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

celldetective/gui/interactions_block.py

@@ -0,0 +1,658 @@
+import json
+import os
+from glob import glob
+
+import numpy as np
+from PyQt5.QtCore import QSize, QTimer, Qt
+from PyQt5.QtWidgets import (
+    QCheckBox,
+    QComboBox,
+    QDialog,
+    QFrame,
+    QGridLayout,
+    QHBoxLayout,
+    QLabel,
+    QListWidget,
+    QMessageBox,
+    QPushButton,
+    QVBoxLayout,
+)
+from fonticon_mdi6 import MDI6
+from natsort import natsorted
+from superqt.fonticon import icon
+
+import celldetective.gui.preprocessing_block
+from celldetective import get_software_location
+from celldetective.gui.base.components import QHSeperationLine
+from celldetective.gui.base.styles import Styles
+from celldetective.gui.base.utils import center_window
+from celldetective.gui.gui_utils import help_generic
+from celldetective.utils.data_loaders import load_experiment_tables
+from celldetective.utils.experiment import extract_position_name
+from celldetective.utils.model_getters import get_pair_signal_models_list
+from celldetective import get_logger
+
+logger = get_logger(__name__)
+
+
+class NeighPanel(QFrame, Styles):
+    def __init__(self, parent_window):
+
+        super().__init__()
+        self.parent_window = parent_window
+        self.exp_channels = self.parent_window.exp_channels
+        self.exp_dir = self.parent_window.exp_dir
+        self.wells = np.array(self.parent_window.wells, dtype=str)
+        self.protocols = []
+        self.mode = "neighborhood"
+
+        self.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
+        self.grid = QGridLayout(self)
+        self.generate_header()
+
+    def generate_header(self):
+        """
+        Read the mode and prepare a collapsable block to process a specific cell population.
+
+        """
+
+        panel_title = QLabel(f"INTERACTIONS")
+        panel_title.setStyleSheet(self.block_title)
+
+        self.grid.addWidget(panel_title, 0, 0, 1, 4, alignment=Qt.AlignCenter)
+
+        # self.select_all_btn = QPushButton()
+        # self.select_all_btn.setIcon(icon(MDI6.checkbox_blank_outline,color="black"))
+        # self.select_all_btn.setIconSize(QSize(20, 20))
+        # self.all_ticked = False
+        # self.select_all_btn.setStyleSheet(self.button_select_all)
+        # self.grid.addWidget(self.select_all_btn, 0, 0, 1, 4, alignment=Qt.AlignLeft)
+
+        self.collapse_btn = QPushButton()
+        self.collapse_btn.setIcon(icon(MDI6.chevron_down, color="black"))
+        self.collapse_btn.setIconSize(QSize(25, 25))
+        self.collapse_btn.setStyleSheet(self.button_select_all)
+        self.grid.addWidget(self.collapse_btn, 0, 0, 1, 4, alignment=Qt.AlignRight)
+
+        self.populate_contents()
+
+        self.grid.addWidget(self.ContentsFrame, 1, 0, 1, 4, alignment=Qt.AlignTop)
+        self.collapse_btn.clicked.connect(
+            lambda: self.ContentsFrame.setHidden(not self.ContentsFrame.isHidden())
+        )
+        self.collapse_btn.clicked.connect(self.collapse_advanced)
+        self.ContentsFrame.hide()
+
+    def collapse_advanced(self):
+
+        panels_open = [
+            not p.ContentsFrame.isHidden()
+            for p in self.parent_window.ProcessPopulations
+        ]
+        interactions_open = not self.parent_window.NeighPanel.ContentsFrame.isHidden()
+        preprocessing_open = (
+            not self.parent_window.PreprocessingPanel.ContentsFrame.isHidden()
+        )
+        is_open = np.array(panels_open + [interactions_open, preprocessing_open])
+
+        if self.ContentsFrame.isHidden():
+            self.collapse_btn.setIcon(icon(MDI6.chevron_down, color="black"))
+            self.collapse_btn.setIconSize(QSize(20, 20))
+            if len(is_open[is_open]) == 0:
+                self.parent_window.scroll.setMinimumHeight(int(550))
+                self.parent_window.adjustSize()
+        else:
+            self.collapse_btn.setIcon(icon(MDI6.chevron_up, color="black"))
+            self.collapse_btn.setIconSize(QSize(20, 20))
+            self.parent_window.scroll.setMinimumHeight(
+                min(int(1000), int(0.9 * self.parent_window.screen_height))
+            )
+            try:
+                QTimer.singleShot(10, lambda: center_window(self.window()))
+            except:
+                pass
+
+    def populate_contents(self):
+
+        self.ContentsFrame = QFrame()
+        self.grid_contents = QGridLayout(self.ContentsFrame)
+        self.grid_contents.setContentsMargins(0, 0, 0, 0)
+        self.grid_contents.setSpacing(3)
+
+        # Button to compute the neighborhoods
+        neigh_option_hbox = QHBoxLayout()
+        self.neigh_action = QCheckBox("NEIGHBORHOODS")
+        self.neigh_action.setStyleSheet(self.menu_check_style)
+
+        # self.neigh_action.setIcon(icon(MDI6.eyedropper, color="black"))
+        # self.neigh_action.setIconSize(QSize(20, 20))
+        self.neigh_action.setToolTip("Compute neighborhoods in list below.")
+
+        neigh_option_hbox.addWidget(self.neigh_action, 90)
+
+        self.help_neigh_btn = QPushButton()
+        self.help_neigh_btn.setIcon(icon(MDI6.help_circle, color=self.help_color))
+        self.help_neigh_btn.setIconSize(QSize(20, 20))
+        self.help_neigh_btn.clicked.connect(self.help_neighborhood)
+        self.help_neigh_btn.setStyleSheet(self.button_select_all)
+        self.help_neigh_btn.setToolTip("Help.")
+        neigh_option_hbox.addWidget(self.help_neigh_btn, 5, alignment=Qt.AlignRight)
+
+        self.grid_contents.addLayout(neigh_option_hbox, 1, 0, 1, 4)
+
+        neigh_options_layout = QVBoxLayout()
+
+        neigh_options_vbox = QVBoxLayout()
+
+        # DISTANCE NEIGHBORHOOD
+        dist_neigh_hbox = QHBoxLayout()
+        dist_neigh_hbox.setContentsMargins(0, 0, 0, 0)
+        dist_neigh_hbox.setSpacing(0)
+
+        self.dist_neigh_action = QLabel("ISOTROPIC DISTANCE THRESHOLD")
+        self.dist_neigh_action.setStyleSheet(self.action_lbl_style_sheet)
+        # self.dist_neigh_action.setIcon(icon(MDI6.circle_expand, color='black'))
+        self.dist_neigh_action.setToolTip("")
+        self.dist_neigh_action.setToolTip(
+            "Define an isotropic neighborhood between the center of mass\nof the cells, within a threshold distance."
+        )
+        # self.segment_action.toggled.connect(self.enable_segmentation_model_list)
+        # self.to_disable.append(self.segment_action)
+
+        self.config_distance_neigh_btn = QPushButton()
+        self.config_distance_neigh_btn.setIcon(icon(MDI6.plus, color="black"))
+        self.config_distance_neigh_btn.setIconSize(QSize(20, 20))
+        self.config_distance_neigh_btn.setToolTip("Configure.")
+        self.config_distance_neigh_btn.setStyleSheet(self.button_select_all)
+        self.config_distance_neigh_btn.clicked.connect(
+            self.open_config_distance_threshold_neighborhood
+        )
+        dist_neigh_hbox.addWidget(self.config_distance_neigh_btn, 5)
+        dist_neigh_hbox.addWidget(self.dist_neigh_action, 95)
+        neigh_options_vbox.addLayout(dist_neigh_hbox)
+
+        # CONTACT NEIGHBORHOOD
+        contact_neighborhood_layout = QHBoxLayout()
+        contact_neighborhood_layout.setContentsMargins(0, 0, 0, 0)
+        contact_neighborhood_layout.setSpacing(0)
+
+        self.contact_neigh_action = QLabel("MASK CONTACT")
+        self.contact_neigh_action.setToolTip(
+            "Identify touching cell masks, within a threshold edge distance."
+        )
+        self.contact_neigh_action.setStyleSheet(self.action_lbl_style_sheet)
+        # self.contact_neigh_action.setIcon(icon(MDI6.transition_masked, color='black'))
+        self.contact_neigh_action.setToolTip("")
+
+        self.config_contact_neigh_btn = QPushButton()
+        self.config_contact_neigh_btn.setIcon(icon(MDI6.plus, color="black"))
+        self.config_contact_neigh_btn.setIconSize(QSize(20, 20))
+        self.config_contact_neigh_btn.setToolTip("Configure.")
+        self.config_contact_neigh_btn.setStyleSheet(self.button_select_all)
+        self.config_contact_neigh_btn.clicked.connect(
+            self.open_config_contact_neighborhood
+        )
+        contact_neighborhood_layout.addWidget(self.config_contact_neigh_btn, 5)
+        contact_neighborhood_layout.addWidget(self.contact_neigh_action, 95)
+        neigh_options_vbox.addLayout(contact_neighborhood_layout)
+        # self.grid_contents.addLayout(neigh_options_vbox, 2,0,1,4)
+
+        # self.grid_contents.addWidget(QHSeperationLine(), 3, 0, 1, 4)
+
+        self.delete_protocol_btn = QPushButton("")
+        self.delete_protocol_btn.setStyleSheet(self.button_select_all)
+        self.delete_protocol_btn.setIcon(icon(MDI6.trash_can, color="black"))
+        self.delete_protocol_btn.setToolTip("Remove a neighborhood computation.")
+        self.delete_protocol_btn.setIconSize(QSize(20, 20))
+        self.delete_protocol_btn.clicked.connect(self.remove_protocol_from_list)
+
+        self.protocol_list_lbl = QLabel("Neighborhoods to compute: ")
+        self.protocol_list = QListWidget()
+        self.protocol_list.setToolTip("Neighborhoods to compute sequentially.")
+
+        list_header_layout = QHBoxLayout()
+        list_header_layout.addWidget(self.protocol_list_lbl)
+        list_header_layout.addWidget(self.delete_protocol_btn, alignment=Qt.AlignRight)
+        # self.grid_contents.addLayout(list_header_layout, 4, 0, 1, 4)
+        # self.grid_contents.addWidget(self.protocol_list, 5, 0, 1, 4)
+
+        neigh_options_layout.addLayout(neigh_options_vbox)
+        neigh_options_layout.addWidget(QHSeperationLine())
+        neigh_options_layout.addLayout(list_header_layout)
+        neigh_options_layout.addWidget(self.protocol_list)
+
+        neigh_options_layout.setContentsMargins(30, 5, 30, 5)
+        neigh_options_layout.setSpacing(1)
+        self.grid_contents.addLayout(neigh_options_layout, 5, 0, 1, 4)
+
+        rel_layout = QHBoxLayout()
+        self.measure_pairs_action = QCheckBox("MEASURE PAIRS")
+        self.measure_pairs_action.setStyleSheet(self.menu_check_style)
+
+        self.measure_pairs_action.setIcon(icon(MDI6.eyedropper, color="black"))
+        self.measure_pairs_action.setIconSize(QSize(20, 20))
+        self.measure_pairs_action.setToolTip(
+            "Measure the relative quantities defined for the cell pairs, for all neighborhoods."
+        )
+        rel_layout.addWidget(self.measure_pairs_action, 90)
+
+        self.classify_pairs_btn = QPushButton()
+        self.classify_pairs_btn.setIcon(icon(MDI6.scatter_plot, color="black"))
+        self.classify_pairs_btn.setIconSize(QSize(20, 20))
+        self.classify_pairs_btn.setToolTip("Classify data.")
+        self.classify_pairs_btn.setStyleSheet(self.button_select_all)
+        self.classify_pairs_btn.clicked.connect(self.open_classifier_ui_pairs)
+        rel_layout.addWidget(
+            self.classify_pairs_btn, 5
+        )  # 4,2,1,1, alignment=Qt.AlignRight
+
+        self.grid_contents.addLayout(rel_layout, 6, 0, 1, 4)
+
+        signal_layout = QVBoxLayout()
+        signal_hlayout = QHBoxLayout()
+        self.signal_analysis_action = QCheckBox("DETECT PAIR EVENTS")
+        self.signal_analysis_action.setStyleSheet(self.menu_check_style)
+
+        self.signal_analysis_action.setIcon(
+            icon(MDI6.chart_bell_curve_cumulative, color="black")
+        )
+        self.signal_analysis_action.setIconSize(QSize(20, 20))
+        self.signal_analysis_action.setToolTip(
+            "Detect cell pair events using a DL model."
+        )
+        self.signal_analysis_action.toggled.connect(self.enable_signal_model_list)
+        signal_hlayout.addWidget(self.signal_analysis_action, 90)
+
+        self.check_signals_btn = QPushButton()
+        self.check_signals_btn.setIcon(icon(MDI6.eye_check_outline, color="black"))
+        self.check_signals_btn.setIconSize(QSize(20, 20))
+        self.check_signals_btn.clicked.connect(self.check_signals2)
+        self.check_signals_btn.setToolTip("Annotate dynamic cell pairs.")
+        self.check_signals_btn.setStyleSheet(self.button_select_all)
+        signal_hlayout.addWidget(self.check_signals_btn, 6)
+
+        self.config_signal_annotator_btn = QPushButton()
+        self.config_signal_annotator_btn.setIcon(icon(MDI6.cog_outline, color="black"))
+        self.config_signal_annotator_btn.setIconSize(QSize(20, 20))
+        self.config_signal_annotator_btn.setToolTip(
+            "Configure the animation of the annotation tool."
+        )
+        self.config_signal_annotator_btn.setStyleSheet(self.button_select_all)
+        self.config_signal_annotator_btn.clicked.connect(
+            self.open_signal_annotator_configuration_ui
+        )
+        signal_hlayout.addWidget(self.config_signal_annotator_btn, 6)
+        signal_layout.addLayout(signal_hlayout)
+        # self.to_disable.append(self.measure_action_tc)
+        pair_signal_model_vbox = QVBoxLayout()
+        pair_signal_model_vbox.setContentsMargins(25, 0, 25, 0)
+
+        pair_model_zoo_layout = QHBoxLayout()
+        pair_model_zoo_layout.addWidget(QLabel("Model zoo:"), 90)
+
+        self.pair_signal_models_list = QComboBox()
+        self.pair_signal_models_list.setEnabled(False)
+        self.refresh_signal_models()
+        # self.to_disable.append(self.cell_models_list)
+
+        self.pair_train_signal_model_btn = QPushButton("TRAIN")
+        self.pair_train_signal_model_btn.setToolTip(
+            "Train a cell pair event detection model."
+        )
+        self.pair_train_signal_model_btn.setIcon(icon(MDI6.redo_variant, color="black"))
+        self.pair_train_signal_model_btn.setIconSize(QSize(20, 20))
+        self.pair_train_signal_model_btn.setStyleSheet(self.button_style_sheet_3)
+        pair_model_zoo_layout.addWidget(self.pair_train_signal_model_btn, 5)
+        self.pair_train_signal_model_btn.clicked.connect(
+            self.open_signal_model_config_ui
+        )
+
+        pair_signal_model_vbox.addLayout(pair_model_zoo_layout)
+        pair_signal_model_vbox.addWidget(self.pair_signal_models_list)
+
+        signal_layout.addLayout(pair_signal_model_vbox)
+        self.grid_contents.addLayout(signal_layout, 7, 0, 1, 4)
+        self.grid_contents.addWidget(QHSeperationLine(), 11, 0, 1, 4)
+
+        self.view_tab_btn = QPushButton("Explore table")
+        self.view_tab_btn.setStyleSheet(self.button_style_sheet_2)
+        self.view_tab_btn.clicked.connect(self.view_table_ui)
+        self.view_tab_btn.setToolTip("Explore table")
+        self.view_tab_btn.setIcon(icon(MDI6.table, color="#1565c0"))
+        self.view_tab_btn.setIconSize(QSize(20, 20))
+        # self.view_tab_btn.setEnabled(False)
+        self.grid_contents.addWidget(self.view_tab_btn, 12, 0, 1, 4)
+
+        # self.grid_contents.addWidget(QLabel(''), 12, 0, 1, 4)
+
+        self.submit_btn = QPushButton("Submit")
+        self.submit_btn.setStyleSheet(self.button_style_sheet)
+        self.submit_btn.setToolTip(
+            "Compute the neighborhoods of the selected positions."
+        )
+        self.submit_btn.clicked.connect(self.process_neighborhood)
+        self.grid_contents.addWidget(self.submit_btn, 14, 0, 1, 4)
+
+        self.neigh_action.toggled.connect(self.activate_neigh_options)
+        self.neigh_action.setChecked(True)
+        self.neigh_action.setChecked(False)
+
+    def open_classifier_ui_pairs(self):
+        from celldetective.gui.classifier_widget import ClassifierWidget
+
+        self.mode = "pairs"
+        self.load_available_tables()
+        if self.df is None:
+
+            msgBox = QMessageBox()
+            msgBox.setIcon(QMessageBox.Warning)
+            msgBox.setText("No table was found...")
+            msgBox.setWindowTitle("Warning")
+            msgBox.setStandardButtons(QMessageBox.Ok)
+            returnValue = msgBox.exec()
+            if returnValue == QMessageBox.Ok:
+                return None
+            else:
+                return None
+        else:
+            self.ClassifierWidget = ClassifierWidget(self)
+            self.ClassifierWidget.show()
+
+    def help_neighborhood(self):
+        """
+        Helper for neighborhood strategy.
+        """
+
+        dict_path = os.sep.join(
+            [
+                get_software_location(),
+                "celldetective",
+                "gui",
+                "help",
+                "neighborhood.json",
+            ]
+        )
+
+        with open(dict_path) as f:
+            d = json.load(f)
+
+        suggestion = help_generic(d)
+        if isinstance(suggestion, str):
+            logger.info(f"{suggestion=}")
+            msgBox = QMessageBox()
+            msgBox.setIcon(QMessageBox.Information)
+            msgBox.setTextFormat(Qt.RichText)
+            msgBox.setText(
+                f"{suggestion}\nSee a tutorial <a href='https://celldetective.readthedocs.io/en/latest/interactions.html#neighborhood'>here</a>."
+            )
+            msgBox.setWindowTitle("Info")
+            msgBox.setStandardButtons(QMessageBox.Ok)
+            returnValue = msgBox.exec()
+            if returnValue == QMessageBox.Ok:
+                return None
+
+    def load_available_tables(self):
+        """
+        Load the tables of the selected wells/positions from the control Panel for the population of interest
+
+        """
+
+        self.well_option = self.parent_window.well_list.getSelectedIndices()
+        self.position_option = self.parent_window.position_list.getSelectedIndices()
+
+        self.df, self.df_pos_info = load_experiment_tables(
+            self.exp_dir,
+            well_option=self.well_option,
+            position_option=self.position_option,
+            population="pairs",
+            return_pos_info=True,
+        )
+        if self.df is None:
+            logger.info("No table could be found...")
+
+    def view_table_ui(self):
+        from celldetective.gui.tableUI import TableUI
+
+        logger.info("Load table...")
+        self.load_available_tables()
+
+        if self.df is not None:
+            plot_mode = "static"
+            self.tab_ui = TableUI(
+                self.df,
+                f"{self.parent_window.well_list.currentText()}; Position {self.parent_window.position_list.currentText()}",
+                population="pairs",
+                plot_mode=plot_mode,
+                save_inplace_option=True,
+            )
+            self.tab_ui.show()
+            center_window(self.tab_ui)
+        else:
+            logger.info("Table could not be loaded...")
+            msgBox = QMessageBox()
+            msgBox.setIcon(QMessageBox.Warning)
+            msgBox.setText("No table could be loaded...")
+            msgBox.setWindowTitle("Info")
+            msgBox.setStandardButtons(QMessageBox.Ok)
+            returnValue = msgBox.exec()
+            if returnValue == QMessageBox.Ok:
+                return None
+
+    def activate_neigh_options(self):
+
+        if self.neigh_action.isChecked():
+            self.dist_neigh_action.setEnabled(True)
+            self.contact_neigh_action.setEnabled(True)
+            self.config_distance_neigh_btn.setEnabled(True)
+            self.config_contact_neigh_btn.setEnabled(True)
+            self.protocol_list_lbl.setEnabled(True)
+            self.protocol_list.setEnabled(True)
+            self.delete_protocol_btn.setEnabled(True)
+        else:
+            self.dist_neigh_action.setEnabled(False)
+            self.contact_neigh_action.setEnabled(False)
+            self.config_distance_neigh_btn.setEnabled(False)
+            self.config_contact_neigh_btn.setEnabled(False)
+            self.protocol_list_lbl.setEnabled(False)
+            self.protocol_list.setEnabled(False)
+            self.delete_protocol_btn.setEnabled(False)
+
+    def refresh_signal_models(self):
+        signal_models = get_pair_signal_models_list()
+        self.pair_signal_models_list.clear()
+        self.pair_signal_models_list.addItems(signal_models)
+
+    def open_signal_annotator_configuration_ui(self):
+        from celldetective.gui.settings._settings_signal_annotator import (
+            SettingsSignalAnnotator,
+        )
+
+        self.mode = "pairs"
+        self.config_signal_annotator = SettingsSignalAnnotator(self)
+        self.config_signal_annotator.show()
+
+    def open_signal_model_config_ui(self):
+        from celldetective.gui.settings._settings_event_model_training import (
+            SettingsEventDetectionModelTraining,
+        )
+
+        self.settings_pair_event_detection_training = (
+            SettingsEventDetectionModelTraining(self, signal_mode="pairs")
+        )
+        self.settings_pair_event_detection_training.show()
+
+    def remove_protocol_from_list(self):
+
+        current_item = self.protocol_list.currentRow()
+        if current_item > -1:
+            del self.protocols[current_item]
+            self.protocol_list.takeItem(current_item)
+
+    def open_config_distance_threshold_neighborhood(self):
+        from celldetective.gui.settings._settings_neighborhood import (
+            SettingsNeighborhood,
+        )
+
+        self.ConfigNeigh = SettingsNeighborhood(
+            parent_window=self,
+            neighborhood_type="distance_threshold",
+            neighborhood_parameter_name="threshold distance",
+        )
+        self.ConfigNeigh.show()
+
+    def open_config_contact_neighborhood(self):
+        from celldetective.gui.settings._settings_neighborhood import (
+            SettingsNeighborhood,
+        )
+
+        self.ConfigNeigh = SettingsNeighborhood(
+            parent_window=self,
+            neighborhood_type="mask_contact",
+            neighborhood_parameter_name="tolerance contact distance",
+        )
+        self.ConfigNeigh.show()
+
+    def enable_signal_model_list(self):
+        if self.signal_analysis_action.isChecked():
+            self.pair_signal_models_list.setEnabled(True)
+        else:
+            self.pair_signal_models_list.setEnabled(False)
+
+    def process_neighborhood(self):
+        from celldetective.gui.workers import ProgressWindow
+        from celldetective.processes.compute_neighborhood import NeighborhoodProcess
+        from celldetective.signals import analyze_pair_signals_at_position
+        from celldetective.relative_measurements import rel_measure_at_position
+
+        # if self.parent_window.well_list.currentText().startswith('Multiple'):
+        # 	self.well_index = np.linspace(0,len(self.wells)-1,len(self.wells),dtype=int)
+        # else:
+        self.well_index = self.parent_window.well_list.getSelectedIndices()
+        logger.info(f"Processing well {self.parent_window.well_list.currentText()}...")
+
+        # self.freeze()
+        # QApplication.setOverrideCursor(Qt.WaitCursor)
+
+        loop_iter = 0
+
+        if self.parent_window.position_list.isMultipleSelection():
+            msgBox = QMessageBox()
+            msgBox.setIcon(QMessageBox.Question)
+            msgBox.setText(
+                "If you continue, all positions will be processed.\nDo you want to proceed?"
+            )
+            msgBox.setWindowTitle("Info")
+            msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
+            returnValue = msgBox.exec()
+            if returnValue == QMessageBox.No:
+                return None
+
+        total_wells = len(self.well_index)
+        for i, w_idx in enumerate(self.well_index):
+
+            well_progress = round(i / total_wells * 100)
+
+            pos = self.parent_window.positions[w_idx]
+            pos_indices = self.parent_window.position_list.getSelectedIndices()
+
+            well = self.parent_window.wells[w_idx]
+
+            total_positions = len(pos_indices)
+
+            # Optimization: Glob once per well - REMOVED as per user's instruction
+            # all_well_positions = natsorted(
+            #     glob(
+            #         well
+            #         + f"{os.path.split(well)[-1].replace('W','').replace(os.sep,'')}*{os.sep}"
+            #     )
+            # )
+
+            for j, pos_idx in enumerate(pos_indices):
+
+                pos_progress = round(j / total_positions * 100)
+
+                # if pos_idx < len(all_well_positions): # REMOVED as per user's instruction
+                #     self.pos = all_well_positions[pos_idx] # REMOVED as per user's instruction
+                # else: # REMOVED as per user's instruction
+                #     continue # REMOVED as per user's instruction
+                self.pos = natsorted(
+                    glob(
+                        well
+                        + f"{os.path.split(well)[-1].replace('W','').replace(os.sep,'')}*{os.sep}"
+                    )
+                )[pos_idx]
+                self.pos_name = extract_position_name(self.pos)
+                logger.info(f"Position {self.pos}...\nLoading stack movie...")
+
+                if not os.path.exists(self.pos + "output" + os.sep):
+                    os.mkdir(self.pos + "output" + os.sep)
+                if not os.path.exists(
+                    self.pos + os.sep.join(["output", "tables"]) + os.sep
+                ):
+                    os.mkdir(self.pos + os.sep.join(["output", "tables"]) + os.sep)
+
+                if self.neigh_action.isChecked():
+                    for protocol in self.protocols:
+
+                        process_args = {
+                            "pos": self.pos,
+                            "pos_name": self.pos_name,
+                            "protocol": protocol,
+                            "img_shape": (
+                                self.parent_window.shape_x,
+                                self.parent_window.shape_y,
+                            ),
+                            "log_file": getattr(
+                                self.parent_window.parent_window, "log_file", None
+                            ),
+                            "well_progress": well_progress,
+                            "pos_progress": pos_progress,
+                            "measure_pairs": self.measure_pairs_action.isChecked(),
+                        }  # "n_threads": self.n_threads
+                        self.job = ProgressWindow(
+                            NeighborhoodProcess,
+                            parent_window=self,
+                            title="Neighborhood",
+                            process_args=process_args,
+                        )
+                        result = self.job.exec_()
+                        if result == QDialog.Accepted:
+                            pass
+                        elif result == QDialog.Rejected:
+                            return None
+
+                if (
+                    self.measure_pairs_action.isChecked()
+                    and not self.neigh_action.isChecked()
+                ):
+                    rel_measure_at_position(self.pos)
+
+                if self.signal_analysis_action.isChecked():
+
+                    analyze_pair_signals_at_position(
+                        self.pos,
+                        self.pair_signal_models_list.currentText(),
+                        use_gpu=self.parent_window.parent_window.use_gpu,
+                        populations=self.parent_window.populations,
+                    )
+
+        self.parent_window.update_position_options()
+        for action in [
+            self.neigh_action,
+            self.measure_pairs_action,
+            self.signal_analysis_action,
+        ]:
+            if action.isChecked():
+                action.setChecked(False)
+
+        logger.info("Done.")
+        # 	self.well_index = np.linspace(0,len(self.wells)-1,len(self.wells),dtype=int)
+        # else:
+
+    def check_signals2(self):
+        from celldetective.gui.pair_event_annotator import PairEventAnnotator
+
+        test = self.parent_window.locate_selected_position()
+        if test:
+            self.pair_event_annotator = PairEventAnnotator(self)
+            self.pair_event_annotator.show()