel(QFrame, Styles):
 		self.track_action.setStyleSheet(self.menu_check_style)
 		self.track_action.setIcon(icon(MDI6.chart_timeline_variant,color="black"))
 		self.track_action.setIconSize(QSize(20, 20))
-		self.track_action.setToolTip("Track the target cells using bTrack.")
+		self.track_action.setToolTip(f"Track the {self.mode[:-1]} cells.")
 		grid_track.addWidget(self.track_action, 75)
 
 		self.delete_tracks_btn = QPushButton()
@@ -307,7 +307,7 @@ class ProcessPanel(QFrame, Styles):
 		self.check_tracking_result_btn = QPushButton()
 		self.check_tracking_result_btn.setIcon(icon(MDI6.eye_check_outline,color="black"))
 		self.check_tracking_result_btn.setIconSize(QSize(20, 20))
-		self.check_tracking_result_btn.setToolTip("View raw bTrack output in napari.")
+		self.check_tracking_result_btn.setToolTip("View tracking output in napari.")
 		self.check_tracking_result_btn.setStyleSheet(self.button_select_all)
 		self.check_tracking_result_btn.clicked.connect(self.open_napari_tracking)
 		self.check_tracking_result_btn.setEnabled(False)
@@ -845,14 +845,16 @@ class ProcessPanel(QFrame, Styles):
 
 			# self.stack = None
 		self.parent_window.update_position_options()
-		if self.segment_action.isChecked():
-			self.segment_action.setChecked(False)
+
+		for action in [self.segment_action, self.track_action, self.measure_action, self.signal_analysis_action]:
+			if action.isChecked():
+				action.setChecked(False)
 
 		self.cellpose_calibrated = False
 
 	def open_napari_tracking(self):
 		print(f'View the tracks before post-processing for position {self.parent_window.pos} in napari...')
-		control_tracking_btrack(self.parent_window.pos, prefix=self.parent_window.movie_prefix, population=self.mode, threads=self.parent_window.parent_window.n_threads)
+		control_tracks(self.parent_window.pos, prefix=self.parent_window.movie_prefix, population=self.mode, threads=self.parent_window.parent_window.n_threads)
 
 	def view_table_ui(self):
 

{celldetective-1.3.4.post1 → celldetective-1.3.5}/celldetective/gui/signal_annotator.py

@@ -457,8 +457,10 @@ class SignalAnnotator(QMainWindow, Styles):
 		cols = np.array(self.df_tracks.columns)
 		self.class_cols = np.array([c.startswith('class') for c in list(self.df_tracks.columns)])
 		self.class_cols = list(cols[self.class_cols])
-		self.class_cols.remove('class_id')
-		self.class_cols.remove('class_color')
+		if 'class_id' in self.class_cols:
+			self.class_cols.remove('class_id')
+		if 'class_color' in self.class_cols:
+			self.class_cols.remove('class_color')
 		self.class_choice_cb.addItems(self.class_cols)
 		idx = self.class_choice_cb.findText(self.target_class)
 		self.class_choice_cb.setCurrentIndex(idx)