boris-behav-obs 9.7.1__py3-none-any.whl → 9.7.15__py3-none-any.whl

boris/plot_waveform_rt.py

@@ -156,7 +156,7 @@ class Plot_waveform_RT(QWidget):
         self.interval += 5 * action
         self.plot_waveform(current_time=self.time_mem, force_plot=True)
 
-    def plot_waveform(self, current_time: float, force_plot: bool = False):
+    def plot_waveform(self, current_time: float, force_plot: bool = False) -> None:
         """
         plot sound waveform centered on the current time
 
@@ -172,6 +172,9 @@ class Plot_waveform_RT(QWidget):
 
         self.ax.clear()
 
+        if current_time is None:
+            return
+
         # start
         if current_time <= self.interval / 2:
             time_ = np.linspace(

boris/plugins.py

@@ -24,6 +24,8 @@ import logging
 import numpy as np
 import pandas as pd
 from pathlib import Path
+import copy
+import inspect
 
 from PySide6.QtGui import QAction
 from PySide6.QtWidgets import QMessageBox
@@ -297,6 +299,7 @@ def run_plugin(self, plugin_name):
 
     logging.debug(f"{plugin_path=}")
 
+    # check if plugin file exists
     if not Path(plugin_path).is_file():
         QMessageBox.critical(self, cfg.programName, f"The plugin {plugin_path} was not found.")
         return
@@ -308,27 +311,7 @@ def run_plugin(self, plugin_name):
     if not selected_observations:
         return
 
-    logging.info("preparing dataframe for plugin")
-
-    message, df = project_functions.project2dataframe(self.pj, selected_observations)
-    if message:
-        logging.critical(message)
-        QMessageBox.critical(self, cfg.programName, message)
-        return
-
-    logging.info("done")
-
-    """
-    logging.debug("dataframe info")
-    logging.debug(f"{df.info()}")
-    logging.debug(f"{df.head()}")
-    """
-
-    # filter the dataframe with parameters
-    logging.info("filtering dataframe for plugin")
-    filtered_df = plugin_df_filter(df, observations_list=selected_observations, parameters=parameters)
-    logging.info("done")
-
+    # Python plugin
     if Path(plugin_path).suffix == ".py":
         # load plugin as module
         module_name = Path(plugin_path).stem
@@ -347,9 +330,48 @@ def run_plugin(self, plugin_name):
             f"{plugin_module.__plugin_name__} loaded v.{getattr(plugin_module, '__version__')} v. {getattr(plugin_module, '__version_date__')}"
         )
 
-        # run plugin
-        plugin_results = plugin_module.run(filtered_df)
+        # check arguments required by the run function of the plugin
+        dataframe_required = False
+        project_required = False
+        # for param in inspect.signature(plugin_module.run).parameters.values():
+        for name, annotation in inspect.getfullargspec(plugin_module.run).annotations.items():
+            if name == "df" and annotation is pd.DataFrame:
+                dataframe_required = True
+            if name == "project" and annotation is dict:
+                project_required = True
+
+        # create arguments for the plugin run function
+        plugin_kwargs: dict = {}
+
+        if dataframe_required:
+            logging.info("preparing dataframe for plugin")
+            message, df = project_functions.project2dataframe(self.pj, selected_observations)
+            if message:
+                logging.critical(message)
+                QMessageBox.critical(self, cfg.programName, message)
+                return
+            logging.info("done")
+
+            # filter the dataframe with parameters
+            logging.info("filtering dataframe for plugin")
+            filtered_df = plugin_df_filter(df, observations_list=selected_observations, parameters=parameters)
+            logging.info("done")
 
+            plugin_kwargs["df"] = filtered_df
+
+        if project_required:
+            pj_copy = copy.deepcopy(self.pj)
+
+            # remove unselected observations from project
+            for obs_id in self.pj[cfg.OBSERVATIONS]:
+                if obs_id not in selected_observations:
+                    del pj_copy[cfg.OBSERVATIONS][obs_id]
+
+            plugin_kwargs["project"] = pj_copy
+
+        plugin_results = plugin_module.run(**plugin_kwargs)
+
+    # R plugin
     if Path(plugin_path).suffix in (".R", ".r"):
         try:
             from rpy2 import robjects
@@ -360,6 +382,21 @@ def run_plugin(self, plugin_name):
             QMessageBox.critical(self, cfg.programName, "The rpy2 Python module is not installed. R plugins cannot be used")
             return
 
+        logging.info("preparing dataframe for plugin")
+
+        message, df = project_functions.project2dataframe(self.pj, selected_observations)
+        if message:
+            logging.critical(message)
+            QMessageBox.critical(self, cfg.programName, message)
+            return
+
+        logging.info("done")
+
+        # filter the dataframe with parameters
+        logging.info("filtering dataframe for plugin")
+        filtered_df = plugin_df_filter(df, observations_list=selected_observations, parameters=parameters)
+        logging.info("done")
+
         # Read code from file
         try:
             with open(plugin_path, "r") as f:

boris/preferences.py

@@ -55,14 +55,38 @@ class Preferences(QDialog, Ui_prefDialog):
         self.pbOK.clicked.connect(self.accept)
         self.pbCancel.clicked.connect(self.reject)
 
+        self.pb_reset_spectro_values.clicked.connect(self.reset_spectro_values)
+        self.cb_use_vmin_vmax.toggled.connect(self.cb_vmin_vmax_changed)
+
         self.flag_refresh = False
 
         # Create a monospace QFont
-        monospace_font = QFont("Courier New")  # or "Monospace", "Consolas", "Liberation Mono", etc.
+        monospace_font = QFont("Courier New")
         monospace_font.setStyleHint(QFont.Monospace)
         monospace_font.setPointSize(12)
         self.pte_plugin_code.setFont(monospace_font)
 
+    def reset_spectro_values(self):
+        """
+        reset spectrogram values to default
+        """
+        self.cbSpectrogramColorMap.setCurrentIndex(cfg.SPECTROGRAM_COLOR_MAPS.index(cfg.SPECTROGRAM_DEFAULT_COLOR_MAP))
+        self.sb_time_interval.setValue(cfg.SPECTROGRAM_DEFAULT_TIME_INTERVAL)
+        self.cb_window_type.setCurrentText(cfg.SPECTROGRAM_DEFAULT_WINDOW_TYPE)
+        self.cb_NFFT.setCurrentText(cfg.SPECTROGRAM_DEFAULT_NFFT)
+        self.sb_noverlap.setValue(cfg.SPECTROGRAM_DEFAULT_NOVERLAP)
+        self.cb_use_vmin_vmax.setChecked(cfg.SPECTROGRAM_USE_VMIN_VMAX_DEFAULT)
+        self.cb_vmin_vmax_changed()
+        self.sb_vmin.setValue(cfg.SPECTROGRAM_DEFAULT_VMIN)
+        self.sb_vmax.setValue(cfg.SPECTROGRAM_DEFAULT_VMAX)
+
+    def cb_vmin_vmax_changed(self):
+        """
+        activate or de-activate vmin and vmax
+        """
+        for w in (self.sb_vmin, self.sb_vmax, self.label_vmin, self.label_vmin_2, self.label_vmax, self.label_vmax_2):
+            w.setEnabled(self.cb_use_vmin_vmax.isChecked())
+
     def browse_plugins_dir(self):
         """
         get the personal plugins directory
@@ -99,7 +123,7 @@ class Preferences(QDialog, Ui_prefDialog):
             dialog.MessageDialog(
                 "BORIS",
                 ("Refresh will re-initialize all your preferences and close BORIS"),
-                [cfg.CANCEL, "Refresh preferences"],
+                (cfg.CANCEL, "Refresh preferences"),
             )
             == "Refresh preferences"
         ):
@@ -221,6 +245,9 @@ 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
@@ -345,6 +372,11 @@ def preferences(self):
     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))
+    # use vmin/xmax
+    preferencesWindow.cb_use_vmin_vmax.setChecked(
+        self.config_param.get(cfg.SPECTROGRAM_USE_VMIN_VMAX, cfg.SPECTROGRAM_USE_VMIN_VMAX_DEFAULT)
+    )
+    preferencesWindow.cb_vmin_vmax_changed()
     # vmin
     preferencesWindow.sb_vmin.setValue(self.config_param.get(cfg.SPECTROGRAM_VMIN, cfg.SPECTROGRAM_DEFAULT_VMIN))
     # vmax
@@ -367,7 +399,7 @@ def preferences(self):
 
     while True:
         if preferencesWindow.exec():
-            if preferencesWindow.sb_vmin.value() >= preferencesWindow.sb_vmax.value():
+            if preferencesWindow.cb_use_vmin_vmax.isChecked() and 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
 
@@ -418,6 +450,9 @@ def preferences(self):
 
             self.beep_every = preferencesWindow.sbBeepEvery.value()
 
+            # frame step size
+            # self.config_param[cfg.FRAME_STEP_SIZE] = preferencesWindow.sb_frame_step_size.value()
+
             self.alertNoFocalSubject = preferencesWindow.cbAlertNoFocalSubject.isChecked()
 
             self.trackingCursorAboveEvent = preferencesWindow.cbTrackingCursorAboveEvent.isChecked()
@@ -478,6 +513,8 @@ def preferences(self):
             self.config_param[cfg.SPECTROGRAM_NFFT] = preferencesWindow.cb_NFFT.currentText()
             # noverlap
             self.config_param[cfg.SPECTROGRAM_NOVERLAP] = preferencesWindow.sb_noverlap.value()
+            # use vmin/vmax
+            self.config_param[cfg.SPECTROGRAM_USE_VMIN_VMAX] = preferencesWindow.cb_use_vmin_vmax.isChecked()
             # vmin
             self.config_param[cfg.SPECTROGRAM_VMIN] = preferencesWindow.sb_vmin.value()
             # vmax
@@ -499,3 +536,6 @@ def preferences(self):
 
         else:
             break
+
+    # activate main window
+    self.activateWindow()

boris/preferences_ui.py

@@ -3,7 +3,7 @@
 ################################################################################
 ## Form generated from reading UI file 'preferences.ui'
 ##
-## Created by: Qt User Interface Compiler version 6.9.0
+## Created by: Qt User Interface Compiler version 6.10.0
 ##
 ## WARNING! All changes made in this file will be lost when recompiling UI file!
 ################################################################################
@@ -27,7 +27,7 @@ class Ui_prefDialog(object):
         if not prefDialog.objectName():
             prefDialog.setObjectName(u"prefDialog")
         prefDialog.setWindowModality(Qt.WindowModality.WindowModal)
-        prefDialog.resize(904, 554)
+        prefDialog.resize(899, 757)
         self.horizontalLayout_17 = QHBoxLayout(prefDialog)
         self.horizontalLayout_17.setObjectName(u"horizontalLayout_17")
         self.verticalLayout_2 = QVBoxLayout()
@@ -145,11 +145,10 @@ class Ui_prefDialog(object):
 
         self.horizontalLayout_4.addWidget(self.label_4)
 
-        self.sbffSpeed = QSpinBox(self.tab_observations)
+        self.sbffSpeed = QDoubleSpinBox(self.tab_observations)
         self.sbffSpeed.setObjectName(u"sbffSpeed")
-        self.sbffSpeed.setMinimum(0)
-        self.sbffSpeed.setMaximum(10000)
-        self.sbffSpeed.setValue(10)
+        self.sbffSpeed.setDecimals(3)
+        self.sbffSpeed.setMaximum(1000000.000000000000000)
 
         self.horizontalLayout_4.addWidget(self.sbffSpeed)
 
@@ -244,6 +243,26 @@ class Ui_prefDialog(object):
 
         self.verticalLayout.addWidget(self.cb_pause_before_addevent)
 
+        self.horizontalLayout_23 = QHBoxLayout()
+        self.horizontalLayout_23.setObjectName(u"horizontalLayout_23")
+        self.label_24 = QLabel(self.tab_observations)
+        self.label_24.setObjectName(u"label_24")
+        self.label_24.setEnabled(False)
+
+        self.horizontalLayout_23.addWidget(self.label_24)
+
+        self.sb_frame_step_size = QSpinBox(self.tab_observations)
+        self.sb_frame_step_size.setObjectName(u"sb_frame_step_size")
+        self.sb_frame_step_size.setEnabled(False)
+        self.sb_frame_step_size.setMinimum(1)
+        self.sb_frame_step_size.setMaximum(1000)
+        self.sb_frame_step_size.setValue(1)
+
+        self.horizontalLayout_23.addWidget(self.sb_frame_step_size)
+
+
+        self.verticalLayout.addLayout(self.horizontalLayout_23)
+
         self.verticalSpacer_4 = QSpacerItem(20, 391, QSizePolicy.Policy.Minimum, QSizePolicy.Policy.Expanding)
 
         self.verticalLayout.addItem(self.verticalSpacer_4)
@@ -256,35 +275,35 @@ class Ui_prefDialog(object):
         self.splitter_2 = QSplitter(self.tab_analysis_plugins)
         self.splitter_2.setObjectName(u"splitter_2")
         self.splitter_2.setOrientation(Qt.Orientation.Horizontal)
-        self.widget = QWidget(self.splitter_2)
-        self.widget.setObjectName(u"widget")
-        self.verticalLayout_11 = QVBoxLayout(self.widget)
+        self.layoutWidget = QWidget(self.splitter_2)
+        self.layoutWidget.setObjectName(u"layoutWidget")
+        self.verticalLayout_11 = QVBoxLayout(self.layoutWidget)
         self.verticalLayout_11.setObjectName(u"verticalLayout_11")
         self.verticalLayout_11.setContentsMargins(0, 0, 0, 0)
-        self.label_13 = QLabel(self.widget)
+        self.label_13 = QLabel(self.layoutWidget)
         self.label_13.setObjectName(u"label_13")
 
         self.verticalLayout_11.addWidget(self.label_13)
 
-        self.lv_all_plugins = QListWidget(self.widget)
+        self.lv_all_plugins = QListWidget(self.layoutWidget)
         self.lv_all_plugins.setObjectName(u"lv_all_plugins")
 
         self.verticalLayout_11.addWidget(self.lv_all_plugins)
 
-        self.label_15 = QLabel(self.widget)
+        self.label_15 = QLabel(self.layoutWidget)
         self.label_15.setObjectName(u"label_15")
 
         self.verticalLayout_11.addWidget(self.label_15)
 
         self.horizontalLayout_16 = QHBoxLayout()
         self.horizontalLayout_16.setObjectName(u"horizontalLayout_16")
-        self.le_personal_plugins_dir = QLineEdit(self.widget)
+        self.le_personal_plugins_dir = QLineEdit(self.layoutWidget)
         self.le_personal_plugins_dir.setObjectName(u"le_personal_plugins_dir")
         self.le_personal_plugins_dir.setReadOnly(True)
 
         self.horizontalLayout_16.addWidget(self.le_personal_plugins_dir)
 
-        self.pb_browse_plugins_dir = QPushButton(self.widget)
+        self.pb_browse_plugins_dir = QPushButton(self.layoutWidget)
         self.pb_browse_plugins_dir.setObjectName(u"pb_browse_plugins_dir")
 
         self.horizontalLayout_16.addWidget(self.pb_browse_plugins_dir)
@@ -292,49 +311,49 @@ class Ui_prefDialog(object):
 
         self.verticalLayout_11.addLayout(self.horizontalLayout_16)
 
-        self.lw_personal_plugins = QListWidget(self.widget)
+        self.lw_personal_plugins = QListWidget(self.layoutWidget)
         self.lw_personal_plugins.setObjectName(u"lw_personal_plugins")
 
         self.verticalLayout_11.addWidget(self.lw_personal_plugins)
 
-        self.splitter_2.addWidget(self.widget)
+        self.splitter_2.addWidget(self.layoutWidget)
         self.splitter = QSplitter(self.splitter_2)
         self.splitter.setObjectName(u"splitter")
         self.splitter.setOrientation(Qt.Orientation.Vertical)
-        self.widget1 = QWidget(self.splitter)
-        self.widget1.setObjectName(u"widget1")
-        self.verticalLayout_12 = QVBoxLayout(self.widget1)
+        self.layoutWidget1 = QWidget(self.splitter)
+        self.layoutWidget1.setObjectName(u"layoutWidget1")
+        self.verticalLayout_12 = QVBoxLayout(self.layoutWidget1)
         self.verticalLayout_12.setObjectName(u"verticalLayout_12")
         self.verticalLayout_12.setContentsMargins(0, 0, 0, 0)
-        self.label_14 = QLabel(self.widget1)
+        self.label_14 = QLabel(self.layoutWidget1)
         self.label_14.setObjectName(u"label_14")
 
         self.verticalLayout_12.addWidget(self.label_14)
 
-        self.pte_plugin_description = QPlainTextEdit(self.widget1)
+        self.pte_plugin_description = QPlainTextEdit(self.layoutWidget1)
         self.pte_plugin_description.setObjectName(u"pte_plugin_description")
         self.pte_plugin_description.setReadOnly(True)
 
         self.verticalLayout_12.addWidget(self.pte_plugin_description)
 
-        self.splitter.addWidget(self.widget1)
-        self.widget2 = QWidget(self.splitter)
-        self.widget2.setObjectName(u"widget2")
-        self.verticalLayout_14 = QVBoxLayout(self.widget2)
+        self.splitter.addWidget(self.layoutWidget1)
+        self.layoutWidget2 = QWidget(self.splitter)
+        self.layoutWidget2.setObjectName(u"layoutWidget2")
+        self.verticalLayout_14 = QVBoxLayout(self.layoutWidget2)
         self.verticalLayout_14.setObjectName(u"verticalLayout_14")
         self.verticalLayout_14.setContentsMargins(0, 0, 0, 0)
-        self.label_23 = QLabel(self.widget2)
+        self.label_23 = QLabel(self.layoutWidget2)
         self.label_23.setObjectName(u"label_23")
 
         self.verticalLayout_14.addWidget(self.label_23)
 
-        self.pte_plugin_code = QPlainTextEdit(self.widget2)
+        self.pte_plugin_code = QPlainTextEdit(self.layoutWidget2)
         self.pte_plugin_code.setObjectName(u"pte_plugin_code")
         self.pte_plugin_code.setLineWrapMode(QPlainTextEdit.LineWrapMode.NoWrap)
 
         self.verticalLayout_14.addWidget(self.pte_plugin_code)
 
-        self.splitter.addWidget(self.widget2)
+        self.splitter.addWidget(self.layoutWidget2)
         self.splitter_2.addWidget(self.splitter)
 
         self.verticalLayout_15.addWidget(self.splitter_2)
@@ -394,6 +413,20 @@ class Ui_prefDialog(object):
         self.groupBox.setObjectName(u"groupBox")
         self.verticalLayout_8 = QVBoxLayout(self.groupBox)
         self.verticalLayout_8.setObjectName(u"verticalLayout_8")
+        self.horizontalLayout_24 = QHBoxLayout()
+        self.horizontalLayout_24.setObjectName(u"horizontalLayout_24")
+        self.pb_reset_spectro_values = QPushButton(self.groupBox)
+        self.pb_reset_spectro_values.setObjectName(u"pb_reset_spectro_values")
+
+        self.horizontalLayout_24.addWidget(self.pb_reset_spectro_values)
+
+        self.horizontalSpacer_9 = QSpacerItem(40, 20, QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Minimum)
+
+        self.horizontalLayout_24.addItem(self.horizontalSpacer_9)
+
+
+        self.verticalLayout_8.addLayout(self.horizontalLayout_24)
+
         self.horizontalLayout_7 = QHBoxLayout()
         self.horizontalLayout_7.setObjectName(u"horizontalLayout_7")
         self.label_7 = QLabel(self.groupBox)
@@ -502,12 +535,26 @@ class Ui_prefDialog(object):
 
         self.verticalLayout_8.addLayout(self.horizontalLayout_20)
 
+        self.horizontalLayout_25 = QHBoxLayout()
+        self.horizontalLayout_25.setObjectName(u"horizontalLayout_25")
+        self.cb_use_vmin_vmax = QCheckBox(self.groupBox)
+        self.cb_use_vmin_vmax.setObjectName(u"cb_use_vmin_vmax")
+
+        self.horizontalLayout_25.addWidget(self.cb_use_vmin_vmax)
+
+        self.horizontalSpacer_10 = QSpacerItem(40, 20, QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Minimum)
+
+        self.horizontalLayout_25.addItem(self.horizontalSpacer_10)
+
+
+        self.verticalLayout_8.addLayout(self.horizontalLayout_25)
+
         self.horizontalLayout_21 = QHBoxLayout()
         self.horizontalLayout_21.setObjectName(u"horizontalLayout_21")
-        self.label_19 = QLabel(self.groupBox)
-        self.label_19.setObjectName(u"label_19")
+        self.label_vmin = QLabel(self.groupBox)
+        self.label_vmin.setObjectName(u"label_vmin")
 
-        self.horizontalLayout_21.addWidget(self.label_19)
+        self.horizontalLayout_21.addWidget(self.label_vmin)
 
         self.sb_vmin = QSpinBox(self.groupBox)
         self.sb_vmin.setObjectName(u"sb_vmin")
@@ -517,10 +564,10 @@ class Ui_prefDialog(object):
 
         self.horizontalLayout_21.addWidget(self.sb_vmin)
 
-        self.label_21 = QLabel(self.groupBox)
-        self.label_21.setObjectName(u"label_21")
+        self.label_vmin_2 = QLabel(self.groupBox)
+        self.label_vmin_2.setObjectName(u"label_vmin_2")
 
-        self.horizontalLayout_21.addWidget(self.label_21)
+        self.horizontalLayout_21.addWidget(self.label_vmin_2)
 
         self.horizontalSpacer_7 = QSpacerItem(40, 20, QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Minimum)
 
@@ -531,10 +578,10 @@ class Ui_prefDialog(object):
 
         self.horizontalLayout_22 = QHBoxLayout()
         self.horizontalLayout_22.setObjectName(u"horizontalLayout_22")
-        self.label_20 = QLabel(self.groupBox)
-        self.label_20.setObjectName(u"label_20")
+        self.label_vmax = QLabel(self.groupBox)
+        self.label_vmax.setObjectName(u"label_vmax")
 
-        self.horizontalLayout_22.addWidget(self.label_20)
+        self.horizontalLayout_22.addWidget(self.label_vmax)
 
         self.sb_vmax = QSpinBox(self.groupBox)
         self.sb_vmax.setObjectName(u"sb_vmax")
@@ -544,10 +591,10 @@ class Ui_prefDialog(object):
 
         self.horizontalLayout_22.addWidget(self.sb_vmax)
 
-        self.label_22 = QLabel(self.groupBox)
-        self.label_22.setObjectName(u"label_22")
+        self.label_vmax_2 = QLabel(self.groupBox)
+        self.label_vmax_2.setObjectName(u"label_vmax_2")
 
-        self.horizontalLayout_22.addWidget(self.label_22)
+        self.horizontalLayout_22.addWidget(self.label_vmax_2)
 
         self.horizontalSpacer_8 = QSpacerItem(40, 20, QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Minimum)
 
@@ -676,7 +723,7 @@ class Ui_prefDialog(object):
 
         self.retranslateUi(prefDialog)
 
-        self.tabWidget.setCurrentIndex(2)
+        self.tabWidget.setCurrentIndex(4)
 
 
         QMetaObject.connectSlotsByName(prefDialog)
@@ -707,6 +754,7 @@ class Ui_prefDialog(object):
         self.cbTrackingCursorAboveEvent.setText(QCoreApplication.translate("prefDialog", u"Tracking cursor above current event", None))
         self.cbAlertNoFocalSubject.setText(QCoreApplication.translate("prefDialog", u"Alert if focal subject is not set", None))
         self.cb_pause_before_addevent.setText(QCoreApplication.translate("prefDialog", u"Pause media before \"Add event\" command", None))
+        self.label_24.setText(QCoreApplication.translate("prefDialog", u"Frame step size", None))
         self.tabWidget.setTabText(self.tabWidget.indexOf(self.tab_observations), QCoreApplication.translate("prefDialog", u"Observations", None))
         self.label_13.setText(QCoreApplication.translate("prefDialog", u"BORIS plugins", None))
         self.label_15.setText(QCoreApplication.translate("prefDialog", u"Personal plugins", None))
@@ -719,6 +767,7 @@ class Ui_prefDialog(object):
         self.pbBrowseFFmpegCacheDir.setText(QCoreApplication.translate("prefDialog", u"...", None))
         self.tabWidget.setTabText(self.tabWidget.indexOf(self.tab_ffmpeg), QCoreApplication.translate("prefDialog", u"FFmpeg framework", None))
         self.groupBox.setTitle(QCoreApplication.translate("prefDialog", u"Spectrogram", None))
+        self.pb_reset_spectro_values.setText(QCoreApplication.translate("prefDialog", u"Reset to default values", None))
         self.label_7.setText(QCoreApplication.translate("prefDialog", u"Color map", None))
         self.label_12.setText(QCoreApplication.translate("prefDialog", u"Default time interval (s)", None))
         self.label_16.setText(QCoreApplication.translate("prefDialog", u"Window type", None))
@@ -733,10 +782,11 @@ class Ui_prefDialog(object):
         self.cb_NFFT.setItemText(3, QCoreApplication.translate("prefDialog", u"2048", None))
 
         self.label_18.setText(QCoreApplication.translate("prefDialog", u"noverlap", None))
-        self.label_19.setText(QCoreApplication.translate("prefDialog", u"vmin", None))
-        self.label_21.setText(QCoreApplication.translate("prefDialog", u"dBFS", None))
-        self.label_20.setText(QCoreApplication.translate("prefDialog", u"vmax", None))
-        self.label_22.setText(QCoreApplication.translate("prefDialog", u"dBFS", None))
+        self.cb_use_vmin_vmax.setText(QCoreApplication.translate("prefDialog", u"Use vmin/vmax", None))
+        self.label_vmin.setText(QCoreApplication.translate("prefDialog", u"vmin", None))
+        self.label_vmin_2.setText(QCoreApplication.translate("prefDialog", u"dBFS", None))
+        self.label_vmax.setText(QCoreApplication.translate("prefDialog", u"vmax", None))
+        self.label_vmax_2.setText(QCoreApplication.translate("prefDialog", u"dBFS", None))
         self.tabWidget.setTabText(self.tabWidget.indexOf(self.tab_spectro), QCoreApplication.translate("prefDialog", u"Spectrogram/Wave form", None))
         self.label_10.setText(QCoreApplication.translate("prefDialog", u"<html><head/><body><p>List of colors for behaviors. See <a href=\"https://matplotlib.org/api/colors_api.html\"><span style=\" text-decoration: underline; color:#0000ff;\">matplotlib colors</span></a></p></body></html>", None))
         self.pb_reset_behav_colors.setText(QCoreApplication.translate("prefDialog", u"Reset colors to default", None))

boris/project.py

@@ -1977,7 +1977,7 @@ class projectDialog(QDialog, Ui_dlgProject):
         self.pj[cfg.INDEPENDENT_VARIABLES] = dict(self.indVar)
 
         # converters
-        converters = {}
+        converters: dict = {}
         for row in range(self.tw_converters.rowCount()):
             converters[self.tw_converters.item(row, 0).text()] = {
                 "name": self.tw_converters.item(row, 0).text(),

boris/project_functions.py

@@ -22,25 +22,22 @@ Copyright 2012-2025 Olivier Friard
 import gzip
 import json
 import logging
-import pandas as pd
-import numpy as np
-from pathlib import Path
 import sys
 from decimal import Decimal as dec
+from pathlib import Path
 from shutil import copyfile
-from typing import List, Tuple, Dict
+from typing import Dict, List, Tuple
 
+import numpy as np
+import pandas as pd
 import tablib
-from PySide6.QtWidgets import QMessageBox, QTableWidgetItem, QAbstractItemView
 from PySide6.QtCore import Qt
+from PySide6.QtWidgets import QAbstractItemView, QMessageBox, QTableWidgetItem
 
 from . import config as cfg
-from . import db_functions
-from . import dialog
-from . import observation_operations
+from . import db_functions, dialog, observation_operations, version
 from . import portion as I
 from . import utilities as util
-from . import version
 
 
 def check_observation_exhaustivity(
@@ -425,6 +422,9 @@ def check_project_integrity(
     r = check_coded_behaviors(pj)
     if r:
         out += f"The following behaviors are not defined in the ethogram: <b>{', '.join(r)}</b><br>"
+        flag_all_behaviors_defined = False
+    else:
+        flag_all_behaviors_defined = True
 
     # check for unpaired state events
     for obs_id in pj[cfg.OBSERVATIONS]:
@@ -577,26 +577,27 @@ def check_project_integrity(
     obs_results: dict = {}
     for obs_id in pj[cfg.OBSERVATIONS]:
         for event_idx, event in enumerate(pj[cfg.OBSERVATIONS][obs_id][cfg.EVENTS]):
-            # event[2]
             for idx in pj[cfg.ETHOGRAM]:
-                if pj[cfg.ETHOGRAM][idx]["code"] == event[2]:
+                if pj[cfg.ETHOGRAM][idx][cfg.BEHAVIOR_CODE] == event[cfg.EVENT_BEHAVIOR_FIELD_IDX]:
                     break
             else:
-                raise
-            if (not event[3]) and not pj[cfg.ETHOGRAM][idx][cfg.MODIFIERS]:
+                # behavior not defined in ethogram
                 continue
 
-            if len(event[3].split("|")) != len(pj[cfg.ETHOGRAM][idx][cfg.MODIFIERS]):
-                print("behavior", event[2])
-                print(f"modifier(s) #{event[3]}#", len(event[3].split("|")))
-                print(pj[cfg.ETHOGRAM][idx]["code"], pj[cfg.ETHOGRAM][idx][cfg.MODIFIERS])
-                print()
+            if (not event[cfg.EVENT_MODIFIER_FIELD_IDX]) and not pj[cfg.ETHOGRAM][idx][cfg.MODIFIERS]:  # no modifiers
+                continue
+
+            if len(event[cfg.EVENT_MODIFIER_FIELD_IDX].split("|")) != len(pj[cfg.ETHOGRAM][idx][cfg.MODIFIERS]):
+                # print("behavior", event[cfg.EVENT_BEHAVIOR_FIELD_IDX])
+                # print(f"modifier(s) #{event[cfg.EVENT_MODIFIER_FIELD_IDX]}#", len(event[cfg.EVENT_MODIFIER_FIELD_IDX].split("|")))
+                # print(pj[cfg.ETHOGRAM][idx]["code"], pj[cfg.ETHOGRAM][idx][cfg.MODIFIERS])
+                # print()
                 if obs_id not in obs_results:
                     obs_results[obs_id] = []
 
                 obs_results[obs_id].append(
                     (
-                        f"Event #{event_idx}: the coded modifiers for {event[2]} are {len(event[3].split('|'))} "
+                        f"Event #{event_idx}: the coded modifiers for {event[cfg.EVENT_BEHAVIOR_FIELD_IDX]} are {len(event[cfg.EVENT_MODIFIER_FIELD_IDX].split('|'))} "
                         f"but {len(pj[cfg.ETHOGRAM][idx][cfg.MODIFIERS])} sets were defined in ethogram."
                     )
                 )
@@ -1425,6 +1426,7 @@ def open_project_json(project_file_name: str) -> tuple:
                 pj[cfg.OBSERVATIONS][obs][cfg.TYPE] = cfg.MEDIA
 
             # convert old media list in new one
+            d1: dict = {}
             if len(pj[cfg.OBSERVATIONS][obs][cfg.FILE]):
                 d1 = {cfg.PLAYER1: [pj[cfg.OBSERVATIONS][obs][cfg.FILE][0]]}
 
@@ -1470,6 +1472,17 @@ def open_project_json(project_file_name: str) -> tuple:
             pj[cfg.PROJECT_VERSION] = cfg.project_format_version
             projectChanged = True
 
+    # check if behavioral categories are stored as a list
+    if cfg.BEHAVIORAL_CATEGORIES_CONF in pj:
+        if isinstance(pj[cfg.BEHAVIORAL_CATEGORIES_CONF], list):
+            # convert to dict
+            pj[cfg.BEHAVIORAL_CATEGORIES_CONF] = {str(idx): {"name": bc} for idx, bc in enumerate(pj[cfg.BEHAVIORAL_CATEGORIES_CONF])}
+            logging.info("Behavioral categories was converted from a list to a dictionary")
+            projectChanged = True
+    else:
+        pj[cfg.BEHAVIORAL_CATEGORIES_CONF] = dict()
+        projectChanged = True
+
     # add category key if not found
     for idx in pj[cfg.ETHOGRAM]:
         if cfg.BEHAVIOR_CATEGORY not in pj[cfg.ETHOGRAM][idx]:
@@ -1789,7 +1802,7 @@ def explore_project(self) -> None:
     if results:
         self.results_dialog = dialog.View_explore_project_results()
         self.results_dialog.setWindowTitle("Explore project results")
-        self.results_dialog.setWindowFlags(Qt.WindowStaysOnTopHint)
+        self.results_dialog.setWindowFlags(Qt.WindowType.WindowStaysOnTopHint)
         self.results_dialog.double_click_signal.connect(double_click_explore_project)
         txt = f"<b>{len(results)}</b> events"
         txt2 = ""