boris-behav-obs 8.16.6__py3-none-any.whl → 9.7.2__py3-none-any.whl

boris/preferences.py

@@ -1,7 +1,7 @@
 """
 BORIS
 Behavioral Observation Research Interactive Software
-Copyright 2012-2023 Olivier Friard
+Copyright 2012-2025 Olivier Friard
 
 This file is part of BORIS.
 
@@ -22,26 +22,30 @@ This file is part of BORIS.
 
 import logging
 import os
-import pathlib
+from pathlib import Path
 import sys
-
 from . import dialog
 from . import gui_utilities
 from . import menu_options
 from . import config as cfg
 from . import config_file
+from . import plugins
 
 from .preferences_ui import Ui_prefDialog
 
-from PyQt5.QtWidgets import QDialog, QFileDialog
+from PySide6.QtWidgets import QDialog, QFileDialog, QListWidgetItem, QMessageBox
+from PySide6.QtCore import Qt
+from PySide6.QtGui import QFont
 
 
 class Preferences(QDialog, Ui_prefDialog):
     def __init__(self, parent=None):
-
         super().__init__()
         self.setupUi(self)
 
+        # plugins
+        self.pb_browse_plugins_dir.clicked.connect(self.browse_plugins_dir)
+
         self.pbBrowseFFmpegCacheDir.clicked.connect(self.browseFFmpegCacheDir)
 
         self.pb_reset_behav_colors.clicked.connect(self.reset_behav_colors)
@@ -52,7 +56,40 @@ class Preferences(QDialog, Ui_prefDialog):
         self.pbCancel.clicked.connect(self.reject)
 
         self.flag_refresh = False
-        self.flag_reset_frames_memory = False
+
+        # Create a monospace QFont
+        monospace_font = QFont("Courier New")  # or "Monospace", "Consolas", "Liberation Mono", etc.
+        monospace_font.setStyleHint(QFont.Monospace)
+        monospace_font.setPointSize(12)
+        self.pte_plugin_code.setFont(monospace_font)
+
+    def browse_plugins_dir(self):
+        """
+        get the personal plugins directory
+        """
+        directory = QFileDialog.getExistingDirectory(None, "Select the plugins directory", self.le_personal_plugins_dir.text())
+        if not directory:
+            return
+
+        self.le_personal_plugins_dir.setText(directory)
+        self.lw_personal_plugins.clear()
+        for file_ in Path(directory).glob("*.py"):
+            if file_.name.startswith("_"):
+                continue
+            plugin_name = plugins.get_plugin_name(file_)
+            if plugin_name is None:
+                continue
+            # check if personal plugin name is in BORIS plugins (case sensitive)
+            if plugin_name in [self.lv_all_plugins.item(i).text() for i in range(self.lv_all_plugins.count())]:
+                continue
+            item = QListWidgetItem(plugin_name)
+            item.setFlags(item.flags() | Qt.ItemIsUserCheckable)
+            item.setCheckState(Qt.Checked)
+            item.setData(100, str(file_))
+            self.lw_personal_plugins.addItem(item)
+
+        if self.lw_personal_plugins.count() == 0:
+            QMessageBox.warning(self, cfg.programName, f"No plugin found in {directory}")
 
     def refresh_preferences(self):
         """
@@ -61,7 +98,7 @@ class Preferences(QDialog, Ui_prefDialog):
         if (
             dialog.MessageDialog(
                 "BORIS",
-                ("Refresh will re-initialize " "all your preferences and close BORIS"),
+                ("Refresh will re-initialize all your preferences and close BORIS"),
                 [cfg.CANCEL, "Refresh preferences"],
             )
             == "Refresh preferences"
@@ -73,11 +110,11 @@ class Preferences(QDialog, Ui_prefDialog):
         """
         allow user select a cache dir for ffmpeg images
         """
-        FFmpegCacheDir = QFileDialog().getExistingDirectory(
+        FFmpegCacheDir = QFileDialog.getExistingDirectory(
             self,
             "Select a directory",
             os.path.expanduser("~"),
-            options=QFileDialog().ShowDirsOnly,
+            options=QFileDialog.ShowDirsOnly,
         )
         if FFmpegCacheDir:
             self.leFFmpegCacheDir.setText(FFmpegCacheDir)
@@ -104,6 +141,63 @@ def preferences(self):
     show preferences window
     """
 
+    def show_plugin_info(item):
+        """
+        display information about the clicked plugin
+        """
+
+        if item.text() not in self.config_param[cfg.ANALYSIS_PLUGINS]:
+            return
+
+        plugin_path = item.data(100)
+
+        # Python plugins
+        if Path(plugin_path).suffix == ".py":
+            import importlib
+
+            module_name = Path(plugin_path).stem
+            spec = importlib.util.spec_from_file_location(module_name, plugin_path)
+            plugin_module = importlib.util.module_from_spec(spec)
+            spec.loader.exec_module(plugin_module)
+            attributes_list = dir(plugin_module)
+
+            out: list = []
+            out.append((plugin_module.__plugin_name__ + "\n") if "__plugin_name__" in attributes_list else "No plugin name provided")
+            out.append(plugin_module.__author__ if "__author__" in attributes_list else "No author provided")
+            version_str: str = ""
+            if "__version__" in attributes_list:
+                version_str += str(plugin_module.__version__)
+            if "__version_date__" in attributes_list:
+                version_str += " " if version_str else ""
+                version_str += f"({plugin_module.__version_date__})"
+
+            out.append(f"Version: {version_str}\n" if version_str else "No version provided")
+
+            # out.append(plugin_module.run.__doc__.strip())
+            # description
+            if "__description__" in attributes_list:
+                out.append("Description:\n")
+            out.append(plugin_module.__description__ if "__description__" in attributes_list else "No description provided")
+
+            preferencesWindow.pte_plugin_description.setPlainText("\n".join(out))
+
+        # R plugins
+        if Path(plugin_path).suffix == ".R":
+            plugin_description = plugins.get_r_plugin_description(plugin_path)
+            if plugin_description is not None:
+                preferencesWindow.pte_plugin_description.setPlainText("\n".join(plugin_description.split("\\n")))
+            else:
+                preferencesWindow.pte_plugin_description.setPlainText("No description provided")
+
+        # display plugin code
+        try:
+            with open(plugin_path, "r") as f_in:
+                plugin_code = f_in.read()
+        except Exception:
+            plugin_code = "Not available"
+
+        preferencesWindow.pte_plugin_code.setPlainText(plugin_code)
+
     preferencesWindow = Preferences()
     preferencesWindow.tabWidget.setCurrentIndex(0)
 
@@ -114,9 +208,7 @@ def preferences(self):
         preferencesWindow.cbTimeFormat.setCurrentIndex(1)
 
     preferencesWindow.sbffSpeed.setValue(self.fast)
-    preferencesWindow.cb_adapt_fast_jump.setChecked(
-        self.config_param.get(cfg.ADAPT_FAST_JUMP, False)
-    )
+    preferencesWindow.cb_adapt_fast_jump.setChecked(self.config_param.get(cfg.ADAPT_FAST_JUMP, False))
     preferencesWindow.sbRepositionTimeOffset.setValue(self.repositioningTimeOffset)
     preferencesWindow.sbSpeedStep.setValue(self.play_rate_step)
     # automatic backup
@@ -129,18 +221,17 @@ def preferences(self):
     preferencesWindow.cbConfirmSound.setChecked(self.confirmSound)
     # beep every
     preferencesWindow.sbBeepEvery.setValue(self.beep_every)
+    # frame step size
+    #preferencesWindow.sb_frame_step_size.setValue(self.config_param.get(cfg.FRAME_STEP_SIZE, cfg.FRAME_STEP_SIZE_DEFAULT_VALUE))
+
     # alert no focal subject
     preferencesWindow.cbAlertNoFocalSubject.setChecked(self.alertNoFocalSubject)
     # tracking cursor above event
-    preferencesWindow.cbTrackingCursorAboveEvent.setChecked(
-        self.trackingCursorAboveEvent
-    )
+    preferencesWindow.cbTrackingCursorAboveEvent.setChecked(self.trackingCursorAboveEvent)
     # check for new version
     preferencesWindow.cbCheckForNewVersion.setChecked(self.checkForNewVersion)
     # display subtitles
-    preferencesWindow.cb_display_subtitles.setChecked(
-        self.config_param[cfg.DISPLAY_SUBTITLES]
-    )
+    preferencesWindow.cb_display_subtitles.setChecked(self.config_param.get(cfg.DISPLAY_SUBTITLES, False))
     # pause before add event
     preferencesWindow.cb_pause_before_addevent.setChecked(self.pause_before_addevent)
     # MPV hwdec
@@ -148,18 +239,77 @@ def preferences(self):
     preferencesWindow.cb_hwdec.addItems(cfg.MPV_HWDEC_OPTIONS)
     try:
         preferencesWindow.cb_hwdec.setCurrentIndex(
-            cfg.MPV_HWDEC_OPTIONS.index(
-                self.config_param.get(cfg.MPV_HWDEC, cfg.MPV_HWDEC_DEFAULT_VALUE)
-            )
+            cfg.MPV_HWDEC_OPTIONS.index(self.config_param.get(cfg.MPV_HWDEC, cfg.MPV_HWDEC_DEFAULT_VALUE))
         )
     except Exception:
-        preferencesWindow.cb_hwdec.setCurrentIndex(cfg.MPV_HWDEC_DEFAULT_VALUE)
+        preferencesWindow.cb_hwdec.setCurrentIndex(cfg.MPV_HWDEC_OPTIONS.index(cfg.MPV_HWDEC_DEFAULT_VALUE))
+    # check integrity
+    preferencesWindow.cb_check_integrity_at_opening.setChecked(self.config_param.get(cfg.CHECK_PROJECT_INTEGRITY, True))
+
+    # BORIS plugins
+    preferencesWindow.lv_all_plugins.itemClicked.connect(show_plugin_info)
+
+    preferencesWindow.lv_all_plugins.clear()
+
+    for file_ in (Path(__file__).parent / "analysis_plugins").glob("*.py"):
+        if file_.name.startswith("_"):
+            continue
+        plugin_name = plugins.get_plugin_name(file_)
+        if plugin_name is not None:
+            item = QListWidgetItem(plugin_name)
+            item.setFlags(item.flags() | Qt.ItemIsUserCheckable)
+            if plugin_name in self.config_param.get(cfg.EXCLUDED_PLUGINS, set()):
+                item.setCheckState(Qt.Unchecked)
+            else:
+                item.setCheckState(Qt.Checked)
+            item.setData(100, str(file_))
+            preferencesWindow.lv_all_plugins.addItem(item)
+
+    # personal plugins
+    preferencesWindow.le_personal_plugins_dir.setText(self.config_param.get(cfg.PERSONAL_PLUGINS_DIR, ""))
+    preferencesWindow.lw_personal_plugins.itemClicked.connect(show_plugin_info)
+
+    preferencesWindow.lw_personal_plugins.clear()
+    if self.config_param.get(cfg.PERSONAL_PLUGINS_DIR, ""):
+        # Python plugins
+        for file_ in Path(self.config_param[cfg.PERSONAL_PLUGINS_DIR]).glob("*.py"):
+            if file_.name.startswith("_"):
+                continue
+            plugin_name = plugins.get_plugin_name(file_)
+            if plugin_name is None:
+                continue
+            # check if personal plugin name is in BORIS plugins (case sensitive)
+            if plugin_name in [preferencesWindow.lv_all_plugins.item(i).text() for i in range(preferencesWindow.lv_all_plugins.count())]:
+                continue
+            item = QListWidgetItem(plugin_name)
+            item.setFlags(item.flags() | Qt.ItemIsUserCheckable)
+            if plugin_name in self.config_param.get(cfg.EXCLUDED_PLUGINS, set()):
+                item.setCheckState(Qt.Unchecked)
+            else:
+                item.setCheckState(Qt.Checked)
+            item.setData(100, str(file_))
+            preferencesWindow.lw_personal_plugins.addItem(item)
+
+        # R plugins
+        for file_ in Path(self.config_param[cfg.PERSONAL_PLUGINS_DIR]).glob("*.R"):
+            plugin_name = plugins.get_r_plugin_name(file_)
+            if plugin_name is None:
+                continue
+            # check if personal plugin name is in BORIS plugins (case sensitive)
+            if plugin_name in [preferencesWindow.lv_all_plugins.item(i).text() for i in range(preferencesWindow.lv_all_plugins.count())]:
+                continue
+            item = QListWidgetItem(plugin_name)
+            item.setFlags(item.flags() | Qt.ItemIsUserCheckable)
+            if plugin_name in self.config_param.get(cfg.EXCLUDED_PLUGINS, set()):
+                item.setCheckState(Qt.Unchecked)
+            else:
+                item.setCheckState(Qt.Checked)
+            item.setData(100, str(file_))
+            preferencesWindow.lw_personal_plugins.addItem(item)
 
     # PROJET FILE INDENTATION
     preferencesWindow.combo_project_file_indentation.clear()
-    preferencesWindow.combo_project_file_indentation.addItems(
-        cfg.PROJECT_FILE_INDENTATION_COMBO_OPTIONS
-    )
+    preferencesWindow.combo_project_file_indentation.addItems(cfg.PROJECT_FILE_INDENTATION_COMBO_OPTIONS)
     try:
         preferencesWindow.combo_project_file_indentation.setCurrentIndex(
             cfg.PROJECT_FILE_INDENTATION_OPTIONS.index(
@@ -172,9 +322,7 @@ def preferences(self):
     except Exception:
         preferencesWindow.combo_project_file_indentation.setCurrentText(
             cfg.PROJECT_FILE_INDENTATION_COMBO_OPTIONS[
-                cfg.PROJECT_FILE_INDENTATION_OPTIONS.index(
-                    cfg.PROJECT_FILE_INDENTATION_DEFAULT_VALUE
-                )
+                cfg.PROJECT_FILE_INDENTATION_OPTIONS.index(cfg.PROJECT_FILE_INDENTATION_DEFAULT_VALUE)
             ]
         )
 
@@ -186,29 +334,24 @@ def preferences(self):
     preferencesWindow.cbSpectrogramColorMap.clear()
     preferencesWindow.cbSpectrogramColorMap.addItems(cfg.SPECTROGRAM_COLOR_MAPS)
     try:
-        preferencesWindow.cbSpectrogramColorMap.setCurrentIndex(
-            cfg.SPECTROGRAM_COLOR_MAPS.index(self.spectrogram_color_map)
-        )
-    except Exception:
-        preferencesWindow.cbSpectrogramColorMap.setCurrentIndex(
-            cfg.SPECTROGRAM_COLOR_MAPS.index(cfg.SPECTROGRAM_DEFAULT_COLOR_MAP)
-        )
-
-    try:
-        preferencesWindow.cbSpectrogramColorMap.setCurrentIndex(
-            cfg.SPECTROGRAM_COLOR_MAPS.index(self.spectrogram_color_map)
-        )
+        preferencesWindow.cbSpectrogramColorMap.setCurrentIndex(cfg.SPECTROGRAM_COLOR_MAPS.index(self.spectrogram_color_map))
     except Exception:
-        preferencesWindow.cbSpectrogramColorMap.setCurrentIndex(
-            cfg.SPECTROGRAM_COLOR_MAPS.index(cfg.SPECTROGRAM_DEFAULT_COLOR_MAP)
-        )
-
+        preferencesWindow.cbSpectrogramColorMap.setCurrentIndex(cfg.SPECTROGRAM_COLOR_MAPS.index(cfg.SPECTROGRAM_DEFAULT_COLOR_MAP))
+    # time interval
     try:
         preferencesWindow.sb_time_interval.setValue(self.spectrogram_time_interval)
     except Exception:
-        preferencesWindow.sb_time_interval.setValue(
-            cfg.SPECTROGRAM_DEFAULT_TIME_INTERVAL
-        )
+        preferencesWindow.sb_time_interval.setValue(cfg.SPECTROGRAM_DEFAULT_TIME_INTERVAL)
+    # window type
+    preferencesWindow.cb_window_type.setCurrentText(self.config_param.get(cfg.SPECTROGRAM_WINDOW_TYPE, cfg.SPECTROGRAM_DEFAULT_WINDOW_TYPE))
+    # NFFT
+    preferencesWindow.cb_NFFT.setCurrentText(self.config_param.get(cfg.SPECTROGRAM_NFFT, cfg.SPECTROGRAM_DEFAULT_NFFT))
+    # noverlap
+    preferencesWindow.sb_noverlap.setValue(self.config_param.get(cfg.SPECTROGRAM_NOVERLAP, cfg.SPECTROGRAM_DEFAULT_NOVERLAP))
+    # vmin
+    preferencesWindow.sb_vmin.setValue(self.config_param.get(cfg.SPECTROGRAM_VMIN, cfg.SPECTROGRAM_DEFAULT_VMIN))
+    # vmax
+    preferencesWindow.sb_vmax.setValue(self.config_param.get(cfg.SPECTROGRAM_VMAX, cfg.SPECTROGRAM_DEFAULT_VMAX))
 
     # behavior colors
     if not self.plot_colors:
@@ -218,109 +361,147 @@ def preferences(self):
     # category colors
     if not self.behav_category_colors:
         self.behav_category_colors = cfg.CATEGORY_COLORS_LIST
-    preferencesWindow.te_category_colors.setPlainText(
-        "\n".join(self.behav_category_colors)
-    )
+    preferencesWindow.te_category_colors.setPlainText("\n".join(self.behav_category_colors))
+
+    # interface
+    preferencesWindow.sb_toolbar_icon_size.setValue(self.config_param.get(cfg.TOOLBAR_ICON_SIZE, cfg.DEFAULT_TOOLBAR_ICON_SIZE_VALUE))
 
     gui_utilities.restore_geometry(preferencesWindow, "preferences", (700, 500))
 
-    if preferencesWindow.exec_():
+    while True:
+        if preferencesWindow.exec():
+            if preferencesWindow.sb_vmin.value() >= preferencesWindow.sb_vmax.value():
+                QMessageBox.warning(self, cfg.programName, "Spectrogram parameters: the vmin value must be lower than the vmax value.")
+                continue
 
-        gui_utilities.save_geometry(preferencesWindow, "preferences")
+            if preferencesWindow.sb_noverlap.value() >= int(preferencesWindow.cb_NFFT.currentText()):
+                QMessageBox.warning(self, cfg.programName, "Spectrogram parameters: the noverlap value must be lower than the NFFT value.")
+                continue
 
-        if preferencesWindow.flag_refresh:
-            # refresh preferences remove the config file
+            gui_utilities.save_geometry(preferencesWindow, "preferences")
 
-            logging.debug("flag refresh ")
+            if preferencesWindow.flag_refresh:
+                # refresh preferences remove the config file
 
-            self.config_param["refresh_preferences"] = True
-            self.close()
-            # check if refresh canceled for not saved project
-            if "refresh_preferences" in self.config_param:
-                if (pathlib.Path.home() / ".boris").exists():
-                    os.remove(pathlib.Path.home() / ".boris")
-                sys.exit()
+                logging.debug("flag refresh ")
 
-        if preferencesWindow.cbTimeFormat.currentIndex() == 0:
-            self.timeFormat = cfg.S
+                self.config_param["refresh_preferences"] = True
+                self.close()
+                # check if refresh canceled for not saved project
+                if "refresh_preferences" in self.config_param:
+                    if (Path.home() / ".boris").exists():
+                        os.remove(Path.home() / ".boris")
+                    sys.exit()
 
-        if preferencesWindow.cbTimeFormat.currentIndex() == 1:
-            self.timeFormat = cfg.HHMMSS
+            if preferencesWindow.cbTimeFormat.currentIndex() == 0:
+                self.timeFormat = cfg.S
 
-        self.fast = preferencesWindow.sbffSpeed.value()
+            if preferencesWindow.cbTimeFormat.currentIndex() == 1:
+                self.timeFormat = cfg.HHMMSS
 
-        self.config_param[
-            cfg.ADAPT_FAST_JUMP
-        ] = preferencesWindow.cb_adapt_fast_jump.isChecked()
+            self.fast = preferencesWindow.sbffSpeed.value()
 
-        self.repositioningTimeOffset = preferencesWindow.sbRepositionTimeOffset.value()
+            self.config_param[cfg.ADAPT_FAST_JUMP] = preferencesWindow.cb_adapt_fast_jump.isChecked()
 
-        self.play_rate_step = preferencesWindow.sbSpeedStep.value()
+            self.repositioningTimeOffset = preferencesWindow.sbRepositionTimeOffset.value()
 
-        self.automaticBackup = preferencesWindow.sbAutomaticBackup.value()
-        if self.automaticBackup:
-            self.automaticBackupTimer.start(self.automaticBackup * 60000)
-        else:
-            self.automaticBackupTimer.stop()
+            self.play_rate_step = preferencesWindow.sbSpeedStep.value()
 
-        self.behav_seq_separator = preferencesWindow.leSeparator.text()
+            self.automaticBackup = preferencesWindow.sbAutomaticBackup.value()
+            if self.automaticBackup:
+                self.automaticBackupTimer.start(self.automaticBackup * 60000)
+            else:
+                self.automaticBackupTimer.stop()
 
-        self.close_the_same_current_event = (
-            preferencesWindow.cbCloseSameEvent.isChecked()
-        )
+            self.behav_seq_separator = preferencesWindow.leSeparator.text()
 
-        self.confirmSound = preferencesWindow.cbConfirmSound.isChecked()
+            self.close_the_same_current_event = preferencesWindow.cbCloseSameEvent.isChecked()
 
-        self.beep_every = preferencesWindow.sbBeepEvery.value()
+            self.confirmSound = preferencesWindow.cbConfirmSound.isChecked()
 
-        self.alertNoFocalSubject = preferencesWindow.cbAlertNoFocalSubject.isChecked()
+            self.beep_every = preferencesWindow.sbBeepEvery.value()
 
-        self.trackingCursorAboveEvent = (
-            preferencesWindow.cbTrackingCursorAboveEvent.isChecked()
-        )
+            # frame step size
+            #self.config_param[cfg.FRAME_STEP_SIZE] = preferencesWindow.sb_frame_step_size.value()
 
-        self.checkForNewVersion = preferencesWindow.cbCheckForNewVersion.isChecked()
+            self.alertNoFocalSubject = preferencesWindow.cbAlertNoFocalSubject.isChecked()
 
-        self.config_param[
-            cfg.DISPLAY_SUBTITLES
-        ] = preferencesWindow.cb_display_subtitles.isChecked()
+            self.trackingCursorAboveEvent = preferencesWindow.cbTrackingCursorAboveEvent.isChecked()
 
-        self.pause_before_addevent = (
-            preferencesWindow.cb_pause_before_addevent.isChecked()
-        )
+            self.checkForNewVersion = preferencesWindow.cbCheckForNewVersion.isChecked()
 
-        # MPV hwdec
-        self.config_param[cfg.MPV_HWDEC] = cfg.MPV_HWDEC_OPTIONS[
-            preferencesWindow.cb_hwdec.currentIndex()
-        ]
+            self.config_param[cfg.DISPLAY_SUBTITLES] = preferencesWindow.cb_display_subtitles.isChecked()
 
-        # project file indentation
-        self.config_param[
-            cfg.PROJECT_FILE_INDENTATION
-        ] = cfg.PROJECT_FILE_INDENTATION_OPTIONS[
-            preferencesWindow.combo_project_file_indentation.currentIndex()
-        ]
+            self.pause_before_addevent = preferencesWindow.cb_pause_before_addevent.isChecked()
 
-        if self.observationId:
-            self.load_tw_events(self.observationId)
-            self.display_statusbar_info(self.observationId)
+            # MPV hwdec
+            self.config_param[cfg.MPV_HWDEC] = cfg.MPV_HWDEC_OPTIONS[preferencesWindow.cb_hwdec.currentIndex()]
 
-        self.ffmpeg_cache_dir = preferencesWindow.leFFmpegCacheDir.text()
+            # check project integrity
+            self.config_param[cfg.CHECK_PROJECT_INTEGRITY] = preferencesWindow.cb_check_integrity_at_opening.isChecked()
 
-        # spectrogram
-        self.spectrogram_color_map = (
-            preferencesWindow.cbSpectrogramColorMap.currentText()
-        )
-        # self.spectrogramHeight = preferencesWindow.sbSpectrogramHeight.value()
-        self.spectrogram_time_interval = preferencesWindow.sb_time_interval.value()
-
-        # behav colors
-        self.plot_colors = preferencesWindow.te_behav_colors.toPlainText().split()
-        # category colors
-        self.behav_category_colors = (
-            preferencesWindow.te_category_colors.toPlainText().split()
-        )
+            # update BORIS analysis plugins
+            self.config_param[cfg.ANALYSIS_PLUGINS] = {}
+            self.config_param[cfg.EXCLUDED_PLUGINS] = set()
+            for i in range(preferencesWindow.lv_all_plugins.count()):
+                if preferencesWindow.lv_all_plugins.item(i).checkState() == Qt.Checked:
+                    self.config_param[cfg.ANALYSIS_PLUGINS][preferencesWindow.lv_all_plugins.item(i).text()] = (
+                        preferencesWindow.lv_all_plugins.item(i).data(100)
+                    )
+                else:
+                    self.config_param[cfg.EXCLUDED_PLUGINS].add(preferencesWindow.lv_all_plugins.item(i).text())
 
-        menu_options.update_menu(self)
+            # update personal plugins
+            self.config_param[cfg.PERSONAL_PLUGINS_DIR] = preferencesWindow.le_personal_plugins_dir.text()
+            for i in range(preferencesWindow.lw_personal_plugins.count()):
+                if preferencesWindow.lw_personal_plugins.item(i).checkState() == Qt.Checked:
+                    self.config_param[cfg.ANALYSIS_PLUGINS][preferencesWindow.lw_personal_plugins.item(i).text()] = (
+                        preferencesWindow.lw_personal_plugins.item(i).data(100)
+                    )
+                else:
+                    self.config_param[cfg.EXCLUDED_PLUGINS].add(preferencesWindow.lw_personal_plugins.item(i).text())
 
-        config_file.save(self)
+            plugins.load_plugins(self)
+            plugins.add_plugins_to_menu(self)
+
+            # project file indentation
+            self.config_param[cfg.PROJECT_FILE_INDENTATION] = cfg.PROJECT_FILE_INDENTATION_OPTIONS[
+                preferencesWindow.combo_project_file_indentation.currentIndex()
+            ]
+
+            if self.observationId:
+                self.load_tw_events(self.observationId)
+                self.display_statusbar_info(self.observationId)
+
+            self.ffmpeg_cache_dir = preferencesWindow.leFFmpegCacheDir.text()
+
+            # spectrogram
+            self.spectrogram_color_map = preferencesWindow.cbSpectrogramColorMap.currentText()
+            self.spectrogram_time_interval = preferencesWindow.sb_time_interval.value()
+            # window type
+            self.config_param[cfg.SPECTROGRAM_WINDOW_TYPE] = preferencesWindow.cb_window_type.currentText()
+            # NFFT
+            self.config_param[cfg.SPECTROGRAM_NFFT] = preferencesWindow.cb_NFFT.currentText()
+            # noverlap
+            self.config_param[cfg.SPECTROGRAM_NOVERLAP] = preferencesWindow.sb_noverlap.value()
+            # vmin
+            self.config_param[cfg.SPECTROGRAM_VMIN] = preferencesWindow.sb_vmin.value()
+            # vmax
+            self.config_param[cfg.SPECTROGRAM_VMAX] = preferencesWindow.sb_vmax.value()
+
+            # behav colors
+            self.plot_colors = preferencesWindow.te_behav_colors.toPlainText().split()
+            # category colors
+            self.behav_category_colors = preferencesWindow.te_category_colors.toPlainText().split()
+
+            # interface
+            self.config_param[cfg.TOOLBAR_ICON_SIZE] = preferencesWindow.sb_toolbar_icon_size.value()
+
+            menu_options.update_menu(self)
+
+            config_file.save(self)
+
+            break
+
+        else:
+            break