celldetective 1.2.2.post2__py3-none-any.whl → 1.3.0.post1__py3-none-any.whl

celldetective/__init__.py

@@ -1,3 +1,4 @@
+from ._version import __version__
 #from .tracking import track, clean_trajectories
 #from .measure import contour_of_instance_segmentation
 

celldetective/_version.py

@@ -0,0 +1 @@
+__version__ = "1.3.0.post1"

celldetective/events.py

@@ -117,6 +117,11 @@ def compute_survival(df, class_of_interest, t_event, t_reference=None, FrameToMi
 	event_times = df.groupby(['position','TRACK_ID'])[t_event].min().values
 	max_times = df.groupby(['position','TRACK_ID'])['FRAME'].max().values
 
+	if t_reference=="0" or t_reference==0:
+		t_reference = None
+		left_censored = False
+		first_detections = None
+
 	if t_reference is not None:
 		left_censored = True
 		assert t_reference in cols,"The reference time cannot be found in the dataframe..."

celldetective/gui/about.py

@@ -4,6 +4,7 @@ from PyQt5.QtCore import Qt
 from celldetective.utils import get_software_location
 import os
 from celldetective.gui.gui_utils import center_window
+from celldetective._version import __version__
 
 class AboutWidget(QWidget):
 
@@ -27,7 +28,7 @@ class AboutWidget(QWidget):
 									""")
 		layout.addWidget(self.soft_name, alignment=Qt.AlignCenter)
 
-		self.version_lbl = QLabel(f"Version X.X.X <a href=\"https://github.com/remyeltorro/celldetective/releases\">(release notes)</a>")
+		self.version_lbl = QLabel(f"Version {__version__} <a href=\"https://github.com/remyeltorro/celldetective/releases\">(release notes)</a>")
 		self.version_lbl.setOpenExternalLinks(True)
 		layout.addWidget(self.version_lbl, alignment=Qt.AlignCenter)
 

celldetective/gui/classifier_widget.py

@@ -10,7 +10,7 @@ import numpy as np
 import matplotlib.pyplot as plt
 import json
 
-from celldetective.gui.gui_utils import FigureCanvas, center_window, color_from_status, help_generic
+from celldetective.gui.gui_utils import FigureCanvas, center_window, color_from_status, help_generic, color_from_class
 from celldetective.gui import Styles
 from celldetective.utils import get_software_location
 from celldetective.measure import classify_cells_from_query, interpret_track_classification
@@ -242,42 +242,50 @@ class ClassifierWidget(QWidget, Styles):
 
 	def update_props_scatter(self, feature_changed=True):
 
-		if not self.project_times:
-			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,self.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_class(c) for c in self.df[self.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())
-
-
-		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)
+		class_name = self.class_name
+
+		try:
+
+			if not self.project_times:
+				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.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)
+			
+			if feature_changed:
+				self.propscanvas.canvas.toolbar.update()
+			self.propscanvas.canvas.draw_idle()
 		
-		if feature_changed:
-			self.propscanvas.canvas.toolbar.update()
-		self.propscanvas.canvas.draw_idle()
+		except Exception as e:
+			pass
 
 	def apply_property_query(self):
 		
 		query = self.property_query_le.text()
-		self.df = classify_cells_from_query(self.df, self.class_name, query)
+		self.df = classify_cells_from_query(self.df, self.name_le.text(), query)
+		self.class_name = "status_"+self.name_le.text()
 		if self.df is None:
 			msgBox = QMessageBox()
 			msgBox.setIcon(QMessageBox.Warning)
@@ -287,7 +295,6 @@ class ClassifierWidget(QWidget, Styles):
 			returnValue = msgBox.exec()
 			if returnValue == QMessageBox.Ok:
 				return None
-
 		self.update_props_scatter()
 
 	def set_frame(self, value):
@@ -346,6 +353,7 @@ class ClassifierWidget(QWidget, Styles):
 					return None
 
 			name_map = {self.class_name: self.class_name_user}
+			print(f"{name_map=}")
 			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)
 
@@ -374,6 +382,8 @@ class ClassifierWidget(QWidget, Styles):
 			#self.df[self.group_name_user] = self.df[self.group_name_user].replace({0: 1, 1: 0})
 			self.df.reset_index(inplace=True, drop=True)
 
+		if 'custom' in list(self.df.columns):
+			self.df = self.df.drop(['custom'],axis=1)
 
 		for pos,pos_group in self.df.groupby('position'):
 			pos_group.to_csv(pos+os.sep.join(['output', 'tables', f'trajectories_{self.mode}.csv']), index=False)

celldetective/gui/control_panel.py

@@ -138,14 +138,6 @@ class ControlPanel(QMainWindow, Styles):
 		self.edit_config_button.clicked.connect(self.open_config_editor)
 		self.edit_config_button.setStyleSheet(self.button_select_all)
 
-		self.exp_options_layout = QHBoxLayout()
-		self.exp_options_layout.addWidget(experiment_label, 32, alignment=Qt.AlignRight)
-		self.exp_options_layout.addWidget(QLabel(name), 65, alignment=Qt.AlignLeft)
-		self.exp_options_layout.addWidget(self.folder_exp_btn, 5, alignment=Qt.AlignRight)
-		self.exp_options_layout.addWidget(self.edit_config_button, 5, alignment=Qt.AlignRight)
-		self.grid.addLayout(self.exp_options_layout, 0,0,1,3)
-
-		well_layout = QHBoxLayout()
 		self.well_list = QComboBox()
 		thresh = 32
 		self.well_truncated = [w[:thresh - 3]+'...' if len(w)>thresh else w for w in self.well_labels]		
@@ -156,7 +148,6 @@ class ControlPanel(QMainWindow, Styles):
 		self.well_list.activated.connect(self.display_positions)
 		self.to_disable.append(self.well_list)
 
-		position_layout = QHBoxLayout()
 		self.position_list = QComboBox()
 		self.position_list.addItems(["*"])
 		self.position_list.addItems(self.positions[0])
@@ -172,27 +163,46 @@ class ControlPanel(QMainWindow, Styles):
 		self.view_stack_btn.clicked.connect(self.view_current_stack)
 		self.view_stack_btn.setEnabled(False)
 
-		well_layout.setContentsMargins(0,0,0,0)
 		well_lbl = QLabel('Well: ')
 		well_lbl.setAlignment(Qt.AlignRight)
-		well_layout.addWidget(well_lbl, 32)
-		well_layout.addWidget(self.well_list, 68)
-		self.grid.addLayout(well_layout, 1, 0, 1, 3)
 
-		position_layout.setContentsMargins(0,0,0,0)
 		pos_lbl = QLabel('Position: ')
 		pos_lbl.setAlignment(Qt.AlignRight)
-		position_layout.addWidget(pos_lbl, 32)
 
-		subposition_layout = QHBoxLayout()
-		subposition_layout.addWidget(self.position_list, 95)
-		subposition_layout.addWidget(self.view_stack_btn, 5)
-		position_layout.addLayout(subposition_layout, 68)
-		self.grid.addLayout(position_layout, 2, 0, 1, 3)
-
-		
 		hsep = QHSeperationLine()
-		self.grid.addWidget(hsep, 5, 0, 1, 3)
+
+		## LAYOUT
+
+		# Header layout
+		vbox = QVBoxLayout()
+		self.grid.addLayout(vbox, 0,0,1,3)
+
+		# Experiment row
+		exp_hbox = QHBoxLayout()
+		exp_hbox.addWidget(experiment_label, 25, alignment=Qt.AlignRight)
+		exp_subhbox = QHBoxLayout()
+		exp_subhbox.addWidget(QLabel(name), 90, alignment=Qt.AlignLeft)
+		exp_subhbox.addWidget(self.folder_exp_btn, 5, alignment=Qt.AlignRight)
+		exp_subhbox.addWidget(self.edit_config_button, 5, alignment=Qt.AlignRight)
+		exp_hbox.addLayout(exp_subhbox, 75)
+		vbox.addLayout(exp_hbox)
+
+		# Well row
+		well_hbox = QHBoxLayout()
+		well_hbox.addWidget(well_lbl, 25, alignment=Qt.AlignVCenter)
+		well_hbox.addWidget(self.well_list, 75)
+		vbox.addLayout(well_hbox)
+
+		# Position row
+		position_hbox = QHBoxLayout()
+		position_hbox.addWidget(pos_lbl, 25, alignment=Qt.AlignVCenter)
+		pos_subhbox = QHBoxLayout()
+		pos_subhbox.addWidget(self.position_list, 95)
+		pos_subhbox.addWidget(self.view_stack_btn, 5)
+		position_hbox.addLayout(pos_subhbox, 75)
+		vbox.addLayout(position_hbox)
+
+		vbox.addWidget(hsep)
 
 	def locate_image(self):
 

celldetective/gui/gui_utils.py

@@ -768,7 +768,7 @@ def color_from_status(status, recently_modified=False):
 		else:
 			return 'k'
 
-def color_from_state(state):
+def color_from_state(state, recently_modified=False):
 
 	"""
 	Generate a color map based on unique values in the provided state array.
@@ -797,9 +797,15 @@ def color_from_state(state):
 	unique_values = np.unique(state)
 	color_map={}
 	for value in unique_values:
-		color_map[value] = plt.cm.tab10(value)
-		if value == 99:
+		if np.isnan(value):
+			value = "nan"
 			color_map[value] = 'k'
+		elif value==0:
+			color_map[value] = 'tab:blue'
+		elif value==1:
+			color_map[value] = 'tab:red'
+		else:
+			color_map[value] = plt.cm.tab10(value)
 
 	return color_map