boris-behav-obs 8.12__py3-none-any.whl → 9.7.6__py3-none-any.whl

boris/latency.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
@@ -18,9 +18,7 @@ Copyright 2012-2023 Olivier Friard
   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
   MA 02110-1301, USA.
 
-"""
 
-"""
 Module for analyzing the latency of behaviors after another behavior(s) (marker)
 
 """
@@ -31,7 +29,7 @@ from . import dialog
 from . import select_observations
 from . import project_functions, observation_operations
 
-from PyQt5.QtWidgets import QMessageBox
+from PySide6.QtWidgets import QMessageBox
 
 
 def get_latency(self):
@@ -43,10 +41,9 @@ def get_latency(self):
         None,
         cfg.programName,
         (
-            f"This function is experimental. Please test it and report any bug at <br>"
+            "This function is experimental. Please test it and report any bug at <br>"
             '<a href="https://github.com/olivierfriard/BORIS/issues">'
             "https://github.com/olivierfriard/BORIS/issues</a><br>"
-            "or by email (See the About page on the BORIS web site.<br><br>"
             "Thank you for your collaboration!"
         ),
         QMessageBox.Ok | QMessageBox.Default,
@@ -83,10 +80,10 @@ def get_latency(self):
         )
         return
 
-    parameters = select_subj_behav.choose_obs_subj_behav_category(
+    parameters: dict = select_subj_behav.choose_obs_subj_behav_category(
         self,
         selected_observations,
-        flagShowExcludeBehaviorsWoEvents=False,
+        show_exclude_non_coded_behaviors=False,
         window_title="Select the marker behaviors (stimulus)",
         n_observations=len(selected_observations),
     )
@@ -102,10 +99,10 @@ def get_latency(self):
     marker_subjects = parameters[cfg.SELECTED_SUBJECTS]
     include_marker_modifiers = parameters[cfg.INCLUDE_MODIFIERS]
 
-    # print(f"{marker_behaviors=} {marker_subjects=} {include_marker_modifiers=}")
+    print(f"{marker_behaviors=} {marker_subjects=} {include_marker_modifiers=}")
 
-    parameters = select_subj_behav.choose_obs_subj_behav_category(
-        self, selected_observations, flagShowExcludeBehaviorsWoEvents=False, window_title="Select the latency behaviors"
+    parameters: dict = select_subj_behav.choose_obs_subj_behav_category(
+        self, selected_observations, show_exclude_non_coded_behaviors=False, window_title="Select the latency behaviors"
     )
     if not parameters[cfg.SELECTED_SUBJECTS] or not parameters[cfg.SELECTED_BEHAVIORS]:
         return
@@ -113,11 +110,11 @@ def get_latency(self):
     latency_subjects = parameters[cfg.SELECTED_SUBJECTS]
     include_latency_modifiers = parameters[cfg.INCLUDE_MODIFIERS]
 
-    # print(f"{latency_behaviors=} {latency_subjects=} {include_latency_modifiers=}")
+    print(f"{latency_behaviors=} {latency_subjects=} {include_latency_modifiers=}")
 
-    results = {}
+    results: dict = {}
     for obs_id in selected_observations:
-        # print(f"{obs_id=}")
+        print(f"{obs_id=}")
 
         events_with_status = project_functions.events_start_stop(
             self.pj[cfg.ETHOGRAM],
@@ -125,7 +122,17 @@ def get_latency(self):
             self.pj[cfg.OBSERVATIONS][obs_id][cfg.TYPE],
         )
 
+        print(f"{events_with_status=}")
+
         for idx, event in enumerate(events_with_status):
+            print(f"{event=}")
+
+            print(f"{event[cfg.EVENT_STATUS_FIELD_IDX]=}")
+
+            print(f"{event[cfg.EVENT_BEHAVIOR_FIELD_IDX]=}")
+
+            print(f"{event[cfg.EVENT_SUBJECT_FIELD_IDX]=}")
+
             if all(
                 (
                     event[cfg.EVENT_STATUS_FIELD_IDX] in (cfg.START, cfg.POINT),
@@ -138,11 +145,13 @@ def get_latency(self):
                     ),
                 )
             ):
-
                 if include_marker_modifiers:
                     marker = event[cfg.EVENT_TIME_FIELD_IDX : cfg.EVENT_MODIFIER_FIELD_IDX + 1]
                 else:
                     marker = event[cfg.EVENT_TIME_FIELD_IDX : cfg.EVENT_BEHAVIOR_FIELD_IDX + 1]
+
+                print(f"{marker=}")
+
                 if marker not in results:
                     results[marker] = {}
 
@@ -164,20 +173,19 @@ def get_latency(self):
                             ),
                         )
                     ):
-
-                        # print(event, event2)
+                        print(event, event2)
                         if include_latency_modifiers:
                             latency = event2[cfg.EVENT_SUBJECT_FIELD_IDX : cfg.EVENT_MODIFIER_FIELD_IDX + 1]
                         else:
                             latency = event2[cfg.EVENT_SUBJECT_FIELD_IDX : cfg.EVENT_BEHAVIOR_FIELD_IDX + 1]
 
                         # print(f"{marker=}")
-                        # print(f"{latency=}")
-                        if not latency in results[marker]:
+                        print(f"{latency=}")
+                        if latency not in results[marker]:
                             results[marker][latency] = []
-                        results[marker][latency].append(
-                            event2[cfg.EVENT_TIME_FIELD_IDX] - event[cfg.EVENT_TIME_FIELD_IDX]
-                        )
+                        results[marker][latency].append(event2[cfg.EVENT_TIME_FIELD_IDX] - event[cfg.EVENT_TIME_FIELD_IDX])
+
+                        print(f"{results[marker][latency]=}")
 
                     # check if new marker
                     if all(
@@ -208,7 +216,6 @@ def get_latency(self):
     out = ""
 
     for marker in sorted(results.keys()):
-
         subject = cfg.NO_FOCAL_SUBJECT if marker[cfg.EVENT_SUBJECT_FIELD_IDX] == "" else marker[1]
         if include_marker_modifiers:
             out += f"Marker: <b>{marker[cfg.EVENT_BEHAVIOR_FIELD_IDX]}</b> at {marker[cfg.EVENT_TIME_FIELD_IDX]} s (subject: {subject} - modifiers: {marker[cfg.EVENT_MODIFIER_FIELD_IDX]})<br><br>"
@@ -223,7 +230,7 @@ def get_latency(self):
 
             out += "first occurrence: "
             out += f"{sorted(results[marker][behav])[0]} s<br>"
-            out += f"all occurrences: "
+            out += "all occurrences: "
 
             out += ", ".join([f"{x} s" for x in sorted(results[marker][behav])])
             out += "<br><br>"

boris/measurement_widget.py

@@ -1,8 +1,7 @@
-#!/usr/bin/env python3
 """
 BORIS
 Behavioral Observation Research Interactive Software
-Copyright 2012-2023 Olivier Friard
+Copyright 2012-2025 Olivier Friard
 
 This file is part of BORIS.
 
@@ -23,10 +22,10 @@ This file is part of BORIS.
 
 import logging
 
-from PyQt5.QtCore import pyqtSignal
+from PySide6.QtCore import Signal
 
-# from PyQt5.QtGui import *
-from PyQt5.QtWidgets import (
+# from PySide6.QtGui import *
+from PySide6.QtWidgets import (
     QApplication,
     QWidget,
     QRadioButton,
@@ -40,14 +39,14 @@ from PyQt5.QtWidgets import (
     QFileDialog,
     QMessageBox,
 )
-from boris import dialog
-from boris.config import YES, NO, CANCEL, programName
+from . import dialog
+from . import config as cfg
 
 
 class wgMeasurement(QWidget):
     """ """
 
-    closeSignal, clearSignal = pyqtSignal(), pyqtSignal()
+    closeSignal, clearSignal = Signal(), Signal()
     flagSaved = True
     draw_mem = []
 
@@ -112,7 +111,7 @@ class wgMeasurement(QWidget):
         self.pbSave = QPushButton("Save results", clicked=self.pbSave_clicked)
         hbox3.addWidget(self.pbSave)
 
-        self.pbClose = QPushButton("Close", clicked=self.pbClose_clicked)
+        self.pbClose = QPushButton(cfg.CLOSE, clicked=self.pbClose_clicked)
         hbox3.addWidget(self.pbClose)
 
         vbox.addLayout(hbox3)
@@ -128,13 +127,13 @@ class wgMeasurement(QWidget):
     def pbClose_clicked(self):
         if not self.flagSaved:
             response = dialog.MessageDialog(
-                programName,
+                cfg.programName,
                 "The current results are not saved. Do you want to save results before closing?",
-                [YES, NO, CANCEL],
+                [cfg.YES, cfg.NO, cfg.CANCEL],
             )
-            if response == YES:
+            if response == cfg.YES:
                 self.pbSave_clicked()
-            if response == CANCEL:
+            if response == cfg.CANCEL:
                 return
         self.closeSignal.emit()
 
@@ -143,19 +142,16 @@ class wgMeasurement(QWidget):
         save results
         """
         if self.pte.toPlainText():
-            fileName, _ = QFileDialog().getSaveFileName(
-                self, "Save measurement results", "", "Text files (*.txt);;All files (*)"
-            )
+            fileName, _ = QFileDialog().getSaveFileName(self, "Save measurement results", "", "Text files (*.txt);;All files (*)")
             if fileName:
                 with open(fileName, "w") as f:
                     f.write(self.pte.toPlainText())
                 self.flagSaved = True
         else:
-            QMessageBox.information(self, programName, "There are no results to save")
+            QMessageBox.information(self, cfg.programName, "There are no results to save")
 
 
 if __name__ == "__main__":
-
     import sys
 
     app = QApplication(sys.argv)

boris/media_file.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.
 
@@ -20,13 +20,13 @@ This file is part of BORIS.
 
 """
 
-import logging
+from PySide6.QtWidgets import QFileDialog
 
 from . import config as cfg
 from . import utilities as util
 from . import dialog
 from . import project_functions
-from PyQt5.QtWidgets import QFileDialog
+from . import utilities as util
 
 
 def get_info(self) -> None:
@@ -34,22 +34,23 @@ def get_info(self) -> None:
     show info about media file (current media file if an observation is opened)
     """
 
-    def media_analysis_str(ffmpeg_bin, media_full_path):
-
+    def media_analysis_str(ffmpeg_bin: str, media_full_path: str) -> str:
         r = util.accurate_media_analysis(ffmpeg_bin, media_full_path)
 
         if "error" in r:
             ffmpeg_output = f"File path: {media_full_path}<br><br>{r['error']}<br><br>"
         else:
-            ffmpeg_output = f"<br><b>{r['analysis_program'] } analysis</b><br>"
+            ffmpeg_output = f"<br><b>{r['analysis_program']} analysis</b><br>"
 
             ffmpeg_output += (
                 f"File path: <b>{media_full_path}</b><br><br>"
                 f"Duration: {r['duration']} seconds ({util.convertTime(self.timeFormat, r['duration'])})<br>"
-                f"Resolution: {r['resolution']}<br>"
+                f"FPS: {r['fps']}<br>"
+                f"Resolution: {r['resolution']} pixels<br>"
+                f"Format long name: {r.get('format_long_name', cfg.NA)}<br>"
+                f"Creation time: {r.get('creation_time', cfg.NA)}<br>"
                 f"Number of frames: {r['frames_number']}<br>"
                 f"Bitrate: {util.smart_size_format(r['bitrate'])}   <br>"
-                f"FPS: {r['fps']}<br>"
                 f"Has video: {r['has_video']}<br>"
                 f"Has audio: {r['has_audio']}<br>"
                 f"File size: {util.smart_size_format(r.get('file size', cfg.NA))}<br>"
@@ -60,7 +61,6 @@ def get_info(self) -> None:
         return ffmpeg_output
 
     if self.observationId and self.playerType == cfg.MEDIA:
-
         tot_output: str = ""
 
         for i, dw in enumerate(self.dw_player):
@@ -72,6 +72,12 @@ def get_info(self) -> None:
 
             mpv_output = (
                 "<b>MPV information</b><br>"
+                f"Duration: {dw.player.duration} seconds ({util.seconds2time(dw.player.duration)})<br>"
+                # "Position: {} %<br>"
+                f"FPS: {dw.player.container_fps}<br>"
+                # "Rate: {}<br>"
+                f"Resolution: {dw.player.width}x{dw.player.height} pixels<br>"
+                # "Scale: {}<br>"
                 f"Video format: {dw.player.video_format}<br>"
                 # "State: {}<br>"
                 # "Media Resource Location: {}<br>"
@@ -79,12 +85,6 @@ def get_info(self) -> None:
                 # "Track: {}/{}<br>"
                 f"Number of media in media list: {dw.player.playlist_count}<br>"
                 f"Current time position: {dw.player.time_pos}<br>"
-                f"duration: {dw.player.duration}<br>"
-                # "Position: {} %<br>"
-                f"FPS: {dw.player.container_fps}<br>"
-                # "Rate: {}<br>"
-                f"Video size: {dw.player.width}x{dw.player.height}<br>"
-                # "Scale: {}<br>"
                 f"Aspect ratio: {round(dw.player.width / dw.player.height, 3)}<br>"
                 # "is seekable? {}<br>"
                 # "has_vout? {}<br>"
@@ -101,9 +101,7 @@ def get_info(self) -> None:
             tot_output += mpv_output + ffmpeg_output + "<br><hr>"
 
     else:  # no open observation
-
-        fn = QFileDialog().getOpenFileNames(self, "Select a media file", "", "Media files (*)")
-        file_paths = fn[0] if type(fn) is tuple else fn
+        file_paths, _ = QFileDialog().getOpenFileNames(self, "Select a media file", "", "Media files (*)")
         if not file_paths:
             return
 
@@ -112,6 +110,6 @@ def get_info(self) -> None:
             tot_output += media_analysis_str(self.ffmpeg_bin, file_path)
 
     self.results = dialog.Results_dialog()
-    self.results.setWindowTitle(cfg.programName + " - Media file information")
+    self.results.setWindowTitle(f"{cfg.programName} - Media file information")
     self.results.ptText.appendHtml(tot_output)
     self.results.show()

boris/menu_options.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
@@ -19,9 +19,9 @@ Copyright 2012-2023 Olivier Friard
   MA 02110-1301, USA.
 """
 
-
 import logging
 from . import config as cfg
+from PySide6.QtCore import QSize
 
 
 def update_windows_title(self):
@@ -57,6 +57,13 @@ def update_menu(self):
 
     update_windows_title(self)
 
+    self.toolBar.setIconSize(
+        QSize(
+            self.config_param.get(cfg.TOOLBAR_ICON_SIZE, cfg.DEFAULT_TOOLBAR_ICON_SIZE_VALUE),
+            self.config_param.get(cfg.TOOLBAR_ICON_SIZE, cfg.DEFAULT_TOOLBAR_ICON_SIZE_VALUE),
+        )
+    )
+
     # enabled if project loaded
     for action in (
         self.actionEdit_project,
@@ -65,9 +72,9 @@ def update_menu(self):
         self.actionExport_project,
         self.actionCheck_project,
         self.actionClose_project,
-        self.actionSend_project,
         self.actionNew_observation,
         self.actionRemove_path_from_media_files,
+        self.action_create_observations,
         self.action_obs_list,
         self.actionExport_observations_list,
         self.actionExplore_project,
@@ -136,7 +143,10 @@ def update_menu(self):
         self.actionJumpForward,
         self.actionJumpBackward,
         self.actionJumpTo,
+        self.action_change_time_offset_of_players,
+        self.action_deinterlace,
         self.actionZoom_level,
+        self.actionRotate_current_video,
         self.actionDisplay_subtitles,
         self.actionPlay,
         self.actionReset,
@@ -156,12 +166,12 @@ def update_menu(self):
         self.menuImage_overlay_on_video_2,
         self.actionAdd_image_overlay_on_video,
         self.actionRemove_image_overlay,
+        self.actionAdd_frame_indexes,
     ):
-
         action.setEnabled(self.playerType == cfg.MEDIA)
 
     # geometric measurements
-    self.action_geometric_measurements.setEnabled(observation_is_active and self.geometric_measurements_mode == False)
+    self.action_geometric_measurements.setEnabled(observation_is_active and self.geometric_measurements_mode is False)
     self.actionCoding_pad.setEnabled(observation_is_active)
     self.actionSubjects_pad.setEnabled(observation_is_active)
     self.actionBehaviors_coding_map.setEnabled(observation_is_active)
@@ -187,6 +197,7 @@ def update_menu(self):
         self.action_behavior_binary_table,
         self.action_advanced_event_filtering,
         self.action_latency,
+        self.action_cooccurence,
         self.menuPlot_events,
         self.menuInter_rater_reliability,
         self.menuSimilarities,
@@ -196,7 +207,7 @@ def update_menu(self):
         w.setEnabled(project_contains_obs)
 
     # statusbar labels
-    for w in [self.lbTimeOffset, self.lbSpeed, self.lb_obs_time_interval]:
+    for w in (self.lbTimeOffset, self.lb_obs_time_interval):
         w.setVisible(self.playerType == cfg.MEDIA)
 
     logging.debug("function: menu_options finished")