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

celldetective/gui/tableUI.py

@@ -1,499 +1,113 @@
-from PyQt5.QtWidgets import QRadioButton, QButtonGroup, QTableView, QAction, QMenu,QFileDialog, QLineEdit, QHBoxLayout, QPushButton, QVBoxLayout, QComboBox, QLabel, QCheckBox, QMessageBox
+from PyQt5.QtWidgets import (
+    QRadioButton,
+    QButtonGroup,
+    QTableView,
+    QAction,
+    QMenu,
+    QFileDialog,
+    QHBoxLayout,
+    QPushButton,
+    QVBoxLayout,
+    QComboBox,
+    QLabel,
+    QCheckBox,
+    QMessageBox,
+)
 from PyQt5.QtCore import Qt
-from PyQt5.QtGui import QBrush, QColor, QDoubleValidator
-import pandas as pd
-import matplotlib.pyplot as plt
-
-from celldetective.gui.table_ops.merge_groups import MergeGroupWidget
-
-plt.rcParams['svg.fonttype'] = 'none'
-from celldetective.gui.gui_utils import FigureCanvas, center_window, QHSeperationLine, GenericOpColWidget, PandasModel
-from celldetective.utils import differentiate_per_track, collapse_trajectories_by_status, test_2samp_generic, safe_log
-from celldetective.neighborhood import extract_neighborhood_in_pair_table
+from PyQt5.QtGui import QBrush, QColor
+
+from celldetective.gui.gui_utils import (
+    PandasModel,
+)
+from celldetective.gui.base.figure_canvas import FigureCanvas
+from celldetective.gui.base.utils import center_window
+from celldetective.gui.table_ops._maths import DifferentiateColWidget, OperationOnColsWidget, CalibrateColWidget, \
+    AbsColWidget, LogColWidget
+from celldetective.gui.table_ops._merge_one_hot import MergeOneHotWidget
+from celldetective.gui.table_ops._query_table import QueryWidget
+from celldetective.gui.table_ops._rename_col import RenameColWidget
 from celldetective.relative_measurements import expand_pair_table
+from celldetective.utils.data_cleaning import collapse_trajectories_by_status
+from celldetective.utils.stats import test_2samp_generic
 import numpy as np
-import seaborn as sns
-import matplotlib.cm as mcm
 import os
-from celldetective.gui import CelldetectiveWidget, CelldetectiveMainWindow
-from superqt import QColormapComboBox, QLabeledSlider, QSearchableComboBox
-from superqt.fonticon import icon
-from fonticon_mdi6 import MDI6
+from celldetective.gui.base.components import (
+    CelldetectiveWidget,
+    CelldetectiveMainWindow,
+    QHSeperationLine,
+)
+from superqt import QColormapComboBox, QSearchableComboBox
 from math import floor
+from celldetective import get_logger
+from celldetective.utils.types import test_bool_array
 
-from matplotlib import colormaps
-import matplotlib.cm
-
-
-class QueryWidget(CelldetectiveWidget):
-
-	def __init__(self, parent_window):
-
-		super().__init__()
-		self.parent_window = parent_window
-
-		self.setWindowTitle("Filter table")
-		# Create the QComboBox and add some items
+logger = get_logger(__name__)
 
-		layout = QHBoxLayout(self)
-		layout.setContentsMargins(30,30,30,30)
-		self.query_le = QLineEdit()
-		layout.addWidget(self.query_le, 70)
-
-		self.submit_btn = QPushButton('submit')
-		self.submit_btn.clicked.connect(self.filter_table)
-		layout.addWidget(self.submit_btn, 30)
-		center_window(self)
-
-	def filter_table(self):
-		try:
-			query_text = self.query_le.text() #.replace('class', '`class`')
-			tab = self.parent_window.data.query(query_text)
-			self.subtable = TableUI(tab, query_text, plot_mode="static", population=self.parent_window.population)
-			self.subtable.show()
-			self.close()
-		except Exception as e:
-			print(e)
-			return None
 
+class PivotTableUI(CelldetectiveWidget):
 
-class MergeOneHotWidget(CelldetectiveWidget):
+    def __init__(self, data, title="", mode=None, *args, **kwargs):
 
-	def __init__(self, parent_window, selected_columns=None):
+        CelldetectiveWidget.__init__(self, *args, **kwargs)
 
-		super().__init__()
-		self.parent_window = parent_window
-		self.selected_columns = selected_columns
+        self.data = data
+        self.title = title
+        self.mode = mode
 
-		self.setWindowTitle("Merge one-hot encoded columns...")
-		# Create the QComboBox and add some items
-		center_window(self)
-		
-		self.layout = QVBoxLayout(self)
-		self.layout.setContentsMargins(30,30,30,30)
-
-		if self.selected_columns is not None:
-			n_cols = len(self.selected_columns)
-		else:
-			n_cols = 2
-
-		name_hbox = QHBoxLayout()
-		name_hbox.addWidget(QLabel('New categorical column: '), 33)
-		self.new_col_le = QLineEdit()
-		self.new_col_le.setText('categorical_')
-		self.new_col_le.textChanged.connect(self.allow_merge)
-		name_hbox.addWidget(self.new_col_le, 66)
-		self.layout.addLayout(name_hbox)
-
-
-		self.layout.addWidget(QLabel('Source columns: '))
-
-		self.cbs = [QSearchableComboBox() for i in range(n_cols)]
-		self.cbs_layout = QVBoxLayout()
-
-		for i in range(n_cols):
-			lay = QHBoxLayout()
-			lay.addWidget(QLabel(f'column {i}: '), 33)
-			self.cbs[i].addItems(['--']+list(self.parent_window.data.columns))
-			if self.selected_columns is not None:
-				self.cbs[i].setCurrentText(self.selected_columns[i])
-			lay.addWidget(self.cbs[i], 66)
-			self.cbs_layout.addLayout(lay)
-
-		self.layout.addLayout(self.cbs_layout)
-
-		hbox = QHBoxLayout()
-		self.add_col_btn = QPushButton('Add column')
-		self.add_col_btn.clicked.connect(self.add_col)
-		self.add_col_btn.setStyleSheet(self.button_add)
-		self.add_col_btn.setIcon(icon(MDI6.plus,color="black"))
-
-		hbox.addWidget(QLabel(''), 50)
-		hbox.addWidget(self.add_col_btn, 50, alignment=Qt.AlignRight)
-		self.layout.addLayout(hbox)
-
-		self.submit_btn = QPushButton('Merge')
-		self.submit_btn.setStyleSheet(self.button_style_sheet)
-		self.submit_btn.clicked.connect(self.merge_cols)
-		self.layout.addWidget(self.submit_btn, 30)
-
-		self.setAttribute(Qt.WA_DeleteOnClose)
-
-	def add_col(self):
-		self.cbs.append(QSearchableComboBox())
-		self.cbs[-1].addItems(['--']+list(self.parent_window.data.columns))
-		lay = QHBoxLayout()
-		lay.addWidget(QLabel(f'column {len(self.cbs)-1}: '), 33)
-		lay.addWidget(self.cbs[-1], 66)
-		self.cbs_layout.addLayout(lay)	
-
-	def merge_cols(self):
-		
-		self.parent_window.data[self.new_col_le.text()] = self.parent_window.data.loc[:,list(self.selected_columns)].idxmax(axis=1)
-		self.parent_window.model = PandasModel(self.parent_window.data)
-		self.parent_window.table_view.setModel(self.parent_window.model)
-		self.close()
-
-	def allow_merge(self):
-
-		if self.new_col_le.text()=='':
-			self.submit_btn.setEnabled(False)
-		else:
-			self.submit_btn.setEnabled(True)
-
-
-class DifferentiateColWidget(CelldetectiveWidget):
-
-	def __init__(self, parent_window, column=None):
-
-		super().__init__()
-		self.parent_window = parent_window
-		self.column = column
-
-		self.setWindowTitle("d/dt")
-		# Create the QComboBox and add some items
-		center_window(self)
-		
-		layout = QVBoxLayout(self)
-		layout.setContentsMargins(30,30,30,30)
-
-		self.measurements_cb = QComboBox()
-		self.measurements_cb.addItems(list(self.parent_window.data.columns))
-		if self.column is not None:
-			idx = self.measurements_cb.findText(self.column)
-			self.measurements_cb.setCurrentIndex(idx)
-
-		measurement_layout = QHBoxLayout()
-		measurement_layout.addWidget(QLabel('measurements: '), 25)
-		measurement_layout.addWidget(self.measurements_cb, 75)
-		layout.addLayout(measurement_layout)
-
-		self.window_size_slider = QLabeledSlider()
-		self.window_size_slider.setRange(1,int(np.nanmax(self.parent_window.data.FRAME.to_numpy())))
-		self.window_size_slider.setValue(3)
-		window_layout = QHBoxLayout()
-		window_layout.addWidget(QLabel('window size: '), 25)
-		window_layout.addWidget(self.window_size_slider, 75)
-		layout.addLayout(window_layout)
-
-		self.backward_btn = QRadioButton('backward')
-		self.bi_btn = QRadioButton('bi')
-		self.bi_btn.click()
-		self.forward_btn = QRadioButton('forward')
-		self.mode_btn_group = QButtonGroup()
-		self.mode_btn_group.addButton(self.backward_btn)
-		self.mode_btn_group.addButton(self.bi_btn)
-		self.mode_btn_group.addButton(self.forward_btn)
-
-		mode_layout = QHBoxLayout()
-		mode_layout.addWidget(QLabel('mode: '),25)
-		mode_sublayout = QHBoxLayout()
-		mode_sublayout.addWidget(self.backward_btn, 33, alignment=Qt.AlignCenter)
-		mode_sublayout.addWidget(self.bi_btn, 33, alignment=Qt.AlignCenter)
-		mode_sublayout.addWidget(self.forward_btn, 33, alignment=Qt.AlignCenter)
-		mode_layout.addLayout(mode_sublayout, 75)
-		layout.addLayout(mode_layout)
-
-		self.submit_btn = QPushButton('Compute')
-		self.submit_btn.setStyleSheet(self.button_style_sheet)
-		self.submit_btn.clicked.connect(self.compute_derivative_and_add_new_column)
-		layout.addWidget(self.submit_btn, 30)
-
-		self.setAttribute(Qt.WA_DeleteOnClose)
-
-
-	def compute_derivative_and_add_new_column(self):
-		
-		if self.bi_btn.isChecked():
-			mode = 'bi'
-		elif self.forward_btn.isChecked():
-			mode = 'forward'
-		elif self.backward_btn.isChecked():
-			mode = 'backward'
-		self.parent_window.data = differentiate_per_track(self.parent_window.data,
-														  self.measurements_cb.currentText(),
-														  window_size=self.window_size_slider.value(),
-														  mode=mode)
-		self.parent_window.model = PandasModel(self.parent_window.data)
-		self.parent_window.table_view.setModel(self.parent_window.model)
-		self.close()
-
-
-
-class OperationOnColsWidget(CelldetectiveWidget):
-
-	def __init__(self, parent_window, column1=None, column2=None, operation='divide'):
-
-		super().__init__()
-		self.parent_window = parent_window
-		self.column1 = column1
-		self.column2 = column2
-		self.operation = operation
-
-		self.setWindowTitle(self.operation)
-		# Create the QComboBox and add some items
-		center_window(self)
-		
-		layout = QVBoxLayout(self)
-		layout.setContentsMargins(30,30,30,30)
-
-		self.col1_cb = QComboBox()
-		self.col1_cb.addItems(list(self.parent_window.data.columns))
-		if self.column1 is not None:
-			idx = self.col1_cb.findText(self.column1)
-			self.col1_cb.setCurrentIndex(idx)
-
-		numerator_layout = QHBoxLayout()
-		numerator_layout.addWidget(QLabel('column 1: '), 25)
-		numerator_layout.addWidget(self.col1_cb, 75)
-		layout.addLayout(numerator_layout)
-
-		self.col2_cb = QComboBox()
-		self.col2_cb.addItems(list(self.parent_window.data.columns))
-		if self.column2 is not None:
-			idx = self.col2_cb.findText(self.column2)
-			self.col2_cb.setCurrentIndex(idx)
-
-		denominator_layout = QHBoxLayout()
-		denominator_layout.addWidget(QLabel('column 2: '), 25)
-		denominator_layout.addWidget(self.col2_cb, 75)
-		layout.addLayout(denominator_layout)
-
-		self.submit_btn = QPushButton('Compute')
-		self.submit_btn.setStyleSheet(self.button_style_sheet)
-		self.submit_btn.clicked.connect(self.compute)
-		layout.addWidget(self.submit_btn, 30)
-
-		self.setAttribute(Qt.WA_DeleteOnClose)
-
-	def compute(self):
-
-		test = self._check_cols_before_operation()
-		if not test:
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText(f"Operation could not be performed, one of the column types is object...")
-			msgBox.setWindowTitle("Warning")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return None
-			else:
-				return None
-		else:
-			if self.operation=='divide':
-				name = f"{self.col1_txt}/{self.col2_txt}"
-				with np.errstate(divide='ignore', invalid='ignore'):
-					res = np.true_divide(self.col1, self.col2)
-					res[res == np.inf] = np.nan
-					res[self.col1!=self.col1] = np.nan
-					res[self.col2!=self.col2] = np.nan
-					self.parent_window.data[name] = res
-
-			elif self.operation=='multiply':
-				name = f"{self.col1_txt}*{self.col2_txt}"
-				res = np.multiply(self.col1, self.col2)
-
-			elif self.operation=='add':
-				name = f"{self.col1_txt}+{self.col2_txt}"
-				res = np.add(self.col1, self.col2)
-
-			elif self.operation=='subtract':
-				name = f"{self.col1_txt}-{self.col2_txt}"
-				res = np.subtract(self.col1, self.col2)				
-			
-			self.parent_window.data[name] = res
-			self.parent_window.model = PandasModel(self.parent_window.data)
-			self.parent_window.table_view.setModel(self.parent_window.model)
-			self.close()
-
-	def _check_cols_before_operation(self):
-
-		self.col1_txt = self.col1_cb.currentText()
-		self.col2_txt = self.col2_cb.currentText()
-		
-		self.col1 = self.parent_window.data[self.col1_txt].to_numpy()
-		self.col2 = self.parent_window.data[self.col2_txt].to_numpy()
-
-		test = np.all([self.col1.dtype!='O', self.col2.dtype!='O'])
-
-		return test
-
-
-class CalibrateColWidget(GenericOpColWidget):
-	
-	def __init__(self, *args, **kwargs):
-
-		super().__init__(title="Calibrate data", *args, **kwargs)	
-
-		self.floatValidator = QDoubleValidator()
-		self.calibration_factor_le = QLineEdit('1')
-		self.calibration_factor_le.setPlaceholderText('multiplicative calibration factor...')
-		self.calibration_factor_le.setValidator(self.floatValidator)
-
-		self.units_le = QLineEdit('um')
-		self.units_le.setPlaceholderText('units...')
-
-		self.calibration_factor_le.textChanged.connect(self.check_valid_params)
-		self.units_le.textChanged.connect(self.check_valid_params)
-
-		calib_layout = QHBoxLayout()
-		calib_layout.addWidget(QLabel('calibration factor: '), 33)
-		calib_layout.addWidget(self.calibration_factor_le, 66)
-		self.sublayout.addLayout(calib_layout)
-
-		units_layout = QHBoxLayout()
-		units_layout.addWidget(QLabel('units: '), 33)
-		units_layout.addWidget(self.units_le, 66)
-		self.sublayout.addLayout(units_layout)
-
-		# info_layout = QHBoxLayout()
-		# info_layout.addWidget(QLabel('For reference: '))
-		# self.sublayout.addLayout(info_layout)
-
-		# info_layout2 = QHBoxLayout()
-		# info_layout2.addWidget(QLabel(f'PxToUm = {self.parent_window.parent_window.parent_window.PxToUm}'), 50)
-		# info_layout2.addWidget(QLabel(f'FrameToMin = {self.parent_window.parent_window.parent_window.FrameToMin}'), 50)
-		# self.sublayout.addLayout(info_layout2)
-
-	def check_valid_params(self):
-		
-		try:
-			factor = float(self.calibration_factor_le.text().replace(',','.'))
-			factor_valid = True
-		except Exception as e:
-			factor_valid = False
-
-		if self.units_le.text()=='':
-			units_valid = False
-		else:
-			units_valid = True
-
-		if factor_valid and units_valid:
-			self.submit_btn.setEnabled(True)
-		else:
-			self.submit_btn.setEnabled(False)
-
-	def compute(self):
-		self.parent_window.data[self.measurements_cb.currentText()+f'[{self.units_le.text()}]'] = self.parent_window.data[self.measurements_cb.currentText()] * float(self.calibration_factor_le.text().replace(',','.'))
-		
-
-class AbsColWidget(GenericOpColWidget):
-	
-	def __init__(self, *args, **kwargs):
-
-		super().__init__(title="abs(.)", *args, **kwargs)
-
-	def compute(self):
-		self.parent_window.data['|'+self.measurements_cb.currentText()+'|'] = self.parent_window.data[self.measurements_cb.currentText()].abs()
+        self.setWindowTitle(title)
+        print("tab to show: ", self.data)
 
-class LogColWidget(GenericOpColWidget):
-	
-	def __init__(self, *args, **kwargs):
+        self.table = QTableView(self)
 
-		super().__init__(title="log10(.)", *args, **kwargs)
+        self.v_layout = QVBoxLayout()
+        self.information_label = QLabel("Information about color code...")
+        self.v_layout.addWidget(self.information_label)
+        self.v_layout.addWidget(self.table)
+        self.setLayout(self.v_layout)
 
-	def compute(self):
-		self.parent_window.data['log10('+self.measurements_cb.currentText()+')'] = safe_log(self.parent_window.data[self.measurements_cb.currentText()].values)
+        self.showdata()
 
+        if self.mode == "cliff":
+            self.color_cells_cliff()
+        elif self.mode == "pvalue":
+            self.color_cells_pvalue()
 
-class RenameColWidget(CelldetectiveWidget):
+        self.table.resizeColumnsToContents()
+        self.setAttribute(Qt.WA_DeleteOnClose)
+        center_window(self)
 
-	def __init__(self, parent_window, column=None):
+    def showdata(self):
+        self.model = PandasModel(self.data)
+        self.table.setModel(self.model)
 
-		super().__init__()
-		self.parent_window = parent_window
-		self.column = column
-		if self.column is None:
-			self.column = ''
+    def set_cell_color(self, row, column, color="red"):
+        self.model.change_color(
+            row, column, QBrush(QColor(color))
+        )  # eval(f"Qt.{color}")
 
-		self.setWindowTitle("Rename column")
-		# Create the QComboBox and add some items
-		center_window(self)
-		
-		layout = QHBoxLayout(self)
-		layout.setContentsMargins(30,30,30,30)
-		self.new_col_name = QLineEdit()
-		self.new_col_name.setText(self.column)
-		layout.addWidget(self.new_col_name, 70)
+    def color_cells_cliff(self):
 
-		self.submit_btn = QPushButton('rename')
-		self.submit_btn.clicked.connect(self.rename_col)
-		layout.addWidget(self.submit_btn, 30)
-		self.setAttribute(Qt.WA_DeleteOnClose)
+        color_codes = {
+            "negligible": "#eff3ff",  # Green
+            "small": "#bdd7e7",  # Yellow
+            "medium": "#6baed6",  # Orange
+            "large": "#2171b5",  # Red
+        }
 
-	def rename_col(self):
-		
-		old_name = self.column
-		new_name = self.new_col_name.text()
-		self.parent_window.data = self.parent_window.data.rename(columns={old_name: new_name})
-
-		self.parent_window.model = PandasModel(self.parent_window.data)
-		self.parent_window.table_view.setModel(self.parent_window.model)
-		self.close()
+        for i in range(self.data.shape[0]):
+            for j in range(self.data.shape[1]):
+                value = self.data.iloc[i, j]
+                if value < 0.147:
+                    self.set_cell_color(i, j, color_codes["negligible"])
+                elif value < 0.33:
+                    self.set_cell_color(i, j, color_codes["small"])
+                elif value < 0.474:
+                    self.set_cell_color(i, j, color_codes["medium"])
+                elif value >= 0.474:
+                    self.set_cell_color(i, j, color_codes["large"])
 
-class PivotTableUI(CelldetectiveWidget):
-
-	def __init__(self, data, title="", mode=None, *args, **kwargs):
-
-		CelldetectiveWidget.__init__(self, *args, **kwargs)
-		
-		self.data = data
-		self.title = title
-		self.mode = mode
-
-		self.setWindowTitle(title)
-		print("tab to show: ",self.data)
-
-		self.table = QTableView(self)
-
-		self.v_layout = QVBoxLayout()
-		self.information_label = QLabel('Information about color code...')
-		self.v_layout.addWidget(self.information_label)
-		self.v_layout.addWidget(self.table)
-		self.setLayout(self.v_layout)
-
-		self.showdata()
-
-		if self.mode=="cliff":
-			self.color_cells_cliff()
-		elif self.mode=="pvalue":
-			self.color_cells_pvalue()
-
-		self.table.resizeColumnsToContents()
-		self.setAttribute(Qt.WA_DeleteOnClose)
-		center_window(self)
-
-	def showdata(self):
-		self.model = PandasModel(self.data)
-		self.table.setModel(self.model)
-
-	def set_cell_color(self, row, column, color='red'):
-		self.model.change_color(row, column, QBrush(QColor(color))) #eval(f"Qt.{color}")
-
-	def color_cells_cliff(self):
-
-		color_codes = {
-			"negligible": "#eff3ff",  # Green
-			"small": "#bdd7e7",       # Yellow
-			"medium": "#6baed6",      # Orange
-			"large": "#2171b5"        # Red
-		}
-
-		for i in range(self.data.shape[0]):
-			for j in range(self.data.shape[1]):
-				value = self.data.iloc[i,j]
-				if value < 0.147:
-					self.set_cell_color(i,j,color_codes['negligible'])
-				elif value < 0.33:
-					self.set_cell_color(i,j,color_codes['small'])
-				elif value < 0.474:
-					self.set_cell_color(i,j,color_codes['medium'])
-				elif value >= 0.474:
-					self.set_cell_color(i,j,color_codes['large'])
-	
-		# Create the HTML text for the label
-		html_caption = f"""
+        # Create the HTML text for the label
+        html_caption = f"""
 		<p style="background-color:black; padding: 5px; font-weight:bold;">
 			<span style="color:{color_codes['negligible']}">Negligible</span>, 
 			<span style="color:{color_codes['small']}">Small</span>, 
@@ -501,33 +115,33 @@ class PivotTableUI(CelldetectiveWidget):
 			<span style="color:{color_codes['large']}">Large</span>
 		</p>
 		"""
-		self.information_label.setText(html_caption)
-
-	def color_cells_pvalue(self):
-
-		color_codes = {
-			"ns": "#fee5d9",
-			"*": "#fcae91",
-			"**": "#fb6a4a",
-			"***": "#de2d26",
-			"****": "#a50f15"
-		}
-
-		for i in range(self.data.shape[0]):
-			for j in range(self.data.shape[1]):
-				value = self.data.iloc[i,j]
-				if value <= 0.0001:
-					self.set_cell_color(i,j,color_codes['****'])
-				elif value <= 0.001:
-					self.set_cell_color(i,j,color_codes['***'])
-				elif value <= 0.01:
-					self.set_cell_color(i,j,color_codes['**'])
-				elif value <= 0.05:
-					self.set_cell_color(i,j,color_codes['*'])
-				elif value > 0.05:
-					self.set_cell_color(i,j,color_codes['ns'])
-		
-		html_caption = f"""
+        self.information_label.setText(html_caption)
+
+    def color_cells_pvalue(self):
+
+        color_codes = {
+            "ns": "#fee5d9",
+            "*": "#fcae91",
+            "**": "#fb6a4a",
+            "***": "#de2d26",
+            "****": "#a50f15",
+        }
+
+        for i in range(self.data.shape[0]):
+            for j in range(self.data.shape[1]):
+                value = self.data.iloc[i, j]
+                if value <= 0.0001:
+                    self.set_cell_color(i, j, color_codes["****"])
+                elif value <= 0.001:
+                    self.set_cell_color(i, j, color_codes["***"])
+                elif value <= 0.01:
+                    self.set_cell_color(i, j, color_codes["**"])
+                elif value <= 0.05:
+                    self.set_cell_color(i, j, color_codes["*"])
+                elif value > 0.05:
+                    self.set_cell_color(i, j, color_codes["ns"])
+
+        html_caption = f"""
 		<p style="background-color:black; padding: 5px; font-weight:bold;">
 			<span style="color:{color_codes['ns']}">ns</span>, 
 			<span style="color:{color_codes['*']}">*</span>, 
@@ -536,1207 +150,1557 @@ class PivotTableUI(CelldetectiveWidget):
 			<span style="color:{color_codes['****']}">****</span>
 		</p>
 		"""
-		self.information_label.setText(html_caption)
-
-class TableUI(CelldetectiveMainWindow):
-
-	def __init__(self, data, title, population='targets',plot_mode="plot_track_signals", save_inplace_option=False, collapse_tracks_option=True, *args, **kwargs):
-
-		CelldetectiveMainWindow.__init__(self, *args, **kwargs)
-
-		self.setWindowTitle(title)
-		self.setGeometry(100,100,1000,400)
-		center_window(self)
-		self.title = title
-		self.plot_mode = plot_mode
-		self.population = population
-		self.numerics = ['int16', 'int32', 'int64', 'float16', 'float32', 'float64']
-		self.groupby_cols = ['position', 'TRACK_ID']
-		self.tracks = False
-		self.save_inplace_option = save_inplace_option
-		self.collapse_tracks_option = collapse_tracks_option
-
-		if self.population=='pairs':
-			self.groupby_cols = ['position','reference_population', 'neighbor_population','REFERENCE_ID', 'NEIGHBOR_ID']
-			self.tracks = True # for now
-		else:
-			if 'TRACK_ID' in data.columns:
-				if not np.all(data['TRACK_ID'].isnull()):
-					self.tracks = True
-		
-		self.data = data
-
-		self._createMenuBar()
-		self._createActions()
-
-		self.table_view = QTableView(self)
-		self.setCentralWidget(self.table_view)
-
-		# Set the model for the table view
-
-		self.model = PandasModel(data)
-		self.table_view.setModel(self.model)
-		self.table_view.resizeColumnsToContents()
-
-	def resizeEvent(self, event):
-
-		super().resizeEvent(event)
-
-		try:
-			self.fig.tight_layout()
-		except:
-			pass
-
-	def _createActions(self):
-
-		self.save_as = QAction("&Save as...", self)
-		self.save_as.triggered.connect(self.save_as_csv)
-		self.save_as.setShortcut("Ctrl+s")
-		self.fileMenu.addAction(self.save_as)
-
-		if self.save_inplace_option:
-			self.save_inplace = QAction("&Save inplace...", self)
-			self.save_inplace.triggered.connect(self.save_as_csv_inplace_per_pos)
-			#self.save_inplace.setShortcut("Ctrl+s")
-			self.fileMenu.addAction(self.save_inplace)
-
-		self.plot_action = QAction("&Plot...", self)
-		self.plot_action.triggered.connect(self.plot)
-		self.plot_action.setShortcut("Ctrl+p")
-		self.fileMenu.addAction(self.plot_action)		
-
-		self.plot_inst_action = QAction("&Plot instantaneous...", self)
-		self.plot_inst_action.triggered.connect(self.plot_instantaneous)
-		self.plot_inst_action.setShortcut("Ctrl+i")
-		self.fileMenu.addAction(self.plot_inst_action)	
-
-		self.groupby_action = QAction("&Collapse tracks...", self)
-		self.groupby_action.triggered.connect(self.set_projection_mode_tracks)
-		self.groupby_action.setShortcut("Ctrl+g")
-		self.fileMenu.addAction(self.groupby_action)
-		if not self.tracks or not self.collapse_tracks_option:
-			self.groupby_action.setEnabled(False)
-
-		if self.population=='pairs':
-
-			self.groupby_pairs_in_neigh_action = QAction("&Collapse pairs in neighborhood...", self)
-			self.groupby_pairs_in_neigh_action.triggered.connect(self.collapse_pairs_in_neigh)
-			self.fileMenu.addAction(self.groupby_pairs_in_neigh_action)
-
-		if 'FRAME' in list(self.data.columns):
-			self.groupby_time_action = QAction("&Group by frames...", self)
-			self.groupby_time_action.triggered.connect(self.groupby_time_table)
-			self.groupby_time_action.setShortcut("Ctrl+t")
-			self.fileMenu.addAction(self.groupby_time_action)
-
-		self.query_action = QAction('Query...', self)
-		self.query_action.triggered.connect(self.perform_query)
-		self.fileMenu.addAction(self.query_action)
-
-		self.delete_action = QAction('&Delete...', self)
-		self.delete_action.triggered.connect(self.delete_columns)
-		self.delete_action.setShortcut(Qt.Key_Delete)
-		self.editMenu.addAction(self.delete_action)
-
-		self.rename_col_action = QAction('&Rename...', self)
-		self.rename_col_action.triggered.connect(self.rename_column)
-		#self.rename_col_action.setShortcut(Qt.Key_Delete)
-		self.editMenu.addAction(self.rename_col_action)
-
-		if self.population=='pairs':
-			self.merge_action = QAction('&Merge...', self)
-			self.merge_action.triggered.connect(self.merge_tables)
-			#self.rename_col_action.setShortcut(Qt.Key_Delete)
-			self.editMenu.addAction(self.merge_action)
-
-		self.calibrate_action = QAction('&Calibrate...', self)
-		self.calibrate_action.triggered.connect(self.calibrate_selected_feature)
-		self.calibrate_action.setShortcut("Ctrl+C")
-		self.mathMenu.addAction(self.calibrate_action)
-		
-		self.merge_classification_action = QAction('&Merge states...', self)
-		self.merge_classification_action.triggered.connect(self.merge_classification_features)
-		self.mathMenu.addAction(self.merge_classification_action)
-
-		self.derivative_action = QAction('&Differentiate...', self)
-		self.derivative_action.triggered.connect(self.differenciate_selected_feature)
-		self.derivative_action.setShortcut("Ctrl+D")
-		self.mathMenu.addAction(self.derivative_action)
-		if not self.tracks:
-			self.derivative_action.setEnabled(False)
-
-		self.abs_action = QAction('&Absolute value...', self)
-		self.abs_action.triggered.connect(self.take_abs_of_selected_feature)
-		#self.derivative_action.setShortcut("Ctrl+D")
-		self.mathMenu.addAction(self.abs_action)
-
-		self.log_action = QAction('&Log (decimal)...', self)
-		self.log_action.triggered.connect(self.take_log_of_selected_feature)
-		#self.derivative_action.setShortcut("Ctrl+D")
-		self.mathMenu.addAction(self.log_action)
-
-
-		self.divide_action = QAction('&Divide...', self)
-		self.divide_action.triggered.connect(self.divide_signals)
-		#self.derivative_action.setShortcut("Ctrl+D")
-		self.mathMenu.addAction(self.divide_action)
-
-		self.multiply_action = QAction('&Multiply...', self)
-		self.multiply_action.triggered.connect(self.multiply_signals)
-		#self.derivative_action.setShortcut("Ctrl+D")
-		self.mathMenu.addAction(self.multiply_action)	
-
-		self.add_action = QAction('&Add...', self)
-		self.add_action.triggered.connect(self.add_signals)
-		#self.derivative_action.setShortcut("Ctrl+D")
-		self.mathMenu.addAction(self.add_action)	
-
-		self.subtract_action = QAction('&Subtract...', self)
-		self.subtract_action.triggered.connect(self.subtract_signals)
-		#self.derivative_action.setShortcut("Ctrl+D")
-		self.mathMenu.addAction(self.subtract_action)	
-
-
-		# self.onehot_action = QAction('&One hot to categorical...', self)
-		# self.onehot_action.triggered.connect(self.transform_one_hot_cols_to_categorical)
-		# #self.onehot_action.setShortcut("Ctrl+D")
-		# self.mathMenu.addAction(self.onehot_action)		
-
-	def collapse_pairs_in_neigh(self):
-
-		self.selectNeighWidget = CelldetectiveWidget()
-		self.selectNeighWidget.setMinimumWidth(480)
-		self.selectNeighWidget.setWindowTitle('Set neighborhood of interest')
-		
-		layout = QVBoxLayout()
-		self.selectNeighWidget.setLayout(layout)
-
-		self.reference_lbl = QLabel('reference population: ')
-		self.reference_pop_cb = QComboBox()
-		ref_pops = self.data['reference_population'].unique()
-		self.reference_pop_cb.addItems(ref_pops)
-		self.reference_pop_cb.currentIndexChanged.connect(self.update_neighborhoods)
-
-		reference_hbox = QHBoxLayout()
-		reference_hbox.addWidget(self.reference_lbl, 33)
-		reference_hbox.addWidget(self.reference_pop_cb, 66)
-		layout.addLayout(reference_hbox)
-
-		self.neigh_lbl = QLabel('neighborhod: ')
-		self.neigh_cb = QComboBox()
-		neigh_cols = [c.replace('status_','') for c in list(self.data.loc[self.data['reference_population']==self.reference_pop_cb.currentText()].columns) if c.startswith('status_neighborhood')]
-		self.neigh_cb.addItems(neigh_cols)
-
-		neigh_hbox = QHBoxLayout()
-		neigh_hbox.addWidget(self.neigh_lbl, 33)
-		neigh_hbox.addWidget(self.neigh_cb, 66)
-		layout.addLayout(neigh_hbox)
-
-		contact_hbox = QHBoxLayout()
-		self.contact_only_check = QCheckBox('keep only pairs in contact')
-		self.contact_only_check.setChecked(True)
-		contact_hbox.addWidget(self.contact_only_check, alignment=Qt.AlignLeft)
-		layout.addLayout(contact_hbox)
-
-		self.groupby_pair_rb = QRadioButton('Group by pair')
-		self.groupby_reference_rb = QRadioButton('Group by reference')
-		self.groupby_pair_rb.setChecked(True)
-
-		groupby_hbox = QHBoxLayout()
-		groupby_hbox.addWidget(QLabel('collapse option: '), 33)
-		groupby_hbox.addWidget(self.groupby_pair_rb, (100-33)//2)
-		groupby_hbox.addWidget(self.groupby_reference_rb, (100-33)//2)
-		layout.addLayout(groupby_hbox)
-
-		self.apply_neigh_btn = QPushButton('Set')
-		self.apply_neigh_btn.setStyleSheet(self.button_style_sheet)
-		self.apply_neigh_btn.clicked.connect(self.prepare_table_at_neighborhood)
-
-		apply_hbox = QHBoxLayout()
-		apply_hbox.addWidget(QLabel(''),33)
-		apply_hbox.addWidget(self.apply_neigh_btn,66)
-		layout.addLayout(apply_hbox)
-
-		self.selectNeighWidget.show()
-		center_window(self.selectNeighWidget)
-
-	def prepare_table_at_neighborhood(self):
-
-		ref_pop = self.reference_pop_cb.currentText()
-		neighborhood = self.neigh_cb.currentText()
-		status_neigh = 'status_'+neighborhood
-
-		if 'self' in neighborhood:
-			neighbor_pop = ref_pop
-
-		neigh_col = neighborhood.replace('status_','')
-		if '_(' in neigh_col and ')_' in neigh_col:
-			neighbor_pop = neigh_col.split('_(')[-1].split(')_')[0].split('-')[-1]
-		else:
-			if ref_pop=='targets':
-				neighbor_pop = 'effectors'
-			if ref_pop=='effectors':
-				neighbor_pop = "targets"
-
-		data = extract_neighborhood_in_pair_table(self.data, neighborhood_key=neighborhood, contact_only=self.contact_only_check.isChecked(), reference_population=ref_pop)
-
-		if self.groupby_pair_rb.isChecked():
-			self.groupby_cols = ['position', 'REFERENCE_ID', 'NEIGHBOR_ID']
-		elif self.groupby_reference_rb.isChecked():
-			self.groupby_cols = ['position', 'REFERENCE_ID']
-
-		self.current_data = data
-		skip_projection = False
-		if 'reference_tracked' in list(self.current_data.columns):
-			print(f"{self.current_data['reference_tracked']=} {(self.current_data['reference_tracked']==False)=} {np.all(self.current_data['reference_tracked']==False)=}")
-			if np.all(self.current_data['reference_tracked'].astype(bool)==False):
-				# reference not tracked
-				if self.groupby_reference_rb.isChecked():
-					self.groupby_cols = ['position', 'FRAME', 'REFERENCE_ID']
-				elif self.groupby_pair_rb.isChecked():
-					print('The reference cells seem to not be tracked. No collapse can be performed.')
-					skip_projection=True
-			else:
-				if np.all(self.current_data['neighbors_tracked'].astype(bool)==False):
-					# neighbors not tracked
-					if self.groupby_pair_rb.isChecked():
-						print('The neighbor cells seem to not be tracked. No collapse can be performed.')
-						skip_projection=True				
-					elif self.groupby_reference_rb.isChecked():
-						self.groupby_cols = ['position', 'REFERENCE_ID'] # think about what would be best
-
-		if not skip_projection:
-			self.set_projection_mode_tracks()
-
-	def update_neighborhoods(self):
-		
-		neigh_cols = [c.replace('status_','') for c in list(self.data.loc[self.data['reference_population']==self.reference_pop_cb.currentText()].columns) if c.startswith('status_neighborhood')]
-		self.neigh_cb.clear()
-		self.neigh_cb.addItems(neigh_cols)		
-
-	def merge_tables(self):
-
-		df_expanded = expand_pair_table(self.data)
-		self.subtable = TableUI(df_expanded, 'merge', plot_mode = "static", population='pairs')
-		self.subtable.show()	
-
-
-	def delete_columns(self):
-
-		x = self.table_view.selectedIndexes()
-		col_idx = np.unique(np.array([l.column() for l in x]))
-		cols = np.array(list(self.data.columns))
-
-		msgBox = QMessageBox()
-		msgBox.setIcon(QMessageBox.Question)
-		msgBox.setText(f"You are about to delete columns {cols[col_idx]}... Do you want to proceed?")
-		msgBox.setWindowTitle("Info")
-		msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
-		returnValue = msgBox.exec()
-		if returnValue == QMessageBox.No:
-			return None
-
-		self.data = self.data.drop(list(cols[col_idx]),axis=1)
-		self.model = PandasModel(self.data)
-		self.table_view.setModel(self.model)
-
-	def rename_column(self):
-
-		x = self.table_view.selectedIndexes()
-		col_idx = np.unique(np.array([l.column() for l in x]))
-
-		if len(col_idx) == 0:
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Question)
-			msgBox.setText(f"Please select a column first.")
-			msgBox.setWindowTitle("Warning")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return None
-			else:
-				return None
-			
-		cols = np.array(list(self.data.columns))
-		selected_col = str(cols[col_idx][0])
-
-		self.renameWidget = RenameColWidget(self, selected_col)
-		self.renameWidget.show()
-
-	def save_as_csv_inplace_per_pos(self):
-
-		print("Saving each table in its respective position folder...")
-		for pos,pos_group in self.data.groupby(['position']):
-			invalid_cols = [c for c in list(pos_group.columns) if c.startswith('Unnamed')]
-			if len(invalid_cols)>0:
-				pos_group = pos_group.drop(invalid_cols, axis=1)
-			pos_group.to_csv(pos[0]+os.sep.join(['output', 'tables', f'trajectories_{self.population}.csv']), index=False)
-		print("Done...")
-
-	def divide_signals(self):
-
-		x = self.table_view.selectedIndexes()
-		col_idx = np.unique(np.array([l.column() for l in x]))
-		if isinstance(col_idx, (list, np.ndarray)):
-			cols = np.array(list(self.data.columns))
-			if len(col_idx)>0:
-				selected_col1 = str(cols[col_idx[0]])
-				if len(col_idx)>1:
-					selected_col2 = str(cols[col_idx[1]])
-				else:
-					selected_col2 = None
-			else:
-				selected_col1 = None
-				selected_col2 = None
-		else:
-			selected_col1 = None
-			selected_col2 = None
-
-		self.divWidget = OperationOnColsWidget(self, column1=selected_col1, column2=selected_col2, operation='divide')
-		self.divWidget.show()
-
-
-	def multiply_signals(self):
-
-		x = self.table_view.selectedIndexes()
-		col_idx = np.unique(np.array([l.column() for l in x]))
-		if isinstance(col_idx, (list, np.ndarray)):
-			cols = np.array(list(self.data.columns))
-			if len(col_idx)>0:
-				selected_col1 = str(cols[col_idx[0]])
-				if len(col_idx)>1:
-					selected_col2 = str(cols[col_idx[1]])
-				else:
-					selected_col2 = None
-			else:
-				selected_col1 = None
-				selected_col2 = None
-		else:
-			selected_col1 = None
-			selected_col2 = None
-
-		self.mulWidget = OperationOnColsWidget(self, column1=selected_col1, column2=selected_col2, operation='multiply')
-		self.mulWidget.show()
-
-	def add_signals(self):
-
-		x = self.table_view.selectedIndexes()
-		col_idx = np.unique(np.array([l.column() for l in x]))
-		if isinstance(col_idx, (list, np.ndarray)):
-			cols = np.array(list(self.data.columns))
-			if len(col_idx)>0:
-				selected_col1 = str(cols[col_idx[0]])
-				if len(col_idx)>1:
-					selected_col2 = str(cols[col_idx[1]])
-				else:
-					selected_col2 = None
-			else:
-				selected_col1 = None
-				selected_col2 = None
-		else:
-			selected_col1 = None
-			selected_col2 = None
-
-		self.addiWidget = OperationOnColsWidget(self, column1=selected_col1, column2=selected_col2, operation='add')
-		self.addiWidget.show()
-
-	def subtract_signals(self):
-
-		x = self.table_view.selectedIndexes()
-		col_idx = np.unique(np.array([l.column() for l in x]))
-		if isinstance(col_idx, (list, np.ndarray)):
-			cols = np.array(list(self.data.columns))
-			if len(col_idx)>0:
-				selected_col1 = str(cols[col_idx[0]])
-				if len(col_idx)>1:
-					selected_col2 = str(cols[col_idx[1]])
-				else:
-					selected_col2 = None
-			else:
-				selected_col1 = None
-				selected_col2 = None
-		else:
-			selected_col1 = None
-			selected_col2 = None
-
-		self.subWidget = OperationOnColsWidget(self, column1=selected_col1, column2=selected_col2, operation='subtract')
-		self.subWidget.show()
-
-
-	def differenciate_selected_feature(self):
-		
-		# check only one col selected and assert is numerical
-		# open widget to select window parameters, directionality
-		# create new col
-		
-		x = self.table_view.selectedIndexes()
-		col_idx = np.unique(np.array([l.column() for l in x]))
-		if isinstance(col_idx, (list, np.ndarray)):
-			cols = np.array(list(self.data.columns))
-			if len(col_idx)>0:
-				selected_col = str(cols[col_idx[0]])
-			else:
-				selected_col = None
-		else:
-			selected_col = None
-
-		self.diffWidget = DifferentiateColWidget(self, selected_col)
-		self.diffWidget.show()
-
-	def take_log_of_selected_feature(self):
-		
-		# check only one col selected and assert is numerical
-		# open widget to select window parameters, directionality
-		# create new col
-		
-		x = self.table_view.selectedIndexes()
-		col_idx = np.unique(np.array([l.column() for l in x]))
-		if isinstance(col_idx, (list, np.ndarray)):
-			cols = np.array(list(self.data.columns))
-			if len(col_idx)>0:
-				selected_col = str(cols[col_idx[0]])
-			else:
-				selected_col = None
-		else:
-			selected_col = None
-
-		self.LogWidget = LogColWidget(self, selected_col)
-		self.LogWidget.show()
-		
-	def merge_classification_features(self):
-		
-		x = self.table_view.selectedIndexes()
-		col_idx = np.unique(np.array([l.column() for l in x]))
-		
-		col_selection = []
-		if isinstance(col_idx, (list, np.ndarray)):
-			cols = np.array(list(self.data.columns))
-			if len(col_idx) > 0:
-				selected_cols = cols[col_idx]
-				col_selection.extend(selected_cols)
-		
-		self.merge_classification_widget = MergeGroupWidget(self, columns = col_selection)
-		self.merge_classification_widget.show()
-
-
-	def calibrate_selected_feature(self):
-		
-		x = self.table_view.selectedIndexes()
-		col_idx = np.unique(np.array([l.column() for l in x]))
-		if isinstance(col_idx, (list, np.ndarray)):
-			cols = np.array(list(self.data.columns))
-			if len(col_idx)>0:
-				selected_col = str(cols[col_idx[0]])
-			else:
-				selected_col = None
-		else:
-			selected_col = None
-
-		self.calWidget = CalibrateColWidget(self, selected_col)
-		self.calWidget.show()
-
-
-	def take_abs_of_selected_feature(self):
-		
-		# check only one col selected and assert is numerical
-		# open widget to select window parameters, directionality
-		# create new col
-		
-		x = self.table_view.selectedIndexes()
-		col_idx = np.unique(np.array([l.column() for l in x]))
-		if isinstance(col_idx, (list, np.ndarray)):
-			cols = np.array(list(self.data.columns))
-			if len(col_idx)>0:
-				selected_col = str(cols[col_idx[0]])
-			else:
-				selected_col = None
-		else:
-			selected_col = None
-
-		self.absWidget = AbsColWidget(self, selected_col)
-		self.absWidget.show()
-
-
-	def transform_one_hot_cols_to_categorical(self):
-
-		x = self.table_view.selectedIndexes()
-		col_idx = np.unique(np.array([l.column() for l in x]))
-		selected_cols = None
-		if isinstance(col_idx, (list, np.ndarray)):
-			cols = np.array(list(self.data.columns))
-			if len(col_idx)>0:
-				selected_col = str(cols[col_idx[0]])
-
-		self.mergewidget = MergeOneHotWidget(self, selected_columns=selected_cols)
-		self.mergewidget.show()
-
-
-	def groupby_time_table(self):
-
-		"""
-		
-		Perform a time average across each track for all features
-
-		"""
+        self.information_label.setText(html_caption)
 
-		num_df = self.data.select_dtypes(include=self.numerics)
 
-		timeseries = num_df.groupby(["FRAME"]).sum().copy()
-		timeseries["timeline"] = timeseries.index
-		self.subtable = TableUI(timeseries,"Group by frames", plot_mode="plot_timeseries")
-		self.subtable.show()
-
-	def perform_query(self):
-
-		"""
-		
-		Perform a time average across each track for all features
+class TableUI(CelldetectiveMainWindow):
 
-		"""
-		self.query_widget = QueryWidget(self)
-		self.query_widget.show()
-
-		# num_df = self.data.select_dtypes(include=self.numerics)
-
-		# timeseries = num_df.groupby("FRAME").mean().copy()
-		# timeseries["timeline"] = timeseries.index
-		# self.subtable = TableUI(timeseries,"Group by frames", plot_mode="plot_timeseries")
-		# self.subtable.show()
-
-	def set_projection_mode_neigh(self):
-
-		self.groupby_cols = ['position', 'reference_population', 'neighbor_population', 'NEIGHBOR_ID', 'FRAME']
-		self.current_data = self.data
-		self.set_projection_mode_tracks()
-
-	def set_projection_mode_ref(self):
-		
-		self.groupby_cols = ['position', 'reference_population', 'neighbor_population', 'REFERENCE_ID', 'FRAME']
-		self.current_data = self.data
-		self.set_projection_mode_tracks()
-
-	def set_projection_mode_tracks(self):
-		
-		self.current_data = self.data
-
-		self.projectionWidget = CelldetectiveWidget()
-		self.projectionWidget.setMinimumWidth(500)
-		self.projectionWidget.setWindowTitle('Set projection mode')
-		
-		layout = QVBoxLayout()
-		self.projectionWidget.setLayout(layout)
-
-		self.projection_option = QRadioButton('global operation: ')
-		self.projection_option.setToolTip('Collapse the cell track measurements with an operation over each track.')
-		self.projection_option.setChecked(True)
-		self.projection_option.toggled.connect(self.enable_projection_options)
-		self.projection_op_cb = QComboBox()
-		self.projection_op_cb.addItems(['mean','median','min','max','first','last','prod','sum'])
-
-		projection_layout = QHBoxLayout()
-		projection_layout.addWidget(self.projection_option, 33)
-		projection_layout.addWidget(self.projection_op_cb, 66)
-		layout.addLayout(projection_layout)
-
-		self.event_time_option = QRadioButton('@event time: ')
-		self.event_time_option.setToolTip('Pick the measurements at a specific event time.')
-		self.event_time_option.toggled.connect(self.enable_projection_options)
-		self.event_times_cb = QComboBox()
-		cols = np.array(self.data.columns)
-		time_cols = np.array([c.startswith('t_') for c in cols])
-		time_cols = list(cols[time_cols])
-		if 't0' in list(self.data.columns):
-			time_cols.append('t0')
-		self.event_times_cb.addItems(time_cols)
-		self.event_times_cb.setEnabled(False)
-
-		event_time_layout = QHBoxLayout()
-		event_time_layout.addWidget(self.event_time_option, 33)
-		event_time_layout.addWidget(self.event_times_cb, 66)
-		layout.addLayout(event_time_layout)
-
-
-		self.per_status_option = QRadioButton('per status: ')
-		self.per_status_option.setToolTip('Collapse the cell track measurements independently for each of the cell state.')
-		self.per_status_option.toggled.connect(self.enable_projection_options)
-		self.per_status_cb = QComboBox()
-		self.status_operation = QComboBox()
-		self.status_operation.setEnabled(False)
-		self.status_operation.addItems(['mean','median','min','max', 'prod', 'sum'])
-
-		status_cols = np.array([c.startswith('status_') or c.startswith('group_') for c in cols])
-		status_cols = list(cols[status_cols])
-		if 'status' in list(self.data.columns):
-			status_cols.append('status')
-		self.per_status_cb.addItems(status_cols)
-		self.per_status_cb.setEnabled(False)
-
-		per_status_layout = QHBoxLayout()
-		per_status_layout.addWidget(self.per_status_option, 33)
-		per_status_layout.addWidget(self.per_status_cb, 66)
-		layout.addLayout(per_status_layout)
-
-		status_operation_layout = QHBoxLayout()
-		status_operation_layout.addWidget(QLabel('operation: '), 33, alignment=Qt.AlignRight)
-		status_operation_layout.addWidget(self.status_operation, 66)
-		layout.addLayout(status_operation_layout)
-
-		self.btn_projection_group = QButtonGroup()
-		self.btn_projection_group.addButton(self.projection_option)
-		self.btn_projection_group.addButton(self.event_time_option)
-		self.btn_projection_group.addButton(self.per_status_option)
-
-		apply_layout = QHBoxLayout()
-
-		self.set_projection_btn = QPushButton('Apply')
-		self.set_projection_btn.setStyleSheet(self.button_style_sheet)
-		self.set_projection_btn.clicked.connect(self.set_proj_mode)
-		apply_layout.addWidget(QLabel(''), 33)
-		apply_layout.addWidget(self.set_projection_btn,33)
-		apply_layout.addWidget(QLabel(''),33)
-		layout.addLayout(apply_layout)
-
-		self.projectionWidget.show()
-		center_window(self.projectionWidget)
-
-	def enable_projection_options(self):
-
-		if self.projection_option.isChecked():
-			self.projection_op_cb.setEnabled(True)
-			self.event_times_cb.setEnabled(False)
-			self.per_status_cb.setEnabled(False)
-			self.status_operation.setEnabled(False)
-		elif self.event_time_option.isChecked():
-			self.projection_op_cb.setEnabled(False)
-			self.event_times_cb.setEnabled(True)
-			self.per_status_cb.setEnabled(False)
-			self.status_operation.setEnabled(False)
-		elif self.per_status_option.isChecked():
-			self.projection_op_cb.setEnabled(False)
-			self.event_times_cb.setEnabled(False)
-			self.per_status_cb.setEnabled(True)
-			self.status_operation.setEnabled(True)
-
-	def set_1D_plot_params(self):
-
-		self.plot1Dparams = CelldetectiveWidget()
-		self.plot1Dparams.setWindowTitle('Set 1D plot parameters')
-		
-		layout = QVBoxLayout()
-		self.plot1Dparams.setLayout(layout)
-
-		layout.addWidget(QLabel('Representations: '))
-		self.hist_check = QCheckBox('histogram')
-		self.kde_check = QCheckBox('KDE plot')
-		self.count_check = QCheckBox('countplot')
-		self.ecdf_check = QCheckBox('ECDF plot')
-		self.line_check = QCheckBox('line plot')
-		self.scat_check = QCheckBox('scatter plot')
-		self.swarm_check = QCheckBox('swarm')
-		self.violin_check = QCheckBox('violin')
-		self.strip_check = QCheckBox('strip')
-		self.box_check = QCheckBox('boxplot')
-		self.boxenplot_check = QCheckBox('boxenplot')
-
-		self.sep_line = QHSeperationLine()
-		self.pvalue_check = QCheckBox("Compute KS test p-value?")
-		self.effect_size_check = QCheckBox("Compute effect size?\n(Cliff's Delta)")
-
-		layout.addWidget(self.hist_check)
-		layout.addWidget(self.kde_check)
-		layout.addWidget(self.count_check)
-		layout.addWidget(self.ecdf_check)
-		layout.addWidget(self.line_check)
-		layout.addWidget(self.scat_check)
-		layout.addWidget(self.swarm_check)
-		layout.addWidget(self.violin_check)
-		layout.addWidget(self.strip_check)
-		layout.addWidget(self.box_check)
-		layout.addWidget(self.boxenplot_check)
-		layout.addWidget(self.sep_line)
-		layout.addWidget(self.pvalue_check)
-		layout.addWidget(self.effect_size_check)
-
-		self.x_cb = QSearchableComboBox()
-		self.x_cb.addItems(['--']+list(self.data.columns))
-
-		self.y_cb = QSearchableComboBox()
-		self.y_cb.addItems(['--']+list(self.data.columns))
-
-		self.hue_cb = QSearchableComboBox()
-		self.hue_cb.addItems(['--']+list(self.data.columns))
-		idx = self.hue_cb.findText('--')
-		self.hue_cb.setCurrentIndex(idx)
-
-		# Set selected column
-
-		try:
-			x = self.table_view.selectedIndexes()
-			col_idx = np.array([l.column() for l in x])
-			row_idx = np.array([l.row() for l in x])
-			column_names = self.data.columns
-			unique_cols = np.unique(col_idx)[0]
-			y = column_names[unique_cols]
-			idx = self.y_cb.findText(y)
-			self.y_cb.setCurrentIndex(idx)
-		except:
-			pass
-
-		hbox = QHBoxLayout()
-		hbox.addWidget(QLabel('x: '), 33)
-		hbox.addWidget(self.x_cb, 66)
-		layout.addLayout(hbox)
-
-		hbox = QHBoxLayout()
-		hbox.addWidget(QLabel('y: '), 33)
-		hbox.addWidget(self.y_cb, 66)
-		layout.addLayout(hbox)
-
-		hbox = QHBoxLayout()
-		hbox.addWidget(QLabel('hue: '), 33)
-		hbox.addWidget(self.hue_cb, 66)
-		layout.addLayout(hbox)
-
-		self.cmap_cb = QColormapComboBox()
-		all_cms = list(colormaps)
-		for cm in all_cms:
-			if hasattr(matplotlib.cm, str(cm).lower()):
-				try:
-					self.cmap_cb.addColormap(cm.lower())
-				except:
-					pass
-					
-		hbox = QHBoxLayout()
-		hbox.addWidget(QLabel('colormap: '), 33)
-		hbox.addWidget(self.cmap_cb, 66)
-		layout.addLayout(hbox)
-
-		self.plot1d_btn = QPushButton('set')
-		self.plot1d_btn.setStyleSheet(self.button_style_sheet)
-		self.plot1d_btn.clicked.connect(self.plot1d)
-		layout.addWidget(self.plot1d_btn)
-
-		self.plot1Dparams.show()
-		center_window(self.plot1Dparams)
-
-
-	def plot1d(self):
-
-		self.x_option = False
-		if self.x_cb.currentText()!='--':
-			self.x_option = True
-			self.x = self.x_cb.currentText()
-
-		self.fig, self.ax = plt.subplots(1,1,figsize=(4,3))
-		self.plot1dWindow = FigureCanvas(self.fig, title="scatter")
-		self.ax.clear()
-
-		cmap = getattr(mcm, self.cmap_cb.currentText())
-
-		try:
-			self.hue_variable = self.hue_cb.currentText()
-			colors = [cmap(i / len(self.data[self.hue_variable].unique())) for i in range(len(self.data[self.hue_variable].unique()))]
-		except:
-			colors = None
-
-		if self.hue_cb.currentText()=='--':
-			self.hue_variable = None
-
-		if self.y_cb.currentText()=='--':
-			self.y = None
-		else:
-			self.y = self.y_cb.currentText()
-
-		if self.x_cb.currentText()=='--':
-			self.x = None
-		else:
-			self.x = self.x_cb.currentText()
-
-		legend=True
-		
-		if self.hist_check.isChecked():
-			if self.x is not None:
-				sns.histplot(data=self.data, x=self.x, hue=self.hue_variable, legend=legend, ax=self.ax, palette=colors, kde=True, common_norm=False, stat='density')
-				legend = False
-			elif self.x is None and self.y is not None:
-				sns.histplot(data=self.data, x=self.y, hue=self.hue_variable, legend=legend, ax=self.ax, palette=colors, kde=True, common_norm=False, stat='density')
-				legend = False
-			else:
-				pass
-
-		if self.kde_check.isChecked():
-			if self.x is not None:
-				sns.kdeplot(data=self.data, x=self.x, hue=self.hue_variable, legend=legend, ax=self.ax, palette=colors, cut=0)
-				legend = False
-			elif self.x is None and self.y is not None:
-				sns.kdeplot(data=self.data, x=self.y, hue=self.hue_variable, legend=legend, ax=self.ax, palette=colors, cut=0)
-				legend = False	
-			else:
-				pass
-
-		if self.count_check.isChecked():
-			sns.countplot(data=self.data, x=self.x, hue=self.hue_variable, legend=legend, ax=self.ax, palette=colors)
-			legend = False
-
-
-		if self.ecdf_check.isChecked():
-			if self.x is not None:
-				sns.ecdfplot(data=self.data, x=self.x, hue=self.hue_variable, legend=legend, ax=self.ax, palette=colors)
-				legend = False
-			elif self.x is None and self.y is not None:
-				sns.ecdfplot(data=self.data, x=self.y, hue=self.hue_variable, legend=legend, ax=self.ax, palette=colors)
-				legend = False
-			else:
-				pass
-				
-		if self.line_check.isChecked():
-			if self.x_option:
-				sns.lineplot(data=self.data, x=self.x,y=self.y, hue=self.hue_variable,legend=legend, ax=self.ax, palette=colors)
-				legend = False
-			else:
-				print('please provide a -x variable...')
-				pass
-
-		if self.scat_check.isChecked():
-			if self.x_option:
-				sns.scatterplot(data=self.data, x=self.x,y=self.y, hue=self.hue_variable,legend=legend, ax=self.ax, palette=colors)
-				legend = False
-			else:
-				print('please provide a -x variable...')
-				pass
-
-		if self.swarm_check.isChecked():
-			if self.x_option:
-				sns.swarmplot(data=self.data, x=self.x,y=self.y,dodge=True, hue=self.hue_variable,legend=legend, ax=self.ax, palette=colors)
-				legend = False
-			else:
-				sns.swarmplot(data=self.data, y=self.y,dodge=True, hue=self.hue_variable,legend=legend, ax=self.ax, palette=colors)
-				legend = False
-
-		if self.violin_check.isChecked():
-			if self.x_option:
-				sns.violinplot(data=self.data,x=self.x, y=self.y,dodge=True, ax=self.ax, hue=self.hue_variable, legend=legend, palette=colors)
-				legend = False
-			else:
-				sns.violinplot(data=self.data, y=self.y,dodge=True, hue=self.hue_variable,legend=legend, ax=self.ax, palette=colors, cut=0)
-				legend = False
-
-		if self.box_check.isChecked():
-			if self.x_option:
-				sns.boxplot(data=self.data, x=self.x, y=self.y,dodge=True, hue=self.hue_variable,legend=legend, ax=self.ax, fill=False,palette=colors, linewidth=2,)
-				legend = False
-			else:
-				sns.boxplot(data=self.data, y=self.y,dodge=True, hue=self.hue_variable,legend=legend, ax=self.ax, fill=False,palette=colors, linewidth=2,)
-				legend = False
-
-		if self.boxenplot_check.isChecked():
-			if self.x_option:
-				sns.boxenplot(data=self.data, x=self.x, y=self.y,dodge=True, hue=self.hue_variable,legend=legend, ax=self.ax, fill=False,palette=colors, linewidth=2,)
-				legend = False
-			else:
-				sns.boxenplot(data=self.data, y=self.y,dodge=True, hue=self.hue_variable,legend=legend, ax=self.ax, fill=False,palette=colors, linewidth=2,)
-				legend = False
-
-		if self.strip_check.isChecked():
-			if self.x_option:
-				sns.stripplot(data=self.data, x = self.x, y=self.y,dodge=True, ax=self.ax, hue=self.hue_variable, legend=legend, palette=colors)
-				legend = False
-			else:
-				sns.stripplot(data=self.data, y=self.y,dodge=True, ax=self.ax, hue=self.hue_variable, legend=legend, palette=colors)
-				legend = False
-
-		plt.tight_layout()
-		self.fig.set_facecolor('none')  # or 'None'
-		self.fig.canvas.setStyleSheet("background-color: transparent;")
-		self.plot1dWindow.canvas.draw()
-		self.plot1dWindow.show()
-
-		if self.effect_size_check.isChecked():
-			self.compute_effect_size()
-		if self.pvalue_check.isChecked():
-			self.compute_pvalue()
-
-	def extract_groupby_cols(self):
-
-		x = self.x
-		y = self.y
-		hue_variable = self.hue_variable
-
-		if self.hist_check.isChecked() or self.ecdf_check.isChecked() or self.kde_check.isChecked():
-			y = self.x
-			x = None
-
-		groupby_cols = []
-		if x is not None:
-			groupby_cols.append(x)
-		if hue_variable is not None:
-			groupby_cols.append(hue_variable)
-
-		return groupby_cols, y
-
-	def compute_effect_size(self):
-
-		if self.count_check.isChecked() or self.scat_check.isChecked():
-			print('Please select a valid plot representation to compute effect size (histogram, boxplot, etc.)...')
-			return None
-
-		groupby_cols, y = self.extract_groupby_cols()
-		pivot = test_2samp_generic(self.data, feature=y, groupby_cols=groupby_cols, method="cliffs_delta")
-		self.effect_size_table = PivotTableUI(pivot, title="Effect size (Cliff's Delta)", mode="cliff")
-		self.effect_size_table.show()
-
-	def compute_pvalue(self):
-
-		if self.count_check.isChecked() or self.scat_check.isChecked():
-			print('Please select a valid plot representation to compute effect size (histogram, boxplot, etc.)...')
-			return None
-
-		groupby_cols, y = self.extract_groupby_cols()
-		pivot = test_2samp_generic(self.data, feature=y, groupby_cols=groupby_cols, method="ks_2samp")
-		self.pval_table = PivotTableUI(pivot, title="p-value (1-sided KS test)", mode="pvalue")
-		self.pval_table.show()
-
-
-	def set_proj_mode(self):
-		
-		self.static_columns = ['well_index', 'well_name', 'pos_name', 'position', 'well', 'status', 't0', 'class','cell_type','concentration', 'antibody', 'pharmaceutical_agent','TRACK_ID','position', 'neighbor_population', 'reference_population', 'NEIGHBOR_ID', 'REFERENCE_ID', 'FRAME']
-
-		if self.projection_option.isChecked():
-
-			self.projection_mode = self.projection_op_cb.currentText()
-			group_table = getattr(
-				self.current_data.groupby(self.groupby_cols), self.projection_mode
-			)(numeric_only=True)
-
-			for c in self.static_columns:
-				try:
-					group_table[c] = self.current_data.groupby(self.groupby_cols)[c].apply(lambda x: x.unique()[0])
-				except Exception as e:
-					print(e)
-					pass
-			
-			if self.population=='pairs':
-				for col in reversed(self.groupby_cols): #['neighbor_population', 'reference_population', 'NEIGHBOR_ID', 'REFERENCE_ID']
-					if col in group_table:
-						first_column = group_table.pop(col)
-						group_table.insert(0, col, first_column)				
-			else:
-				for col in ['TRACK_ID']:
-					first_column = group_table.pop(col) 
-					group_table.insert(0, col, first_column)
-				group_table.pop('FRAME')
-
-
-		elif self.event_time_option.isChecked():
-
-			time_of_interest = self.event_times_cb.currentText()
-			self.projection_mode = f"measurements at {time_of_interest}"
-			new_table = []
-			for tid,group in self.current_data.groupby(self.groupby_cols):
-				time = group[time_of_interest].values[0]
-				if time==time:
-					time = floor(time) # floor for onset
-				else:
-					continue
-				frames = group['FRAME'].values
-				values = group.loc[group['FRAME']==time,:].to_numpy()
-				if len(values)>0:
-					values = dict(zip(list(self.current_data.columns), values[0]))
-					for k,c in enumerate(self.groupby_cols):
-						values.update({c: tid[k]})
-					new_table.append(values)
-			
-			group_table = pd.DataFrame(new_table)
-			if self.population=='pairs':
-				for col in self.groupby_cols[1:]:
-					first_column = group_table.pop(col) 
-					group_table.insert(0, col, first_column)				
-			else:
-				for col in ['TRACK_ID']:
-					first_column = group_table.pop(col) 
-					group_table.insert(0, col, first_column)
-				
-			group_table = group_table.sort_values(by=self.groupby_cols+['FRAME'],ignore_index=True)
-			group_table = group_table.reset_index(drop=True)
-
-
-		elif self.per_status_option.isChecked():
-			self.projection_mode = self.status_operation.currentText()
-			group_table = collapse_trajectories_by_status(self.current_data, status=self.per_status_cb.currentText(),population=self.population, projection=self.status_operation.currentText(), groupby_columns=self.groupby_cols)
-
-		self.subtable = TableUI(group_table,f"Group by tracks: {self.projection_mode}", plot_mode="static", collapse_tracks_option=False)
-		self.subtable.show()
-
-		self.projectionWidget.close()
-
-	# def groupby_track_table(self):
-
-	# 	"""
-		
-	# 	Perform a time average across each track for all features
-
-	# 	"""
-
-	# 	self.subtable = TrajectoryTablePanel(self.data.groupby("TRACK_ID").mean(),"Group by tracks", plot_mode="scatter")
-	# 	self.subtable.show()
-
-	def _createMenuBar(self):
-		menuBar = self.menuBar()
-		self.fileMenu = QMenu("&File", self)
-		menuBar.addMenu(self.fileMenu)
-		self.editMenu = QMenu("&Edit", self)
-		menuBar.addMenu(self.editMenu)
-		self.mathMenu = QMenu('&Math', self)
-		menuBar.addMenu(self.mathMenu)
-
-	def save_as_csv(self):
-		options = QFileDialog.Options()
-		options |= QFileDialog.ReadOnly
-		file_name, _ = QFileDialog.getSaveFileName(self, "Save as .csv", "","CSV Files (*.csv);;All Files (*)", options=options)
-		if file_name:
-			if not file_name.endswith(".csv"):
-				file_name += ".csv"
-			invalid_cols = [c for c in list(self.data.columns) if c.startswith('Unnamed')]
-			if len(invalid_cols)>0:
-				self.data = self.data.drop(invalid_cols, axis=1)
-			self.data.to_csv(file_name, index=False)
-
-	def test_bool(self, array):
-		if array.dtype=="bool":
-			return np.array(array, dtype=int)
-		else:
-			return array
-
-	def plot_instantaneous(self):
-		
-		if self.plot_mode=='plot_track_signals':
-			self.plot_mode = 'static'
-			self.plot()
-			self.plot_mode = 'plot_track_signals'
-		elif self.plot_mode=="static":
-			self.plot()
-
-	def plot(self):
-		if self.plot_mode == "static":
-	
-			x = self.table_view.selectedIndexes()
-			col_idx = [l.column() for l in x]
-			row_idx = [l.row() for l in x]
-			column_names = self.data.columns
-			unique_cols = np.unique(col_idx)
-
-			if len(unique_cols)==1 or len(unique_cols)==0:
-				self.set_1D_plot_params()
-
-			if len(unique_cols) == 2:
-
-				print("two columns, plot mode")
-				x1 = self.test_bool(self.data.iloc[row_idx, unique_cols[0]])
-				x2 = self.test_bool(self.data.iloc[row_idx, unique_cols[1]])
-
-				self.fig, self.ax = plt.subplots(1, 1, figsize=(4,3))
-				self.scatter_wdw = FigureCanvas(self.fig, title="scatter")
-				self.ax.clear()
-				self.ax.scatter(x1,x2)
-				self.ax.set_xlabel(column_names[unique_cols[0]])
-				self.ax.set_ylabel(column_names[unique_cols[1]])
-				plt.tight_layout()
-				self.fig.set_facecolor('none')  # or 'None'
-				self.fig.canvas.setStyleSheet("background-color: transparent;")
-				self.scatter_wdw.canvas.draw()
-				self.scatter_wdw.show()
-
-			else:
-				print("please select less columns")
-
-		elif self.plot_mode == "plot_timeseries":
-			print("mode plot frames")
-			x = self.table_view.selectedIndexes()
-			col_idx = np.array([l.column() for l in x])
-			row_idx = np.array([l.row() for l in x])
-			column_names = self.data.columns
-			unique_cols = np.unique(col_idx)
-
-			self.fig, self.ax = plt.subplots(1, 1, figsize=(4, 3))
-			self.plot_wdw = FigureCanvas(self.fig, title="scatter")
-			self.ax.clear()
-			for k in range(len(unique_cols)):
-				row_idx_i = row_idx[np.where(col_idx == unique_cols[k])[0]]
-				y = self.data.iloc[row_idx_i, unique_cols[k]]
-				self.ax.plot(self.data["timeline"][row_idx_i], y, label=column_names[unique_cols[k]])
-
-			self.ax.legend()
-			self.ax.set_xlabel("time [frame]")
-			self.ax.set_ylabel(self.title)
-			plt.tight_layout()
-			self.fig.set_facecolor('none')  # or 'None'
-			self.fig.canvas.setStyleSheet("background-color: transparent;")
-			self.plot_wdw.canvas.draw()
-			plt.show()
-
-		elif self.plot_mode == "plot_track_signals":
-
-			print("mode plot track signals")
-			print('we plot here')
-
-			x = self.table_view.selectedIndexes()
-			col_idx = np.array([l.column() for l in x])
-			row_idx = np.array([l.row() for l in x])
-			column_names = self.data.columns
-			unique_cols = np.unique(col_idx)
-
-			if len(unique_cols) > 2:
-				fig,ax = plt.subplots(1, 1, figsize=(7, 5.5))
-				for k in range(len(unique_cols)):
-
-					row_idx_i = row_idx[np.where(col_idx == unique_cols[k])[0]]
-					y = self.data.iloc[row_idx_i, unique_cols[k]]
-					print(unique_cols[k])
-					for w,well_group in self.data.groupby(['well_name']):
-						for pos,pos_group in well_group.groupby(['pos_name']):
-							for tid,group_track in pos_group.groupby(self.groupby_cols[1:]):
-								ax.plot(group_track["FRAME"], group_track[column_names[unique_cols[k]]],label=column_names[unique_cols[k]])
-					#ax.plot(self.data["FRAME"][row_idx_i], y, label=column_names[unique_cols[k]])
-				ax.legend()
-				ax.set_xlabel("time [frame]")
-				ax.set_ylabel(self.title)
-				plt.tight_layout()
-				plt.show(block=False)
-
-			if len(unique_cols) == 2:
-
-				self.fig, self.ax = plt.subplots(1, 1, figsize=(4, 3))
-				self.scatter_wdw = FigureCanvas(self.fig, title="scatter")
-				self.ax.clear()
-				for tid,group in self.data.groupby(self.groupby_cols[1:]):
-					self.ax.plot(group[column_names[unique_cols[0]]], group[column_names[unique_cols[1]]], marker="o")
-				self.ax.set_xlabel(column_names[unique_cols[0]])
-				self.ax.set_ylabel(column_names[unique_cols[1]])
-				plt.tight_layout()
-				self.fig.set_facecolor('none')  # or 'None'
-				self.fig.canvas.setStyleSheet("background-color: transparent;")
-				self.scatter_wdw.canvas.draw()
-				self.scatter_wdw.show()
-
-			if len(unique_cols) == 1:
-				
-				self.fig, self.ax = plt.subplots(1, 1, figsize=(4, 3))
-				self.plot_wdw = FigureCanvas(self.fig, title="scatter")
-				self.ax.clear()
-				
-				# if 't0' in list(self.data.columns):
-				# 	ref_time_col = 't0'
-				# else:
-				# 	ref_time_col = 'FRAME'
-
-				for w,well_group in self.data.groupby(['well_name']):
-					for pos,pos_group in well_group.groupby(['pos_name']):
-						for tid,group_track in pos_group.groupby(self.groupby_cols[1:]):
-							self.ax.plot(group_track["FRAME"], group_track[column_names[unique_cols[0]]],c="k", alpha = 0.1)
-				self.ax.set_xlabel(r"$t$ [frame]")
-				self.ax.set_ylabel(column_names[unique_cols[0]])
-				plt.tight_layout()
-				self.fig.set_facecolor('none')  # or 'None'
-				self.fig.canvas.setStyleSheet("background-color: transparent;")
-				self.plot_wdw.canvas.draw()
-				self.plot_wdw.show()
+    def __init__(
+        self,
+        data,
+        title,
+        population="targets",
+        plot_mode="plot_track_signals",
+        save_inplace_option=False,
+        collapse_tracks_option=True,
+        *args,
+        **kwargs,
+    ):
+
+        CelldetectiveMainWindow.__init__(self, *args, **kwargs)
+
+        self.setWindowTitle(title)
+        self.setGeometry(100, 100, 1000, 400)
+        center_window(self)
+        self.title = title
+        self.plot_mode = plot_mode
+        self.population = population
+        self.numerics = ["int16", "int32", "int64", "float16", "float32", "float64"]
+        self.groupby_cols = ["position", "TRACK_ID"]
+        self.tracks = False
+        self.save_inplace_option = save_inplace_option
+        self.collapse_tracks_option = collapse_tracks_option
+
+        if self.population == "pairs":
+            self.groupby_cols = [
+                "position",
+                "reference_population",
+                "neighbor_population",
+                "REFERENCE_ID",
+                "NEIGHBOR_ID",
+            ]
+            self.tracks = True  # for now
+        else:
+            if "TRACK_ID" in data.columns:
+                if not np.all(data["TRACK_ID"].isnull()):
+                    self.tracks = True
+
+        self.data = data
+
+        self._createMenuBar()
+        self._create_actions()
+
+        self.table_view = QTableView(self)
+        self.setCentralWidget(self.table_view)
+
+        # Set the model for the table view
+
+        import matplotlib.pyplot as plt
+
+        plt.rcParams["svg.fonttype"] = "none"
+
+        self.model = PandasModel(data)
+        self.table_view.setModel(self.model)
+        self.table_view.resizeColumnsToContents()
+
+    def resizeEvent(self, event):
+
+        super().resizeEvent(event)
+
+        try:
+            self.fig.tight_layout()
+        except:
+            pass
+
+    def _create_actions(self):
+
+        self.save_as = QAction("&Save as...", self)
+        self.save_as.triggered.connect(self.save_as_csv)
+        self.save_as.setShortcut("Ctrl+s")
+        self.fileMenu.addAction(self.save_as)
+
+        if self.save_inplace_option:
+            self.save_inplace = QAction("&Save inplace...", self)
+            self.save_inplace.triggered.connect(self.save_as_csv_inplace_per_pos)
+            # self.save_inplace.setShortcut("Ctrl+s")
+            self.fileMenu.addAction(self.save_inplace)
+
+        self.plot_action = QAction("&Plot...", self)
+        self.plot_action.triggered.connect(self.plot)
+        self.plot_action.setShortcut("Ctrl+p")
+        self.fileMenu.addAction(self.plot_action)
+
+        self.plot_inst_action = QAction("&Plot instantaneous...", self)
+        self.plot_inst_action.triggered.connect(self.plot_instantaneous)
+        self.plot_inst_action.setShortcut("Ctrl+i")
+        self.fileMenu.addAction(self.plot_inst_action)
+
+        self.groupby_action = QAction("&Collapse tracks...", self)
+        self.groupby_action.triggered.connect(self.set_projection_mode_tracks)
+        self.groupby_action.setShortcut("Ctrl+g")
+        self.fileMenu.addAction(self.groupby_action)
+        if not self.tracks or not self.collapse_tracks_option:
+            self.groupby_action.setEnabled(False)
+
+        if self.population == "pairs":
+
+            self.groupby_pairs_in_neigh_action = QAction(
+                "&Collapse pairs in neighborhood...", self
+            )
+            self.groupby_pairs_in_neigh_action.triggered.connect(
+                self.collapse_pairs_in_neigh
+            )
+            self.fileMenu.addAction(self.groupby_pairs_in_neigh_action)
+
+        if "FRAME" in list(self.data.columns):
+            self.groupby_time_action = QAction("&Group by frames...", self)
+            self.groupby_time_action.triggered.connect(self.groupby_time_table)
+            self.groupby_time_action.setShortcut("Ctrl+t")
+            self.fileMenu.addAction(self.groupby_time_action)
+
+        self.query_action = QAction("Query...", self)
+        self.query_action.triggered.connect(self.perform_query)
+        self.fileMenu.addAction(self.query_action)
+
+        self.delete_action = QAction("&Delete...", self)
+        self.delete_action.triggered.connect(self.delete_columns)
+        self.delete_action.setShortcut(Qt.Key_Delete)
+        self.editMenu.addAction(self.delete_action)
+
+        self.rename_col_action = QAction("&Rename...", self)
+        self.rename_col_action.triggered.connect(self.rename_column)
+        # self.rename_col_action.setShortcut(Qt.Key_Delete)
+        self.editMenu.addAction(self.rename_col_action)
+
+        if self.population == "pairs":
+            self.merge_action = QAction("&Merge...", self)
+            self.merge_action.triggered.connect(self.merge_tables)
+            # self.rename_col_action.setShortcut(Qt.Key_Delete)
+            self.editMenu.addAction(self.merge_action)
+
+        self.calibrate_action = QAction("&Calibrate...", self)
+        self.calibrate_action.triggered.connect(self.calibrate_selected_feature)
+        self.calibrate_action.setShortcut("Ctrl+C")
+        self.mathMenu.addAction(self.calibrate_action)
+
+        self.merge_classification_action = QAction("&Merge states...", self)
+        self.merge_classification_action.triggered.connect(
+            self.merge_classification_features
+        )
+        self.mathMenu.addAction(self.merge_classification_action)
+
+        self.derivative_action = QAction("&Differentiate...", self)
+        self.derivative_action.triggered.connect(self.differenciate_selected_feature)
+        self.derivative_action.setShortcut("Ctrl+D")
+        self.mathMenu.addAction(self.derivative_action)
+        if not self.tracks:
+            self.derivative_action.setEnabled(False)
+
+        self.abs_action = QAction("&Absolute value...", self)
+        self.abs_action.triggered.connect(self.take_abs_of_selected_feature)
+        # self.derivative_action.setShortcut("Ctrl+D")
+        self.mathMenu.addAction(self.abs_action)
+
+        self.log_action = QAction("&Log (decimal)...", self)
+        self.log_action.triggered.connect(self.take_log_of_selected_feature)
+        # self.derivative_action.setShortcut("Ctrl+D")
+        self.mathMenu.addAction(self.log_action)
+
+        self.divide_action = QAction("&Divide...", self)
+        self.divide_action.triggered.connect(self.divide_signals)
+        # self.derivative_action.setShortcut("Ctrl+D")
+        self.mathMenu.addAction(self.divide_action)
+
+        self.multiply_action = QAction("&Multiply...", self)
+        self.multiply_action.triggered.connect(self.multiply_signals)
+        # self.derivative_action.setShortcut("Ctrl+D")
+        self.mathMenu.addAction(self.multiply_action)
+
+        self.add_action = QAction("&Add...", self)
+        self.add_action.triggered.connect(self.add_signals)
+        # self.derivative_action.setShortcut("Ctrl+D")
+        self.mathMenu.addAction(self.add_action)
+
+        self.subtract_action = QAction("&Subtract...", self)
+        self.subtract_action.triggered.connect(self.subtract_signals)
+        # self.derivative_action.setShortcut("Ctrl+D")
+        self.mathMenu.addAction(self.subtract_action)
+
+        # self.onehot_action = QAction('&One hot to categorical...', self)
+        # self.onehot_action.triggered.connect(self.transform_one_hot_cols_to_categorical)
+        # #self.onehot_action.setShortcut("Ctrl+D")
+        # self.mathMenu.addAction(self.onehot_action)
+
+    def collapse_pairs_in_neigh(self):
+
+        self.selectNeighWidget = CelldetectiveWidget()
+        self.selectNeighWidget.setMinimumWidth(480)
+        self.selectNeighWidget.setWindowTitle("Set neighborhood of interest")
+
+        layout = QVBoxLayout()
+        self.selectNeighWidget.setLayout(layout)
+
+        self.reference_lbl = QLabel("reference population: ")
+        self.reference_pop_cb = QComboBox()
+        ref_pops = self.data["reference_population"].unique()
+        self.reference_pop_cb.addItems(ref_pops)
+        self.reference_pop_cb.currentIndexChanged.connect(self.update_neighborhoods)
+
+        reference_hbox = QHBoxLayout()
+        reference_hbox.addWidget(self.reference_lbl, 33)
+        reference_hbox.addWidget(self.reference_pop_cb, 66)
+        layout.addLayout(reference_hbox)
+
+        self.neigh_lbl = QLabel("neighborhod: ")
+        self.neigh_cb = QComboBox()
+        neigh_cols = [
+            c.replace("status_", "")
+            for c in list(
+                self.data.loc[
+                    self.data["reference_population"]
+                    == self.reference_pop_cb.currentText()
+                ].columns
+            )
+            if c.startswith("status_neighborhood")
+        ]
+        self.neigh_cb.addItems(neigh_cols)
+
+        neigh_hbox = QHBoxLayout()
+        neigh_hbox.addWidget(self.neigh_lbl, 33)
+        neigh_hbox.addWidget(self.neigh_cb, 66)
+        layout.addLayout(neigh_hbox)
+
+        contact_hbox = QHBoxLayout()
+        self.contact_only_check = QCheckBox("keep only pairs in contact")
+        self.contact_only_check.setChecked(True)
+        contact_hbox.addWidget(self.contact_only_check, alignment=Qt.AlignLeft)
+        layout.addLayout(contact_hbox)
+
+        self.groupby_pair_rb = QRadioButton("Group by pair")
+        self.groupby_reference_rb = QRadioButton("Group by reference")
+        self.groupby_pair_rb.setChecked(True)
+
+        groupby_hbox = QHBoxLayout()
+        groupby_hbox.addWidget(QLabel("collapse option: "), 33)
+        groupby_hbox.addWidget(self.groupby_pair_rb, (100 - 33) // 2)
+        groupby_hbox.addWidget(self.groupby_reference_rb, (100 - 33) // 2)
+        layout.addLayout(groupby_hbox)
+
+        self.apply_neigh_btn = QPushButton("Set")
+        self.apply_neigh_btn.setStyleSheet(self.button_style_sheet)
+        self.apply_neigh_btn.clicked.connect(self.prepare_table_at_neighborhood)
+
+        apply_hbox = QHBoxLayout()
+        apply_hbox.addWidget(QLabel(""), 33)
+        apply_hbox.addWidget(self.apply_neigh_btn, 66)
+        layout.addLayout(apply_hbox)
+
+        self.selectNeighWidget.show()
+        center_window(self.selectNeighWidget)
+
+    def prepare_table_at_neighborhood(self):
+
+        ref_pop = self.reference_pop_cb.currentText()
+        neighborhood = self.neigh_cb.currentText()
+        status_neigh = "status_" + neighborhood
+
+        if "self" in neighborhood:
+            neighbor_pop = ref_pop
+
+        neigh_col = neighborhood.replace("status_", "")
+        if "_(" in neigh_col and ")_" in neigh_col:
+            neighbor_pop = neigh_col.split("_(")[-1].split(")_")[0].split("-")[-1]
+        else:
+            if ref_pop == "targets":
+                neighbor_pop = "effectors"
+            if ref_pop == "effectors":
+                neighbor_pop = "targets"
+
+        from celldetective.neighborhood import extract_neighborhood_in_pair_table
+
+        data = extract_neighborhood_in_pair_table(
+            self.data,
+            neighborhood_key=neighborhood,
+            contact_only=self.contact_only_check.isChecked(),
+            reference_population=ref_pop,
+        )
+
+        if self.groupby_pair_rb.isChecked():
+            self.groupby_cols = ["position", "REFERENCE_ID", "NEIGHBOR_ID"]
+        elif self.groupby_reference_rb.isChecked():
+            self.groupby_cols = ["position", "REFERENCE_ID"]
+
+        self.current_data = data
+        skip_projection = False
+        if "reference_tracked" in list(self.current_data.columns):
+            print(
+                f"{self.current_data['reference_tracked']=} {(self.current_data['reference_tracked']==False)=} {np.all(self.current_data['reference_tracked']==False)=}"
+            )
+            if np.all(self.current_data["reference_tracked"].astype(bool) == False):
+                # reference not tracked
+                if self.groupby_reference_rb.isChecked():
+                    self.groupby_cols = ["position", "FRAME", "REFERENCE_ID"]
+                elif self.groupby_pair_rb.isChecked():
+                    print(
+                        "The reference cells seem to not be tracked. No collapse can be performed."
+                    )
+                    skip_projection = True
+            else:
+                if np.all(self.current_data["neighbors_tracked"].astype(bool) == False):
+                    # neighbors not tracked
+                    if self.groupby_pair_rb.isChecked():
+                        print(
+                            "The neighbor cells seem to not be tracked. No collapse can be performed."
+                        )
+                        skip_projection = True
+                    elif self.groupby_reference_rb.isChecked():
+                        self.groupby_cols = [
+                            "position",
+                            "REFERENCE_ID",
+                        ]  # think about what would be best
+
+        if not skip_projection:
+            self.set_projection_mode_tracks()
+
+    def update_neighborhoods(self):
+
+        neigh_cols = [
+            c.replace("status_", "")
+            for c in list(
+                self.data.loc[
+                    self.data["reference_population"]
+                    == self.reference_pop_cb.currentText()
+                ].columns
+            )
+            if c.startswith("status_neighborhood")
+        ]
+        self.neigh_cb.clear()
+        self.neigh_cb.addItems(neigh_cols)
+
+    def merge_tables(self):
+
+        df_expanded = expand_pair_table(self.data)
+        self.subtable = TableUI(
+            df_expanded, "merge", plot_mode="static", population="pairs"
+        )
+        self.subtable.show()
+
+    def delete_columns(self):
+
+        x = self.table_view.selectedIndexes()
+        col_idx = np.unique(np.array([l.column() for l in x]))
+        cols = np.array(list(self.data.columns))
+
+        msgBox = QMessageBox()
+        msgBox.setIcon(QMessageBox.Question)
+        msgBox.setText(
+            f"You are about to delete columns {cols[col_idx]}... Do you want to proceed?"
+        )
+        msgBox.setWindowTitle("Info")
+        msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
+        return_value = msgBox.exec()
+        if return_value == QMessageBox.No:
+            return None
+
+        self.data = self.data.drop(list(cols[col_idx]), axis=1)
+        self.model = PandasModel(self.data)
+        self.table_view.setModel(self.model)
+
+    def rename_column(self):
+
+        x = self.table_view.selectedIndexes()
+        col_idx = np.unique(np.array([l.column() for l in x]))
+
+        if len(col_idx) == 0:
+            msg_box = QMessageBox()
+            msg_box.setIcon(QMessageBox.Question)
+            msg_box.setText(f"Please select a column first.")
+            msg_box.setWindowTitle("Warning")
+            msg_box.setStandardButtons(QMessageBox.Ok)
+            returnValue = msg_box.exec()
+            if returnValue == QMessageBox.Ok:
+                return None
+            else:
+                return None
+
+        cols = np.array(list(self.data.columns))
+        selected_col = str(cols[col_idx][0])
+
+        self.renameWidget = RenameColWidget(self, selected_col)
+        self.renameWidget.show()
+
+    def save_as_csv_inplace_per_pos(self):
+
+        print("Saving each table in its respective position folder...")
+        for pos, pos_group in self.data.groupby(["position"]):
+            invalid_cols = [
+                c for c in list(pos_group.columns) if c.startswith("Unnamed")
+            ]
+            if len(invalid_cols) > 0:
+                pos_group = pos_group.drop(invalid_cols, axis=1)
+            pos_group.to_csv(
+                pos[0]
+                + os.sep.join(
+                    ["output", "tables", f"trajectories_{self.population}.csv"]
+                ),
+                index=False,
+            )
+        print("Done...")
+
+    def divide_signals(self):
+
+        x = self.table_view.selectedIndexes()
+        col_idx = np.unique(np.array([l.column() for l in x]))
+        if isinstance(col_idx, (list, np.ndarray)):
+            cols = np.array(list(self.data.columns))
+            if len(col_idx) > 0:
+                selected_col1 = str(cols[col_idx[0]])
+                if len(col_idx) > 1:
+                    selected_col2 = str(cols[col_idx[1]])
+                else:
+                    selected_col2 = None
+            else:
+                selected_col1 = None
+                selected_col2 = None
+        else:
+            selected_col1 = None
+            selected_col2 = None
+
+        self.divWidget = OperationOnColsWidget(
+            self, column1=selected_col1, column2=selected_col2, operation="divide"
+        )
+        self.divWidget.show()
+
+    def multiply_signals(self):
+
+        x = self.table_view.selectedIndexes()
+        col_idx = np.unique(np.array([l.column() for l in x]))
+        if isinstance(col_idx, (list, np.ndarray)):
+            cols = np.array(list(self.data.columns))
+            if len(col_idx) > 0:
+                selected_col1 = str(cols[col_idx[0]])
+                if len(col_idx) > 1:
+                    selected_col2 = str(cols[col_idx[1]])
+                else:
+                    selected_col2 = None
+            else:
+                selected_col1 = None
+                selected_col2 = None
+        else:
+            selected_col1 = None
+            selected_col2 = None
+
+        self.mulWidget = OperationOnColsWidget(
+            self, column1=selected_col1, column2=selected_col2, operation="multiply"
+        )
+        self.mulWidget.show()
+
+    def add_signals(self):
+
+        x = self.table_view.selectedIndexes()
+        col_idx = np.unique(np.array([l.column() for l in x]))
+        if isinstance(col_idx, (list, np.ndarray)):
+            cols = np.array(list(self.data.columns))
+            if len(col_idx) > 0:
+                selected_col1 = str(cols[col_idx[0]])
+                if len(col_idx) > 1:
+                    selected_col2 = str(cols[col_idx[1]])
+                else:
+                    selected_col2 = None
+            else:
+                selected_col1 = None
+                selected_col2 = None
+        else:
+            selected_col1 = None
+            selected_col2 = None
+
+        self.addiWidget = OperationOnColsWidget(
+            self, column1=selected_col1, column2=selected_col2, operation="add"
+        )
+        self.addiWidget.show()
+
+    def subtract_signals(self):
+
+        x = self.table_view.selectedIndexes()
+        col_idx = np.unique(np.array([l.column() for l in x]))
+        if isinstance(col_idx, (list, np.ndarray)):
+            cols = np.array(list(self.data.columns))
+            if len(col_idx) > 0:
+                selected_col1 = str(cols[col_idx[0]])
+                if len(col_idx) > 1:
+                    selected_col2 = str(cols[col_idx[1]])
+                else:
+                    selected_col2 = None
+            else:
+                selected_col1 = None
+                selected_col2 = None
+        else:
+            selected_col1 = None
+            selected_col2 = None
+
+        self.subWidget = OperationOnColsWidget(
+            self, column1=selected_col1, column2=selected_col2, operation="subtract"
+        )
+        self.subWidget.show()
+
+    def differenciate_selected_feature(self):
+
+        # check only one col selected and assert is numerical
+        # open widget to select window parameters, directionality
+        # create new col
+
+        x = self.table_view.selectedIndexes()
+        col_idx = np.unique(np.array([l.column() for l in x]))
+        if isinstance(col_idx, (list, np.ndarray)):
+            cols = np.array(list(self.data.columns))
+            if len(col_idx) > 0:
+                selected_col = str(cols[col_idx[0]])
+            else:
+                selected_col = None
+        else:
+            selected_col = None
+
+        self.diffWidget = DifferentiateColWidget(self, selected_col)
+        self.diffWidget.show()
+
+    def take_log_of_selected_feature(self):
+
+        # check only one col selected and assert is numerical
+        # open widget to select window parameters, directionality
+        # create new col
+
+        x = self.table_view.selectedIndexes()
+        col_idx = np.unique(np.array([l.column() for l in x]))
+        if isinstance(col_idx, (list, np.ndarray)):
+            cols = np.array(list(self.data.columns))
+            if len(col_idx) > 0:
+                selected_col = str(cols[col_idx[0]])
+            else:
+                selected_col = None
+        else:
+            selected_col = None
+
+        self.LogWidget = LogColWidget(self, selected_col)
+        self.LogWidget.show()
+
+    def merge_classification_features(self):
+
+        x = self.table_view.selectedIndexes()
+        col_idx = np.unique(np.array([l.column() for l in x]))
+
+        col_selection = []
+        if isinstance(col_idx, (list, np.ndarray)):
+            cols = np.array(list(self.data.columns))
+            if len(col_idx) > 0:
+                selected_cols = cols[col_idx]
+                col_selection.extend(selected_cols)
+
+        # Lazy load MergeGroupWidget
+        from celldetective.gui.table_ops._merge_groups import MergeGroupWidget
+
+        self.merge_classification_widget = MergeGroupWidget(self, columns=col_selection)
+        self.merge_classification_widget.show()
+
+    def calibrate_selected_feature(self):
+
+        x = self.table_view.selectedIndexes()
+        col_idx = np.unique(np.array([l.column() for l in x]))
+        if isinstance(col_idx, (list, np.ndarray)):
+            cols = np.array(list(self.data.columns))
+            if len(col_idx) > 0:
+                selected_col = str(cols[col_idx[0]])
+            else:
+                selected_col = None
+        else:
+            selected_col = None
+
+        self.calWidget = CalibrateColWidget(self, selected_col)
+        self.calWidget.show()
+
+    def take_abs_of_selected_feature(self):
+
+        # check only one col selected and assert is numerical
+        # open widget to select window parameters, directionality
+        # create new col
+
+        x = self.table_view.selectedIndexes()
+        col_idx = np.unique(np.array([l.column() for l in x]))
+        if isinstance(col_idx, (list, np.ndarray)):
+            cols = np.array(list(self.data.columns))
+            if len(col_idx) > 0:
+                selected_col = str(cols[col_idx[0]])
+            else:
+                selected_col = None
+        else:
+            selected_col = None
+
+        self.absWidget = AbsColWidget(self, selected_col)
+        self.absWidget.show()
+
+    def transform_one_hot_cols_to_categorical(self):
+
+        x = self.table_view.selectedIndexes()
+        col_idx = np.unique(np.array([l.column() for l in x]))
+        selected_cols = None
+        if isinstance(col_idx, (list, np.ndarray)):
+            cols = np.array(list(self.data.columns))
+            if len(col_idx) > 0:
+                selected_col = str(cols[col_idx[0]])
+
+        self.mergewidget = MergeOneHotWidget(self, selected_columns=selected_cols)
+        self.mergewidget.show()
+
+    def groupby_time_table(self):
+        """
+
+        Perform a time average across each track for all features
+
+        """
+
+        num_df = self.data.select_dtypes(include=self.numerics)
+
+        timeseries = num_df.groupby(["FRAME"]).sum().copy()
+        timeseries["timeline"] = timeseries.index
+        self.subtable = TableUI(
+            timeseries, "Group by frames", plot_mode="plot_timeseries"
+        )
+        self.subtable.show()
+
+    def perform_query(self):
+        """
+
+        Perform a time average across each track for all features
+
+        """
+        self.query_widget = QueryWidget(self)
+        self.query_widget.show()
+
+        # num_df = self.data.select_dtypes(include=self.numerics)
+
+        # timeseries = num_df.groupby("FRAME").mean().copy()
+        # timeseries["timeline"] = timeseries.index
+        # self.subtable = TableUI(timeseries,"Group by frames", plot_mode="plot_timeseries")
+        # self.subtable.show()
+
+    def set_projection_mode_neigh(self):
+
+        self.groupby_cols = [
+            "position",
+            "reference_population",
+            "neighbor_population",
+            "NEIGHBOR_ID",
+            "FRAME",
+        ]
+        self.current_data = self.data
+        self.set_projection_mode_tracks()
+
+    def set_projection_mode_ref(self):
+
+        self.groupby_cols = [
+            "position",
+            "reference_population",
+            "neighbor_population",
+            "REFERENCE_ID",
+            "FRAME",
+        ]
+        self.current_data = self.data
+        self.set_projection_mode_tracks()
+
+    def set_projection_mode_tracks(self):
+
+        self.current_data = self.data
+
+        self.projectionWidget = CelldetectiveWidget()
+        self.projectionWidget.setMinimumWidth(500)
+        self.projectionWidget.setWindowTitle("Set projection mode")
+
+        layout = QVBoxLayout()
+        self.projectionWidget.setLayout(layout)
+
+        self.projection_option = QRadioButton("global operation: ")
+        self.projection_option.setToolTip(
+            "Collapse the cell track measurements with an operation over each track."
+        )
+        self.projection_option.setChecked(True)
+        self.projection_option.toggled.connect(self.enable_projection_options)
+        self.projection_op_cb = QComboBox()
+        self.projection_op_cb.addItems(
+            ["mean", "median", "min", "max", "first", "last", "prod", "sum"]
+        )
+
+        projection_layout = QHBoxLayout()
+        projection_layout.addWidget(self.projection_option, 33)
+        projection_layout.addWidget(self.projection_op_cb, 66)
+        layout.addLayout(projection_layout)
+
+        self.event_time_option = QRadioButton("@event time: ")
+        self.event_time_option.setToolTip(
+            "Pick the measurements at a specific event time."
+        )
+        self.event_time_option.toggled.connect(self.enable_projection_options)
+        self.event_times_cb = QComboBox()
+        cols = np.array(self.data.columns)
+        time_cols = np.array([c.startswith("t_") for c in cols])
+        time_cols = list(cols[time_cols])
+        if "t0" in list(self.data.columns):
+            time_cols.append("t0")
+        self.event_times_cb.addItems(time_cols)
+        self.event_times_cb.setEnabled(False)
+
+        event_time_layout = QHBoxLayout()
+        event_time_layout.addWidget(self.event_time_option, 33)
+        event_time_layout.addWidget(self.event_times_cb, 66)
+        layout.addLayout(event_time_layout)
+
+        self.per_status_option = QRadioButton("per status: ")
+        self.per_status_option.setToolTip(
+            "Collapse the cell track measurements independently for each of the cell state."
+        )
+        self.per_status_option.toggled.connect(self.enable_projection_options)
+        self.per_status_cb = QComboBox()
+        self.status_operation = QComboBox()
+        self.status_operation.setEnabled(False)
+        self.status_operation.addItems(["mean", "median", "min", "max", "prod", "sum"])
+
+        status_cols = np.array(
+            [c.startswith("status_") or c.startswith("group_") for c in cols]
+        )
+        status_cols = list(cols[status_cols])
+        if "status" in list(self.data.columns):
+            status_cols.append("status")
+        self.per_status_cb.addItems(status_cols)
+        self.per_status_cb.setEnabled(False)
+
+        per_status_layout = QHBoxLayout()
+        per_status_layout.addWidget(self.per_status_option, 33)
+        per_status_layout.addWidget(self.per_status_cb, 66)
+        layout.addLayout(per_status_layout)
+
+        status_operation_layout = QHBoxLayout()
+        status_operation_layout.addWidget(
+            QLabel("operation: "), 33, alignment=Qt.AlignRight
+        )
+        status_operation_layout.addWidget(self.status_operation, 66)
+        layout.addLayout(status_operation_layout)
+
+        self.btn_projection_group = QButtonGroup()
+        self.btn_projection_group.addButton(self.projection_option)
+        self.btn_projection_group.addButton(self.event_time_option)
+        self.btn_projection_group.addButton(self.per_status_option)
+
+        apply_layout = QHBoxLayout()
+
+        self.set_projection_btn = QPushButton("Apply")
+        self.set_projection_btn.setStyleSheet(self.button_style_sheet)
+        self.set_projection_btn.clicked.connect(self.set_proj_mode)
+        apply_layout.addWidget(QLabel(""), 33)
+        apply_layout.addWidget(self.set_projection_btn, 33)
+        apply_layout.addWidget(QLabel(""), 33)
+        layout.addLayout(apply_layout)
+
+        self.projectionWidget.show()
+        center_window(self.projectionWidget)
+
+    def enable_projection_options(self):
+
+        if self.projection_option.isChecked():
+            self.projection_op_cb.setEnabled(True)
+            self.event_times_cb.setEnabled(False)
+            self.per_status_cb.setEnabled(False)
+            self.status_operation.setEnabled(False)
+        elif self.event_time_option.isChecked():
+            self.projection_op_cb.setEnabled(False)
+            self.event_times_cb.setEnabled(True)
+            self.per_status_cb.setEnabled(False)
+            self.status_operation.setEnabled(False)
+        elif self.per_status_option.isChecked():
+            self.projection_op_cb.setEnabled(False)
+            self.event_times_cb.setEnabled(False)
+            self.per_status_cb.setEnabled(True)
+            self.status_operation.setEnabled(True)
+
+    def set_1D_plot_params(self):
+
+        self.plot1Dparams = CelldetectiveWidget()
+        self.plot1Dparams.setWindowTitle("Set 1D plot parameters")
+
+        layout = QVBoxLayout()
+        self.plot1Dparams.setLayout(layout)
+
+        layout.addWidget(QLabel("Representations: "))
+        self.hist_check = QCheckBox("histogram")
+        self.kde_check = QCheckBox("KDE plot")
+        self.count_check = QCheckBox("countplot")
+        self.ecdf_check = QCheckBox("ECDF plot")
+        self.line_check = QCheckBox("line plot")
+        self.scat_check = QCheckBox("scatter plot")
+        self.swarm_check = QCheckBox("swarm")
+        self.violin_check = QCheckBox("violin")
+        self.strip_check = QCheckBox("strip")
+        self.box_check = QCheckBox("boxplot")
+        self.boxenplot_check = QCheckBox("boxenplot")
+
+        self.sep_line = QHSeperationLine()
+        self.pvalue_check = QCheckBox("Compute KS test p-value?")
+        self.effect_size_check = QCheckBox("Compute effect size?\n(Cliff's Delta)")
+
+        layout.addWidget(self.hist_check)
+        layout.addWidget(self.kde_check)
+        layout.addWidget(self.count_check)
+        layout.addWidget(self.ecdf_check)
+        layout.addWidget(self.line_check)
+        layout.addWidget(self.scat_check)
+        layout.addWidget(self.swarm_check)
+        layout.addWidget(self.violin_check)
+        layout.addWidget(self.strip_check)
+        layout.addWidget(self.box_check)
+        layout.addWidget(self.boxenplot_check)
+        layout.addWidget(self.sep_line)
+        layout.addWidget(self.pvalue_check)
+        layout.addWidget(self.effect_size_check)
+
+        self.x_cb = QSearchableComboBox()
+        self.x_cb.addItems(["--"] + list(self.data.columns))
+
+        self.y_cb = QSearchableComboBox()
+        self.y_cb.addItems(["--"] + list(self.data.columns))
+
+        self.hue_cb = QSearchableComboBox()
+        self.hue_cb.addItems(["--"] + list(self.data.columns))
+        idx = self.hue_cb.findText("--")
+        self.hue_cb.setCurrentIndex(idx)
+
+        # Set selected column
+
+        try:
+            x = self.table_view.selectedIndexes()
+            col_idx = np.array([l.column() for l in x])
+            row_idx = np.array([l.row() for l in x])
+            column_names = self.data.columns
+            unique_cols = np.unique(col_idx)[0]
+            y = column_names[unique_cols]
+            idx = self.y_cb.findText(y)
+            self.y_cb.setCurrentIndex(idx)
+        except:
+            pass
+
+        hbox = QHBoxLayout()
+        hbox.addWidget(QLabel("x: "), 33)
+        hbox.addWidget(self.x_cb, 66)
+        layout.addLayout(hbox)
+
+        hbox = QHBoxLayout()
+        hbox.addWidget(QLabel("y: "), 33)
+        hbox.addWidget(self.y_cb, 66)
+        layout.addLayout(hbox)
+
+        hbox = QHBoxLayout()
+        hbox.addWidget(QLabel("hue: "), 33)
+        hbox.addWidget(self.hue_cb, 66)
+        layout.addLayout(hbox)
+
+        from matplotlib import colormaps
+        import matplotlib.cm
+
+        self.cmap_cb = QColormapComboBox()
+        all_cms = list(colormaps)
+        for cm in all_cms:
+            if hasattr(matplotlib.cm, str(cm).lower()):
+                try:
+                    self.cmap_cb.addColormap(cm.lower())
+                except:
+                    pass
+
+        hbox = QHBoxLayout()
+        hbox.addWidget(QLabel("colormap: "), 33)
+        hbox.addWidget(self.cmap_cb, 66)
+        layout.addLayout(hbox)
+
+        self.plot1d_btn = QPushButton("set")
+        self.plot1d_btn.setStyleSheet(self.button_style_sheet)
+        self.plot1d_btn.clicked.connect(self.plot1d)
+        layout.addWidget(self.plot1d_btn)
+
+        self.plot1Dparams.show()
+        center_window(self.plot1Dparams)
+
+    def plot1d(self):
+
+        self.x_option = False
+        if self.x_cb.currentText() != "--":
+            self.x_option = True
+            self.x = self.x_cb.currentText()
+
+        import matplotlib.pyplot as plt
+        import seaborn as sns
+        import matplotlib.cm as mcm
+
+        self.fig, self.ax = plt.subplots(1, 1, figsize=(4, 3))
+        self.plot1dWindow = FigureCanvas(self.fig, title="scatter")
+        self.ax.clear()
+
+        cmap = getattr(mcm, self.cmap_cb.currentText())
+
+        try:
+            self.hue_variable = self.hue_cb.currentText()
+            colors = [
+                cmap(i / len(self.data[self.hue_variable].unique()))
+                for i in range(len(self.data[self.hue_variable].unique()))
+            ]
+        except:
+            colors = None
+
+        if self.hue_cb.currentText() == "--":
+            self.hue_variable = None
+
+        if self.y_cb.currentText() == "--":
+            self.y = None
+        else:
+            self.y = self.y_cb.currentText()
+
+        if self.x_cb.currentText() == "--":
+            self.x = None
+        else:
+            self.x = self.x_cb.currentText()
+
+        legend = True
+
+        if self.hist_check.isChecked():
+            if self.x is not None:
+                sns.histplot(
+                    data=self.data,
+                    x=self.x,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    ax=self.ax,
+                    palette=colors,
+                    kde=True,
+                    common_norm=False,
+                    stat="density",
+                )
+                legend = False
+            elif self.x is None and self.y is not None:
+                sns.histplot(
+                    data=self.data,
+                    x=self.y,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    ax=self.ax,
+                    palette=colors,
+                    kde=True,
+                    common_norm=False,
+                    stat="density",
+                )
+                legend = False
+            else:
+                pass
+
+        if self.kde_check.isChecked():
+            if self.x is not None:
+                sns.kdeplot(
+                    data=self.data,
+                    x=self.x,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    ax=self.ax,
+                    palette=colors,
+                    cut=0,
+                )
+                legend = False
+            elif self.x is None and self.y is not None:
+                sns.kdeplot(
+                    data=self.data,
+                    x=self.y,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    ax=self.ax,
+                    palette=colors,
+                    cut=0,
+                )
+                legend = False
+            else:
+                pass
+
+        if self.count_check.isChecked():
+            sns.countplot(
+                data=self.data,
+                x=self.x,
+                hue=self.hue_variable,
+                legend=legend,
+                ax=self.ax,
+                palette=colors,
+            )
+            legend = False
+
+        if self.ecdf_check.isChecked():
+            if self.x is not None:
+                sns.ecdfplot(
+                    data=self.data,
+                    x=self.x,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    ax=self.ax,
+                    palette=colors,
+                )
+                legend = False
+            elif self.x is None and self.y is not None:
+                sns.ecdfplot(
+                    data=self.data,
+                    x=self.y,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    ax=self.ax,
+                    palette=colors,
+                )
+                legend = False
+            else:
+                pass
+
+        if self.line_check.isChecked():
+            if self.x_option:
+                sns.lineplot(
+                    data=self.data,
+                    x=self.x,
+                    y=self.y,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    ax=self.ax,
+                    palette=colors,
+                )
+                legend = False
+            else:
+                print("please provide a -x variable...")
+                pass
+
+        if self.scat_check.isChecked():
+            if self.x_option:
+                sns.scatterplot(
+                    data=self.data,
+                    x=self.x,
+                    y=self.y,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    ax=self.ax,
+                    palette=colors,
+                )
+                legend = False
+            else:
+                print("please provide a -x variable...")
+                pass
+
+        if self.swarm_check.isChecked():
+            if self.x_option:
+                sns.swarmplot(
+                    data=self.data,
+                    x=self.x,
+                    y=self.y,
+                    dodge=True,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    ax=self.ax,
+                    palette=colors,
+                )
+                legend = False
+            else:
+                sns.swarmplot(
+                    data=self.data,
+                    y=self.y,
+                    dodge=True,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    ax=self.ax,
+                    palette=colors,
+                )
+                legend = False
+
+        if self.violin_check.isChecked():
+            if self.x_option:
+                sns.violinplot(
+                    data=self.data,
+                    x=self.x,
+                    y=self.y,
+                    dodge=True,
+                    ax=self.ax,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    palette=colors,
+                )
+                legend = False
+            else:
+                sns.violinplot(
+                    data=self.data,
+                    y=self.y,
+                    dodge=True,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    ax=self.ax,
+                    palette=colors,
+                    cut=0,
+                )
+                legend = False
+
+        if self.box_check.isChecked():
+            if self.x_option:
+                sns.boxplot(
+                    data=self.data,
+                    x=self.x,
+                    y=self.y,
+                    dodge=True,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    ax=self.ax,
+                    fill=False,
+                    palette=colors,
+                    linewidth=2,
+                )
+                legend = False
+            else:
+                sns.boxplot(
+                    data=self.data,
+                    y=self.y,
+                    dodge=True,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    ax=self.ax,
+                    fill=False,
+                    palette=colors,
+                    linewidth=2,
+                )
+                legend = False
+
+        if self.boxenplot_check.isChecked():
+            if self.x_option:
+                sns.boxenplot(
+                    data=self.data,
+                    x=self.x,
+                    y=self.y,
+                    dodge=True,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    ax=self.ax,
+                    fill=False,
+                    palette=colors,
+                    linewidth=2,
+                )
+                legend = False
+            else:
+                sns.boxenplot(
+                    data=self.data,
+                    y=self.y,
+                    dodge=True,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    ax=self.ax,
+                    fill=False,
+                    palette=colors,
+                    linewidth=2,
+                )
+                legend = False
+
+        if self.strip_check.isChecked():
+            if self.x_option:
+                sns.stripplot(
+                    data=self.data,
+                    x=self.x,
+                    y=self.y,
+                    dodge=True,
+                    ax=self.ax,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    palette=colors,
+                )
+                legend = False
+            else:
+                sns.stripplot(
+                    data=self.data,
+                    y=self.y,
+                    dodge=True,
+                    ax=self.ax,
+                    hue=self.hue_variable,
+                    legend=legend,
+                    palette=colors,
+                )
+                legend = False
+
+        plt.tight_layout()
+        self.fig.set_facecolor("none")  # or 'None'
+        self.fig.canvas.setStyleSheet("background-color: transparent;")
+        self.plot1dWindow.canvas.draw()
+        self.plot1dWindow.show()
+
+        if self.effect_size_check.isChecked():
+            self.compute_effect_size()
+        if self.pvalue_check.isChecked():
+            self.compute_pvalue()
+
+    def extract_groupby_cols(self):
+
+        x = self.x
+        y = self.y
+        hue_variable = self.hue_variable
+
+        if (
+            self.hist_check.isChecked()
+            or self.ecdf_check.isChecked()
+            or self.kde_check.isChecked()
+        ):
+            y = self.x
+            x = None
+
+        groupby_cols = []
+        if x is not None:
+            groupby_cols.append(x)
+        if hue_variable is not None:
+            groupby_cols.append(hue_variable)
+
+        return groupby_cols, y
+
+    def compute_effect_size(self):
+
+        if self.count_check.isChecked() or self.scat_check.isChecked():
+            print(
+                "Please select a valid plot representation to compute effect size (histogram, boxplot, etc.)..."
+            )
+            return None
+
+        groupby_cols, y = self.extract_groupby_cols()
+        pivot = test_2samp_generic(
+            self.data, feature=y, groupby_cols=groupby_cols, method="cliffs_delta"
+        )
+        self.effect_size_table = PivotTableUI(
+            pivot, title="Effect size (Cliff's Delta)", mode="cliff"
+        )
+        self.effect_size_table.show()
+
+    def compute_pvalue(self):
+
+        if self.count_check.isChecked() or self.scat_check.isChecked():
+            print(
+                "Please select a valid plot representation to compute effect size (histogram, boxplot, etc.)..."
+            )
+            return None
+
+        groupby_cols, y = self.extract_groupby_cols()
+        pivot = test_2samp_generic(
+            self.data, feature=y, groupby_cols=groupby_cols, method="ks_2samp"
+        )
+        self.pval_table = PivotTableUI(
+            pivot, title="p-value (1-sided KS test)", mode="pvalue"
+        )
+        self.pval_table.show()
+
+    def set_proj_mode(self):
+
+        self.static_columns = [
+            "well_index",
+            "well_name",
+            "pos_name",
+            "position",
+            "well",
+            "status",
+            "t0",
+            "class",
+            "cell_type",
+            "concentration",
+            "antibody",
+            "pharmaceutical_agent",
+            "TRACK_ID",
+            "position",
+            "neighbor_population",
+            "reference_population",
+            "NEIGHBOR_ID",
+            "REFERENCE_ID",
+            "FRAME",
+        ]
+
+        if self.projection_option.isChecked():
+
+            self.projection_mode = self.projection_op_cb.currentText()
+            op = getattr(
+                self.current_data.groupby(self.groupby_cols), self.projection_mode
+            )
+            group_table = op(self.current_data.groupby(self.groupby_cols))
+
+            for c in self.static_columns:
+                try:
+                    group_table[c] = self.current_data.groupby(self.groupby_cols)[
+                        c
+                    ].apply(lambda x: x.unique()[0])
+                except Exception as e:
+                    print(e)
+                    pass
+
+            if self.population == "pairs":
+                for col in reversed(
+                    self.groupby_cols
+                ):  # ['neighbor_population', 'reference_population', 'NEIGHBOR_ID', 'REFERENCE_ID']
+                    if col in group_table:
+                        first_column = group_table.pop(col)
+                        group_table.insert(0, col, first_column)
+            else:
+                for col in ["TRACK_ID"]:
+                    first_column = group_table.pop(col)
+                    group_table.insert(0, col, first_column)
+                group_table.pop("FRAME")
+
+        elif self.event_time_option.isChecked():
+
+            time_of_interest = self.event_times_cb.currentText()
+            self.projection_mode = f"measurements at {time_of_interest}"
+            new_table = []
+            for tid, group in self.current_data.groupby(self.groupby_cols):
+                time = group[time_of_interest].values[0]
+                if time == time:
+                    time = floor(time)  # floor for onset
+                else:
+                    continue
+                frames = group["FRAME"].values
+                values = group.loc[group["FRAME"] == time, :].to_numpy()
+                if len(values) > 0:
+                    values = dict(zip(list(self.current_data.columns), values[0]))
+                    for k, c in enumerate(self.groupby_cols):
+                        values.update({c: tid[k]})
+                    new_table.append(values)
+            import pandas as pd
+
+            group_table = pd.DataFrame(new_table)
+            if self.population == "pairs":
+                for col in self.groupby_cols[1:]:
+                    first_column = group_table.pop(col)
+                    group_table.insert(0, col, first_column)
+            else:
+                for col in ["TRACK_ID"]:
+                    first_column = group_table.pop(col)
+                    group_table.insert(0, col, first_column)
+
+            group_table = group_table.sort_values(
+                by=self.groupby_cols + ["FRAME"], ignore_index=True
+            )
+            group_table = group_table.reset_index(drop=True)
+
+        elif self.per_status_option.isChecked():
+            self.projection_mode = self.status_operation.currentText()
+            group_table = collapse_trajectories_by_status(
+                self.current_data,
+                status=self.per_status_cb.currentText(),
+                population=self.population,
+                projection=self.status_operation.currentText(),
+                groupby_columns=self.groupby_cols,
+            )
+
+        self.subtable = TableUI(
+            group_table,
+            f"Group by tracks: {self.projection_mode}",
+            plot_mode="static",
+            collapse_tracks_option=False,
+        )
+        self.subtable.show()
+
+        self.projectionWidget.close()
+
+    # def groupby_track_table(self):
+
+    # 	"""
+
+    # 	Perform a time average across each track for all features
+
+    # 	"""
+
+    # 	self.subtable = TrajectoryTablePanel(self.data.groupby("TRACK_ID").mean(),"Group by tracks", plot_mode="scatter")
+    # 	self.subtable.show()
+
+    def _createMenuBar(self):
+        menuBar = self.menuBar()
+        self.fileMenu = QMenu("&File", self)
+        menuBar.addMenu(self.fileMenu)
+        self.editMenu = QMenu("&Edit", self)
+        menuBar.addMenu(self.editMenu)
+        self.mathMenu = QMenu("&Math", self)
+        menuBar.addMenu(self.mathMenu)
+
+    def save_as_csv(self):
+        options = QFileDialog.Options()
+        options |= QFileDialog.ReadOnly
+        file_name, _ = QFileDialog.getSaveFileName(
+            self,
+            "Save as .csv",
+            "",
+            "CSV Files (*.csv);;All Files (*)",
+            options=options,
+        )
+        if file_name:
+            if not file_name.endswith(".csv"):
+                file_name += ".csv"
+            invalid_cols = [
+                c for c in list(self.data.columns) if c.startswith("Unnamed")
+            ]
+            if len(invalid_cols) > 0:
+                self.data = self.data.drop(invalid_cols, axis=1)
+            self.data.to_csv(file_name, index=False)
+
+    def plot_instantaneous(self):
+
+        if self.plot_mode == "plot_track_signals":
+            self.plot_mode = "static"
+            self.plot()
+            self.plot_mode = "plot_track_signals"
+        elif self.plot_mode == "static":
+            self.plot()
+
+    def plot(self):
+        import matplotlib.pyplot as plt
+
+        if self.plot_mode == "static":
+
+            x = self.table_view.selectedIndexes()
+            col_idx = [l.column() for l in x]
+            row_idx = [l.row() for l in x]
+            column_names = self.data.columns
+            unique_cols = np.unique(col_idx)
+
+            if len(unique_cols) == 1 or len(unique_cols) == 0:
+                self.set_1D_plot_params()
+
+            if len(unique_cols) == 2:
+
+                print("two columns, plot mode")
+                x1 = test_bool_array(self.data.iloc[row_idx, unique_cols[0]])
+                x2 = test_bool_array(self.data.iloc[row_idx, unique_cols[1]])
+
+                self.fig, self.ax = plt.subplots(1, 1, figsize=(4, 3))
+                self.scatter_wdw = FigureCanvas(self.fig, title="scatter")
+                self.ax.clear()
+                self.ax.scatter(x1, x2)
+                self.ax.set_xlabel(column_names[unique_cols[0]])
+                self.ax.set_ylabel(column_names[unique_cols[1]])
+                plt.tight_layout()
+                self.fig.set_facecolor("none")  # or 'None'
+                self.fig.canvas.setStyleSheet("background-color: transparent;")
+                self.scatter_wdw.canvas.draw()
+                self.scatter_wdw.show()
+
+            else:
+                print("please select less columns")
+
+        elif self.plot_mode == "plot_timeseries":
+            print("mode plot frames")
+            x = self.table_view.selectedIndexes()
+            col_idx = np.array([l.column() for l in x])
+            row_idx = np.array([l.row() for l in x])
+            column_names = self.data.columns
+            unique_cols = np.unique(col_idx)
+
+            self.fig, self.ax = plt.subplots(1, 1, figsize=(4, 3))
+            self.plot_wdw = FigureCanvas(self.fig, title="scatter")
+            self.ax.clear()
+            for k in range(len(unique_cols)):
+                row_idx_i = row_idx[np.where(col_idx == unique_cols[k])[0]]
+                y = self.data.iloc[row_idx_i, unique_cols[k]]
+                self.ax.plot(
+                    self.data["timeline"][row_idx_i],
+                    y,
+                    label=column_names[unique_cols[k]],
+                )
+
+            self.ax.legend()
+            self.ax.set_xlabel("time [frame]")
+            self.ax.set_ylabel(self.title)
+            plt.tight_layout()
+            self.fig.set_facecolor("none")  # or 'None'
+            self.fig.canvas.setStyleSheet("background-color: transparent;")
+            self.plot_wdw.canvas.draw()
+            plt.show()
+
+        elif self.plot_mode == "plot_track_signals":
+
+            print("mode plot track signals")
+            print("we plot here")
+
+            x = self.table_view.selectedIndexes()
+            col_idx = np.array([l.column() for l in x])
+            row_idx = np.array([l.row() for l in x])
+            column_names = self.data.columns
+            unique_cols = np.unique(col_idx)
+
+            if len(unique_cols) > 2:
+                fig, ax = plt.subplots(1, 1, figsize=(7, 5.5))
+                for k in range(len(unique_cols)):
+
+                    row_idx_i = row_idx[np.where(col_idx == unique_cols[k])[0]]
+                    y = self.data.iloc[row_idx_i, unique_cols[k]]
+                    print(unique_cols[k])
+                    for w, well_group in self.data.groupby(["well_name"]):
+                        for pos, pos_group in well_group.groupby(["pos_name"]):
+                            for tid, group_track in pos_group.groupby(
+                                self.groupby_cols[1:]
+                            ):
+                                ax.plot(
+                                    group_track["FRAME"],
+                                    group_track[column_names[unique_cols[k]]],
+                                    label=column_names[unique_cols[k]],
+                                )
+                    # ax.plot(self.data["FRAME"][row_idx_i], y, label=column_names[unique_cols[k]])
+                ax.legend()
+                ax.set_xlabel("time [frame]")
+                ax.set_ylabel(self.title)
+                plt.tight_layout()
+                plt.show(block=False)
+
+            if len(unique_cols) == 2:
+
+                self.fig, self.ax = plt.subplots(1, 1, figsize=(4, 3))
+                self.scatter_wdw = FigureCanvas(self.fig, title="scatter")
+                self.ax.clear()
+                for tid, group in self.data.groupby(self.groupby_cols[1:]):
+                    self.ax.plot(
+                        group[column_names[unique_cols[0]]],
+                        group[column_names[unique_cols[1]]],
+                        marker="o",
+                    )
+                self.ax.set_xlabel(column_names[unique_cols[0]])
+                self.ax.set_ylabel(column_names[unique_cols[1]])
+                plt.tight_layout()
+                self.fig.set_facecolor("none")  # or 'None'
+                self.fig.canvas.setStyleSheet("background-color: transparent;")
+                self.scatter_wdw.canvas.draw()
+                self.scatter_wdw.show()
+
+            if len(unique_cols) == 1:
+
+                self.fig, self.ax = plt.subplots(1, 1, figsize=(4, 3))
+                self.plot_wdw = FigureCanvas(self.fig, title="scatter")
+                self.ax.clear()
+
+                # if 't0' in list(self.data.columns):
+                # 	ref_time_col = 't0'
+                # else:
+                # 	ref_time_col = 'FRAME'
+
+                for w, well_group in self.data.groupby(["well_name"]):
+                    for pos, pos_group in well_group.groupby(["pos_name"]):
+                        for tid, group_track in pos_group.groupby(
+                            self.groupby_cols[1:]
+                        ):
+                            self.ax.plot(
+                                group_track["FRAME"],
+                                group_track[column_names[unique_cols[0]]],
+                                c="k",
+                                alpha=0.1,
+                            )
+                self.ax.set_xlabel(r"$t$ [frame]")
+                self.ax.set_ylabel(column_names[unique_cols[0]])
+                plt.tight_layout()
+                self.fig.set_facecolor("none")  # or 'None'
+                self.fig.canvas.setStyleSheet("background-color: transparent;")
+                self.plot_wdw.canvas.draw()
+                self.plot_wdw.show()