boris-behav-obs 8.16.6__py3-none-any.whl → 9.7.1__py3-none-any.whl

boris/connections.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
@@ -19,8 +19,8 @@ Copyright 2012-2023 Olivier Friard
   MA 02110-1301, USA.
 """
 
-from PyQt5.QtCore import Qt, QTimer
-from PyQt5.QtWidgets import QAction
+from PySide6.QtCore import Qt, QTimer
+from PySide6.QtGui import QAction
 
 from . import config as cfg
 from . import (
@@ -37,6 +37,7 @@ from . import (
     import_observations,
     irr,
     latency,
+    cooccurence,
     media_file,
     observation_operations,
     preferences,
@@ -69,9 +70,7 @@ def connections(self):
     self.actionExport_project.triggered.connect(lambda: project_import_export.export_project_as_pickle_object(self.pj))
     self.actionClose_project.triggered.connect(self.close_project)
 
-    self.action_media_file_and_images_directories_relative_path.triggered.connect(
-        self.set_media_files_path_relative_to_project_dir
-    )
+    self.action_media_file_and_images_directories_relative_path.triggered.connect(self.set_media_files_path_relative_to_project_dir)
     self.action_data_files_relative_path.triggered.connect(self.set_data_files_path_relative_to_project_dir)
 
     self.action_remove_media_files_and_images_directories_path.triggered.connect(self.remove_media_files_path)
@@ -84,19 +83,16 @@ def connections(self):
     self.actionQuit.triggered.connect(self.actionQuit_activated)
 
     # menu observations
-    self.actionNew_observation.triggered.connect(
-        lambda: observation_operations.new_observation(self, mode=cfg.NEW, obsId="")
-    )
+    self.actionNew_observation.triggered.connect(lambda: observation_operations.new_observation(self, mode=cfg.NEW, obsId=""))
 
-    self.actionOpen_observation.triggered.connect(
-        lambda: observation_operations.open_observation(self, mode=cfg.OBS_START)
-    )
+    self.actionOpen_observation.triggered.connect(lambda: observation_operations.open_observation(self, mode=cfg.OBS_START))
     self.actionView_observation.triggered.connect(lambda: observation_operations.open_observation(self, mode=cfg.VIEW))
     self.actionEdit_observation_2.triggered.connect(lambda: observation_operations.edit_observation(self))
     self.actionObservationsList.triggered.connect(lambda: observation_operations.observations_list(self))
 
     self.actionClose_observation.triggered.connect(lambda: observation_operations.close_observation(self))
 
+    self.action_create_observations.triggered.connect(lambda: observation_operations.create_observations(self))
     self.actionRemove_observations.triggered.connect(lambda: observation_operations.remove_observations(self))
 
     self.actionAdd_event.triggered.connect(lambda: event_operations.add_event(self))
@@ -107,22 +103,24 @@ def connections(self):
     self.actionShow_all_events.triggered.connect(lambda: event_operations.show_all_events(self))
 
     # twevent header
-    self.actionConfigure_twEvents_columns.triggered.connect(self.configure_twevents_columns)
+    # self.actionConfigure_twEvents_columns.triggered.connect(self.configure_twevents_columns)
 
-    self.actionExport_observations_list.triggered.connect(
-        lambda: observation_operations.export_observations_list_clicked(self)
-    )
+    # tv_events header
+    self.actionConfigure_tvevents_columns.triggered.connect(self.configure_tvevents_columns)
+
+    self.actionExport_observations_list.triggered.connect(lambda: observation_operations.export_observations_list_clicked(self))
 
     self.actionCheckStateEvents.triggered.connect(lambda: state_events.check_state_events(self, mode="all"))
-    self.actionCheckStateEventsSingleObs.triggered.connect(
-        lambda: state_events.check_state_events(self, mode="current")
-    )
+    self.actionCheckStateEventsSingleObs.triggered.connect(lambda: state_events.check_state_events(self, mode="current"))
     self.actionClose_unpaired_events.triggered.connect(lambda: state_events.fix_unpaired_events(self))
+    self.actionAdd_frame_indexes.triggered.connect(lambda: event_operations.add_frame_indexes(self))
+
     self.actionRunEventOutside.triggered.connect(self.run_event_outside)
 
     self.actionSelect_observations.triggered.connect(lambda: event_operations.select_events_between_activated(self))
 
     self.actionEdit_selected_events.triggered.connect(lambda: event_operations.edit_selected_events(self))
+    self.action_add_comment.triggered.connect(lambda: event_operations.add_comment(self))
     self.actionEdit_event_time.triggered.connect(lambda: event_operations.edit_time_selected_events(self))
 
     self.actionCopy_events.triggered.connect(lambda: event_operations.copy_selected_events(self))
@@ -130,7 +128,7 @@ def connections(self):
 
     self.actionExplore_project.triggered.connect(lambda: project_functions.explore_project(self))
     self.actionFind_events.triggered.connect(lambda: event_operations.find_events(self))
-    self.actionFind_replace_events.triggered.connect(self.find_replace_events)
+    self.actionFind_replace_events.triggered.connect(lambda: event_operations.find_replace_events(self))
     self.actionDelete_all_events.triggered.connect(lambda: event_operations.delete_all_events(self))
     self.actionDelete_selected_events.triggered.connect(lambda: event_operations.delete_selected_events(self))
 
@@ -163,14 +161,16 @@ def connections(self):
     self.actionNumber_of_transitions.triggered.connect(lambda: transitions.transitions_matrix(self, "number"))
 
     self.actionFrequencies_of_transitions_after_behaviors.triggered.connect(
-        lambda: self.transitions_matrix("frequencies_after_behaviors")
+        lambda: transitions.transitions_matrix(self, "frequencies_after_behaviors")
     )
 
     # menu playback
     self.actionJumpTo.triggered.connect(self.jump_to)
     self.action_deinterlace.triggered.connect(lambda: video_operations.deinterlace(self))
+    self.action_change_time_offset_of_players.triggered.connect(lambda: video_operations.change_player_offset(self))
     self.actionZoom_level.triggered.connect(lambda: video_operations.zoom_level(self))
     self.actionRotate_current_video.triggered.connect(lambda: video_operations.rotate_displayed_video(self))
+
     self.actionDisplay_subtitles.triggered.connect(lambda: video_operations.display_subtitles(self))
     self.actionVideo_equalizer.triggered.connect(lambda: video_equalizer.video_equalizer_show(self))
 
@@ -178,9 +178,7 @@ def connections(self):
     self.action_block_dockwidgets.triggered.connect(self.block_dockwidgets)
 
     self.action_create_modifiers_coding_map.triggered.connect(self.modifiers_coding_map_creator)
-    self.action_create_behaviors_coding_map.triggered.connect(
-        lambda: behav_coding_map_creator.behaviors_coding_map_creator(self)
-    )
+    self.action_create_behaviors_coding_map.triggered.connect(lambda: behav_coding_map_creator.behaviors_coding_map_creator(self))
 
     self.actionShow_spectrogram.triggered.connect(lambda: self.show_plot_widget("spectrogram", warning=True))
     self.actionShow_the_sound_waveform.triggered.connect(lambda: self.show_plot_widget("waveform", warning=True))
@@ -198,24 +196,22 @@ def connections(self):
     self.actionAdd_image_overlay_on_video.triggered.connect(lambda: image_overlay.add_image_overlay(self))
     self.actionRemove_image_overlay.triggered.connect(lambda: image_overlay.remove_image_overlay(self))
 
+    self.actionMedia_file_information_2.triggered.connect(lambda: media_file.get_info(self))
     self.actionRecode_resize_video.triggered.connect(lambda: external_processes.ffmpeg_process(self, "reencode_resize"))
     self.actionRotate_video.triggered.connect(lambda: external_processes.ffmpeg_process(self, "rotate"))
     self.actionMerge_media_files.triggered.connect(lambda: external_processes.ffmpeg_process(self, "merge"))
-    self.actionMedia_file_information_2.triggered.connect(lambda: media_file.get_info(self))
+    self.actionCreate_video_spectrogram.triggered.connect(lambda: external_processes.ffmpeg_process(self, "video_spectrogram"))
 
     self.actionCreate_transitions_flow_diagram.triggered.connect(transitions.transitions_dot_script)
     self.actionCreate_transitions_flow_diagram_2.triggered.connect(transitions.transitions_flow_diagram)
 
     # menu Analysis
+
     self.actionTime_budget.triggered.connect(lambda: time_budget_widget.time_budget(self, mode="by_behavior"))
-    self.actionTime_budget_by_behaviors_category.triggered.connect(
-        lambda: time_budget_widget.time_budget(self, mode="by_category")
-    )
+    self.actionTime_budget_by_behaviors_category.triggered.connect(lambda: time_budget_widget.time_budget(self, mode="by_category"))
 
     self.actionTime_budget_report.triggered.connect(lambda: synthetic_time_budget.synthetic_time_budget(self))
-    self.actionSynthetic_binned_time_budget.triggered.connect(
-        lambda: synthetic_time_budget.synthetic_binned_time_budget(self)
-    )
+    self.actionSynthetic_binned_time_budget.triggered.connect(lambda: synthetic_time_budget.synthetic_binned_time_budget(self))
 
     self.actionBehavior_bar_plot.triggered.connect(lambda: self.behaviors_bar_plot(mode="list"))
     self.actionBehavior_bar_plot.setVisible(True)
@@ -229,6 +225,8 @@ def connections(self):
 
     self.action_latency.triggered.connect(lambda: latency.get_latency(self))
 
+    self.action_cooccurence.triggered.connect(lambda: cooccurence.get_cooccurence(self))
+
     # menu Help
     self.actionUser_guide.triggered.connect(self.actionUser_guide_triggered)
     self.actionAbout.triggered.connect(lambda: about.actionAbout_activated(self))
@@ -254,9 +252,7 @@ def connections(self):
     self.actionFrame_forward.triggered.connect(self.next_frame)
 
     self.actionCloseObs.triggered.connect(lambda: observation_operations.close_observation(self))
-    self.actionCurrent_Time_Budget.triggered.connect(
-        lambda: time_budget_widget.time_budget(self, mode="by_behavior", mode2="current")
-    )
+    self.actionCurrent_Time_Budget.triggered.connect(lambda: time_budget_widget.time_budget(self, mode="by_behavior", mode2="current"))
     self.actionPlot_current_observation.triggered.connect(lambda: self.plot_events_triggered(mode="current"))
 
     self.actionPlot_current_time_budget.triggered.connect(lambda: self.behaviors_bar_plot(mode="current"))
@@ -264,10 +260,13 @@ def connections(self):
     self.actionFind_in_current_obs.triggered.connect(lambda: event_operations.find_events(self))
 
     # table Widget double click
-    self.twEvents.itemDoubleClicked.connect(self.twEvents_doubleClicked)
+    # self.twEvents.itemDoubleClicked.connect(self.twEvents_doubleClicked)
     self.twEthogram.itemDoubleClicked.connect(self.twEthogram_doubleClicked)
     self.twSubjects.itemDoubleClicked.connect(self.twSubjects_doubleClicked)
 
+    # events tableview
+    self.tv_events.doubleClicked.connect(self.tv_events_doubleClicked)
+
     # Actions for twEthogram context menu
     self.twEthogram.setContextMenuPolicy(Qt.ActionsContextMenu)
     self.twEthogram.horizontalHeader().sortIndicatorChanged.connect(self.twEthogram_sorted)
@@ -275,7 +274,9 @@ def connections(self):
     self.actionViewBehavior.triggered.connect(self.view_behavior)
     self.twEthogram.addAction(self.actionViewBehavior)
 
-    self.actionFilterBehaviors.triggered.connect(lambda: self.filter_behaviors(table=cfg.ETHOGRAM))
+    self.actionFilterBehaviors.triggered.connect(
+        lambda: self.filter_behaviors(table=cfg.ETHOGRAM, behavior_type=cfg.STATE_EVENT_TYPES + cfg.POINT_EVENT_TYPES)
+    )
     self.twEthogram.addAction(self.actionFilterBehaviors)
 
     self.actionShowAllBehaviors.triggered.connect(self.show_all_behaviors)
@@ -291,49 +292,95 @@ def connections(self):
     self.twSubjects.addAction(self.actionShowAllSubjects)
 
     # actions for twEvents horizontal header menu
-    tw_headers = self.twEvents.horizontalHeader()
-    tw_headers.setContextMenuPolicy(Qt.ActionsContextMenu)
-    tw_headers.addAction(self.actionConfigure_twEvents_columns)
+    # tw_headers = self.twEvents.horizontalHeader()
+    # tw_headers.setContextMenuPolicy(Qt.ActionsContextMenu)
+    # tw_headers.addAction(self.actionConfigure_twEvents_columns)
+
+    tv_headers = self.tv_events.horizontalHeader()
+    tv_headers.setContextMenuPolicy(Qt.ActionsContextMenu)
+    tv_headers.addAction(self.actionConfigure_tvevents_columns)
 
     # Actions for twEvents menu
-    self.twEvents.setContextMenuPolicy(Qt.ActionsContextMenu)
+    # self.twEvents.setContextMenuPolicy(Qt.ActionsContextMenu)
+
+    # self.twEvents.addAction(self.actionAdd_event)
+    # self.twEvents.addAction(self.actionEdit_selected_events)
+    # self.twEvents.addAction(self.actionEdit_event_time)
+
+    # self.twEvents.addAction(self.actionCopy_events)
+    # self.twEvents.addAction(self.actionPaste_events)
+
+    # separator2 = QAction(self)
+    # separator2.setSeparator(True)
+    # self.twEvents.addAction(separator2)
+
+    # self.twEvents.addAction(self.actionFind_events)
+    # self.twEvents.addAction(self.actionFind_replace_events)
+
+    # separator2 = QAction(self)
+    # separator2.setSeparator(True)
+    # self.twEvents.addAction(separator2)
+
+    # self.twEvents.addAction(self.actionFilter_events)
+    # self.twEvents.addAction(self.actionShow_all_events)
 
-    self.twEvents.addAction(self.actionAdd_event)
-    self.twEvents.addAction(self.actionEdit_selected_events)
-    self.twEvents.addAction(self.actionEdit_event_time)
+    # separator2 = QAction(self)
+    # separator2.setSeparator(True)
+    # self.twEvents.addAction(separator2)
 
-    self.twEvents.addAction(self.actionCopy_events)
-    self.twEvents.addAction(self.actionPaste_events)
+    # self.twEvents.addAction(self.actionCheckStateEventsSingleObs)
+    # self.twEvents.addAction(self.actionClose_unpaired_events)
+
+    # self.twEvents.addAction(self.actionRunEventOutside)
+
+    # separator2 = QAction(self)
+    # separator2.setSeparator(True)
+    # self.twEvents.addAction(separator2)
+
+    # self.twEvents.addAction(self.actionDelete_selected_events)
+
+    # Actions for tv_events menu
+    self.tv_events.setContextMenuPolicy(Qt.ActionsContextMenu)
+
+    self.tv_events.addAction(self.actionAdd_event)
+    self.tv_events.addAction(self.actionEdit_selected_events)
+    self.tv_events.addAction(self.action_add_comment)
+
+    self.tv_events.addAction(self.actionEdit_event_time)
+
+    self.tv_events.addAction(self.actionCopy_events)
+    self.tv_events.addAction(self.actionPaste_events)
 
     separator2 = QAction(self)
     separator2.setSeparator(True)
-    self.twEvents.addAction(separator2)
+    self.tv_events.addAction(separator2)
 
-    self.twEvents.addAction(self.actionFind_events)
-    self.twEvents.addAction(self.actionFind_replace_events)
+    self.tv_events.addAction(self.actionFind_events)
+    self.tv_events.addAction(self.actionFind_replace_events)
 
     separator2 = QAction(self)
     separator2.setSeparator(True)
-    self.twEvents.addAction(separator2)
+    self.tv_events.addAction(separator2)
 
-    self.twEvents.addAction(self.actionFilter_events)
-    self.twEvents.addAction(self.actionShow_all_events)
+    self.tv_events.addAction(self.actionFilter_events)
+    self.tv_events.addAction(self.actionShow_all_events)
 
     separator2 = QAction(self)
     separator2.setSeparator(True)
-    self.twEvents.addAction(separator2)
+    self.tv_events.addAction(separator2)
+
+    self.tv_events.addAction(self.actionCheckStateEventsSingleObs)
+    self.tv_events.addAction(self.actionClose_unpaired_events)
 
-    self.twEvents.addAction(self.actionCheckStateEventsSingleObs)
-    self.twEvents.addAction(self.actionClose_unpaired_events)
+    self.tv_events.addAction(self.actionAdd_frame_indexes)
 
-    self.twEvents.addAction(self.actionRunEventOutside)
+    self.tv_events.addAction(self.actionRunEventOutside)
 
     separator2 = QAction(self)
     separator2.setSeparator(True)
-    self.twEvents.addAction(separator2)
+    self.tv_events.addAction(separator2)
 
-    self.twEvents.addAction(self.actionDelete_selected_events)
-    # self.twEvents.addAction(self.actionDelete_all_events)
+    self.tv_events.addAction(self.actionDelete_selected_events)
 
     # Actions for twSubjects context menu
     self.actionDeselectCurrentSubject.triggered.connect(lambda: self.update_subject(""))

boris/converters.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.
 
@@ -22,14 +22,10 @@ This file is part of BORIS.
 
 import sys
 import json
-import urllib.error
-import urllib.parse
 import urllib.request
 
 
-from PyQt5.QtCore import *
-from PyQt5.QtGui import *
-from PyQt5.QtWidgets import *
+from PySide6.QtWidgets import QMessageBox, QTableWidgetItem, QFileDialog, QInputDialog, QLineEdit
 
 from . import dialog
 from . import config as cfg
@@ -113,12 +109,8 @@ def modify_converter(self):
         w.setEnabled(False)
 
     self.le_converter_name.setText(self.tw_converters.item(self.tw_converters.selectedIndexes()[0].row(), 0).text())
-    self.le_converter_description.setText(
-        self.tw_converters.item(self.tw_converters.selectedIndexes()[0].row(), 1).text()
-    )
-    self.pteCode.setPlainText(
-        self.tw_converters.item(self.tw_converters.selectedIndexes()[0].row(), 2).text().replace("@", "\n")
-    )
+    self.le_converter_description.setText(self.tw_converters.item(self.tw_converters.selectedIndexes()[0].row(), 1).text())
+    self.pteCode.setPlainText(self.tw_converters.item(self.tw_converters.selectedIndexes()[0].row(), 2).text().replace("@", "\n"))
 
     self.row_in_modification = self.tw_converters.selectedIndexes()[0].row()
 
@@ -153,9 +145,7 @@ def save_converter(self):
         return
 
     if not self.le_converter_name.text().replace("_", "a").isalnum():
-        QMessageBox.critical(
-            self, "BORIS", "Forbidden characters are used in converter name.<br>Use a..z, A..Z, 0..9 _"
-        )
+        QMessageBox.critical(self, "BORIS", "Forbidden characters are used in converter name.<br>Use a..z, A..Z, 0..9 _")
         return
 
     # test code with exec
@@ -164,7 +154,7 @@ def save_converter(self):
         QMessageBox.critical(self, "BORIS", "The converter must have Python code")
         return
 
-    function = code_2_func(self, self.le_converter_name.text(), code)
+    function = code_2_func(self, name=self.le_converter_name.text(), code=code)
 
     try:
         exec(function)
@@ -247,8 +237,7 @@ def load_converters_from_file_repo(self, mode: str):
 
     converters_from_file = {}
     if mode == "file":
-        fn = QFileDialog(self).getOpenFileName(self, "Load converters from file", "", "All files (*)")
-        file_name = fn[0] if type(fn) is tuple else fn
+        file_name, _ = QFileDialog.getOpenFileName(self, "Load converters from file", "", "All files (*)")
 
         if file_name:
             with open(file_name, "r") as f_in:
@@ -259,35 +248,25 @@ def load_converters_from_file_repo(self, mode: str):
                     return
 
     if mode == "repo":
-
-        converters_repo_URL = "http://www.boris.unito.it/archive/converters.json"
+        converters_repo_URL = "https://www.boris.unito.it/static/converters.json"
         try:
             converters_from_repo = urllib.request.urlopen(converters_repo_URL).read().strip().decode("utf-8")
         except Exception:
-            QMessageBox.critical(
-                self, cfg.programName, "An error occured during retrieving converters from BORIS remote repository"
-            )
+            QMessageBox.critical(self, cfg.programName, "An error occured during retrieving converters from BORIS remote repository")
             return
 
         try:
             converters_from_file = eval(converters_from_repo)["BORIS converters"]
         except Exception:
-            QMessageBox.critical(
-                self, cfg.programName, "An error occured during retrieving converters from BORIS remote repository"
-            )
+            QMessageBox.critical(self, cfg.programName, "An error occured during retrieving converters from BORIS remote repository")
             return
 
     if converters_from_file:
-
-        diag_choose_conv = dialog.ChooseObservationsToImport(
-            "Choose the converters to load:", sorted(list(converters_from_file.keys()))
-        )
+        diag_choose_conv = dialog.ChooseObservationsToImport("Choose the converters to load:", sorted(list(converters_from_file.keys())))
 
         if diag_choose_conv.exec_():
-
             selected_converters = diag_choose_conv.get_selected_observations()
             if selected_converters:
-
                 # extract converter names from table
                 converter_names = []
                 for row in range(self.tw_converters.rowCount()):
@@ -325,7 +304,7 @@ def load_converters_from_file_repo(self, mode: str):
                         else:
                             continue
                     # test if code does not produce error
-                    function = self.code_2_func(converter_name, converters_from_file[converter]["code"])
+                    function = code_2_func(self, name=converter_name, code=converters_from_file[converter]["code"])
 
                     try:
                         exec(function)
@@ -333,10 +312,7 @@ def load_converters_from_file_repo(self, mode: str):
                         QMessageBox.critical(
                             self,
                             "BORIS",
-                            (
-                                f"The code of {converter_name} converter produces an error: "
-                                f"<br><b>{sys.exc_info()[1]}</b>"
-                            ),
+                            (f"The code of {converter_name} converter produces an error: <br><b>{sys.exc_info()[1]}</b>"),
                         )
 
                     self.tw_converters.setRowCount(self.tw_converters.rowCount() + 1)