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

celldetective/gui/settings/_settings_neighborhood.py

@@ -1,6 +1,17 @@
-from PyQt5.QtWidgets import QApplication, QComboBox, QFrame, QCheckBox, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
+from PyQt5.QtWidgets import (
+    QApplication,
+    QComboBox,
+    QFrame,
+    QCheckBox,
+    QVBoxLayout,
+    QLabel,
+    QHBoxLayout,
+    QPushButton,
+)
 from PyQt5.QtCore import Qt, QSize
-from celldetective.gui.gui_utils import center_window, ListWidget, DistanceChoice
+from celldetective.gui.gui_utils import DistanceChoice
+from celldetective.gui.base.list_widget import ListWidget
+from celldetective.gui.base.utils import center_window
 from superqt.fonticon import icon
 from fonticon_mdi6 import MDI6
 import numpy as np
@@ -8,492 +19,567 @@ import json
 import os
 from glob import glob
 import pandas as pd
-from celldetective.gui.viewers import CellSizeViewer, CellEdgeVisualizer
-from celldetective.gui import CelldetectiveWidget
+from celldetective.gui.viewers.contour_viewer import CellEdgeVisualizer
+from celldetective.gui.viewers.size_viewer import CellSizeViewer
+
+from celldetective.gui.base.components import CelldetectiveWidget
 
 
 class SettingsNeighborhood(CelldetectiveWidget):
-	
-	"""
-	Widget to configure neighborhood measurements.
-
-	"""
-
-	def __init__(self, neighborhood_type='distance_threshold',neighborhood_parameter_name='threshold distance', parent_window=None, *args, **kwargs):
-		
-		super().__init__(*args, **kwargs)
-		self.parent_window = parent_window
-		self.attr_parent = self.parent_window.parent_window
-
-		self.neighborhood_type = neighborhood_type
-		self.neighborhood_parameter_name = neighborhood_parameter_name
-
-		self.setWindowTitle('Configure neighborhoods')
-		self.neigh_instructions = self.attr_parent.exp_dir + os.sep.join(["configs","neighborhood_instructions.json"])
-		self.clear_previous = False
-		self.not_status_reference = False
-		self.not_status_neighbor = False	
-
-		self.screen_height = self.attr_parent.screen_height
-		self.setMinimumWidth(750)
-		self.setMinimumHeight(int(0.5*self.screen_height))
-		self.setMaximumHeight(int(0.95*self.screen_height))
-		
-		self.generate_main_layout()
-		self.load_previous_neighborhood_instructions()
-		center_window(self)
-
-	def generate_main_layout(self):
-
-		main_layout = QVBoxLayout(self)
-		main_layout.setContentsMargins(30,30,30,30)
-
-		populations_layout = QHBoxLayout()
-
-		# Reference population
-		self.reference_population_frame = QFrame()
-		self.reference_population_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
-		self.populate_reference_frame()
-		populations_layout.addWidget(self.reference_population_frame, 50)
-
-		# Neighbor population
-		self.neigh_population_frame = QFrame()
-		self.neigh_population_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
-		self.populate_neighbor_frame()
-		populations_layout.addWidget(self.neigh_population_frame, 50)
-		main_layout.addLayout(populations_layout)
-
-		# Measurements
-
-		self.measurement_frame = QFrame()
-		self.measurement_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
-		self.populate_measurement_frame()
-		# if self.neighborhood_type=='distance_threshold':
-		# 	self.populate_radii_frame()
-		# elif self.neighborhood_type=='mask_contact':
-		# 	self.populate_contact_frame()
-		main_layout.addWidget(self.measurement_frame)
-
-		self.clear_previous_btn = QCheckBox('clear previous neighborhoods')
-		self.clear_previous_btn.setToolTip('Clear all previous neighborhood measurements.')
-		self.clear_previous_btn.setIcon(icon(MDI6.broom, color='black'))
-
-		main_layout.addWidget(self.clear_previous_btn, alignment=Qt.AlignRight)
-
-		main_layout.addWidget(QLabel(''))
-		self.submit_btn = QPushButton('Set')
-		self.submit_btn.setStyleSheet(self.button_style_sheet)
-		self.submit_btn.clicked.connect(self.write_instructions)
-		main_layout.addWidget(self.submit_btn)
-
-		self.adjustSize()
-		QApplication.processEvents()
-
-	def populate_measurement_frame(self):
-		
-		"""
-		Add widgets and layout in the radii frame.
-		"""
-
-		grid = QVBoxLayout(self.measurement_frame)
-
-		self.dist_lbl = QLabel(f"NEIGHBORHOOD {self.neighborhood_parameter_name.upper()}")
-		self.dist_lbl.setStyleSheet(self.block_title)
-		grid.addWidget(self.dist_lbl, alignment=Qt.AlignCenter)
-
-		self.ContentsMeasurements = QFrame()
-		layout = QVBoxLayout(self.ContentsMeasurements)
-		layout.setContentsMargins(0,0,0,0)
-
-		list_header_layout = QHBoxLayout()
-		meas = self.neighborhood_parameter_name.split(' ')[-1]
-		lbl = QLabel(f'{meas} [px]:')
-		lbl.setToolTip('')
-		list_header_layout.addWidget(lbl, 85)
-
-		self.delete_measurement_btn = QPushButton("")
-		self.delete_measurement_btn.setStyleSheet(self.button_select_all)
-		self.delete_measurement_btn.setIcon(icon(MDI6.trash_can,color="black"))
-		self.delete_measurement_btn.setToolTip("Remove measurement.")
-		self.delete_measurement_btn.setIconSize(QSize(20, 20))
-		list_header_layout.addWidget(self.delete_measurement_btn, 5)
-
-		self.add_measurement_btn = QPushButton("")
-		self.add_measurement_btn.setStyleSheet(self.button_select_all)
-		self.add_measurement_btn.setIcon(icon(MDI6.plus,color="black"))
-		self.add_measurement_btn.setToolTip("Add a neighborhood measurement.")
-		self.add_measurement_btn.setIconSize(QSize(20, 20))	
-		list_header_layout.addWidget(self.add_measurement_btn, 5)
-
-		self.viewer_btn = QPushButton()
-		self.viewer_btn.setStyleSheet(self.button_select_all)
-		self.viewer_btn.setIcon(icon(MDI6.image_check, color="black"))
-		self.viewer_btn.setToolTip("View stack and set measurement.")
-		self.viewer_btn.setIconSize(QSize(20, 20))
-		if self.neighborhood_type=='distance_threshold':
-			self.viewer_btn.clicked.connect(self.view_current_stack_with_circle)
-		elif self.neighborhood_type=='mask_contact':
-			self.viewer_btn.clicked.connect(self.view_current_stack_with_edge)			
-		list_header_layout.addWidget(self.viewer_btn, 5)
-
-		layout.addLayout(list_header_layout)
-
-		self.measurements_list = ListWidget(DistanceChoice, initial_features=[], dtype=int)
-		self.measurements_list.setToolTip('Neighborhoods to compute.')
-		layout.addWidget(self.measurements_list)
-
-		self.delete_measurement_btn.clicked.connect(self.measurements_list.removeSel)
-		self.add_measurement_btn.clicked.connect(self.measurements_list.addItem)
-
-		grid.addWidget(self.ContentsMeasurements)
-
-	def view_current_stack_with_circle(self):
-		
-		self.parent_window.parent_window.locate_image()
-		if self.parent_window.parent_window.current_stack is not None:
-			self.viewer = CellSizeViewer(
-										  initial_diameter = 100,
-										  parent_list_widget = self.measurements_list.list_widget,
-										  set_radius_in_list = True,
-										  stack_path=self.parent_window.parent_window.current_stack,
-										  window_title=f'Position {self.parent_window.parent_window.position_list.currentText()}',
-										  frame_slider = True,
-										  contrast_slider = True,
-										  channel_cb = True,
-										  diameter_slider_range = (0,300),
-										  channel_names = self.parent_window.parent_window.exp_channels,
-										  n_channels = self.parent_window.parent_window.nbr_channels,
-										  PxToUm = 1,
-										 )
-			self.viewer.show()
-
-	def view_current_stack_with_edge(self):
-		
-		self.attr_parent.locate_image()
-		if self.attr_parent.current_stack is not None:
-			self.viewer = CellEdgeVisualizer(
-										  cell_type=self.reference_population_cb.currentText(),
-										  edge_range=(1,30),
-										  invert=True,
-										  initial_edge=3,
-										  parent_list_widget = self.measurements_list.list_widget,
-										  stack_path=self.attr_parent.current_stack,
-										  window_title=f'Position {self.attr_parent.position_list.currentText()}',
-										  frame_slider = True,
-										  contrast_slider = True,
-										  channel_cb = True,
-										  channel_names = self.attr_parent.exp_channels,
-										  n_channels = self.attr_parent.nbr_channels,
-										  PxToUm = 1,
-										 )
-			self.viewer.show()
-
-
-	def populate_reference_frame(self):
-		
-		"""
-		Add widgets and layout in the reference population frame.
-		"""
-
-		grid = QVBoxLayout(self.reference_population_frame)
-		grid.setSpacing(15)
-		self.ref_lbl = QLabel("REFERENCE")
-		self.ref_lbl.setStyleSheet(self.block_title)
-		self.ref_lbl.setToolTip('Reference population settings.')
-		grid.addWidget(self.ref_lbl, 30, alignment=Qt.AlignCenter)
-
-		self.ContentsReference = QFrame()
-		layout = QVBoxLayout(self.ContentsReference)
-		layout.setContentsMargins(15,15,15,15)
-
-		population_layout = QHBoxLayout()
-		population_layout.addWidget(QLabel('population: '),30)
-		self.reference_population_cb = QComboBox()
-		self.reference_population_cb.addItems(self.parent_window.parent_window.populations)
-		self.reference_population_cb.setToolTip('Select a reference population.')
-		population_layout.addWidget(self.reference_population_cb,70)
-		layout.addLayout(population_layout)
-
-		status_layout = QHBoxLayout()
-
-		#status_layout.addWidget(QLabel('status: '), 30)
-
-		status_sublayout = QHBoxLayout()
-		self.reference_population_status_cb = QComboBox()
-		self.reference_population_status_cb.setToolTip('Status of the reference population.')
-		self.reference_population_status_cb.hide()
-		status_sublayout.addWidget(self.reference_population_status_cb,95)
-
-		self.reference_switch_status_btn = QPushButton("")
-		self.reference_switch_status_btn.setStyleSheet(self.button_select_all)
-		self.reference_switch_status_btn.setIcon(icon(MDI6.invert_colors,color="black"))
-		self.reference_switch_status_btn.setIconSize(QSize(20, 20))
-		self.reference_switch_status_btn.clicked.connect(self.switch_not_reference)
-		self.reference_switch_status_btn.setToolTip('Invert status values.')
-		self.reference_switch_status_btn.hide()
-
-		status_sublayout.addWidget(self.reference_switch_status_btn, 5)
-
-		status_layout.addLayout(status_sublayout, 70)
-		layout.addLayout(status_layout)
-
-		event_layout = QHBoxLayout()
-		event_layout.addWidget(QLabel('event time: '),30)
-		self.event_time_cb = QComboBox()
-		self.event_time_cb.setToolTip('Compute average neighborhood metrics before and after this event time.')
-		event_layout.addWidget(self.event_time_cb,70)
-		layout.addLayout(event_layout)
-		
-		self.fill_cbs_of_reference_population()
-		self.reference_population_cb.currentIndexChanged.connect(self.fill_cbs_of_reference_population)
-
-		grid.addWidget(self.ContentsReference, 70)
-
-	def populate_neighbor_frame(self):
-
-		"""
-		Add widgets and layout in the neighbor population frame.
-		"""
-
-		grid = QVBoxLayout(self.neigh_population_frame)
-		grid.setSpacing(15)
-		self.ref_lbl = QLabel("NEIGHBOR")
-		self.ref_lbl.setStyleSheet(self.block_title)
-		self.ref_lbl.setToolTip('Neighbor population settings.')
-		grid.addWidget(self.ref_lbl, 30, alignment=Qt.AlignCenter)
-
-		self.ContentsNeigh = QFrame()
-		layout = QVBoxLayout(self.ContentsNeigh)
-		layout.setContentsMargins(15,15,15,15)
-
-		population_layout = QHBoxLayout()
-		population_layout.addWidget(QLabel('population: '),30)
-		self.neighbor_population_cb = QComboBox()
-		self.neighbor_population_cb.addItems(self.parent_window.parent_window.populations)
-		self.neighbor_population_cb.setToolTip('Select a neighbor population.')
-		population_layout.addWidget(self.neighbor_population_cb,70)
-		layout.addLayout(population_layout)
-
-		status_layout = QHBoxLayout()
-
-		status_layout.addWidget(QLabel('status: '), 30)
-		status_sublayout = QHBoxLayout()
-
-		self.neighbor_population_status_cb = QComboBox()
-		self.neighbor_population_status_cb.setToolTip('Status of the neighbor population.')
-		status_sublayout.addWidget(self.neighbor_population_status_cb,95)
-
-		self.neighbor_switch_status_btn = QPushButton("")
-		self.neighbor_switch_status_btn.setStyleSheet(self.button_select_all)
-		self.neighbor_switch_status_btn.setIcon(icon(MDI6.invert_colors,color="black"))
-		self.neighbor_switch_status_btn.setToolTip("Invert status values.")
-		self.neighbor_switch_status_btn.setIconSize(QSize(20, 20))
-		self.neighbor_switch_status_btn.clicked.connect(self.switch_not_neigh)
-		status_sublayout.addWidget(self.neighbor_switch_status_btn, 5)
-		status_layout.addLayout(status_sublayout, 70)
-		layout.addLayout(status_layout)
-
-		self.cumulated_presence_btn = QCheckBox('cumulated presence')
-		self.cumulated_presence_btn.setToolTip("Compute the cumulated presence time of each neighbor around a reference cell.")
-		self.cumulated_presence_btn.setIcon(icon(MDI6.timer_outline, color='black'))
-
-		layout.addWidget(self.cumulated_presence_btn)
-
-		# self.symmetrize_btn = QCheckBox('symmetrize')
-		# self.symmetrize_btn.setToolTip("Write the neighborhood of the neighbor cells with respect to the reference cells.")
-		# layout.addWidget(self.symmetrize_btn)
-		
-		self.fill_cbs_of_neighbor_population()
-		self.neighbor_population_cb.currentIndexChanged.connect(self.fill_cbs_of_neighbor_population)
-
-		grid.addWidget(self.ContentsNeigh, 70)
-
-	def fill_cbs_of_neighbor_population(self):
-
-		population = self.neighbor_population_cb.currentText()
-		class_cols, status_cols, group_cols, time_cols = self.locate_population_specific_columns(population)
-		self.neighbor_population_status_cb.clear()
-		self.neighbor_population_status_cb.addItems(list(np.unique(['--','class', 'status']+class_cols+status_cols+group_cols)))
-
-	def fill_cbs_of_reference_population(self):
-
-		population = self.reference_population_cb.currentText()
-		class_cols, status_cols, group_cols, time_cols = self.locate_population_specific_columns(population)
-		self.event_time_cb.clear()
-		self.event_time_cb.addItems(list(np.unique(['--', 't0']+time_cols)))
-
-	def switch_not_reference(self):
-		
-		self.not_status_reference = not self.not_status_reference
-		if self.not_status_reference:
-			self.reference_switch_status_btn.setIcon(icon(MDI6.invert_colors,color=self.celldetective_blue))
-			self.reference_switch_status_btn.setIconSize(QSize(20, 20))
-		else:
-			self.reference_switch_status_btn.setIcon(icon(MDI6.invert_colors,color="black"))
-			self.reference_switch_status_btn.setIconSize(QSize(20, 20))
-
-	def switch_not_neigh(self):
-		
-		self.not_status_neighbor = not self.not_status_neighbor
-		if self.not_status_neighbor:
-			self.neighbor_switch_status_btn.setIcon(icon(MDI6.invert_colors,color=self.celldetective_blue))
-			self.neighbor_switch_status_btn.setIconSize(QSize(20, 20))
-		else:
-			self.neighbor_switch_status_btn.setIcon(icon(MDI6.invert_colors,color="black"))
-			self.neighbor_switch_status_btn.setIconSize(QSize(20, 20))
-
-
-	def locate_population_specific_columns(self, population):
-
-		# Look for all classes and times
-		tables = glob(self.attr_parent.exp_dir+os.sep.join(['W*','*','output','tables',f'trajectories_{population}.csv']))
-		self.all_columns = []
-		for tab in tables:
-			cols = pd.read_csv(tab, nrows=1).columns.tolist()
-			self.all_columns.extend(cols)
-		self.all_columns = np.unique(self.all_columns)
-
-		class_idx = np.array([s.startswith('class_') for s in self.all_columns])
-		status_idx = np.array([s.startswith('status_') for s in self.all_columns])
-		group_idx = np.array([s.startswith('group_') for s in self.all_columns])		
-		time_idx = np.array([s.startswith('t_') for s in self.all_columns])
-
-		if len(class_idx)>0:
-			class_columns = list(self.all_columns[class_idx])
-			for c in ['class_id', 'class_color']:
-				if c in class_columns:
-					class_columns.remove(c)
-		else:
-			class_columns = []
-
-		if len(status_idx)>0:
-			status_columns = list(self.all_columns[status_idx])
-		else:
-			status_columns = []
-
-		if len(group_idx)>0:
-			group_columns = list(self.all_columns[group_idx])
-		else:
-			group_columns = []
-
-		if len(time_idx)>0:
-			time_columns = list(self.all_columns[time_idx])
-		else:
-			time_columns = []
-
-		return class_columns, status_columns, group_columns, time_columns
-
-	def write_instructions(self):
-
-		"""
-		Write the selected options in a json file for later reading by the software.
-		"""
-
-		print('Writing instructions...')
-		
-		neighborhood_options = {}
-		pop = [self.reference_population_cb.currentText(), self.neighbor_population_cb.currentText()]
-		neighborhood_options.update({'population': pop})
-		
-		status_options = [self.reference_population_status_cb.currentText(), self.neighbor_population_status_cb.currentText()]
-		for k in range(2):
-			if status_options[k]=='--' or status_options[k]=='':
-				status_options[k] = None
-		if pop[0]!=pop[1]:
-			mode = 'two-pop'
-		else:
-			mode = 'self'
-
-		# TO ADAPT
-		distances = self.measurements_list.getItems()
-		neighborhood_options.update({'neighborhood_type': self.neighborhood_type})
-		neighborhood_options.update({'distance': distances})	
-		neighborhood_options.update({'clear_neigh': self.clear_previous_btn.isChecked()})
-		event_time_col = self.event_time_cb.currentText()
-		if event_time_col=='--':
-			event_time_col = None
-		neighborhood_options.update({'event_time_col': event_time_col})		
-
-		neighborhood_kwargs = {'mode': mode, 'status': status_options, 'not_status_option': [self.not_status_reference, self.not_status_neighbor], 
-							  'compute_cum_sum': self.cumulated_presence_btn.isChecked(), 'attention_weight': True, 'symmetrize': False,
-							  'include_dead_weight': True}
-
-		neighborhood_options.update({'neighborhood_kwargs': neighborhood_kwargs})
-
-		print('Neighborhood instructions: ', neighborhood_options)
-		file_name = self.neigh_instructions
-		with open(file_name, 'w') as f:
-			json.dump(neighborhood_options, f, indent=4)
-
-
-		self.parent_window.protocols.append(neighborhood_options)
-		correction_description = ""
-		for index, (key, value) in enumerate(neighborhood_options.items()):
-			if index > 0:
-				correction_description += ", "
-			correction_description += str(key) + " : " + str(value)
-		self.parent_window.protocol_list.addItem(correction_description)
-		
-		print('Done.')
-		self.close()
-
-	def load_previous_neighborhood_instructions(self):
-
-		"""
-		Read the measurmeent options from a previously written json file and format properly for the UI.
-		"""
-
-		print('Reading instructions..')
-		if os.path.exists(self.neigh_instructions):
-			with open(self.neigh_instructions, 'r') as f:
-				
-				neigh_instructions = json.load(f)
-				print(f"Loading the instructions: {neigh_instructions}...")
-
-				if 'neighborhood_type' not in neigh_instructions:
-					neigh_instructions.update({'neighborhood_type': self.neighborhood_type})
-
-				if self.neighborhood_type==neigh_instructions['neighborhood_type']:
-
-					if 'distance' in neigh_instructions:
-						distances = neigh_instructions['distance']
-						distances = [str(d) for d in distances]
-						self.measurements_list.list_widget.clear()
-						self.measurements_list.list_widget.addItems(distances)
-
-					if 'population' in neigh_instructions:
-
-						pop = neigh_instructions['population']
-						idx0 = self.reference_population_cb.findText(pop[0])
-						self.reference_population_cb.setCurrentIndex(idx0)
-						idx1 = self.neighbor_population_cb.findText(pop[1])
-						self.neighbor_population_cb.setCurrentIndex(idx1)
-
-					if 'clear_neigh' in neigh_instructions:
-						clear_neigh = neigh_instructions['clear_neigh']
-						self.clear_previous_btn.setChecked(clear_neigh)
-
-					if 'event_time_col' in neigh_instructions:
-						event_time_col = neigh_instructions['event_time_col']
-						if event_time_col is None:
-							event_time_col = '--'
-						idx = self.event_time_cb.findText(event_time_col)
-						self.event_time_cb.setCurrentIndex(idx)
-
-					if 'neighborhood_kwargs' in neigh_instructions:
-						neighborhood_kwargs = neigh_instructions['neighborhood_kwargs']
-						if 'compute_cum_sum' in neighborhood_kwargs:
-							self.cumulated_presence_btn.setChecked(neighborhood_kwargs['compute_cum_sum'])
-						if 'status' in neighborhood_kwargs:
-							status_options = neighborhood_kwargs['status']
-							status_options = ['--' if s is None else s for s in status_options]
-							idx0 = self.reference_population_status_cb.findText(status_options[0])
-							self.reference_population_status_cb.setCurrentIndex(idx0)
-							idx1 = self.neighbor_population_status_cb.findText(status_options[1])
-							self.neighbor_population_status_cb.setCurrentIndex(idx1)
-						if 'not_status_option' in neighborhood_kwargs:
-							not_status_option = neighborhood_kwargs['not_status_option']
-							if not_status_option[0]:
-								self.reference_switch_status_btn.click()
-							if not_status_option[1]:
-								self.neighbor_switch_status_btn.click()
+    """
+    Widget to configure neighborhood measurements.
+
+    """
+
+    def __init__(
+        self,
+        neighborhood_type="distance_threshold",
+        neighborhood_parameter_name="threshold distance",
+        parent_window=None,
+        *args,
+        **kwargs,
+    ):
+
+        super().__init__(*args, **kwargs)
+        self.parent_window = parent_window
+        self.attr_parent = self.parent_window.parent_window
+
+        self.neighborhood_type = neighborhood_type
+        self.neighborhood_parameter_name = neighborhood_parameter_name
+
+        self.setWindowTitle("Configure neighborhoods")
+        self.neigh_instructions = self.attr_parent.exp_dir + os.sep.join(
+            ["configs", "neighborhood_instructions.json"]
+        )
+        self.clear_previous = False
+        self.not_status_reference = False
+        self.not_status_neighbor = False
+
+        self.screen_height = self.attr_parent.screen_height
+        self.setMinimumWidth(750)
+        self.setMinimumHeight(int(0.5 * self.screen_height))
+        self.setMaximumHeight(int(0.95 * self.screen_height))
+
+        self.generate_main_layout()
+        self.load_previous_neighborhood_instructions()
+        center_window(self)
+
+    def generate_main_layout(self):
+
+        main_layout = QVBoxLayout(self)
+        main_layout.setContentsMargins(30, 30, 30, 30)
+
+        populations_layout = QHBoxLayout()
+
+        # Reference population
+        self.reference_population_frame = QFrame()
+        self.reference_population_frame.setFrameStyle(
+            QFrame.StyledPanel | QFrame.Raised
+        )
+        self.populate_reference_frame()
+        populations_layout.addWidget(self.reference_population_frame, 50)
+
+        # Neighbor population
+        self.neigh_population_frame = QFrame()
+        self.neigh_population_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
+        self.populate_neighbor_frame()
+        populations_layout.addWidget(self.neigh_population_frame, 50)
+        main_layout.addLayout(populations_layout)
+
+        # Measurements
+
+        self.measurement_frame = QFrame()
+        self.measurement_frame.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
+        self.populate_measurement_frame()
+        # if self.neighborhood_type=='distance_threshold':
+        # 	self.populate_radii_frame()
+        # elif self.neighborhood_type=='mask_contact':
+        # 	self.populate_contact_frame()
+        main_layout.addWidget(self.measurement_frame)
+
+        self.clear_previous_btn = QCheckBox("clear previous neighborhoods")
+        self.clear_previous_btn.setToolTip(
+            "Clear all previous neighborhood measurements."
+        )
+        self.clear_previous_btn.setIcon(icon(MDI6.broom, color="black"))
+
+        main_layout.addWidget(self.clear_previous_btn, alignment=Qt.AlignRight)
+
+        main_layout.addWidget(QLabel(""))
+        self.submit_btn = QPushButton("Set")
+        self.submit_btn.setStyleSheet(self.button_style_sheet)
+        self.submit_btn.clicked.connect(self.write_instructions)
+        main_layout.addWidget(self.submit_btn)
+
+        self.adjustSize()
+        QApplication.processEvents()
+
+    def populate_measurement_frame(self):
+        """
+        Add widgets and layout in the radii frame.
+        """
+
+        grid = QVBoxLayout(self.measurement_frame)
+
+        self.dist_lbl = QLabel(
+            f"NEIGHBORHOOD {self.neighborhood_parameter_name.upper()}"
+        )
+        self.dist_lbl.setStyleSheet(self.block_title)
+        grid.addWidget(self.dist_lbl, alignment=Qt.AlignCenter)
+
+        self.ContentsMeasurements = QFrame()
+        layout = QVBoxLayout(self.ContentsMeasurements)
+        layout.setContentsMargins(0, 0, 0, 0)
+
+        list_header_layout = QHBoxLayout()
+        meas = self.neighborhood_parameter_name.split(" ")[-1]
+        lbl = QLabel(f"{meas} [px]:")
+        lbl.setToolTip("")
+        list_header_layout.addWidget(lbl, 85)
+
+        self.delete_measurement_btn = QPushButton("")
+        self.delete_measurement_btn.setStyleSheet(self.button_select_all)
+        self.delete_measurement_btn.setIcon(icon(MDI6.trash_can, color="black"))
+        self.delete_measurement_btn.setToolTip("Remove measurement.")
+        self.delete_measurement_btn.setIconSize(QSize(20, 20))
+        list_header_layout.addWidget(self.delete_measurement_btn, 5)
+
+        self.add_measurement_btn = QPushButton("")
+        self.add_measurement_btn.setStyleSheet(self.button_select_all)
+        self.add_measurement_btn.setIcon(icon(MDI6.plus, color="black"))
+        self.add_measurement_btn.setToolTip("Add a neighborhood measurement.")
+        self.add_measurement_btn.setIconSize(QSize(20, 20))
+        list_header_layout.addWidget(self.add_measurement_btn, 5)
+
+        self.viewer_btn = QPushButton()
+        self.viewer_btn.setStyleSheet(self.button_select_all)
+        self.viewer_btn.setIcon(icon(MDI6.image_check, color="black"))
+        self.viewer_btn.setToolTip("View stack and set measurement.")
+        self.viewer_btn.setIconSize(QSize(20, 20))
+        if self.neighborhood_type == "distance_threshold":
+            self.viewer_btn.clicked.connect(self.view_current_stack_with_circle)
+        elif self.neighborhood_type == "mask_contact":
+            self.viewer_btn.clicked.connect(self.view_current_stack_with_edge)
+        list_header_layout.addWidget(self.viewer_btn, 5)
+
+        layout.addLayout(list_header_layout)
+
+        self.measurements_list = ListWidget(
+            DistanceChoice, initial_features=[], dtype=int
+        )
+        self.measurements_list.setToolTip("Neighborhoods to compute.")
+        layout.addWidget(self.measurements_list)
+
+        self.delete_measurement_btn.clicked.connect(self.measurements_list.removeSel)
+        self.add_measurement_btn.clicked.connect(self.measurements_list.addItem)
+
+        grid.addWidget(self.ContentsMeasurements)
+
+    def view_current_stack_with_circle(self):
+
+        self.parent_window.parent_window.locate_image()
+        if self.parent_window.parent_window.current_stack is not None:
+            self.viewer = CellSizeViewer(
+                initial_diameter=100,
+                parent_list_widget=self.measurements_list.list_widget,
+                set_radius_in_list=True,
+                stack_path=self.parent_window.parent_window.current_stack,
+                window_title=f"Position {self.parent_window.parent_window.position_list.currentText()}",
+                frame_slider=True,
+                contrast_slider=True,
+                channel_cb=True,
+                diameter_slider_range=(0, 300),
+                channel_names=self.parent_window.parent_window.exp_channels,
+                n_channels=self.parent_window.parent_window.nbr_channels,
+                PxToUm=1,
+            )
+            self.viewer.show()
+
+    def view_current_stack_with_edge(self):
+
+        self.attr_parent.locate_image()
+        if self.attr_parent.current_stack is not None:
+            self.viewer = CellEdgeVisualizer(
+                cell_type=self.reference_population_cb.currentText(),
+                edge_range=(1, 30),
+                invert=True,
+                initial_edge=3,
+                parent_list_widget=self.measurements_list.list_widget,
+                stack_path=self.attr_parent.current_stack,
+                window_title=f"Position {self.attr_parent.position_list.currentText()}",
+                frame_slider=True,
+                contrast_slider=True,
+                channel_cb=True,
+                channel_names=self.attr_parent.exp_channels,
+                n_channels=self.attr_parent.nbr_channels,
+                PxToUm=1,
+            )
+            self.viewer.show()
+
+    def populate_reference_frame(self):
+        """
+        Add widgets and layout in the reference population frame.
+        """
+
+        grid = QVBoxLayout(self.reference_population_frame)
+        grid.setSpacing(15)
+        self.ref_lbl = QLabel("REFERENCE")
+        self.ref_lbl.setStyleSheet(self.block_title)
+        self.ref_lbl.setToolTip("Reference population settings.")
+        grid.addWidget(self.ref_lbl, 30, alignment=Qt.AlignCenter)
+
+        self.ContentsReference = QFrame()
+        layout = QVBoxLayout(self.ContentsReference)
+        layout.setContentsMargins(15, 15, 15, 15)
+
+        population_layout = QHBoxLayout()
+        population_layout.addWidget(QLabel("population: "), 30)
+        self.reference_population_cb = QComboBox()
+        self.reference_population_cb.addItems(
+            self.parent_window.parent_window.populations
+        )
+        self.reference_population_cb.setToolTip("Select a reference population.")
+        population_layout.addWidget(self.reference_population_cb, 70)
+        layout.addLayout(population_layout)
+
+        status_layout = QHBoxLayout()
+
+        # status_layout.addWidget(QLabel('status: '), 30)
+
+        status_sublayout = QHBoxLayout()
+        self.reference_population_status_cb = QComboBox()
+        self.reference_population_status_cb.setToolTip(
+            "Status of the reference population."
+        )
+        self.reference_population_status_cb.hide()
+        status_sublayout.addWidget(self.reference_population_status_cb, 95)
+
+        self.reference_switch_status_btn = QPushButton("")
+        self.reference_switch_status_btn.setStyleSheet(self.button_select_all)
+        self.reference_switch_status_btn.setIcon(
+            icon(MDI6.invert_colors, color="black")
+        )
+        self.reference_switch_status_btn.setIconSize(QSize(20, 20))
+        self.reference_switch_status_btn.clicked.connect(self.switch_not_reference)
+        self.reference_switch_status_btn.setToolTip("Invert status values.")
+        self.reference_switch_status_btn.hide()
+
+        status_sublayout.addWidget(self.reference_switch_status_btn, 5)
+
+        status_layout.addLayout(status_sublayout, 70)
+        layout.addLayout(status_layout)
+
+        event_layout = QHBoxLayout()
+        event_layout.addWidget(QLabel("event time: "), 30)
+        self.event_time_cb = QComboBox()
+        self.event_time_cb.setToolTip(
+            "Compute average neighborhood metrics before and after this event time."
+        )
+        event_layout.addWidget(self.event_time_cb, 70)
+        layout.addLayout(event_layout)
+
+        self.fill_cbs_of_reference_population()
+        self.reference_population_cb.currentIndexChanged.connect(
+            self.fill_cbs_of_reference_population
+        )
+
+        grid.addWidget(self.ContentsReference, 70)
+
+    def populate_neighbor_frame(self):
+        """
+        Add widgets and layout in the neighbor population frame.
+        """
+
+        grid = QVBoxLayout(self.neigh_population_frame)
+        grid.setSpacing(15)
+        self.ref_lbl = QLabel("NEIGHBOR")
+        self.ref_lbl.setStyleSheet(self.block_title)
+        self.ref_lbl.setToolTip("Neighbor population settings.")
+        grid.addWidget(self.ref_lbl, 30, alignment=Qt.AlignCenter)
+
+        self.ContentsNeigh = QFrame()
+        layout = QVBoxLayout(self.ContentsNeigh)
+        layout.setContentsMargins(15, 15, 15, 15)
+
+        population_layout = QHBoxLayout()
+        population_layout.addWidget(QLabel("population: "), 30)
+        self.neighbor_population_cb = QComboBox()
+        self.neighbor_population_cb.addItems(
+            self.parent_window.parent_window.populations
+        )
+        self.neighbor_population_cb.setToolTip("Select a neighbor population.")
+        population_layout.addWidget(self.neighbor_population_cb, 70)
+        layout.addLayout(population_layout)
+
+        status_layout = QHBoxLayout()
+
+        status_layout.addWidget(QLabel("status: "), 30)
+        status_sublayout = QHBoxLayout()
+
+        self.neighbor_population_status_cb = QComboBox()
+        self.neighbor_population_status_cb.setToolTip(
+            "Status of the neighbor population."
+        )
+        status_sublayout.addWidget(self.neighbor_population_status_cb, 95)
+
+        self.neighbor_switch_status_btn = QPushButton("")
+        self.neighbor_switch_status_btn.setStyleSheet(self.button_select_all)
+        self.neighbor_switch_status_btn.setIcon(icon(MDI6.invert_colors, color="black"))
+        self.neighbor_switch_status_btn.setToolTip("Invert status values.")
+        self.neighbor_switch_status_btn.setIconSize(QSize(20, 20))
+        self.neighbor_switch_status_btn.clicked.connect(self.switch_not_neigh)
+        status_sublayout.addWidget(self.neighbor_switch_status_btn, 5)
+        status_layout.addLayout(status_sublayout, 70)
+        layout.addLayout(status_layout)
+
+        self.cumulated_presence_btn = QCheckBox("cumulated presence")
+        self.cumulated_presence_btn.setToolTip(
+            "Compute the cumulated presence time of each neighbor around a reference cell."
+        )
+        self.cumulated_presence_btn.setIcon(icon(MDI6.timer_outline, color="black"))
+
+        layout.addWidget(self.cumulated_presence_btn)
+
+        # self.symmetrize_btn = QCheckBox('symmetrize')
+        # self.symmetrize_btn.setToolTip("Write the neighborhood of the neighbor cells with respect to the reference cells.")
+        # layout.addWidget(self.symmetrize_btn)
+
+        self.fill_cbs_of_neighbor_population()
+        self.neighbor_population_cb.currentIndexChanged.connect(
+            self.fill_cbs_of_neighbor_population
+        )
+
+        grid.addWidget(self.ContentsNeigh, 70)
+
+    def fill_cbs_of_neighbor_population(self):
+
+        population = self.neighbor_population_cb.currentText()
+        class_cols, status_cols, group_cols, time_cols = (
+            self.locate_population_specific_columns(population)
+        )
+        self.neighbor_population_status_cb.clear()
+        self.neighbor_population_status_cb.addItems(
+            list(
+                np.unique(
+                    ["--", "class", "status"] + class_cols + status_cols + group_cols
+                )
+            )
+        )
+
+    def fill_cbs_of_reference_population(self):
+
+        population = self.reference_population_cb.currentText()
+        class_cols, status_cols, group_cols, time_cols = (
+            self.locate_population_specific_columns(population)
+        )
+        self.event_time_cb.clear()
+        self.event_time_cb.addItems(list(np.unique(["--", "t0"] + time_cols)))
+
+    def switch_not_reference(self):
+
+        self.not_status_reference = not self.not_status_reference
+        if self.not_status_reference:
+            self.reference_switch_status_btn.setIcon(
+                icon(MDI6.invert_colors, color=self.celldetective_blue)
+            )
+            self.reference_switch_status_btn.setIconSize(QSize(20, 20))
+        else:
+            self.reference_switch_status_btn.setIcon(
+                icon(MDI6.invert_colors, color="black")
+            )
+            self.reference_switch_status_btn.setIconSize(QSize(20, 20))
+
+    def switch_not_neigh(self):
+
+        self.not_status_neighbor = not self.not_status_neighbor
+        if self.not_status_neighbor:
+            self.neighbor_switch_status_btn.setIcon(
+                icon(MDI6.invert_colors, color=self.celldetective_blue)
+            )
+            self.neighbor_switch_status_btn.setIconSize(QSize(20, 20))
+        else:
+            self.neighbor_switch_status_btn.setIcon(
+                icon(MDI6.invert_colors, color="black")
+            )
+            self.neighbor_switch_status_btn.setIconSize(QSize(20, 20))
+
+    def locate_population_specific_columns(self, population):
+
+        # Look for all classes and times
+        tables = glob(
+            self.attr_parent.exp_dir
+            + os.sep.join(
+                ["W*", "*", "output", "tables", f"trajectories_{population}.csv"]
+            )
+        )
+        self.all_columns = []
+        for tab in tables:
+            cols = pd.read_csv(tab, nrows=1).columns.tolist()
+            self.all_columns.extend(cols)
+        self.all_columns = np.unique(self.all_columns)
+
+        class_idx = np.array([s.startswith("class_") for s in self.all_columns])
+        status_idx = np.array([s.startswith("status_") for s in self.all_columns])
+        group_idx = np.array([s.startswith("group_") for s in self.all_columns])
+        time_idx = np.array([s.startswith("t_") for s in self.all_columns])
+
+        if len(class_idx) > 0:
+            class_columns = list(self.all_columns[class_idx])
+            for c in ["class_id", "class_color"]:
+                if c in class_columns:
+                    class_columns.remove(c)
+        else:
+            class_columns = []
+
+        if len(status_idx) > 0:
+            status_columns = list(self.all_columns[status_idx])
+        else:
+            status_columns = []
+
+        if len(group_idx) > 0:
+            group_columns = list(self.all_columns[group_idx])
+        else:
+            group_columns = []
+
+        if len(time_idx) > 0:
+            time_columns = list(self.all_columns[time_idx])
+        else:
+            time_columns = []
+
+        return class_columns, status_columns, group_columns, time_columns
+
+    def write_instructions(self):
+        """
+        Write the selected options in a json file for later reading by the software.
+        """
+
+        print("Writing instructions...")
+
+        neighborhood_options = {}
+        pop = [
+            self.reference_population_cb.currentText(),
+            self.neighbor_population_cb.currentText(),
+        ]
+        neighborhood_options.update({"population": pop})
+
+        status_options = [
+            self.reference_population_status_cb.currentText(),
+            self.neighbor_population_status_cb.currentText(),
+        ]
+        for k in range(2):
+            if status_options[k] == "--" or status_options[k] == "":
+                status_options[k] = None
+        if pop[0] != pop[1]:
+            mode = "two-pop"
+        else:
+            mode = "self"
+
+        # TO ADAPT
+        distances = self.measurements_list.getItems()
+        neighborhood_options.update({"neighborhood_type": self.neighborhood_type})
+        neighborhood_options.update({"distance": distances})
+        neighborhood_options.update(
+            {"clear_neigh": self.clear_previous_btn.isChecked()}
+        )
+        event_time_col = self.event_time_cb.currentText()
+        if event_time_col == "--":
+            event_time_col = None
+        neighborhood_options.update({"event_time_col": event_time_col})
+
+        neighborhood_kwargs = {
+            "mode": mode,
+            "status": status_options,
+            "not_status_option": [self.not_status_reference, self.not_status_neighbor],
+            "compute_cum_sum": self.cumulated_presence_btn.isChecked(),
+            "attention_weight": True,
+            "symmetrize": False,
+            "include_dead_weight": True,
+        }
+
+        neighborhood_options.update({"neighborhood_kwargs": neighborhood_kwargs})
+
+        print("Neighborhood instructions: ", neighborhood_options)
+        file_name = self.neigh_instructions
+        with open(file_name, "w") as f:
+            json.dump(neighborhood_options, f, indent=4)
+
+        self.parent_window.protocols.append(neighborhood_options)
+        correction_description = ""
+        for index, (key, value) in enumerate(neighborhood_options.items()):
+            if index > 0:
+                correction_description += ", "
+            correction_description += str(key) + " : " + str(value)
+        self.parent_window.protocol_list.addItem(correction_description)
+
+        print("Done.")
+        self.close()
+
+    def load_previous_neighborhood_instructions(self):
+        """
+        Read the measurmeent options from a previously written json file and format properly for the UI.
+        """
+
+        print("Reading instructions..")
+        if os.path.exists(self.neigh_instructions):
+            with open(self.neigh_instructions, "r") as f:
+
+                neigh_instructions = json.load(f)
+                print(f"Loading the instructions: {neigh_instructions}...")
+
+                if "neighborhood_type" not in neigh_instructions:
+                    neigh_instructions.update(
+                        {"neighborhood_type": self.neighborhood_type}
+                    )
+
+                if self.neighborhood_type == neigh_instructions["neighborhood_type"]:
+
+                    if "distance" in neigh_instructions:
+                        distances = neigh_instructions["distance"]
+                        distances = [str(d) for d in distances]
+                        self.measurements_list.list_widget.clear()
+                        self.measurements_list.list_widget.addItems(distances)
+
+                    if "population" in neigh_instructions:
+
+                        pop = neigh_instructions["population"]
+                        idx0 = self.reference_population_cb.findText(pop[0])
+                        self.reference_population_cb.setCurrentIndex(idx0)
+                        idx1 = self.neighbor_population_cb.findText(pop[1])
+                        self.neighbor_population_cb.setCurrentIndex(idx1)
+
+                    if "clear_neigh" in neigh_instructions:
+                        clear_neigh = neigh_instructions["clear_neigh"]
+                        self.clear_previous_btn.setChecked(clear_neigh)
+
+                    if "event_time_col" in neigh_instructions:
+                        event_time_col = neigh_instructions["event_time_col"]
+                        if event_time_col is None:
+                            event_time_col = "--"
+                        idx = self.event_time_cb.findText(event_time_col)
+                        self.event_time_cb.setCurrentIndex(idx)
+
+                    if "neighborhood_kwargs" in neigh_instructions:
+                        neighborhood_kwargs = neigh_instructions["neighborhood_kwargs"]
+                        if "compute_cum_sum" in neighborhood_kwargs:
+                            self.cumulated_presence_btn.setChecked(
+                                neighborhood_kwargs["compute_cum_sum"]
+                            )
+                        if "status" in neighborhood_kwargs:
+                            status_options = neighborhood_kwargs["status"]
+                            status_options = [
+                                "--" if s is None else s for s in status_options
+                            ]
+                            idx0 = self.reference_population_status_cb.findText(
+                                status_options[0]
+                            )
+                            self.reference_population_status_cb.setCurrentIndex(idx0)
+                            idx1 = self.neighbor_population_status_cb.findText(
+                                status_options[1]
+                            )
+                            self.neighbor_population_status_cb.setCurrentIndex(idx1)
+                        if "not_status_option" in neighborhood_kwargs:
+                            not_status_option = neighborhood_kwargs["not_status_option"]
+                            if not_status_option[0]:
+                                self.reference_switch_status_btn.click()
+                            if not_status_option[1]:
+                                self.neighbor_switch_status_btn.click()