boris-behav-obs 8.9.16__py3-none-any.whl → 9.7.6__py3-none-any.whl

boris/gui_utilities.py

@@ -1,7 +1,7 @@
 """
 BORIS
 Behavioral Observation Research Interactive Software
-Copyright 2012-2023 Olivier Friard
+Copyright 2012-2025 Olivier Friard
 
   This program is free software; you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
@@ -21,8 +21,18 @@ Copyright 2012-2023 Olivier Friard
 
 import pathlib as pl
 import logging
-from PyQt5.QtCore import QSettings
-from PyQt5.QtWidgets import QWidget
+from PySide6.QtCore import QSettings
+from PySide6.QtWidgets import QWidget, QApplication
+from PySide6.QtGui import QIcon
+
+
+def theme_mode() -> str:
+    """
+    return the theme mode (dark or light) of the OS
+    """
+    palette = QApplication.instance().palette()
+    color = palette.window().color()
+    return "dark" if color.value() < 128 else "light"  # Dark mode if the color value is less than 128
 
 
 def save_geometry(widget: QWidget, widget_name: str):
@@ -30,29 +40,96 @@ def save_geometry(widget: QWidget, widget_name: str):
     save window geometry in ini file
     """
 
-    try:
-        ini_file_path = pl.Path.home() / pl.Path(".boris")
-        if ini_file_path.is_file():
+    ini_file_path = pl.Path.home() / pl.Path(".boris")
+    if ini_file_path.is_file():
+        try:
             settings = QSettings(str(ini_file_path), QSettings.IniFormat)
             settings.setValue(f"{widget_name} geometry", widget.saveGeometry())
-    except Exception:
-        logging.warning(f"error during saving {widget_name} geometry")
+        except Exception:
+            logging.warning(f"error during saving {widget_name} geometry")
 
 
-def restore_geometry(widget: QWidget, widget_name: str, default_geometry):
+def restore_geometry(widget: QWidget, widget_name: str, default_width_height):
     """
     restore window geometry in ini file
     """
 
+    def default_resize(widget, default_width_height):
+        if default_width_height != (0, 0):
+            try:
+                widget.resize(default_width_height[0], default_width_height[1])
+            except Exception:
+                logging.warning("Error during restoring default")
+
+    logging.debug(f"restore geometry function for {widget_name}")
     try:
         ini_file_path = pl.Path.home() / pl.Path(".boris")
         if ini_file_path.is_file():
             settings = QSettings(str(ini_file_path), QSettings.IniFormat)
             widget.restoreGeometry(settings.value(f"{widget_name} geometry"))
+            logging.debug(f"geometry restored for {widget_name}  {settings.value(f'{widget_name} geometry')}")
+        else:
+            default_resize(widget, default_width_height)
     except Exception:
         logging.warning(f"error during restoring {widget_name} geometry")
-        if default_geometry != (0, 0):
-            try:
-                widget.resize(default_geometry[0], default_geometry[1])
-            except Exception:
-                logging.warning(f"error during restoring default")
+        default_resize(widget, default_width_height)
+
+
+def set_icons(self, theme_mode: str) -> None:
+    """
+    set icons of actions
+    """
+
+    # menu
+    self.action_obs_list.setIcon(QIcon(f":/observations_list_{theme_mode}"))
+
+    self.actionTime_budget.setIcon(QIcon(f":/time_budget_{theme_mode}"))
+    self.actionPlot_events2.setIcon(QIcon(f":/plot_events_{theme_mode}"))
+    self.action_advanced_event_filtering.setIcon(QIcon(f":/filter_{theme_mode}"))
+
+    self.actionPreferences.setIcon(QIcon(f":/preferences_{theme_mode}"))
+
+    self.actionPlay.setIcon(QIcon(f":/play_{theme_mode}"))
+    self.actionReset.setIcon(QIcon(f":/reset_{theme_mode}"))
+    self.actionJumpBackward.setIcon(QIcon(f":/jump_backward_{theme_mode}"))
+    self.actionJumpForward.setIcon(QIcon(f":/jump_forward_{theme_mode}"))
+
+    self.actionFaster.setIcon(QIcon(f":/faster_{theme_mode}"))
+    self.actionSlower.setIcon(QIcon(f":/slower_{theme_mode}"))
+    self.actionNormalSpeed.setIcon(QIcon(f":/normal_speed_{theme_mode}"))
+
+    self.actionPrevious.setIcon(QIcon(f":/previous_{theme_mode}"))
+    self.actionNext.setIcon(QIcon(f":/next_{theme_mode}"))
+
+    self.actionSnapshot.setIcon(QIcon(f":/snapshot_{theme_mode}"))
+
+    self.actionFrame_backward.setIcon(QIcon(f":/frame_backward_{theme_mode}"))
+    self.actionFrame_forward.setIcon(QIcon(f":/frame_forward_{theme_mode}"))
+    self.actionCloseObs.setIcon(QIcon(f":/close_observation_{theme_mode}"))
+    self.actionCurrent_Time_Budget.setIcon(QIcon(f":/time_budget_{theme_mode}"))
+    self.actionPlot_current_observation.setIcon(QIcon(f":/plot_events_{theme_mode}"))
+
+    self.actionPlot_events_in_real_time.setIcon(QIcon(f":/plot_real_time_{theme_mode}"))
+
+    self.actionBehavior_bar_plot.setIcon(QIcon(f":/plot_time_budget_{theme_mode}"))
+    self.actionPlot_current_time_budget.setIcon(QIcon(f":/plot_time_budget_{theme_mode}"))
+    self.action_geometric_measurements.setIcon(QIcon(f":/measurement_{theme_mode}"))
+    self.actionFind_in_current_obs.setIcon(QIcon(f":/find_{theme_mode}"))
+    self.actionExplore_project.setIcon(QIcon(f":/explore_{theme_mode}"))
+
+
+def resize_center(app, window, width: int, height: int) -> None:
+    """
+    resize and center window
+    """
+    window.resize(width, height)
+    screen_geometry = app.primaryScreen().geometry()
+    if window.height() > screen_geometry.height():
+        window.resize(window.width(), int(screen_geometry.height() * 0.8))
+    if window.width() > screen_geometry.width():
+        window.resize(screen_geometry.width(), window.height())
+    # center
+    center_x = (screen_geometry.width() - window.width()) // 2
+    center_y = (screen_geometry.height() - window.height()) // 2
+
+    window.move(center_x, center_y)

boris/image_overlay.py

@@ -1,7 +1,7 @@
 """
 BORIS
 Behavioral Observation Research Interactive Software
-Copyright 2012-2023 Olivier Friard
+Copyright 2012-2025 Olivier Friard
 
 
   This program is free software; you can redistribute it and/or modify
@@ -26,16 +26,16 @@ from . import config as cfg
 from . import dialog
 
 
-def add_image_overlay(self):
+def add_image_overlay(self) -> None:
     """
-    add an image overlay on video
+    add an image overlay on video from an image
     """
 
-    logging.debug(f"function add_image_overlay")
+    logging.debug("function add_image_overlay")
 
     try:
         w = dialog.Video_overlay_dialog()
-        items = list([f"Player #{i + 1}" for i, _ in enumerate(self.dw_player)])
+        items = [f"Player #{i + 1}" for i, _ in enumerate(self.dw_player)]
         w.cb_player.addItems(items)
         if not w.exec_():
             return
@@ -57,16 +57,16 @@ def add_image_overlay(self):
         logging.debug("error in add_image_overlay function")
 
 
-def remove_image_overlay(self):
+def remove_image_overlay(self) -> None:
     """
     remove image overlay from all players
     """
-    keys_to_delete = []
+    keys_to_delete: list = []
     for n_player in self.pj[cfg.OBSERVATIONS][self.observationId][cfg.MEDIA_INFO].get(cfg.OVERLAY, {}):
         keys_to_delete.append(n_player)
         try:
             self.overlays[int(n_player) - 1].remove()
-        except:
-            logging.debug("error removing overlay")
+        except Exception:
+            logging.debug("Error removing image overlay")
     for n_player in keys_to_delete:
         del self.pj[cfg.OBSERVATIONS][self.observationId][cfg.MEDIA_INFO][cfg.OVERLAY][n_player]

boris/import_observations.py

@@ -1,7 +1,7 @@
 """
 BORIS
 Behavioral Observation Research Interactive Software
-Copyright 2012-2023 Olivier Friard
+Copyright 2012-2025 Olivier Friard
 
   This program is free software; you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
@@ -19,11 +19,13 @@ Copyright 2012-2023 Olivier Friard
   MA 02110-1301, USA.
 """
 
-
-import json
 import datetime
+import gzip
+import json
+import pandas as pd
+from pathlib import Path
 
-from PyQt5.QtWidgets import (
+from PySide6.QtWidgets import (
     QMessageBox,
     QFileDialog,
 )
@@ -33,17 +35,12 @@ from . import dialog
 from . import utilities as util
 
 
-def import_observations(self):
+def load_observations_from_boris_project(self, project_file_path: str):
     """
-    import observations from project file
+    import observations from a BORIS project file
     """
 
-    fn = QFileDialog().getOpenFileName(
-        None, "Choose a BORIS project file", "", "Project files (*.boris);;All files (*)"
-    )
-    fileName = fn[0] if type(fn) is tuple else fn
-
-    if self.projectFileName and fileName == self.projectFileName:
+    if self.projectFileName and project_file_path == self.projectFileName:
         QMessageBox.critical(
             None,
             cfg.programName,
@@ -53,98 +50,193 @@ def import_observations(self):
         )
         return
 
-    if fileName:
-        try:
-            fromProject = json.loads(open(fileName, "r").read())
-        except Exception:
-            QMessageBox.critical(self, cfg.programName, "This project file seems corrupted")
-            return
+    if project_file_path.endswith(".boris.gz"):
+        file_in = gzip.open(project_file_path, mode="rt", encoding="utf-8")
+    else:
+        file_in = open(project_file_path, "r")
+    file_content = file_in.read()
+
+    try:
+        fromProject = json.loads(file_content)
+    except Exception:
+        QMessageBox.critical(self, cfg.programName, "This project file seems corrupted")
+        return
+
+    # transform time to decimal
+    fromProject = util.convert_time_to_decimal(fromProject)  # function in utilities.py
 
-        # transform time to decimal
-        fromProject = util.convert_time_to_decimal(fromProject)  # function in utilities.py
+    dbc = dialog.ChooseObservationsToImport("Choose the observations to import:", sorted(list(fromProject[cfg.OBSERVATIONS].keys())))
+
+    if not dbc.exec_():
+        return
+    selected_observations = dbc.get_selected_observations()
+    if selected_observations:
+        flagImported = False
+
+        # set of behaviors in current projet ethogram
+        behav_set = set([self.pj[cfg.ETHOGRAM][idx][cfg.BEHAVIOR_CODE] for idx in self.pj[cfg.ETHOGRAM]])
+
+        # set of subjects in current projet
+        subjects_set = set([self.pj[cfg.SUBJECTS][idx][cfg.SUBJECT_NAME] for idx in self.pj[cfg.SUBJECTS]])
+
+        for obs_id in selected_observations:
+            # check if behaviors are in current project ethogram
+            new_behav_set = set(
+                [
+                    event[cfg.EVENT_BEHAVIOR_FIELD_IDX]
+                    for event in fromProject[cfg.OBSERVATIONS][obs_id][cfg.EVENTS]
+                    if event[cfg.EVENT_BEHAVIOR_FIELD_IDX] not in behav_set
+                ]
+            )
+            if new_behav_set:
+                diag_result = dialog.MessageDialog(
+                    cfg.programName,
+                    (f"Some coded behaviors in <b>{obs_id}</b> are not defined in the ethogram:<br><b>{', '.join(new_behav_set)}</b>"),
+                    ["Interrupt import", "Skip observation", "Import observation"],
+                )
+                if diag_result == "Interrupt import":
+                    return
+                if diag_result == "Skip observation":
+                    continue
+
+            # check if subjects are in current project
+            new_subject_set = set(
+                [
+                    event[cfg.EVENT_SUBJECT_FIELD_IDX]
+                    for event in fromProject[cfg.OBSERVATIONS][obs_id][cfg.EVENTS]
+                    if event[cfg.EVENT_SUBJECT_FIELD_IDX] not in subjects_set
+                ]
+            )
+            if new_subject_set and new_subject_set != {""}:
+                diag_result = dialog.MessageDialog(
+                    cfg.programName,
+                    (f"Some coded subjects in <b>{obs_id}</b> are not defined in the project:<br><b>{', '.join(new_subject_set)}</b>"),
+                    ["Interrupt import", "Skip observation", "Import observation"],
+                )
+
+                if diag_result == "Interrupt import":
+                    return
+
+                if diag_result == "Skip observation":
+                    continue
+
+            if obs_id in self.pj[cfg.OBSERVATIONS].keys():
+                diag_result = dialog.MessageDialog(
+                    cfg.programName,
+                    (f"The observation <b>{obs_id}</b>already exists in the current project.<br>"),
+                    ["Interrupt import", "Skip observation", "Rename observation"],
+                )
+                if diag_result == "Interrupt import":
+                    return
+
+                if diag_result == "Rename observation":
+                    self.pj[cfg.OBSERVATIONS][f"{obs_id} (imported at {util.datetime_iso8601(datetime.datetime.now())})"] = dict(
+                        fromProject[cfg.OBSERVATIONS][obs_id]
+                    )
+                    flagImported = True
+            else:
+                self.pj[cfg.OBSERVATIONS][obs_id] = dict(fromProject[cfg.OBSERVATIONS][obs_id])
+                flagImported = True
+
+        if flagImported:
+            QMessageBox.information(self, cfg.programName, "Observations imported successfully")
+            self.project_changed()
+
+
+def load_observations_from_spreadsheet(self, project_file_path: str):
+    """
+    import observations from a spreadsheet file
+    """
+
+    if Path(project_file_path).suffix.lower() == ".xlsx":
+        engine = "openpyxl"
+    elif Path(project_file_path).suffix.lower() == ".ods":
+        engine = "odf"
+    else:
+        return
 
-        dbc = dialog.ChooseObservationsToImport(
-            "Choose the observations to import:", sorted(list(fromProject[cfg.OBSERVATIONS].keys()))
+    try:
+        df = pd.read_excel(project_file_path, sheet_name=0, engine=engine)
+    except Exception:
+        QMessageBox.warning(
+            None,
+            cfg.programName,
+            ("The type of file was not recognized. Must be Microsoft-Excel XLSX format or OpenDocument ODS"),
+            QMessageBox.Ok | QMessageBox.Default,
+            QMessageBox.NoButton,
         )
+        return
 
-        if dbc.exec_():
+    expected_labels: list = ("time", "subject", "code", "modifier", "comment")
+
+    df.columns = df.columns.str.upper()
+
+    for column in expected_labels:
+        if column.upper() not in list(df.columns):
+            QMessageBox.warning(
+                None,
+                cfg.programName,
+                (
+                    f"The {column} column was not found in the file header.<br>"
+                    "For information the current file header contains the following labels:<br>"
+                    f"{'<br>'.join(['<b>' + util.replace_leading_trailing_chars(x, ' ', '&#9608;') + '</b>' for x in df.columns])}<br>"
+                    "<br>"
+                    "The first row of the spreadsheet must contain the following labels:<br>"
+                    f"{'<br>'.join(['<b>' + x + '</b>' for x in expected_labels])}<br>"
+                    "<br>The order is not mandatory."
+                ),
+                QMessageBox.Ok | QMessageBox.Default,
+                QMessageBox.NoButton,
+            )
+            return 1
+    event: dict = {}
+    events: list = []
+    for _, row in df.iterrows():
+        for label in expected_labels:
+            event[label] = row[label.upper()] if str(row[label.upper()]) != "nan" else ""
+        events.append([event["time"], event["subject"], event["code"], event["modifier"], event["comment"]])
+
+    if events:
+        self.pj[cfg.OBSERVATIONS][self.observationId]["events"].extend(events)
+        self.load_tw_events(self.observationId)
+
+        QMessageBox.information(self, cfg.programName, "Observations imported successfully")
+        self.project_changed()
 
-            selected_observations = dbc.get_selected_observations()
-            if selected_observations:
-                flagImported = False
 
-                # set of behaviors in current projet ethogram
-                behav_set = set([self.pj[cfg.ETHOGRAM][idx][cfg.BEHAVIOR_CODE] for idx in self.pj[cfg.ETHOGRAM]])
+def import_observations(self):
+    """
+    import observations from project file
+    """
 
-                # set of subjects in current projet
-                subjects_set = set([self.pj[cfg.SUBJECTS][idx][cfg.SUBJECT_NAME] for idx in self.pj[cfg.SUBJECTS]])
+    file_name, _ = QFileDialog().getOpenFileName(
+        None, "Choose a file", "", "BORIS project files (*.boris *.boris.gz);;Spreadsheet files (*.ods *.xlsx *);;All files (*)"
+    )
 
-                for obsId in selected_observations:
+    if not file_name:
+        return
 
-                    # check if behaviors are in current project ethogram
-                    new_behav_set = set(
-                        [
-                            event[cfg.EVENT_BEHAVIOR_FIELD_IDX]
-                            for event in fromProject[cfg.OBSERVATIONS][obsId][cfg.EVENTS]
-                            if event[cfg.EVENT_BEHAVIOR_FIELD_IDX] not in behav_set
-                        ]
-                    )
-                    if new_behav_set:
-                        diag_result = dialog.MessageDialog(
-                            cfg.programName,
-                            (
-                                f"Some coded behaviors in <b>{obsId}</b> are "
-                                f"not defined in the ethogram:<br><b>{', '.join(new_behav_set)}</b>"
-                            ),
-                            ["Interrupt import", "Skip observation", "Import observation"],
-                        )
-                        if diag_result == "Interrupt import":
-                            return
-                        if diag_result == "Skip observation":
-                            continue
-
-                    # check if subjects are in current project
-                    new_subject_set = set(
-                        [
-                            event[cfg.EVENT_SUBJECT_FIELD_IDX]
-                            for event in fromProject[cfg.OBSERVATIONS][obsId][cfg.EVENTS]
-                            if event[cfg.EVENT_SUBJECT_FIELD_IDX] not in subjects_set
-                        ]
-                    )
-                    if new_subject_set and new_subject_set != {""}:
-                        diag_result = dialog.MessageDialog(
-                            cfg.programName,
-                            (
-                                f"Some coded subjects in <b>{obsId}</b> are not defined in the project:<br>"
-                                f"<b>{', '.join(new_subject_set)}</b>"
-                            ),
-                            ["Interrupt import", "Skip observation", "Import observation"],
-                        )
-
-                        if diag_result == "Interrupt import":
-                            return
-
-                        if diag_result == "Skip observation":
-                            continue
-
-                    if obsId in self.pj[cfg.OBSERVATIONS].keys():
-                        diag_result = dialog.MessageDialog(
-                            cfg.programName,
-                            (f"The observation <b>{obsId}</b>" "already exists in the current project.<br>"),
-                            ["Interrupt import", "Skip observation", "Rename observation"],
-                        )
-                        if diag_result == "Interrupt import":
-                            return
-
-                        if diag_result == "Rename observation":
-                            self.pj[cfg.OBSERVATIONS][
-                                f"{obsId} (imported at {util.datetime_iso8601(datetime.datetime.now())})"
-                            ] = dict(fromProject[cfg.OBSERVATIONS][obsId])
-                            flagImported = True
-                    else:
-                        self.pj[cfg.OBSERVATIONS][obsId] = dict(fromProject[cfg.OBSERVATIONS][obsId])
-                        flagImported = True
-
-                if flagImported:
-                    QMessageBox.information(self, cfg.programName, "Observations imported successfully")
-                    self.project_changed()
+    if file_name.endswith(".boris") or file_name.endswith(".boris.gz"):
+        load_observations_from_boris_project(self, file_name)
+
+    elif Path(file_name).suffix.lower() in (".ods", ".xlsx"):
+        if not self.observationId:
+            QMessageBox.warning(
+                None,
+                cfg.programName,
+                ("Please open or create a new observation before importing from a spreadsheet file"),
+                QMessageBox.Ok,
+                QMessageBox.NoButton,
+            )
+            return
+
+        load_observations_from_spreadsheet(self, file_name)
+
+    else:
+        QMessageBox.warning(
+            None,
+            cfg.programName,
+            ("The type of file was not recognized. Must be a BORIS project or a Microsoft-Excel XLSX format or OpenDocument ODS"),
+            QMessageBox.Ok | QMessageBox.Default,
+            QMessageBox.NoButton,
+        )