celldetective 1.3.9.post5__py3-none-any.whl → 1.4.0__py3-none-any.whl

celldetective/gui/btrack_options.py

@@ -1,9 +1,9 @@
-from PyQt5.QtWidgets import QRadioButton, QButtonGroup, QMainWindow, QApplication, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, QFileDialog, QGridLayout, QTextEdit, QLineEdit, QVBoxLayout, QWidget, QLabel, QHBoxLayout, QPushButton
+from PyQt5.QtWidgets import QRadioButton, QButtonGroup, QApplication, QMessageBox, QScrollArea, QComboBox, QFrame, QCheckBox, QFileDialog, QGridLayout, QTextEdit, QLineEdit, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
 from PyQt5.QtCore import Qt, QSize
 from PyQt5.QtGui import QDoubleValidator
 
 from celldetective.gui.gui_utils import center_window, FeatureChoice, ListWidget, QHSeperationLine, FigureCanvas, help_generic
-from superqt import QLabeledDoubleSlider,QLabeledSlider
+from superqt import QLabeledDoubleSlider, QLabeledSlider
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 from celldetective.utils import extract_experiment_channels, get_software_location
@@ -16,9 +16,10 @@ import os
 import matplotlib.pyplot as plt
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 from glob import glob
-from celldetective.gui import Styles
+from celldetective.gui import CelldetectiveWidget, CelldetectiveMainWindow
 
-class ConfigTracking(QMainWindow, Styles):
+
+class ConfigTracking(CelldetectiveMainWindow):
 	
 	"""
 	UI to set tracking parameters for bTrack.
@@ -34,15 +35,10 @@ class ConfigTracking(QMainWindow, Styles):
 		self.exp_dir = self.parent_window.exp_dir
 		self.floatValidator = QDoubleValidator()
 
-		if self.mode=="targets":
-			self.config_name = os.sep.join(["configs", "btrack_config_targets.json"])
-			self.track_instructions_write_path = self.parent_window.exp_dir + os.sep.join(["configs","tracking_instructions_targets.json"])
-		elif self.mode=="effectors":
-			self.config_name = os.sep.join(["configs","btrack_config_effectors.json"])
-			self.track_instructions_write_path = self.parent_window.exp_dir + os.sep.join(["configs", "tracking_instructions_effectors.json"])
+		self.config_name = os.sep.join(["configs", f"btrack_config_{self.mode}.json"])
+		self.track_instructions_write_path = self.parent_window.exp_dir + os.sep.join(["configs", f"tracking_instructions_{self.mode}.json"])
 		self.soft_path = get_software_location()
 		
-		exp_config = self.exp_dir +"config.ini"
 		self.config_path = self.exp_dir + self.config_name
 		self.channel_names, self.channels = extract_experiment_channels(self.exp_dir)
 		self.channel_names = np.array(self.channel_names)
@@ -66,10 +62,10 @@ class ConfigTracking(QMainWindow, Styles):
 		
 		# Create button widget and layout
 		self.scroll_area = QScrollArea(self)
-		self.button_widget = QWidget()
+		self.button_widget = CelldetectiveWidget()
 		main_layout = QVBoxLayout()
 		self.button_widget.setLayout(main_layout)
-		main_layout.setContentsMargins(30,30,30,30)
+		main_layout.setContentsMargins(30, 30, 30, 30)
 
 		# First collapsable Frame CONFIG
 
@@ -86,7 +82,7 @@ class ConfigTracking(QMainWindow, Styles):
 		self.populate_config_frame()
 
 		tracker_hbox = QHBoxLayout()
-		tracker_hbox.setContentsMargins(15,15,15,15)
+		tracker_hbox.setContentsMargins(15, 15, 15, 15)
 		tracker_hbox.addWidget(self.btrack_option, 50, alignment=Qt.AlignCenter)
 		tracker_hbox.addWidget(self.trackpy_option, 50, alignment=Qt.AlignCenter)
 		main_layout.addLayout(tracker_hbox)
@@ -149,7 +145,6 @@ class ConfigTracking(QMainWindow, Styles):
 			#self.scroll_area.setMinimumHeight(self.minimum_height)
 			#self.adjustSize()
 
-
 	def populate_post_proc_frame(self):
 
 		"""
@@ -172,13 +167,13 @@ class ConfigTracking(QMainWindow, Styles):
 		title_hbox = QHBoxLayout()
 
 		self.collapse_post_proc_btn = QPushButton()
-		self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_down,color="black"))
+		self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_down, color="black"))
 		self.collapse_post_proc_btn.setIconSize(QSize(20, 20))
 		self.collapse_post_proc_btn.setStyleSheet(self.button_select_all)
 		#grid.addWidget(self.collapse_post_proc_btn, 0, 0, 1, 4, alignment=Qt.AlignRight)
 
 		self.help_post_btn = QPushButton()
-		self.help_post_btn.setIcon(icon(MDI6.help_circle,color=self.help_color))
+		self.help_post_btn.setIcon(icon(MDI6.help_circle, color=self.help_color))
 		self.help_post_btn.setIconSize(QSize(20, 20))
 		self.help_post_btn.clicked.connect(self.help_post)
 		self.help_post_btn.setStyleSheet(self.button_select_all)
@@ -188,7 +183,7 @@ class ConfigTracking(QMainWindow, Styles):
 		title_hbox.addWidget(QLabel(), 85, alignment=Qt.AlignCenter)
 		title_hbox.addWidget(self.help_post_btn, 5)
 		title_hbox.addWidget(self.collapse_post_proc_btn, 5)
-		grid.addLayout(title_hbox, 0,0,1,4)
+		grid.addLayout(title_hbox, 0, 0, 1, 4)
 
 		self.generate_post_proc_panel_contents()
 		grid.addWidget(self.ContentsPostProc, 1, 0, 1, 4, alignment=Qt.AlignTop)
@@ -205,13 +200,13 @@ class ConfigTracking(QMainWindow, Styles):
 		is_open = np.array([features_open, config_open, post_open])
 
 		if self.ContentsPostProc.isHidden():
-			self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_down,color="black"))
+			self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_down, color="black"))
 			self.collapse_post_proc_btn.setIconSize(QSize(20, 20))
 			if len(is_open[is_open])==0:
 				self.scroll_area.setMinimumHeight(int(self.minimum_height))
 				self.adjustSize()
 		else:
-			self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_up,color="black"))
+			self.collapse_post_proc_btn.setIcon(icon(MDI6.chevron_up, color="black"))
 			self.collapse_post_proc_btn.setIconSize(QSize(20, 20))
 			self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
 
@@ -222,7 +217,7 @@ class ConfigTracking(QMainWindow, Styles):
 		Helper for track post-processing strategy.
 		"""
 
-		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','track-postprocessing.json'])
+		dict_path = os.sep.join([get_software_location(), 'celldetective', 'gui', 'help', 'track-postprocessing.json'])
 
 		with open(dict_path) as f:
 			d = json.load(f)
@@ -246,7 +241,7 @@ class ConfigTracking(QMainWindow, Styles):
 		Helper for track post-processing strategy.
 		"""
 
-		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','feature-btrack.json'])
+		dict_path = os.sep.join([get_software_location(), 'celldetective', 'gui', 'help', 'feature-btrack.json'])
 
 		with open(dict_path) as f:
 			d = json.load(f)
@@ -300,7 +295,7 @@ class ConfigTracking(QMainWindow, Styles):
 		title_hbox.addWidget(QLabel(), 85, alignment=Qt.AlignCenter)
 		title_hbox.addWidget(self.help_feature_btn, 5)
 		title_hbox.addWidget(self.collapse_features_btn, 5)
-		grid.addLayout(title_hbox, 0,0,1,4)		
+		grid.addLayout(title_hbox, 0, 0, 1, 4)
 
 		self.generate_feature_panel_contents()
 		grid.addWidget(self.ContentsFeatures, 1, 0, 1, 4, alignment=Qt.AlignTop)
@@ -321,13 +316,13 @@ class ConfigTracking(QMainWindow, Styles):
 		is_open = np.array([features_open, config_open, post_open])
 
 		if self.ContentsFeatures.isHidden():
-			self.collapse_features_btn.setIcon(icon(MDI6.chevron_down,color="black"))
+			self.collapse_features_btn.setIcon(icon(MDI6.chevron_down, color="black"))
 			self.collapse_features_btn.setIconSize(QSize(20, 20))
 			if len(is_open[is_open])==0:
 				self.scroll_area.setMinimumHeight(int(self.minimum_height))
 				self.adjustSize()
 		else:
-			self.collapse_features_btn.setIcon(icon(MDI6.chevron_up,color="black"))
+			self.collapse_features_btn.setIcon(icon(MDI6.chevron_up, color="black"))
 			self.collapse_features_btn.setIconSize(QSize(20, 20))
 			self.scroll_area.setMinimumHeight(min(int(930), int(0.9*self.screen_height)))
 
@@ -351,7 +346,7 @@ class ConfigTracking(QMainWindow, Styles):
 		self.min_tracklength_slider.setSingleStep(1)
 		self.min_tracklength_slider.setTickInterval(1)
 		self.min_tracklength_slider.setSingleStep(1)
-		self.min_tracklength_slider.setOrientation(1)
+		self.min_tracklength_slider.setOrientation(Qt.Horizontal)
 		self.min_tracklength_slider.setRange(0,self.parent_window.parent_window.len_movie)
 		self.min_tracklength_slider.setValue(0)
 		tracklength_layout.addWidget(QLabel('Min. tracklength: '),40)
@@ -391,7 +386,6 @@ class ConfigTracking(QMainWindow, Styles):
 
 		layout.addLayout(clean_traj_sublayout)
 
-
 	def generate_feature_panel_contents(self):
 		
 		self.ContentsFeatures = QFrame()
@@ -456,10 +450,9 @@ class ConfigTracking(QMainWindow, Styles):
 
 		# Slider to set vmin & vmax
 		self.haralick_scale_slider = QLabeledDoubleSlider()
-		self.haralick_scale_slider.setSingleStep(0.05)
 		self.haralick_scale_slider.setTickInterval(0.05)
 		self.haralick_scale_slider.setSingleStep(1)
-		self.haralick_scale_slider.setOrientation(1)
+		self.haralick_scale_slider.setOrientation(Qt.Horizontal)
 		self.haralick_scale_slider.setRange(0,1)
 		self.haralick_scale_slider.setValue(0.5)
 		self.haralick_scale_lbl = QLabel('Scale: ')
@@ -671,7 +664,7 @@ class ConfigTracking(QMainWindow, Styles):
 		self.memory_slider.setSingleStep(1)
 		self.memory_slider.setTickInterval(1)
 		self.memory_slider.setSingleStep(1)
-		self.memory_slider.setOrientation(1)
+		self.memory_slider.setOrientation(Qt.Horizontal)
 		self.memory_slider.setRange(0,self.parent_window.parent_window.len_movie)
 		self.memory_slider.setValue(0)
 		memory_layout.addWidget(self.memory_lbl, 30)
@@ -745,7 +738,7 @@ class ConfigTracking(QMainWindow, Styles):
 				copyfile(self.filename, self.config_path)
 			self.load_cell_config()
 		except Exception as e:
-			print(e, modelpath)
+			print(e)
 			return None
 
 	def reset_btrack_config(self):
@@ -994,7 +987,7 @@ class ConfigTracking(QMainWindow, Styles):
 				if 'search_range' in tracking_instructions:
 					search_range = tracking_instructions['search_range']
 					if search_range is not None:
-						self.search_range_le.setText(str(search_range).replace('.',','))				
+						self.search_range_le.setText(str(search_range).replace('.', ','))
 				if 'memory' in tracking_instructions:
 					memory = tracking_instructions['memory']
 					if memory is not None:
@@ -1072,7 +1065,7 @@ class ConfigTracking(QMainWindow, Styles):
 		Load the first frame of the first movie found in the experiment folder as a sample.
 		"""
 
-		movies = glob(self.parent_window.parent_window.exp_dir + os.sep.join(["*","*","movie",self.parent_window.parent_window.movie_prefix+"*.tif"]))
+		movies = glob(self.parent_window.parent_window.exp_dir + os.sep.join(["*", "*", "movie", self.parent_window.parent_window.movie_prefix+"*.tif"]))
 		if len(movies)==0:
 			msgBox = QMessageBox()
 			msgBox.setIcon(QMessageBox.Warning)
@@ -1088,7 +1081,6 @@ class ConfigTracking(QMainWindow, Styles):
 			n_channels = len(self.channels)
 			self.test_frame = load_frames(np.arange(n_channels), stack0, scale=None, normalize_input=False)
 
-
 	def control_haralick_digitalization(self):
 
 		"""

celldetective/gui/classifier_widget.py

@@ -1,7 +1,7 @@
-from PyQt5.QtWidgets import QWidget, QLineEdit, QMessageBox, QHBoxLayout, QVBoxLayout, QPushButton, QLabel, \
+from PyQt5.QtWidgets import QLineEdit, QMessageBox, QHBoxLayout, QVBoxLayout, QPushButton, QLabel, \
 	QCheckBox, QRadioButton, QButtonGroup, QComboBox
 from PyQt5.QtCore import Qt, QSize
-from superqt import QLabeledSlider,QLabeledDoubleSlider, QSearchableComboBox
+from superqt import QLabeledSlider, QLabeledDoubleSlider, QSearchableComboBox
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 
@@ -11,11 +11,11 @@ import matplotlib.pyplot as plt
 import json
 
 from celldetective.gui.gui_utils import FigureCanvas, center_window, color_from_status, help_generic
-from celldetective.gui import Styles
+from celldetective.gui.base_components import CelldetectiveWidget
 from celldetective.utils import get_software_location
 from celldetective.measure import classify_cells_from_query, interpret_track_classification
 
-class ClassifierWidget(QWidget, Styles):
+class ClassifierWidget(CelldetectiveWidget):
 
 	def __init__(self, parent_window):
 
@@ -33,7 +33,7 @@ class ClassifierWidget(QWidget, Styles):
 
 		is_number = np.vectorize(lambda x: np.issubdtype(x, np.number))
 		is_number_test = is_number(self.df.dtypes)
-		self.cols = [col for t,col in zip(is_number_test,self.df.columns) if t]
+		self.cols = [col for t, col in zip(is_number_test, self.df.columns) if t]
 
 		self.class_name = 'custom'
 		self.name_le = QLineEdit(self.class_name)
@@ -44,7 +44,7 @@ class ClassifierWidget(QWidget, Styles):
 
 		
 		layout = QVBoxLayout(self)
-		layout.setContentsMargins(30,30,30,30)
+		layout.setContentsMargins(30, 30, 30, 30)
 
 		name_layout = QHBoxLayout()
 		name_layout.addWidget(QLabel('class name: '), 33)
@@ -55,7 +55,7 @@ class ClassifierWidget(QWidget, Styles):
 		fig_btn_hbox.addWidget(QLabel(''), 95)
 		self.project_times_btn = QPushButton('')
 		self.project_times_btn.setStyleSheet(self.parent_window.parent_window.parent_window.button_select_all)
-		self.project_times_btn.setIcon(icon(MDI6.math_integral,color="black"))
+		self.project_times_btn.setIcon(icon(MDI6.math_integral, color="black"))
 		self.project_times_btn.setToolTip("Project measurements at all times.")
 		self.project_times_btn.setIconSize(QSize(20, 20))
 		self.project_times = False
@@ -70,8 +70,8 @@ class ClassifierWidget(QWidget, Styles):
 		# slider
 		self.frame_slider = QLabeledSlider()
 		self.frame_slider.setSingleStep(1)
-		self.frame_slider.setOrientation(1)
-		self.frame_slider.setRange(0,int(self.df.FRAME.max()) - 1)
+		self.frame_slider.setOrientation(Qt.Horizontal)
+		self.frame_slider.setRange(0, int(self.df.FRAME.max()) - 1)
 		self.frame_slider.setValue(0)
 		self.currentFrame = 0
 
@@ -84,8 +84,8 @@ class ClassifierWidget(QWidget, Styles):
 		# transparency slider
 		self.alpha_slider = QLabeledDoubleSlider()
 		self.alpha_slider.setSingleStep(0.001)
-		self.alpha_slider.setOrientation(1)
-		self.alpha_slider.setRange(0,1)
+		self.alpha_slider.setOrientation(Qt.Horizontal)
+		self.alpha_slider.setRange(0, 1)
 		self.alpha_slider.setValue(1.0)
 		self.alpha_slider.setDecimals(3)
 
@@ -95,8 +95,8 @@ class ClassifierWidget(QWidget, Styles):
 		layout.addLayout(slider_alpha_hbox)
 
 
-		self.features_cb = [QSearchableComboBox() for i in range(2)]
-		self.log_btns = [QPushButton() for i in range(2)]
+		self.features_cb = [QSearchableComboBox() for _ in range(2)]
+		self.log_btns = [QPushButton() for _ in range(2)]
 
 		for i in range(2):
 			hbox_feat = QHBoxLayout()
@@ -106,7 +106,7 @@ class ClassifierWidget(QWidget, Styles):
 			layout.addLayout(hbox_feat)
 
 			self.features_cb[i].clear()
-			self.features_cb[i].addItems(sorted(list(self.cols),key=str.lower))
+			self.features_cb[i].addItems(sorted(list(self.cols), key=str.lower))
 			self.features_cb[i].currentTextChanged.connect(self.update_props_scatter)
 			self.features_cb[i].setCurrentIndex(i)
 
@@ -134,15 +134,15 @@ class ClassifierWidget(QWidget, Styles):
 			self.time_corr.setEnabled(False)
 
 		time_prop_hbox = QHBoxLayout()
-		time_prop_hbox.addWidget(self.time_corr,alignment=Qt.AlignCenter)
+		time_prop_hbox.addWidget(self.time_corr, alignment=Qt.AlignCenter)
 
 		self.help_propagate_btn = QPushButton()
-		self.help_propagate_btn.setIcon(icon(MDI6.help_circle,color=self.help_color))
+		self.help_propagate_btn.setIcon(icon(MDI6.help_circle, color=self.help_color))
 		self.help_propagate_btn.setIconSize(QSize(20, 20))
 		self.help_propagate_btn.clicked.connect(self.help_propagate)
 		self.help_propagate_btn.setStyleSheet(self.button_select_all)
 		self.help_propagate_btn.setToolTip("Help.")
-		time_prop_hbox.addWidget(self.help_propagate_btn,5,alignment=Qt.AlignRight)
+		time_prop_hbox.addWidget(self.help_propagate_btn, 5, alignment=Qt.AlignRight)
 
 		layout.addLayout(time_prop_hbox)
 
@@ -154,23 +154,23 @@ class ClassifierWidget(QWidget, Styles):
 
 		time_corr_layout = QHBoxLayout()
 		time_corr_layout.addWidget(self.unique_state_btn, 33, alignment=Qt.AlignCenter)
-		time_corr_layout.addWidget(self.irreversible_event_btn, 33,alignment=Qt.AlignCenter)
-		time_corr_layout.addWidget(self.transient_event_btn, 33,alignment=Qt.AlignCenter)
+		time_corr_layout.addWidget(self.irreversible_event_btn, 33, alignment=Qt.AlignCenter)
+		time_corr_layout.addWidget(self.transient_event_btn, 33, 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_')]
+		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)
 
 		self.r2_slider = QLabeledDoubleSlider()
 		self.r2_slider.setValue(0.75)
-		self.r2_slider.setRange(0,1)
+		self.r2_slider.setRange(0, 1)
 		self.r2_slider.setSingleStep(0.01)
-		self.r2_slider.setOrientation(1)
+		self.r2_slider.setOrientation(Qt.Horizontal)
 		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.')
 
@@ -196,7 +196,7 @@ class ClassifierWidget(QWidget, Styles):
 			wg.setEnabled(False)
 
 		prereq_layout = QHBoxLayout()
-		prereq_layout.setContentsMargins(30,0,0,0)
+		prereq_layout.setContentsMargins(30, 0, 0, 0)
 		prereq_layout.addWidget(self.prereq_event_check, 20)
 		prereq_layout.addWidget(self.prereq_event_cb, 80)
 		layout.addLayout(prereq_layout)
@@ -212,7 +212,6 @@ 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():
@@ -270,11 +269,10 @@ class ClassifierWidget(QWidget, Styles):
 		Define properties scatter.
 		"""
 
-		self.fig_props, self.ax_props = plt.subplots(figsize=(4,4),tight_layout=True)
+		self.fig_props, self.ax_props = plt.subplots(figsize=(4, 4), tight_layout=True)
 		self.propscanvas = FigureCanvas(self.fig_props, interactive=True)
 		self.fig_props.set_facecolor('none')
-		self.fig_props.canvas.setStyleSheet("background-color: transparent;")
-		self.scat_props = self.ax_props.scatter([],[], color="k", alpha=self.currentAlpha)
+		self.scat_props = self.ax_props.scatter([], [], color="k", alpha=self.currentAlpha)
 		self.propscanvas.canvas.draw_idle()
 		self.propscanvas.canvas.setMinimumHeight(self.screen_height//5)
 
@@ -295,25 +293,24 @@ class ClassifierWidget(QWidget, Styles):
 				self.log_btns[0].setEnabled(True)
 
 			if np.any(self.df[self.features_cb[1].currentText()].to_numpy() <= 0.):
-				if self.ax_props.get_xscale()=='log':
+				if self.ax_props.get_xscale() == 'log':
 					self.log_btns[1].click()
 				self.log_btns[1].setEnabled(False)
 			else:
 				self.log_btns[1].setEnabled(True)
 		except Exception as e:
-			#print(e)
-			pass
+			print(e)
 
 		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_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)
 			else:
-				self.scat_props.set_offsets(self.df[[self.features_cb[1].currentText(),self.features_cb[0].currentText()]].to_numpy())
+				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)
 			
@@ -333,18 +330,18 @@ class ClassifierWidget(QWidget, Styles):
 				
 				x_padding = (max_x - min_x) * 0.05
 				y_padding = (max_y - min_y) * 0.05
-				if x_padding==0:
+				if x_padding == 0:
 					x_padding = 0.05
-				if y_padding==0:
+				if y_padding == 0:
 					y_padding = 0.05
 
-				if min_x==min_x and max_x==max_x:
-					if self.ax_props.get_xscale()=='linear':
+				if min_x == min_x and max_x == max_x:
+					if self.ax_props.get_xscale() == 'linear':
 						self.ax_props.set_xlim(min_x - x_padding, max_x + x_padding)
 					else:
 						self.ax_props.set_xlim(min_x, max_x)
-				if min_y==min_y and max_y==max_y:
-					if self.ax_props.get_yscale()=='linear':
+				if min_y == min_y and max_y == max_y:
+					if self.ax_props.get_yscale() == 'linear':
 						self.ax_props.set_ylim(min_y - y_padding, max_y + y_padding)
 					else:
 						self.ax_props.set_ylim(min_y, max_y)						
@@ -379,7 +376,7 @@ class ClassifierWidget(QWidget, Styles):
 		if self.df is None:
 			msgBox = QMessageBox()
 			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText(f"The query could not be understood. No filtering was applied. {e}")
+			msgBox.setText(f"The query could not be understood. No filtering was applied.")
 			msgBox.setWindowTitle("Warning")
 			msgBox.setStandardButtons(QMessageBox.Ok)
 			returnValue = msgBox.exec()
@@ -390,22 +387,18 @@ class ClassifierWidget(QWidget, Styles):
 		self.update_props_scatter(feature_changed=False)
 
 	def set_frame(self, value):
-		xlim=self.ax_props.get_xlim()
-		ylim=self.ax_props.get_ylim()
+		xlim = self.ax_props.get_xlim()
+		ylim = self.ax_props.get_ylim()
 		self.currentFrame = value
 		self.update_props_scatter(feature_changed=False)
 		self.ax_props.set_xlim(xlim)
 		self.ax_props.set_ylim(ylim)
 
-
 	def set_transparency(self, value):
-		xlim=self.ax_props.get_xlim()
-		ylim=self.ax_props.get_ylim()
+		xlim = self.ax_props.get_xlim()
+		ylim = self.ax_props.get_ylim()
 		self.currentAlpha = value
-		#fc = self.scat_props.get_facecolors()
-		#fc[:, 3] = value
-		#self.scat_props.set_facecolors(fc)
-		#self.propscanvas.canvas.draw_idle()
+
 		self.update_props_scatter(feature_changed=False)
 		self.ax_props.set_xlim(xlim)
 		self.ax_props.set_ylim(ylim)
@@ -413,12 +406,12 @@ class ClassifierWidget(QWidget, Styles):
 	def switch_projection(self):
 		if self.project_times:
 			self.project_times = False
-			self.project_times_btn.setIcon(icon(MDI6.math_integral,color="black"))
+			self.project_times_btn.setIcon(icon(MDI6.math_integral, color="black"))
 			self.project_times_btn.setIconSize(QSize(20, 20))
 			self.frame_slider.setEnabled(True)
 		else:
 			self.project_times = True
-			self.project_times_btn.setIcon(icon(MDI6.math_integral_box,color="black"))
+			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(feature_changed=False)
@@ -432,12 +425,13 @@ class ClassifierWidget(QWidget, Styles):
 
 		if self.time_corr.isChecked():
 			self.class_name_user = 'class_'+self.name_le.text()
-			print(f'User defined class name: {self.class_name_user}.')
+			print(f'User defined class name: {self.class_name_user}...')
 			if self.class_name_user in self.df.columns:
 
 				msgBox = QMessageBox()
 				msgBox.setIcon(QMessageBox.Information)
-				msgBox.setText(f"The class column {self.class_name_user} already exists in the table.\nProceeding will reclassify. Do you want to continue?")
+				msgBox.setText(f"The class column {self.class_name_user} already exists in the table.\nProceeding will "
+							   f"reclassify. Do you want to continue?")
 				msgBox.setWindowTitle("Warning")
 				msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
 				returnValue = msgBox.exec()
@@ -447,7 +441,6 @@ 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)
 
@@ -455,7 +448,7 @@ class ClassifierWidget(QWidget, Styles):
 			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(), transient_event=self.transient_event_btn.isChecked(),r2_threshold=self.r2_slider.value(), pre_event=pre_event)
+			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(), transient_event=self.transient_event_btn.isChecked(), r2_threshold=self.r2_slider.value(), pre_event=pre_event)
 		
 		else:
 			self.group_name_user = 'group_' + self.name_le.text()
@@ -465,7 +458,8 @@ class ClassifierWidget(QWidget, Styles):
 				msgBox = QMessageBox()
 				msgBox.setIcon(QMessageBox.Information)
 				msgBox.setText(
-					f"The group column {self.group_name_user} already exists in the table.\nProceeding will reclassify. Do you want to continue?")
+					f"The group column {self.group_name_user} already exists in the table.\nProceeding will "
+					f"reclassify. Do you want to continue?")
 				msgBox.setWindowTitle("Warning")
 				msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
 				returnValue = msgBox.exec()
@@ -477,18 +471,18 @@ class ClassifierWidget(QWidget, Styles):
 			name_map = {self.class_name: self.group_name_user}
 			self.df = self.df.drop(list(set(name_map.values()) & set(self.df.columns)), axis=1).rename(columns=name_map)
 			print(self.df.columns)
-			#self.df[self.group_name_user] = self.df[self.group_name_user].replace({0: 1, 1: 0})
+			# 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)
+			self.df = self.df.drop(['custom'], axis=1)
 		
-		self.fig_props.set_size_inches(4,3)
+		self.fig_props.set_size_inches(4, 3)
 		self.fig_props.suptitle(self.property_query_le.text(), fontsize=10)
 		self.fig_props.tight_layout()
-		for pos,pos_group in self.df.groupby('position'):
-			self.fig_props.savefig(pos+os.sep.join(['output',f'{self.class_name}.png']), bbox_inches='tight', dpi=300)
-			pos_group.to_csv(pos+os.sep.join(['output', 'tables', f'trajectories_{self.mode}.csv']), index=False)
+		for pos, pos_group in self.df.groupby('position'):
+			self.fig_props.savefig(str(pos)+os.sep.join(['output', f'{self.class_name}.png']), bbox_inches='tight', dpi=300)
+			pos_group.to_csv(str(pos)+os.sep.join(['output', 'tables', f'trajectories_{self.mode}.csv']), index=False)
 
 		self.parent_window.parent_window.update_position_options()
 		self.close()
@@ -500,7 +494,7 @@ class ClassifierWidget(QWidget, Styles):
 		Helper for segmentation strategy between threshold-based and Deep learning.
 		"""
 
-		dict_path = os.sep.join([get_software_location(),'celldetective','gui','help','propagate-classification.json'])
+		dict_path = os.sep.join([get_software_location(), 'celldetective', 'gui', 'help', 'propagate-classification.json'])
 
 		with open(dict_path) as f:
 			d = json.load(f)
@@ -524,53 +518,46 @@ class ClassifierWidget(QWidget, Styles):
 		Switch threshold histogram to log scale. Auto adjust.
 		"""
 
-		if i==1:
+		if i == 1:
 			try:
 				feat_x = self.features_cb[1].currentText()
 				min_x = self.df.dropna(subset=feat_x)[feat_x].min()
 				max_x = self.df.dropna(subset=feat_x)[feat_x].max()
 				x_padding = (max_x - min_x) * 0.05
-				if x_padding==0:
+				if x_padding == 0:
 					x_padding = 0.05
 
-				if self.ax_props.get_xscale()=='linear':
+				if self.ax_props.get_xscale() == 'linear':
 					self.ax_props.set_xlim(min_x, max_x)
 					self.ax_props.set_xscale('log')
-					self.log_btns[i].setIcon(icon(MDI6.math_log,color="#1565c0"))
+					self.log_btns[i].setIcon(icon(MDI6.math_log, color="#1565c0"))
 				else:
 					self.ax_props.set_xscale('linear')
 					self.ax_props.set_xlim(min_x - x_padding, max_x + x_padding)
-					self.log_btns[i].setIcon(icon(MDI6.math_log,color="black"))
+					self.log_btns[i].setIcon(icon(MDI6.math_log, color="black"))
 			except Exception as e:
 				print(e)
-		elif i==0:
+		elif i == 0:
 			try:
 				feat_y = self.features_cb[0].currentText()
 				min_y = self.df.dropna(subset=feat_y)[feat_y].min()
 				max_y = self.df.dropna(subset=feat_y)[feat_y].max()
 				y_padding = (max_y - min_y) * 0.05
-				if y_padding==0:
+				if y_padding == 0:
 					y_padding = 0.05
 
-				if self.ax_props.get_yscale()=='linear':
+				if self.ax_props.get_yscale() == 'linear':
 					self.ax_props.set_ylim(min_y, max_y)
 					self.ax_props.set_yscale('log')
-					self.log_btns[i].setIcon(icon(MDI6.math_log,color="#1565c0"))
+					self.log_btns[i].setIcon(icon(MDI6.math_log, color="#1565c0"))
 				else:
 					self.ax_props.set_yscale('linear')
 					self.ax_props.set_ylim(min_y - y_padding, max_y + y_padding)
-					self.log_btns[i].setIcon(icon(MDI6.math_log,color="black"))
+					self.log_btns[i].setIcon(icon(MDI6.math_log, color="black"))
 			except Exception as e:
 				print(e)
 
 		self.ax_props.autoscale()
 		self.propscanvas.canvas.draw_idle()
 
-		print('Done.')
-
-
-
-
-
-
-
+		print('Done.')