celldetective 1.4.2__py3-none-any.whl → 1.5.0b1__py3-none-any.whl

celldetective/gui/base_annotator.py

@@ -3,12 +3,20 @@ import os
 import numpy as np
 import pandas as pd
 from PyQt5.QtGui import QKeySequence
-from PyQt5.QtWidgets import QApplication, QCheckBox, QFileDialog, QLineEdit, QMessageBox, QHBoxLayout, QRadioButton, \
-	QShortcut, \
-	QVBoxLayout, \
-	QPushButton, \
-	QComboBox, \
-	QLabel
+from PyQt5.QtWidgets import (
+    QApplication,
+    QCheckBox,
+    QFileDialog,
+    QLineEdit,
+    QMessageBox,
+    QHBoxLayout,
+    QRadioButton,
+    QShortcut,
+    QVBoxLayout,
+    QPushButton,
+    QComboBox,
+    QLabel,
+)
 from PyQt5.QtCore import QSize, Qt
 import matplotlib.pyplot as plt
 from matplotlib.ticker import MultipleLocator
@@ -19,768 +27,893 @@ from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 import json
 
-from celldetective.gui import Styles, CelldetectiveWidget, CelldetectiveMainWindow
-from celldetective.utils import get_software_location
-from celldetective.io import auto_load_number_of_frames, extract_experiment_channels, get_experiment_metadata, \
-	get_experiment_labels, load_frames
-from celldetective.gui.gui_utils import FigureCanvas, center_window, color_from_status, color_from_class, ExportPlotBtn
+from celldetective.gui.base.styles import Styles
+from celldetective.gui.base.components import (
+    CelldetectiveWidget,
+    CelldetectiveMainWindow,
+)
+from celldetective import get_software_location
+from celldetective.utils.image_loaders import auto_load_number_of_frames, load_frames
+from celldetective.utils.experiment import (
+    extract_experiment_channels,
+    get_experiment_metadata,
+    get_experiment_labels,
+)
+from celldetective.gui.gui_utils import (
+    color_from_status,
+    color_from_class,
+    ExportPlotBtn,
+)
+from celldetective.gui.base.figure_canvas import FigureCanvas
+from celldetective.gui.base.utils import center_window
 import gc
 
+
 class BaseAnnotator(CelldetectiveMainWindow, Styles):
 
-	def __init__(self, parent_window=None, read_config=True):
-
-		super().__init__()
-		self.parent_window = parent_window
-		self.read_config = read_config
-		
-		self.mode = self.parent_window.mode
-		self.pos = self.parent_window.parent_window.pos
-		self.exp_dir = self.parent_window.exp_dir
-		self.PxToUm = self.parent_window.parent_window.PxToUm
-		self.n_signals = 3
-		self.soft_path = get_software_location()
-		self.recently_modified = False
-		self.selection = []
-		self.MinMaxScaler = MinMaxScaler()
-		self.fraction = 1
-		self.log_scale = False
-
-		self.instructions_path = self.exp_dir + os.sep.join(['configs', f'signal_annotator_config_{self.mode}.json'])
-		self.trajectories_path = self.pos + os.sep.join(['output','tables',f'trajectories_{self.mode}.csv'])
-
-		self.screen_height = self.parent_window.parent_window.parent_window.screen_height
-		self.screen_width = self.parent_window.parent_window.parent_window.screen_width
-		self.value_magnitude = 1
-		
-		self.setMinimumWidth(int(0.8 * self.screen_width))
-		self.setMinimumHeight(int(0.8 * self.screen_height))
-		
-		self.proceed = True
-		self.locate_stack()
-		if not self.proceed:
-			self.close()
-		else:
-			if self.read_config:
-				self.load_annotator_config()
-			self.locate_tracks()
-			self._init_base_widgets()
-	
-	def _init_base_widgets(self):
-		self._init_base_widgets_left()
-		self._init_base_widgets_right()
-	
-	def _init_base_widgets_right(self):
-		pass
-	
-	def _init_base_widgets_left(self):
-		
-		self.class_label = QLabel('event: ')
-		self.class_choice_cb = QComboBox()
-
-		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])
-		try:
-			self.class_cols.remove('class_id')
-		except Exception:
-			pass
-		try:
-			self.class_cols.remove('class_color')
-		except Exception:
-			pass
-
-		self.class_choice_cb.addItems(self.class_cols)
-		self.class_choice_cb.currentIndexChanged.connect(self.compute_status_and_colors)
-
-		self.add_class_btn = QPushButton('')
-		self.add_class_btn.setStyleSheet(self.button_select_all)
-		self.add_class_btn.setIcon(icon(MDI6.plus, color="black"))
-		self.add_class_btn.setToolTip("Add a new event class")
-		self.add_class_btn.setIconSize(QSize(20, 20))
-		self.add_class_btn.clicked.connect(self.create_new_event_class)
-
-		self.del_class_btn = QPushButton('')
-		self.del_class_btn.setStyleSheet(self.button_select_all)
-		self.del_class_btn.setIcon(icon(MDI6.delete, color="black"))
-		self.del_class_btn.setToolTip("Delete an event class")
-		self.del_class_btn.setIconSize(QSize(20, 20))
-		self.del_class_btn.clicked.connect(self.del_event_class)
-		
-		self.cell_info = QLabel('')
-
-		self.correct_btn = QPushButton('correct')
-		self.correct_btn.setIcon(icon(MDI6.redo_variant, color="white"))
-		self.correct_btn.setIconSize(QSize(20, 20))
-		self.correct_btn.setStyleSheet(self.button_style_sheet)
-		self.correct_btn.clicked.connect(self.show_annotation_buttons)
-		self.correct_btn.setEnabled(False)
-
-		self.cancel_btn = QPushButton('cancel')
-		self.cancel_btn.setStyleSheet(self.button_style_sheet_2)
-		self.cancel_btn.setShortcut(QKeySequence("Esc"))
-		self.cancel_btn.setEnabled(False)
-		self.cancel_btn.clicked.connect(self.cancel_selection)
-		
-		self._init_cell_fig_widgets()
-		
-		self.save_btn = QPushButton('Save')
-		self.save_btn.setStyleSheet(self.button_style_sheet)
-		self.save_btn.clicked.connect(self.save_trajectories)
-
-		self.export_btn = QPushButton('')
-		self.export_btn.setStyleSheet(self.button_select_all)
-		self.export_btn.clicked.connect(self.export_signals)
-		self.export_btn.setIcon(icon(MDI6.export, color="black"))
-		self.export_btn.setIconSize(QSize(25, 25))
-
-	def _init_cell_fig_widgets(self):
-		
-		self.generate_signal_choices()
-		self.create_cell_signal_canvas()
-		self.cell_fcanvas.setMinimumHeight(int(0.2 * self.screen_height))
-		
-		self.outliers_check = QCheckBox('Show outliers')
-		self.outliers_check.toggled.connect(self.show_outliers)
-		
-		self.normalize_features_btn = QPushButton('')
-		self.normalize_features_btn.setStyleSheet(self.button_select_all)
-		self.normalize_features_btn.setIcon(icon(MDI6.arrow_collapse_vertical, color="black"))
-		self.normalize_features_btn.setIconSize(QSize(25, 25))
-		self.normalize_features_btn.setFixedSize(QSize(30, 30))
-		self.normalize_features_btn.clicked.connect(self.normalize_features)
-		self.normalized_signals = False
-		
-		self.log_btn = QPushButton()
-		self.log_btn.setIcon(icon(MDI6.math_log, color="black"))
-		self.log_btn.setStyleSheet(self.button_select_all)
-		self.log_btn.clicked.connect(self.switch_to_log)
-	
-		self.export_plot_btn = ExportPlotBtn(self.cell_fig, export_dir = self.exp_dir)
-
-	def close_without_new_class(self):
-		self.newClassWidget.close()
-
-	def init_class_selection_block(self):
-		
-		self.class_hbox = QHBoxLayout()
-		self.class_hbox.setContentsMargins(0,0,0,0)
-		
-		self.class_hbox.addWidget(self.class_label, 25)
-		self.class_hbox.addWidget(self.class_choice_cb, 70)
-		self.class_hbox.addWidget(self.add_class_btn, 5)
-		self.class_hbox.addWidget(self.del_class_btn, 5)
-	
-	def init_options_block(self):
-		self.options_hbox = QHBoxLayout()
-		self.options_hbox.setContentsMargins(0, 0, 0, 0)
-		
-	def init_correction_block(self):
-		self.action_hbox = QHBoxLayout()
-		self.action_hbox.setContentsMargins(0,0,0,0)
-		
-		self.action_hbox.addWidget(self.correct_btn)
-		self.action_hbox.addWidget(self.cancel_btn)
-	
-	def init_plot_buttons_block(self):
-		self.plot_buttons_hbox = QHBoxLayout()
-		self.plot_buttons_hbox.setContentsMargins(0, 0, 0, 0)
-		self.plot_buttons_hbox.addWidget(QLabel(''), 90)
-		self.plot_buttons_hbox.addWidget(self.outliers_check, 5)
-		self.plot_buttons_hbox.addWidget(self.normalize_features_btn, 5)
-		self.plot_buttons_hbox.addWidget(self.log_btn, 5)
-		self.plot_buttons_hbox.addWidget(self.export_plot_btn, 5)
-	
-	def init_save_btn_block(self):
-		
-		self.btn_hbox = QHBoxLayout()
-		self.btn_hbox.setContentsMargins(0,10,0,0)
-		self.btn_hbox.addWidget(self.save_btn, 90)
-		self.btn_hbox.addWidget(self.export_btn, 10)
-
-	def populate_window(self):
-		
-		"""
-		Create the multibox design.
-
-		"""
-
-		# Main layout
-		self.button_widget = CelldetectiveWidget()
-		self.main_layout = QHBoxLayout()
-		self.button_widget.setLayout(self.main_layout)
-		self.main_layout.setContentsMargins(30, 30, 30, 30)
-		
-		# Left panel
-		self.left_panel = QVBoxLayout()
-		self.left_panel.setContentsMargins(30, 5, 30, 5)
-		self.left_panel.setSpacing(3)
-		
-		self.init_class_selection_block()
-		self.left_panel.addLayout(self.class_hbox, 5)
-		self.left_panel.addWidget(self.cell_info,10)
-		
-		self.init_options_block()
-		self.init_correction_block()
-		self.left_panel.addLayout(self.options_hbox, 5)
-		self.left_panel.addLayout(self.action_hbox, 5)
-		
-		self.left_panel.addWidget(self.cell_fcanvas, 45)
-		
-		self.init_plot_buttons_block()
-		self.left_panel.addLayout(self.plot_buttons_hbox, 5)
-	
-		signal_choice_vbox = QVBoxLayout()
-		signal_choice_vbox.setContentsMargins(30, 0, 30, 0)
-		for i in range(len(self.signal_choice_cb)):
-			hlayout = QHBoxLayout()
-			hlayout.addWidget(self.signal_choice_label[i], 20)
-			hlayout.addWidget(self.signal_choice_cb[i], 75)
-			signal_choice_vbox.addLayout(hlayout)
-
-		self.left_panel.addLayout(signal_choice_vbox, 15)
-		
-		self.init_save_btn_block()
-		self.left_panel.addLayout(self.btn_hbox, 5)
-
-		# Right panel
-		self.right_panel = QVBoxLayout()
-		
-		# add left/right to main layout
-		self.main_layout.addLayout(self.left_panel, 35)
-		self.main_layout.addLayout(self.right_panel, 65)
-		self.button_widget.adjustSize()
-		#self.compute_status_and_colors(0)
-
-		self.setCentralWidget(self.button_widget)
-		# self.show()
-		
-		self.del_shortcut = QShortcut(Qt.Key_Delete, self)  # QKeySequence("s")
-		self.del_shortcut.activated.connect(self.shortcut_suppr)
-		self.del_shortcut.setEnabled(False)
-
-		QApplication.processEvents()
-
-	def generate_signal_choices(self):
-
-		self.signal_choice_cb = [QSearchableComboBox() for i in range(self.n_signals)]
-		self.signal_choice_label = [QLabel(f'signal {i + 1}: ') for i in range(self.n_signals)]
-		# self.log_btns = [QPushButton() for i in range(self.n_signals)]
-
-		signals = list(self.df_tracks.columns)
-
-		to_remove = ['FRAME', 'ID', 'POSITION_X', 'POSITION_Y', 'TRACK_ID', 'antibody', 'cell_type',
-					 'class', 'class_color', 'class_id', 'concentration', 'dummy', 'generation',
-					 'group', 'group_color', 'index', 'parent', 'pharmaceutical_agent', 'pos_name',
-					 'position', 'root', 'state', 'status', 'status_color', 't', 't0', 'well',
-					 'well_index', 'well_name', 'x_anim', 'y_anim',
-					 ]
-
-		meta = get_experiment_metadata(self.exp_dir)
-		if meta is not None:
-			keys = list(meta.keys())
-			to_remove.extend(keys)
-
-		labels = get_experiment_labels(self.exp_dir)
-		if labels is not None:
-			keys = list(labels.keys())
-			to_remove.extend(labels)
-
-		for c in to_remove:
-			if c in signals:
-				signals.remove(c)
-
-		for i in range(len(self.signal_choice_cb)):
-			self.signal_choice_cb[i].addItems(['--'] + signals)
-			self.signal_choice_cb[i].setCurrentIndex(i + 1)
-			self.signal_choice_cb[i].currentIndexChanged.connect(self.plot_signals)
-	
-	def on_scatter_pick(self, event):
-		
-		self.event = event
-		
-		self.correct_btn.disconnect()
-		self.correct_btn.clicked.connect(self.show_annotation_buttons)
-		
-		print(f"{self.selection=}")
-		
-		ind = event.ind
-		
-		if len(ind) > 1:
-			# More than one point in vicinity
-			datax, datay = [self.positions[self.framedata][i, 0] for i in ind], [self.positions[self.framedata][i, 1]
-																				 for i in ind]
-			msx, msy = event.mouseevent.xdata, event.mouseevent.ydata
-			dist = np.sqrt((np.array(datax) - msx) ** 2 + (np.array(datay) - msy) ** 2)
-			ind = [ind[np.argmin(dist)]]
-		
-		if len(ind) > 0 and (len(self.selection) == 0):
-			
-			self.selection.append([ind[0], self.framedata])
-			self.select_single_cell(ind[0], self.framedata)
-		
-		elif len(ind) > 0 and len(self.selection) == 1:
-			self.cancel_btn.click()
-		else:
-			pass
-		
-		# self.draw_frame(self.current_frame)
-		# self.fcanvas.canvas.draw()
-		#
-	def load_annotator_config(self):
-
-		"""
-		Load settings from config or set default values.
-		"""
-
-		if os.path.exists(self.instructions_path):
-			with open(self.instructions_path, 'r') as f:
-
-				instructions = json.load(f)
-
-				if 'rgb_mode' in instructions:
-					self.rgb_mode = instructions['rgb_mode']
-				else:
-					self.rgb_mode = False
-
-				if 'percentile_mode' in instructions:
-					self.percentile_mode = instructions['percentile_mode']
-				else:
-					self.percentile_mode = True
-
-				if 'channels' in instructions:
-					self.target_channels = instructions['channels']
-				else:
-					self.target_channels = [[self.channel_names[0], 0.01, 99.99]]
-
-				if 'fraction' in instructions:
-					self.fraction = float(instructions['fraction'])
-				else:
-					self.fraction = 0.25
-
-				if 'interval' in instructions:
-					self.anim_interval = int(instructions['interval'])
-				else:
-					self.anim_interval = 1
-
-				if 'log' in instructions:
-					self.log_option = instructions['log']
-				else:
-					self.log_option = False
-		else:
-			self.rgb_mode = False
-			self.log_option = False
-			self.percentile_mode = True
-			self.target_channels = [[self.channel_names[0], 0.01, 99.99]]
-			self.fraction = 0.25
-			self.anim_interval = 1
-
-
-	def locate_stack(self):
-
-		"""
-		Locate the target movie.
-
-		"""
-
-		movies = glob(self.pos + os.sep.join(["movie", f"{self.parent_window.parent_window.movie_prefix}*.tif"]))
-
-		if len(movies) == 0:
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText("No movie is detected in the experiment folder.\nPlease check the stack prefix...")
-			msgBox.setWindowTitle("Warning")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				self.proceed = False
-				self.close()
-			else:
-				self.close()
-		else:
-			self.stack_path = movies[0]
-			self.len_movie = self.parent_window.parent_window.len_movie
-			len_movie_auto = auto_load_number_of_frames(self.stack_path)
-			if len_movie_auto is not None:
-				self.len_movie = len_movie_auto
-			exp_config = self.exp_dir + "config.ini"
-			self.channel_names, self.channels = extract_experiment_channels(self.exp_dir)
-			self.channel_names = np.array(self.channel_names)
-			self.channels = np.array(self.channels)
-			self.nbr_channels = len(self.channels)
-			self.img = load_frames(0, self.stack_path, normalize_input=False)
-	def create_cell_signal_canvas(self):
-
-		self.cell_fig, self.cell_ax = plt.subplots(tight_layout=True)
-		self.cell_fcanvas = FigureCanvas(self.cell_fig, interactive=True)
-		self.cell_ax.clear()
-
-		spacing = 0.5
-		minorLocator = MultipleLocator(1)
-		self.cell_ax.xaxis.set_minor_locator(minorLocator)
-		self.cell_ax.xaxis.set_major_locator(MultipleLocator(5))
-		self.cell_ax.grid(which='major')
-		self.cell_ax.set_xlabel("time [frame]")
-		self.cell_ax.set_ylabel("signal")
-
-		self.cell_fig.set_facecolor('none')  # or 'None'
-		self.cell_fig.canvas.setStyleSheet("background-color: transparent;")
-
-
-		self.lines = [
-			self.cell_ax.plot([np.linspace(0, self.len_movie - 1, self.len_movie)], [np.zeros((self.len_movie))])[0] for
-			i in range(len(self.signal_choice_cb))]
-		for i in range(len(self.lines)):
-			self.lines[i].set_label(f'signal {i}')
-
-		min_val, max_val = self.cell_ax.get_ylim()
-		self.line_dt, = self.cell_ax.plot([-1, -1], [min_val, max_val], c="k", linestyle="--")
-
-		self.cell_ax.set_xlim(0, self.len_movie)
-		self.cell_ax.legend(fontsize=8)
-		self.cell_fcanvas.canvas.draw()
-	
-	def resizeEvent(self, event):
-		
-		super().resizeEvent(event)
-		try:
-			self.cell_fig.tight_layout()
-		except:
-			pass
-
-	def locate_tracks(self):
-
-		"""
-		Locate the tracks.
-		"""
-
-		if not os.path.exists(self.trajectories_path):
-
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText("The trajectories cannot be detected.")
-			msgBox.setWindowTitle("Warning")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Yes:
-				self.close()
-		else:
-
-			# Load and prep tracks
-			self.df_tracks = pd.read_csv(self.trajectories_path)
-			self.df_tracks = self.df_tracks.sort_values(by=['TRACK_ID', 'FRAME'])
-			self.df_tracks.replace([np.inf, -np.inf], np.nan, inplace=True)
-
-			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])
-			try:
-				self.class_cols.remove('class_id')
-			except:
-				pass
-			try:
-				self.class_cols.remove('class_color')
-			except:
-				pass
-			if len(self.class_cols) > 0:
-				self.class_name = self.class_cols[0]
-				self.expected_status = 'status'
-				suffix = self.class_name.replace('class', '').replace('_', '')
-				if suffix != '':
-					self.expected_status += '_' + suffix
-					self.expected_time = 't_' + suffix
-				else:
-					self.expected_time = 't0'
-				self.time_name = self.expected_time
-				self.status_name = self.expected_status
-			else:
-				self.class_name = 'class'
-				self.time_name = 't0'
-				self.status_name = 'status'
-
-			if self.time_name in self.df_tracks.columns and self.class_name in self.df_tracks.columns and not self.status_name in self.df_tracks.columns:
-				# only create the status column if it does not exist to not erase static classification results
-				self.make_status_column()
-			elif self.time_name in self.df_tracks.columns and self.class_name in self.df_tracks.columns:
-				# all good, do nothing
-				pass
-			else:
-				if not self.status_name in self.df_tracks.columns:
-					self.df_tracks[self.status_name] = 0
-					self.df_tracks['status_color'] = color_from_status(0)
-					self.df_tracks['class_color'] = color_from_class(1)
-
-			if not self.class_name in self.df_tracks.columns:
-				self.df_tracks[self.class_name] = 1
-			if not self.time_name in self.df_tracks.columns:
-				self.df_tracks[self.time_name] = -1
-
-			self.df_tracks['status_color'] = [color_from_status(i) for i in self.df_tracks[self.status_name].to_numpy()]
-			self.df_tracks['class_color'] = [color_from_class(i) for i in self.df_tracks[self.class_name].to_numpy()]
-
-			self.df_tracks = self.df_tracks.dropna(subset=['POSITION_X', 'POSITION_Y'])
-			self.df_tracks['x_anim'] = self.df_tracks['POSITION_X'] * self.fraction
-			self.df_tracks['y_anim'] = self.df_tracks['POSITION_Y'] * self.fraction
-			self.df_tracks['x_anim'] = self.df_tracks['x_anim'].astype(int)
-			self.df_tracks['y_anim'] = self.df_tracks['y_anim'].astype(int)
-			
-			self.extract_scatter_from_trajectories()
-			self.track_of_interest = self.df_tracks['TRACK_ID'].min()
-
-			self.loc_t = []
-			self.loc_idx = []
-			for t in range(len(self.tracks)):
-				indices = np.where(self.tracks[t] == self.track_of_interest)[0]
-				if len(indices) > 0:
-					self.loc_t.append(t)
-					self.loc_idx.append(indices[0])
-
-			self.MinMaxScaler = MinMaxScaler()
-			self.columns_to_rescale = list(self.df_tracks.columns)
-
-			cols_to_remove = ['group', 'group_color', 'status', 'status_color', 'class_color', 'TRACK_ID', 'FRAME',
-							  'x_anim', 'y_anim', 't','dummy','group_color',
-							  'state', 'generation', 'root', 'parent', 'class_id', 'class', 't0', 'POSITION_X',
-							  'POSITION_Y', 'position', 'well', 'well_index', 'well_name', 'pos_name', 'index',
-							  'concentration', 'cell_type', 'antibody', 'pharmaceutical_agent', 'ID'] + self.class_cols
-
-			meta = get_experiment_metadata(self.exp_dir)
-			if meta is not None:
-				keys = list(meta.keys())
-				cols_to_remove.extend(keys)
-
-			labels = get_experiment_labels(self.exp_dir)
-			if labels is not None:
-				keys = list(labels.keys())
-				cols_to_remove.extend(labels)
-
-			cols = np.array(list(self.df_tracks.columns))
-			time_cols = np.array([c.startswith('t_') for c in cols])
-			time_cols = list(cols[time_cols])
-			cols_to_remove += time_cols
-			
-			status_cols = np.array([c.startswith('status_') for c in cols])
-			status_cols = list(cols[status_cols])
-			cols_to_remove += status_cols
-
-			for tr in cols_to_remove:
-				try:
-					self.columns_to_rescale.remove(tr)
-				except:
-					pass
-
-			x = self.df_tracks[self.columns_to_rescale].values
-			self.MinMaxScaler.fit(x)
-	
-	def del_event_class(self):
-
-		msgBox = QMessageBox()
-		msgBox.setIcon(QMessageBox.Warning)
-		msgBox.setText(
-			f"You are about to delete the class {self.class_choice_cb.currentText()}. The associated time and\nstatus will also be deleted. Do you still want to proceed?")
-		msgBox.setWindowTitle("Warning")
-		msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
-		returnValue = msgBox.exec()
-		if returnValue == QMessageBox.No:
-			return None
-		else:
-			class_to_delete = self.class_choice_cb.currentText()
-			time_to_delete = class_to_delete.replace('class', 't')
-			status_to_delete = class_to_delete.replace('class', 'status')
-			cols_to_delete = [class_to_delete, time_to_delete, status_to_delete]
-			for c in cols_to_delete:
-				try:
-					self.df_tracks = self.df_tracks.drop([c], axis=1)
-				except Exception as e:
-					print(e)
-			item_idx = self.class_choice_cb.findText(class_to_delete)
-			self.class_choice_cb.removeItem(item_idx)
-			
-	def normalize_features(self):
-
-		x = self.df_tracks[self.columns_to_rescale].values
-
-		if not self.normalized_signals:
-			x = self.MinMaxScaler.transform(x)
-			self.df_tracks[self.columns_to_rescale] = x
-			self.plot_signals()
-			self.normalized_signals = True
-			self.normalize_features_btn.setIcon(icon(MDI6.arrow_collapse_vertical, color="#1565c0"))
-			self.normalize_features_btn.setIconSize(QSize(25, 25))
-		else:
-			x = self.MinMaxScaler.inverse_transform(x)
-			self.df_tracks[self.columns_to_rescale] = x
-			self.plot_signals()
-			self.normalized_signals = False
-			self.normalize_features_btn.setIcon(icon(MDI6.arrow_collapse_vertical, color="black"))
-			self.normalize_features_btn.setIconSize(QSize(25, 25))
-
-	def switch_to_log(self):
-
-		"""
-		Better would be to create a log(quantity) and plot it...
-		"""
-
-		try:
-			if self.cell_ax.get_yscale()=='linear':
-				ymin,ymax = self.cell_ax.get_ylim()
-				self.cell_ax.set_yscale('log')
-				self.log_btn.setIcon(icon(MDI6.math_log,color="#1565c0"))
-				self.cell_ax.set_ylim(self.value_magnitude, ymax)
-				self.log_scale = True
-			else:
-				self.cell_ax.set_yscale('linear')
-				self.log_btn.setIcon(icon(MDI6.math_log,color="black"))
-				self.log_scale = False
-		except Exception as e:
-			print(e)
-
-		#self.cell_ax.autoscale()
-		self.cell_fcanvas.canvas.draw_idle()
-		
-	def start(self):
-		'''
-		Starts interactive animation. Adds the draw frame command to the GUI
-		handler, calls show to start the event loop.
-		'''
-		self.start_btn.setShortcut(QKeySequence(""))
-
-		self.last_frame_btn.setEnabled(True)
-		self.last_frame_btn.clicked.connect(self.set_last_frame)
-
-		self.first_frame_btn.setEnabled(True)
-		self.first_frame_btn.clicked.connect(self.set_first_frame)
-
-		self.start_btn.hide()
-		self.stop_btn.show()
-
-		self.anim.event_source.start()
-		self.stop_btn.clicked.connect(self.stop)
-		
-	def contrast_slider_action(self):
-
-		"""
-		Recontrast the imshow as the contrast slider is moved.
-		"""
-
-		self.vmin = self.contrast_slider.value()[0]
-		self.vmax = self.contrast_slider.value()[1]
-		self.im.set_clim(vmin=self.vmin, vmax=self.vmax)
-		self.fcanvas.canvas.draw_idle()
-		
-	def show_outliers(self):
-		if self.outliers_check.isChecked():
-			self.show_fliers = True
-			self.plot_signals()
-		else:
-			self.show_fliers = False
-			self.plot_signals()
-
-	def export_signals(self):
-
-		auto_dataset_name = self.pos.split(os.sep)[-4] + '_' + self.pos.split(os.sep)[-2] + '.npy'
-
-		if self.normalized_signals:
-			self.normalize_features_btn.click()
-
-		training_set = []
-		cols = self.df_tracks.columns
-		tracks = np.unique(self.df_tracks["TRACK_ID"].to_numpy())
-
-		for track in tracks:
-			# Add all signals at given track
-			signals = {}
-			for c in cols:
-				signals.update({c: self.df_tracks.loc[self.df_tracks["TRACK_ID"] == track, c].to_numpy()})
-			time_of_interest = self.df_tracks.loc[self.df_tracks["TRACK_ID"] == track, self.time_name].to_numpy()[0]
-			cclass = self.df_tracks.loc[self.df_tracks["TRACK_ID"] == track, self.class_name].to_numpy()[0]
-			signals.update({"time_of_interest": time_of_interest, "class": cclass})
-			# Here auto add all available channels
-			training_set.append(signals)
-
-		pathsave = QFileDialog.getSaveFileName(self, "Select file name", self.exp_dir + auto_dataset_name, ".npy")[0]
-		if pathsave != '':
-			if not pathsave.endswith(".npy"):
-				pathsave += ".npy"
-			try:
-				np.save(pathsave, training_set)
-				print(f'File successfully written in {pathsave}.')
-			except Exception as e:
-				print(f"Error {e}...")
-
-	def create_new_event_class(self):
-
-		# display qwidget to name the event
-		self.newClassWidget = CelldetectiveWidget()
-		self.newClassWidget.setWindowTitle('Create new event class')
-
-		layout = QVBoxLayout()
-		self.newClassWidget.setLayout(layout)
-		name_hbox = QHBoxLayout()
-		name_hbox.addWidget(QLabel('event name: '), 25)
-		self.class_name_le = QLineEdit('event')
-		name_hbox.addWidget(self.class_name_le, 75)
-		layout.addLayout(name_hbox)
-
-		class_labels = ['event', 'no event', 'else']
-		layout.addWidget(QLabel('prefill: '))
-		radio_box = QHBoxLayout()
-		self.class_option_rb = [QRadioButton() for i in range(3)]
-		for i, c in enumerate(self.class_option_rb):
-			if i == 0:
-				c.setChecked(True)
-			c.setText(class_labels[i])
-			radio_box.addWidget(c, 33, alignment=Qt.AlignCenter)
-		layout.addLayout(radio_box)
-
-		btn_hbox = QHBoxLayout()
-		submit_btn = QPushButton('submit')
-		cancel_btn = QPushButton('cancel')
-		btn_hbox.addWidget(cancel_btn, 50)
-		btn_hbox.addWidget(submit_btn, 50)
-		layout.addLayout(btn_hbox)
-
-		submit_btn.clicked.connect(self.write_new_event_class)
-		cancel_btn.clicked.connect(self.close_without_new_class)
-
-		self.newClassWidget.show()
-		center_window(self.newClassWidget)
-
-	def shortcut_suppr(self):
-		self.correct_btn.click()
-		self.suppr_btn.click()
-		self.correct_btn.click()
-
-	def closeEvent(self, event):
-		# result = QMessageBox.question(self,
-		# 			  "Confirm Exit...",
-		# 			  "Are you sure you want to exit ?",
-		# 			  QMessageBox.Yes| QMessageBox.No,
-		# 			  )
-		# del self.img
-		gc.collect()
-	
-	def save_trajectories(self):
-		# specific to signal/static annotator
-		print('Save trajectory function not implemented for BaseAnnotator class...')
-		
-	def cancel_selection(self):
-		print('we are in cancel selection...')
-		self.hide_annotation_buttons()
-		self.correct_btn.setEnabled(False)
-		self.correct_btn.setText('correct')
-		self.cancel_btn.setEnabled(False)
-
-		try:
-			self.selection.pop(0)
-		except Exception as e:
-			pass
-		
-		try:
-			for k, (t, idx) in enumerate(zip(self.loc_t, self.loc_idx)):
-				self.colors[t][idx, 0] = self.previous_color[k][0]
-				#self.colors[t][idx, 1] = self.previous_color[k][1]
-		except Exception as e:
-			pass
-		
+    def __init__(self, parent_window=None, read_config=True):
+
+        super().__init__()
+        self.parent_window = parent_window
+        self.read_config = read_config
+
+        self.mode = self.parent_window.mode
+        self.pos = self.parent_window.parent_window.pos
+        self.exp_dir = self.parent_window.exp_dir
+        self.PxToUm = self.parent_window.parent_window.PxToUm
+        self.n_signals = 3
+        self.soft_path = get_software_location()
+        self.recently_modified = False
+        self.selection = []
+        self.MinMaxScaler = MinMaxScaler()
+        self.fraction = 1
+        self.log_scale = False
+
+        self.instructions_path = self.exp_dir + os.sep.join(
+            ["configs", f"signal_annotator_config_{self.mode}.json"]
+        )
+        self.trajectories_path = self.pos + os.sep.join(
+            ["output", "tables", f"trajectories_{self.mode}.csv"]
+        )
+
+        self.screen_height = (
+            self.parent_window.parent_window.parent_window.screen_height
+        )
+        self.screen_width = self.parent_window.parent_window.parent_window.screen_width
+        self.value_magnitude = 1
+
+        self.setMinimumWidth(int(0.8 * self.screen_width))
+        self.setMinimumHeight(int(0.8 * self.screen_height))
+
+        self.proceed = True
+        self.locate_stack()
+        if not self.proceed:
+            self.close()
+        else:
+            if self.read_config:
+                self.load_annotator_config()
+            self.locate_tracks()
+            self._init_base_widgets()
+
+    def _init_base_widgets(self):
+        self._init_base_widgets_left()
+        self._init_base_widgets_right()
+
+    def _init_base_widgets_right(self):
+        pass
+
+    def _init_base_widgets_left(self):
+
+        self.class_label = QLabel("event: ")
+        self.class_choice_cb = QComboBox()
+
+        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])
+        try:
+            self.class_cols.remove("class_id")
+        except Exception:
+            pass
+        try:
+            self.class_cols.remove("class_color")
+        except Exception:
+            pass
+
+        self.class_choice_cb.addItems(self.class_cols)
+        self.class_choice_cb.currentIndexChanged.connect(self.compute_status_and_colors)
+
+        self.add_class_btn = QPushButton("")
+        self.add_class_btn.setStyleSheet(self.button_select_all)
+        self.add_class_btn.setIcon(icon(MDI6.plus, color="black"))
+        self.add_class_btn.setToolTip("Add a new event class")
+        self.add_class_btn.setIconSize(QSize(20, 20))
+        self.add_class_btn.clicked.connect(self.create_new_event_class)
+
+        self.del_class_btn = QPushButton("")
+        self.del_class_btn.setStyleSheet(self.button_select_all)
+        self.del_class_btn.setIcon(icon(MDI6.delete, color="black"))
+        self.del_class_btn.setToolTip("Delete an event class")
+        self.del_class_btn.setIconSize(QSize(20, 20))
+        self.del_class_btn.clicked.connect(self.del_event_class)
+
+        self.cell_info = QLabel("")
+
+        self.correct_btn = QPushButton("correct")
+        self.correct_btn.setIcon(icon(MDI6.redo_variant, color="white"))
+        self.correct_btn.setIconSize(QSize(20, 20))
+        self.correct_btn.setStyleSheet(self.button_style_sheet)
+        self.correct_btn.clicked.connect(self.show_annotation_buttons)
+        self.correct_btn.setEnabled(False)
+
+        self.cancel_btn = QPushButton("cancel")
+        self.cancel_btn.setStyleSheet(self.button_style_sheet_2)
+        self.cancel_btn.setShortcut(QKeySequence("Esc"))
+        self.cancel_btn.setEnabled(False)
+        self.cancel_btn.clicked.connect(self.cancel_selection)
+
+        self._init_cell_fig_widgets()
+
+        self.save_btn = QPushButton("Save")
+        self.save_btn.setStyleSheet(self.button_style_sheet)
+        self.save_btn.clicked.connect(self.save_trajectories)
+
+        self.export_btn = QPushButton("")
+        self.export_btn.setStyleSheet(self.button_select_all)
+        self.export_btn.clicked.connect(self.export_signals)
+        self.export_btn.setIcon(icon(MDI6.export, color="black"))
+        self.export_btn.setIconSize(QSize(25, 25))
+
+    def _init_cell_fig_widgets(self):
+
+        self.generate_signal_choices()
+        self.create_cell_signal_canvas()
+        self.cell_fcanvas.setMinimumHeight(int(0.2 * self.screen_height))
+
+        self.outliers_check = QCheckBox("Show outliers")
+        self.outliers_check.toggled.connect(self.show_outliers)
+
+        self.normalize_features_btn = QPushButton("")
+        self.normalize_features_btn.setStyleSheet(self.button_select_all)
+        self.normalize_features_btn.setIcon(
+            icon(MDI6.arrow_collapse_vertical, color="black")
+        )
+        self.normalize_features_btn.setIconSize(QSize(25, 25))
+        self.normalize_features_btn.setFixedSize(QSize(30, 30))
+        self.normalize_features_btn.clicked.connect(self.normalize_features)
+        self.normalized_signals = False
+
+        self.log_btn = QPushButton()
+        self.log_btn.setIcon(icon(MDI6.math_log, color="black"))
+        self.log_btn.setStyleSheet(self.button_select_all)
+        self.log_btn.clicked.connect(self.switch_to_log)
+
+        self.export_plot_btn = ExportPlotBtn(self.cell_fig, export_dir=self.exp_dir)
+
+    def close_without_new_class(self):
+        self.newClassWidget.close()
+
+    def init_class_selection_block(self):
+
+        self.class_hbox = QHBoxLayout()
+        self.class_hbox.setContentsMargins(0, 0, 0, 0)
+
+        self.class_hbox.addWidget(self.class_label, 25)
+        self.class_hbox.addWidget(self.class_choice_cb, 70)
+        self.class_hbox.addWidget(self.add_class_btn, 5)
+        self.class_hbox.addWidget(self.del_class_btn, 5)
+
+    def init_options_block(self):
+        self.options_hbox = QHBoxLayout()
+        self.options_hbox.setContentsMargins(0, 0, 0, 0)
+
+    def init_correction_block(self):
+        self.action_hbox = QHBoxLayout()
+        self.action_hbox.setContentsMargins(0, 0, 0, 0)
+
+        self.action_hbox.addWidget(self.correct_btn)
+        self.action_hbox.addWidget(self.cancel_btn)
+
+    def init_plot_buttons_block(self):
+        self.plot_buttons_hbox = QHBoxLayout()
+        self.plot_buttons_hbox.setContentsMargins(0, 0, 0, 0)
+        self.plot_buttons_hbox.addWidget(QLabel(""), 90)
+        self.plot_buttons_hbox.addWidget(self.outliers_check, 5)
+        self.plot_buttons_hbox.addWidget(self.normalize_features_btn, 5)
+        self.plot_buttons_hbox.addWidget(self.log_btn, 5)
+        self.plot_buttons_hbox.addWidget(self.export_plot_btn, 5)
+
+    def init_save_btn_block(self):
+
+        self.btn_hbox = QHBoxLayout()
+        self.btn_hbox.setContentsMargins(0, 10, 0, 0)
+        self.btn_hbox.addWidget(self.save_btn, 90)
+        self.btn_hbox.addWidget(self.export_btn, 10)
+
+    def populate_window(self):
+        """
+        Create the multibox design.
+
+        """
+
+        # Main layout
+        self.button_widget = CelldetectiveWidget()
+        self.main_layout = QHBoxLayout()
+        self.button_widget.setLayout(self.main_layout)
+        self.main_layout.setContentsMargins(30, 30, 30, 30)
+
+        # Left panel
+        self.left_panel = QVBoxLayout()
+        self.left_panel.setContentsMargins(30, 5, 30, 5)
+        self.left_panel.setSpacing(3)
+
+        self.init_class_selection_block()
+        self.left_panel.addLayout(self.class_hbox, 5)
+        self.left_panel.addWidget(self.cell_info, 10)
+
+        self.init_options_block()
+        self.init_correction_block()
+        self.left_panel.addLayout(self.options_hbox, 5)
+        self.left_panel.addLayout(self.action_hbox, 5)
+
+        self.left_panel.addWidget(self.cell_fcanvas, 45)
+
+        self.init_plot_buttons_block()
+        self.left_panel.addLayout(self.plot_buttons_hbox, 5)
+
+        signal_choice_vbox = QVBoxLayout()
+        signal_choice_vbox.setContentsMargins(30, 0, 30, 0)
+        for i in range(len(self.signal_choice_cb)):
+            hlayout = QHBoxLayout()
+            hlayout.addWidget(self.signal_choice_label[i], 20)
+            hlayout.addWidget(self.signal_choice_cb[i], 75)
+            signal_choice_vbox.addLayout(hlayout)
+
+        self.left_panel.addLayout(signal_choice_vbox, 15)
+
+        self.init_save_btn_block()
+        self.left_panel.addLayout(self.btn_hbox, 5)
+
+        # Right panel
+        self.right_panel = QVBoxLayout()
+
+        # add left/right to main layout
+        self.main_layout.addLayout(self.left_panel, 35)
+        self.main_layout.addLayout(self.right_panel, 65)
+        self.button_widget.adjustSize()
+        # self.compute_status_and_colors(0)
+
+        self.setCentralWidget(self.button_widget)
+        # self.show()
+
+        self.del_shortcut = QShortcut(Qt.Key_Delete, self)  # QKeySequence("s")
+        self.del_shortcut.activated.connect(self.shortcut_suppr)
+        self.del_shortcut.setEnabled(False)
+
+        QApplication.processEvents()
+
+    def generate_signal_choices(self):
+
+        self.signal_choice_cb = [QSearchableComboBox() for i in range(self.n_signals)]
+        self.signal_choice_label = [
+            QLabel(f"signal {i + 1}: ") for i in range(self.n_signals)
+        ]
+        # self.log_btns = [QPushButton() for i in range(self.n_signals)]
+
+        signals = list(self.df_tracks.columns)
+
+        to_remove = [
+            "FRAME",
+            "ID",
+            "POSITION_X",
+            "POSITION_Y",
+            "TRACK_ID",
+            "antibody",
+            "cell_type",
+            "class",
+            "class_color",
+            "class_id",
+            "concentration",
+            "dummy",
+            "generation",
+            "group",
+            "group_color",
+            "index",
+            "parent",
+            "pharmaceutical_agent",
+            "pos_name",
+            "position",
+            "root",
+            "state",
+            "status",
+            "status_color",
+            "t",
+            "t0",
+            "well",
+            "well_index",
+            "well_name",
+            "x_anim",
+            "y_anim",
+        ]
+
+        meta = get_experiment_metadata(self.exp_dir)
+        if meta is not None:
+            keys = list(meta.keys())
+            to_remove.extend(keys)
+
+        labels = get_experiment_labels(self.exp_dir)
+        if labels is not None:
+            keys = list(labels.keys())
+            to_remove.extend(labels)
+
+        for c in to_remove:
+            if c in signals:
+                signals.remove(c)
+
+        for i in range(len(self.signal_choice_cb)):
+            self.signal_choice_cb[i].addItems(["--"] + signals)
+            self.signal_choice_cb[i].setCurrentIndex(i + 1)
+            self.signal_choice_cb[i].currentIndexChanged.connect(self.plot_signals)
+
+    def on_scatter_pick(self, event):
+
+        self.event = event
+
+        self.correct_btn.disconnect()
+        self.correct_btn.clicked.connect(self.show_annotation_buttons)
+
+        print(f"{self.selection=}")
+
+        ind = event.ind
+
+        if len(ind) > 1:
+            # More than one point in vicinity
+            datax, datay = [self.positions[self.framedata][i, 0] for i in ind], [
+                self.positions[self.framedata][i, 1] for i in ind
+            ]
+            msx, msy = event.mouseevent.xdata, event.mouseevent.ydata
+            dist = np.sqrt((np.array(datax) - msx) ** 2 + (np.array(datay) - msy) ** 2)
+            ind = [ind[np.argmin(dist)]]
+
+        if len(ind) > 0 and (len(self.selection) == 0):
+
+            self.selection.append([ind[0], self.framedata])
+            self.select_single_cell(ind[0], self.framedata)
+
+        elif len(ind) > 0 and len(self.selection) == 1:
+            self.cancel_btn.click()
+        else:
+            pass
+
+        # self.draw_frame(self.current_frame)
+        # self.fcanvas.canvas.draw()
+        #
+
+    def load_annotator_config(self):
+        """
+        Load settings from config or set default values.
+        """
+
+        if os.path.exists(self.instructions_path):
+            with open(self.instructions_path, "r") as f:
+
+                instructions = json.load(f)
+
+                if "rgb_mode" in instructions:
+                    self.rgb_mode = instructions["rgb_mode"]
+                else:
+                    self.rgb_mode = False
+
+                if "percentile_mode" in instructions:
+                    self.percentile_mode = instructions["percentile_mode"]
+                else:
+                    self.percentile_mode = True
+
+                if "channels" in instructions:
+                    self.target_channels = instructions["channels"]
+                else:
+                    self.target_channels = [[self.channel_names[0], 0.01, 99.99]]
+
+                if "fraction" in instructions:
+                    self.fraction = float(instructions["fraction"])
+                else:
+                    self.fraction = 0.25
+
+                if "interval" in instructions:
+                    self.anim_interval = int(instructions["interval"])
+                else:
+                    self.anim_interval = 1
+
+                if "log" in instructions:
+                    self.log_option = instructions["log"]
+                else:
+                    self.log_option = False
+        else:
+            self.rgb_mode = False
+            self.log_option = False
+            self.percentile_mode = True
+            self.target_channels = [[self.channel_names[0], 0.01, 99.99]]
+            self.fraction = 0.25
+            self.anim_interval = 1
+
+    def locate_stack(self):
+        """
+        Locate the target movie.
+
+        """
+
+        movies = glob(
+            self.pos
+            + os.sep.join(
+                ["movie", f"{self.parent_window.parent_window.movie_prefix}*.tif"]
+            )
+        )
+
+        if len(movies) == 0:
+            msgBox = QMessageBox()
+            msgBox.setIcon(QMessageBox.Warning)
+            msgBox.setText(
+                "No movie is detected in the experiment folder.\nPlease check the stack prefix..."
+            )
+            msgBox.setWindowTitle("Warning")
+            msgBox.setStandardButtons(QMessageBox.Ok)
+            returnValue = msgBox.exec()
+            if returnValue == QMessageBox.Ok:
+                self.proceed = False
+                self.close()
+            else:
+                self.close()
+        else:
+            self.stack_path = movies[0]
+            self.len_movie = self.parent_window.parent_window.len_movie
+            len_movie_auto = auto_load_number_of_frames(self.stack_path)
+            if len_movie_auto is not None:
+                self.len_movie = len_movie_auto
+            exp_config = self.exp_dir + "config.ini"
+            self.channel_names, self.channels = extract_experiment_channels(
+                self.exp_dir
+            )
+            self.channel_names = np.array(self.channel_names)
+            self.channels = np.array(self.channels)
+            self.nbr_channels = len(self.channels)
+            self.img = load_frames(0, self.stack_path, normalize_input=False)
+
+    def create_cell_signal_canvas(self):
+
+        self.cell_fig, self.cell_ax = plt.subplots(tight_layout=True)
+        self.cell_fcanvas = FigureCanvas(self.cell_fig, interactive=True)
+        self.cell_ax.clear()
+
+        spacing = 0.5
+        minorLocator = MultipleLocator(1)
+        self.cell_ax.xaxis.set_minor_locator(minorLocator)
+        self.cell_ax.xaxis.set_major_locator(MultipleLocator(5))
+        self.cell_ax.grid(which="major")
+        self.cell_ax.set_xlabel("time [frame]")
+        self.cell_ax.set_ylabel("signal")
+
+        self.cell_fig.set_facecolor("none")  # or 'None'
+        self.cell_fig.canvas.setStyleSheet("background-color: transparent;")
+
+        self.lines = [
+            self.cell_ax.plot(
+                [np.linspace(0, self.len_movie - 1, self.len_movie)],
+                [np.zeros((self.len_movie))],
+            )[0]
+            for i in range(len(self.signal_choice_cb))
+        ]
+        for i in range(len(self.lines)):
+            self.lines[i].set_label(f"signal {i}")
+
+        min_val, max_val = self.cell_ax.get_ylim()
+        (self.line_dt,) = self.cell_ax.plot(
+            [-1, -1], [min_val, max_val], c="k", linestyle="--"
+        )
+
+        self.cell_ax.set_xlim(0, self.len_movie)
+        self.cell_ax.legend(fontsize=8)
+        self.cell_fcanvas.canvas.draw()
+
+    def resizeEvent(self, event):
+
+        super().resizeEvent(event)
+        try:
+            self.cell_fig.tight_layout()
+        except:
+            pass
+
+    def locate_tracks(self):
+        """
+        Locate the tracks.
+        """
+
+        if not os.path.exists(self.trajectories_path):
+
+            msgBox = QMessageBox()
+            msgBox.setIcon(QMessageBox.Warning)
+            msgBox.setText("The trajectories cannot be detected.")
+            msgBox.setWindowTitle("Warning")
+            msgBox.setStandardButtons(QMessageBox.Ok)
+            returnValue = msgBox.exec()
+            if returnValue == QMessageBox.Yes:
+                self.close()
+        else:
+
+            # Load and prep tracks
+            self.df_tracks = pd.read_csv(self.trajectories_path)
+            self.df_tracks = self.df_tracks.sort_values(by=["TRACK_ID", "FRAME"])
+            self.df_tracks.replace([np.inf, -np.inf], np.nan, inplace=True)
+
+            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])
+            try:
+                self.class_cols.remove("class_id")
+            except:
+                pass
+            try:
+                self.class_cols.remove("class_color")
+            except:
+                pass
+            if len(self.class_cols) > 0:
+                self.class_name = self.class_cols[0]
+                self.expected_status = "status"
+                suffix = self.class_name.replace("class", "").replace("_", "")
+                if suffix != "":
+                    self.expected_status += "_" + suffix
+                    self.expected_time = "t_" + suffix
+                else:
+                    self.expected_time = "t0"
+                self.time_name = self.expected_time
+                self.status_name = self.expected_status
+            else:
+                self.class_name = "class"
+                self.time_name = "t0"
+                self.status_name = "status"
+
+            if (
+                self.time_name in self.df_tracks.columns
+                and self.class_name in self.df_tracks.columns
+                and not self.status_name in self.df_tracks.columns
+            ):
+                # only create the status column if it does not exist to not erase static classification results
+                self.make_status_column()
+            elif (
+                self.time_name in self.df_tracks.columns
+                and self.class_name in self.df_tracks.columns
+            ):
+                # all good, do nothing
+                pass
+            else:
+                if not self.status_name in self.df_tracks.columns:
+                    self.df_tracks[self.status_name] = 0
+                    self.df_tracks["status_color"] = color_from_status(0)
+                    self.df_tracks["class_color"] = color_from_class(1)
+
+            if not self.class_name in self.df_tracks.columns:
+                self.df_tracks[self.class_name] = 1
+            if not self.time_name in self.df_tracks.columns:
+                self.df_tracks[self.time_name] = -1
+
+            self.df_tracks["status_color"] = [
+                color_from_status(i)
+                for i in self.df_tracks[self.status_name].to_numpy()
+            ]
+            self.df_tracks["class_color"] = [
+                color_from_class(i) for i in self.df_tracks[self.class_name].to_numpy()
+            ]
+
+            self.df_tracks = self.df_tracks.dropna(subset=["POSITION_X", "POSITION_Y"])
+            self.df_tracks["x_anim"] = self.df_tracks["POSITION_X"] * self.fraction
+            self.df_tracks["y_anim"] = self.df_tracks["POSITION_Y"] * self.fraction
+            self.df_tracks["x_anim"] = self.df_tracks["x_anim"].astype(int)
+            self.df_tracks["y_anim"] = self.df_tracks["y_anim"].astype(int)
+
+            self.extract_scatter_from_trajectories()
+            self.track_of_interest = self.df_tracks["TRACK_ID"].min()
+
+            self.loc_t = []
+            self.loc_idx = []
+            for t in range(len(self.tracks)):
+                indices = np.where(self.tracks[t] == self.track_of_interest)[0]
+                if len(indices) > 0:
+                    self.loc_t.append(t)
+                    self.loc_idx.append(indices[0])
+
+            self.MinMaxScaler = MinMaxScaler()
+            self.columns_to_rescale = list(self.df_tracks.columns)
+
+            cols_to_remove = [
+                "group",
+                "group_color",
+                "status",
+                "status_color",
+                "class_color",
+                "TRACK_ID",
+                "FRAME",
+                "x_anim",
+                "y_anim",
+                "t",
+                "dummy",
+                "group_color",
+                "state",
+                "generation",
+                "root",
+                "parent",
+                "class_id",
+                "class",
+                "t0",
+                "POSITION_X",
+                "POSITION_Y",
+                "position",
+                "well",
+                "well_index",
+                "well_name",
+                "pos_name",
+                "index",
+                "concentration",
+                "cell_type",
+                "antibody",
+                "pharmaceutical_agent",
+                "ID",
+            ] + self.class_cols
+
+            meta = get_experiment_metadata(self.exp_dir)
+            if meta is not None:
+                keys = list(meta.keys())
+                cols_to_remove.extend(keys)
+
+            labels = get_experiment_labels(self.exp_dir)
+            if labels is not None:
+                keys = list(labels.keys())
+                cols_to_remove.extend(labels)
+
+            cols = np.array(list(self.df_tracks.columns))
+            time_cols = np.array([c.startswith("t_") for c in cols])
+            time_cols = list(cols[time_cols])
+            cols_to_remove += time_cols
+
+            status_cols = np.array([c.startswith("status_") for c in cols])
+            status_cols = list(cols[status_cols])
+            cols_to_remove += status_cols
+
+            for tr in cols_to_remove:
+                try:
+                    self.columns_to_rescale.remove(tr)
+                except:
+                    pass
+
+            x = self.df_tracks[self.columns_to_rescale].values
+            self.MinMaxScaler.fit(x)
+
+    def del_event_class(self):
+
+        msgBox = QMessageBox()
+        msgBox.setIcon(QMessageBox.Warning)
+        msgBox.setText(
+            f"You are about to delete the class {self.class_choice_cb.currentText()}. The associated time and\nstatus will also be deleted. Do you still want to proceed?"
+        )
+        msgBox.setWindowTitle("Warning")
+        msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
+        returnValue = msgBox.exec()
+        if returnValue == QMessageBox.No:
+            return None
+        else:
+            class_to_delete = self.class_choice_cb.currentText()
+            time_to_delete = class_to_delete.replace("class", "t")
+            status_to_delete = class_to_delete.replace("class", "status")
+            cols_to_delete = [class_to_delete, time_to_delete, status_to_delete]
+            for c in cols_to_delete:
+                try:
+                    self.df_tracks = self.df_tracks.drop([c], axis=1)
+                except Exception as e:
+                    print(e)
+            item_idx = self.class_choice_cb.findText(class_to_delete)
+            self.class_choice_cb.removeItem(item_idx)
+
+    def normalize_features(self):
+
+        x = self.df_tracks[self.columns_to_rescale].values
+
+        if not self.normalized_signals:
+            x = self.MinMaxScaler.transform(x)
+            self.df_tracks[self.columns_to_rescale] = x
+            self.plot_signals()
+            self.normalized_signals = True
+            self.normalize_features_btn.setIcon(
+                icon(MDI6.arrow_collapse_vertical, color="#1565c0")
+            )
+            self.normalize_features_btn.setIconSize(QSize(25, 25))
+        else:
+            x = self.MinMaxScaler.inverse_transform(x)
+            self.df_tracks[self.columns_to_rescale] = x
+            self.plot_signals()
+            self.normalized_signals = False
+            self.normalize_features_btn.setIcon(
+                icon(MDI6.arrow_collapse_vertical, color="black")
+            )
+            self.normalize_features_btn.setIconSize(QSize(25, 25))
+
+    def switch_to_log(self):
+        """
+        Better would be to create a log(quantity) and plot it...
+        """
+
+        try:
+            if self.cell_ax.get_yscale() == "linear":
+                ymin, ymax = self.cell_ax.get_ylim()
+                self.cell_ax.set_yscale("log")
+                self.log_btn.setIcon(icon(MDI6.math_log, color="#1565c0"))
+                self.cell_ax.set_ylim(self.value_magnitude, ymax)
+                self.log_scale = True
+            else:
+                self.cell_ax.set_yscale("linear")
+                self.log_btn.setIcon(icon(MDI6.math_log, color="black"))
+                self.log_scale = False
+        except Exception as e:
+            print(e)
+
+        # self.cell_ax.autoscale()
+        self.cell_fcanvas.canvas.draw_idle()
+
+    def start(self):
+        """
+        Starts interactive animation. Adds the draw frame command to the GUI
+        handler, calls show to start the event loop.
+        """
+        self.start_btn.setShortcut(QKeySequence(""))
+
+        self.last_frame_btn.setEnabled(True)
+        self.last_frame_btn.clicked.connect(self.set_last_frame)
+
+        self.first_frame_btn.setEnabled(True)
+        self.first_frame_btn.clicked.connect(self.set_first_frame)
+
+        self.start_btn.hide()
+        self.stop_btn.show()
+
+        self.anim.event_source.start()
+        self.stop_btn.clicked.connect(self.stop)
+
+    def contrast_slider_action(self):
+        """
+        Recontrast the imshow as the contrast slider is moved.
+        """
+
+        self.vmin = self.contrast_slider.value()[0]
+        self.vmax = self.contrast_slider.value()[1]
+        self.im.set_clim(vmin=self.vmin, vmax=self.vmax)
+        self.fcanvas.canvas.draw_idle()
+
+    def show_outliers(self):
+        if self.outliers_check.isChecked():
+            self.show_fliers = True
+            self.plot_signals()
+        else:
+            self.show_fliers = False
+            self.plot_signals()
+
+    def export_signals(self):
+
+        auto_dataset_name = (
+            self.pos.split(os.sep)[-4] + "_" + self.pos.split(os.sep)[-2] + ".npy"
+        )
+
+        if self.normalized_signals:
+            self.normalize_features_btn.click()
+
+        training_set = []
+        cols = self.df_tracks.columns
+        tracks = np.unique(self.df_tracks["TRACK_ID"].to_numpy())
+
+        for track in tracks:
+            # Add all signals at given track
+            signals = {}
+            for c in cols:
+                signals.update(
+                    {
+                        c: self.df_tracks.loc[
+                            self.df_tracks["TRACK_ID"] == track, c
+                        ].to_numpy()
+                    }
+                )
+            time_of_interest = self.df_tracks.loc[
+                self.df_tracks["TRACK_ID"] == track, self.time_name
+            ].to_numpy()[0]
+            cclass = self.df_tracks.loc[
+                self.df_tracks["TRACK_ID"] == track, self.class_name
+            ].to_numpy()[0]
+            signals.update({"time_of_interest": time_of_interest, "class": cclass})
+            # Here auto add all available channels
+            training_set.append(signals)
+
+        pathsave = QFileDialog.getSaveFileName(
+            self, "Select file name", self.exp_dir + auto_dataset_name, ".npy"
+        )[0]
+        if pathsave != "":
+            if not pathsave.endswith(".npy"):
+                pathsave += ".npy"
+            try:
+                np.save(pathsave, training_set)
+                print(f"File successfully written in {pathsave}.")
+            except Exception as e:
+                print(f"Error {e}...")
+
+    def create_new_event_class(self):
+
+        # display qwidget to name the event
+        self.newClassWidget = CelldetectiveWidget()
+        self.newClassWidget.setWindowTitle("Create new event class")
+
+        layout = QVBoxLayout()
+        self.newClassWidget.setLayout(layout)
+        name_hbox = QHBoxLayout()
+        name_hbox.addWidget(QLabel("event name: "), 25)
+        self.class_name_le = QLineEdit("event")
+        name_hbox.addWidget(self.class_name_le, 75)
+        layout.addLayout(name_hbox)
+
+        class_labels = ["event", "no event", "else"]
+        layout.addWidget(QLabel("prefill: "))
+        radio_box = QHBoxLayout()
+        self.class_option_rb = [QRadioButton() for i in range(3)]
+        for i, c in enumerate(self.class_option_rb):
+            if i == 0:
+                c.setChecked(True)
+            c.setText(class_labels[i])
+            radio_box.addWidget(c, 33, alignment=Qt.AlignCenter)
+        layout.addLayout(radio_box)
+
+        btn_hbox = QHBoxLayout()
+        submit_btn = QPushButton("submit")
+        cancel_btn = QPushButton("cancel")
+        btn_hbox.addWidget(cancel_btn, 50)
+        btn_hbox.addWidget(submit_btn, 50)
+        layout.addLayout(btn_hbox)
+
+        submit_btn.clicked.connect(self.write_new_event_class)
+        cancel_btn.clicked.connect(self.close_without_new_class)
+
+        self.newClassWidget.show()
+        center_window(self.newClassWidget)
+
+    def shortcut_suppr(self):
+        self.correct_btn.click()
+        self.suppr_btn.click()
+        self.correct_btn.click()
+
+    def closeEvent(self, event):
+        # result = QMessageBox.question(self,
+        # 			  "Confirm Exit...",
+        # 			  "Are you sure you want to exit ?",
+        # 			  QMessageBox.Yes| QMessageBox.No,
+        # 			  )
+        # del self.img
+        gc.collect()
+
+    def save_trajectories(self):
+        # specific to signal/static annotator
+        print("Save trajectory function not implemented for BaseAnnotator class...")
+
+    def cancel_selection(self):
+        print("we are in cancel selection...")
+        self.hide_annotation_buttons()
+        self.correct_btn.setEnabled(False)
+        self.correct_btn.setText("correct")
+        self.cancel_btn.setEnabled(False)
+
+        try:
+            self.selection.pop(0)
+        except Exception as e:
+            pass
+
+        try:
+            for k, (t, idx) in enumerate(zip(self.loc_t, self.loc_idx)):
+                self.colors[t][idx, 0] = self.previous_color[k][0]
+                # self.colors[t][idx, 1] = self.previous_color[k][1]
+        except Exception as e:
+            pass