boris-behav-obs 9.7.13__py3-none-any.whl → 9.8__py3-none-any.whl

boris/core_ui.py

@@ -912,7 +912,7 @@ class Ui_MainWindow(object):
         self.actionEdit_selected_events.setText(QCoreApplication.translate("MainWindow", u"Edit selected event(s)", None))
         self.actionShow_spectrogram.setText(QCoreApplication.translate("MainWindow", u"Show the sound spectrogram", None))
         self.actionExport_events_as_Praat_TextGrid.setText(QCoreApplication.translate("MainWindow", u"as Praat TextGrid", None))
-        self.actionExtract_events_from_media_files.setText(QCoreApplication.translate("MainWindow", u"Extract sequences from media files", None))
+        self.actionExtract_events_from_media_files.setText(QCoreApplication.translate("MainWindow", u"Extract clips from media files", None))
         self.action_geometric_measurements.setText(QCoreApplication.translate("MainWindow", u"Geometric measurement", None))
         self.actionFrame_forward.setText(QCoreApplication.translate("MainWindow", u"Frame forward", None))
         self.actionFrame_backward.setText(QCoreApplication.translate("MainWindow", u"frame backward", None))

boris/db_functions.py

@@ -1,7 +1,7 @@
 """
 BORIS
 Behavioral Observation Research Interactive Software
-Copyright 2012-2025 Olivier Friard
+Copyright 2012-2026 Olivier Friard
 
 
   This program is free software; you can redistribute it and/or modify
@@ -21,12 +21,12 @@ Copyright 2012-2025 Olivier Friard
 
 """
 
-import sqlite3
 import logging
+import sqlite3
 from typing import Optional, Tuple
+
 from . import config as cfg
-from . import project_functions
-from . import event_operations
+from . import event_operations, project_functions
 
 
 def load_events_in_db(
@@ -39,6 +39,7 @@ def load_events_in_db(
     """
     populate a memory sqlite database with events from selected_observations,
     selected_subjects and selected_behaviors
+    include modifiers
 
     Args:
         pj (dict): project dictionary
@@ -59,16 +60,6 @@ def load_events_in_db(
         if cfg.STATE in pj[cfg.ETHOGRAM][x][cfg.TYPE].upper() and pj[cfg.ETHOGRAM][x][cfg.BEHAVIOR_CODE] in selected_behaviors
     ]
 
-    # selected behaviors defined as point event
-    """
-    point_behaviors_codes = [
-        pj[cfg.ETHOGRAM][x][cfg.BEHAVIOR_CODE]
-        for x in pj[cfg.ETHOGRAM]
-        if cfg.POINT in pj[cfg.ETHOGRAM][x][cfg.TYPE].upper()
-        and pj[cfg.ETHOGRAM][x][cfg.BEHAVIOR_CODE] in selected_behaviors
-    ]
-    """
-
     db = sqlite3.connect(":memory:", isolation_level=None)
 
     """

boris/dialog.py

@@ -1,7 +1,7 @@
 """
 BORIS
 Behavioral Observation Research Interactive Software
-Copyright 2012-2025 Olivier Friard
+Copyright 2012-2026 Olivier Friard
 
 This file is part of BORIS.
 

boris/edit_event.py

@@ -1,7 +1,7 @@
 """
 BORIS
 Behavioral Observation Research Interactive Software
-Copyright 2012-2025 Olivier Friard
+Copyright 2012-2026 Olivier Friard
 
 This file is part of BORIS.
 

boris/event_operations.py

@@ -1,7 +1,7 @@
 """
 BORIS
 Behavioral Observation Research Interactive Software
-Copyright 2012-2025 Olivier Friard
+Copyright 2012-2026 Olivier Friard
 
 
   This program is free software; you can redistribute it and/or modify

boris/events_cursor.py

@@ -1,7 +1,7 @@
 """
 BORIS
 Behavioral Observation Research Interactive Software
-Copyright 2012-2025 Olivier Friard
+Copyright 2012-2026 Olivier Friard
 
 
   This program is free software; you can redistribute it and/or modify

boris/events_snapshots.py

@@ -1,23 +1,22 @@
 """
 BORIS
 Behavioral Observation Research Interactive Software
-Copyright 2012-2025 Olivier Friard
+Copyright 2012-2026 Olivier Friard
 
+This file is part of BORIS.
 
-  This program is free software; you can redistribute it and/or modify
+  BORIS is free software; you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
-  the Free Software Foundation; either version 2 of the License, or
-  (at your option) any later version.
+  the Free Software Foundation; either version 3 of the License, or
+  any later version.
 
-  This program is distributed in the hope that it will be useful,
+  BORIS is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
 
   You should have received a copy of the GNU General Public License
-  along with this program; if not, write to the Free Software
-  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
-  MA 02110-1301, USA.
+  along with this program; if not see <http://www.gnu.org/licenses/>.
 
 """
 
@@ -34,10 +33,10 @@ from . import db_functions, dialog, project_functions, select_observations, sele
 from . import utilities as util
 
 
-def events_snapshots(self):
+def extract_media_snapshots(self):
     """
     create snapshots corresponding to coded events
-    if observations are from media file and media files have video
+    Observations must be from media file and media files must have video
     """
 
     _, selected_observations = select_observations.select_observations2(
@@ -47,7 +46,7 @@ def events_snapshots(self):
         return
 
     # check if obs are MEDIA
-    live_images_obs_list = []
+    live_images_obs_list: list = []
     for obs_id in selected_observations:
         if self.pj[cfg.OBSERVATIONS][obs_id][cfg.TYPE] in [cfg.LIVE, cfg.IMAGES]:
             live_images_obs_list.append(obs_id)
@@ -79,7 +78,7 @@ def events_snapshots(self):
         selected_observations,
         start_coding=dec("NaN"),
         end_coding=dec("NaN"),
-        show_include_modifiers=False,
+        show_include_modifiers=True,
         show_exclude_non_coded_behaviors=False,
         n_observations=len(selected_observations),
     )
@@ -94,7 +93,15 @@ def events_snapshots(self):
         label_caption="Choose parameters",
         elements_list=[
             ("dsb", "Time interval around the events (in seconds)", 0.0, 86400, 1, 0, 3),
-            ("il", "Bitmap format", (("JPG - small size / low quality", ""), ("PNG - big size / high quality", ""))),
+            (
+                "il",
+                "Bitmap format",
+                (
+                    ("JPG - small size / low quality", ""),
+                    ("PNG - big size / high quality", ""),
+                    #    ("WEBP - small size / high quality", "")
+                ),
+            ),
         ],
         title="Extract frames",
     )
@@ -105,6 +112,8 @@ def events_snapshots(self):
         frame_bitmap_format = "jpg"
     elif "PNG" in ib.elements["Bitmap format"].currentText():
         frame_bitmap_format = "png"
+        # elif "WEBP" in ib.elements["Bitmap format"].currentText():
+        #    frame_bitmap_format = "webp"
     else:
         return
 
@@ -113,7 +122,7 @@ def events_snapshots(self):
         self,
         "Choose a directory to extract events",
         os.path.expanduser("~"),
-        options=QFileDialog.ShowDirsOnly,
+        options=QFileDialog.Option.ShowDirsOnly,
     )
     if not export_dir:
         return
@@ -137,10 +146,13 @@ def events_snapshots(self):
             for subject in parameters[cfg.SELECTED_SUBJECTS]:
                 for behavior in parameters[cfg.SELECTED_BEHAVIORS]:
                     cursor.execute(
-                        "SELECT occurence FROM events WHERE observation = ? AND subject = ? AND code = ?",
+                        "SELECT occurence, modifiers FROM events WHERE observation = ? AND subject = ? AND code = ?",
                         (obs_id, subject, behavior),
                     )
-                    rows = [{"occurence": util.float2decimal(r["occurence"])} for r in cursor.fetchall()]
+
+                    rows = tuple(
+                        {"occurence": util.float2decimal(r["occurence"]), "modifiers": r[cfg.MODIFIERS]} for r in cursor.fetchall()
+                    )
 
                     behavior_state = project_functions.event_type(behavior, self.pj[cfg.ETHOGRAM])
 
@@ -165,11 +177,11 @@ def events_snapshots(self):
                                     "The following media file does not have video.<br>"
                                     f"{self.pj[cfg.OBSERVATIONS][obs_id][cfg.FILE][nplayer][mediaFileIdx]}"
                                 ),
-                                [cfg.OK, "Abort"],
+                                (cfg.OK, cfg.ABORT),
                             )
                             if response == cfg.OK:
                                 continue
-                            if response == "Abort":
+                            if response == cfg.ABORT:
                                 return
 
                         # check FPS
@@ -194,11 +206,11 @@ def events_snapshots(self):
                                     "The FPS was not found for the following media file:<br>"
                                     f"{self.pj[cfg.OBSERVATIONS][obs_id][cfg.FILE][nplayer][mediaFileIdx]}"
                                 ),
-                                [cfg.OK, "Abort"],
+                                (cfg.OK, cfg.ABORT),
                             )
                             if response == cfg.OK:
                                 continue
-                            if response == "Abort":
+                            if response == cfg.ABORT:
                                 return
 
                         global_start = dec("0.000") if row["occurence"] < time_interval else round(row["occurence"] - time_interval, 3)
@@ -238,11 +250,11 @@ def events_snapshots(self):
                                             "At the moment it no possible to extract frames "
                                             "for this type of event.<br>"
                                         ),
-                                        [cfg.OK, "Abort"],
+                                        (cfg.OK, cfg.ABORT),
                                     )
                                     if response == cfg.OK:
                                         continue
-                                    if response == "Abort":
+                                    if response == cfg.ABORT:
                                         return
 
                                 # globalStop = round(rows[idx + 1]["occurence"] + time_interval, 3)
@@ -279,17 +291,23 @@ def events_snapshots(self):
                             else:
                                 continue
 
-                        ffmpeg_command = (
-                            f'"{self.ffmpeg_bin}" '
-                            f"-ss {start:.3f} "
-                            f'-i "{media_path}" '
-                            f"-vframes {vframes} "
-                            f'"{export_dir}{os.sep}'
-                            f"{util.safeFileName(obs_id).replace(' ', '-')}"
-                            f"_PLAYER{nplayer}"
-                            f"_{util.safeFileName(subject).replace(' ', '-')}"
-                            f"_{util.safeFileName(behavior).replace(' ', '-')}"
-                            f'_{global_start:.3f}_%08d.{frame_bitmap_format}"'
+                        ffmpeg_command = "".join(
+                            [
+                                f'"{self.ffmpeg_bin}" ',
+                                f'-i "{media_path}" ',
+                                f"-ss {start:.3f} ",
+                                f"-vframes {vframes} ",
+                                f'"{export_dir}{os.sep}',
+                                f"{util.safeFileName(obs_id).replace(' ', '-')}",
+                                f"_PLAYER{nplayer}",
+                                f"_{util.safeFileName(subject).replace(' ', '-')}",
+                                f"_{util.safeFileName(behavior).replace(' ', '-')}",
+                                f"_{global_start:.3f}_%08d",
+                                f"_{util.safeFileName(row[cfg.MODIFIERS].replace('|', '+')).replace(' ', '-')}"
+                                if parameters[cfg.INCLUDE_MODIFIERS] and row[cfg.MODIFIERS]
+                                else "",
+                                f'.{frame_bitmap_format}"',
+                            ]
                         )
 
                         logging.debug(f"ffmpeg command: {ffmpeg_command}")
@@ -300,10 +318,10 @@ def events_snapshots(self):
     self.statusbar.showMessage(f"Frames extracted in {export_dir}", 0)
 
 
-def extract_events(self):
+def extract_media_clips(self):
     """
-    extract sub-sequences from media files corresponding to coded events with FFmpeg
-    in case of point event, from -n to +n seconds are extracted (n is asked to user)
+    extract with FFmpeg sub-sequences from media files corresponding to coded events
+    In case of point event, from -n to +n seconds are extracted (n is asked to user)
     """
 
     _, selected_observations = select_observations.select_observations2(
@@ -312,14 +330,14 @@ def extract_events(self):
     if not selected_observations:
         return
 
-    # check if obs are MEDIA
-    live_images_obs_list = []
+    # check if obs are from media files
+    live_images_obs_list: list = []
     for obs_id in selected_observations:
-        if self.pj[cfg.OBSERVATIONS][obs_id][cfg.TYPE] in [cfg.LIVE, cfg.IMAGES]:
+        if self.pj[cfg.OBSERVATIONS][obs_id][cfg.TYPE] in (cfg.LIVE, cfg.IMAGES):
             live_images_obs_list.append(obs_id)
 
     if live_images_obs_list:
-        out = "The following observations are live observations or observation from pictures and will be removed from analysis<br><br>"
+        out = "The following observations are live observations or observation from pictures and will be removed<br><br>"
         out += "<br>".join(live_images_obs_list)
         results = dialog.Results_dialog()
         results.setWindowTitle(cfg.programName)
@@ -345,7 +363,7 @@ def extract_events(self):
         selected_observations,
         start_coding=dec("NaN"),
         end_coding=dec("NaN"),
-        show_include_modifiers=False,
+        show_include_modifiers=True,
         show_exclude_non_coded_behaviors=False,
     )
     if parameters == {}:
@@ -377,7 +395,7 @@ def extract_events(self):
         self,
         "Choose a directory to extract events",
         os.path.expanduser("~"),
-        options=QFileDialog.ShowDirsOnly,
+        options=QFileDialog.Option.ShowDirsOnly,
     )
     if not export_dir:
         return
@@ -393,7 +411,7 @@ def extract_events(self):
     self.statusBar().showMessage("Extracting sequences from media files")
     QApplication.processEvents()
 
-    ffmpeg_extract_command: str = '"{ffmpeg_bin}" -ss {start} -i "{input_}" -y -t {duration} {codecs} '
+    ffmpeg_extract_command: str = '"{ffmpeg_bin}"-i "{input_}" -ss {start} -y -t {duration} {codecs} '
     mem_command: str = ""
     for obs_id in selected_observations:
         for nplayer in self.pj[cfg.OBSERVATIONS][obs_id][cfg.FILE]:
@@ -407,11 +425,12 @@ def extract_events(self):
             for subject in parameters[cfg.SELECTED_SUBJECTS]:
                 for behavior in parameters[cfg.SELECTED_BEHAVIORS]:
                     cursor.execute(
-                        "SELECT occurence FROM events WHERE observation = ? AND subject = ? AND code = ?",
+                        "SELECT occurence, modifiers FROM events WHERE observation = ? AND subject = ? AND code = ?",
                         (obs_id, subject, behavior),
                     )
-                    rows = [{"occurence": util.float2decimal(r["occurence"])} for r in cursor.fetchall()]
-
+                    rows = tuple(
+                        {"occurence": util.float2decimal(r["occurence"]), "modifiers": r[cfg.MODIFIERS]} for r in cursor.fetchall()
+                    )
                     behavior_state = project_functions.event_type(behavior, self.pj[cfg.ETHOGRAM])
                     if behavior_state in cfg.STATE_EVENT_TYPES and len(rows) % 2:  # unpaired events
                         continue
@@ -433,7 +452,7 @@ def extract_events(self):
                                     dialog.MessageDialog(
                                         cfg.programName,
                                         f"The media file {self.pj[cfg.OBSERVATIONS][obs_id][cfg.FILE][nplayer][mediaFileIdx]} does not have a video stream",
-                                        ["Continue", "Abort"],
+                                        ("Continue", "Abort"),
                                     )
                                     == "Abort"
                                 ):
@@ -461,9 +480,9 @@ def extract_events(self):
                                     dialog.MessageDialog(
                                         cfg.programName,
                                         f"The media file {self.pj[cfg.OBSERVATIONS][obs_id][cfg.FILE][nplayer][mediaFileIdx]} does not have an audio stream",
-                                        ["Continue", "Abort"],
+                                        ("Continue", cfg.ABORT),
                                     )
-                                    == "Abort"
+                                    == cfg.ABORT
                                 ):
                                     return
                                 else:
@@ -509,11 +528,11 @@ def extract_events(self):
                                             "The event extends on 2 successive video. "
                                             " At the moment it is not possible to extract this type of event.<br>"
                                         ),
-                                        [cfg.OK, "Abort"],
+                                        (cfg.OK, cfg.ABORT),
                                     )
                                     if response == cfg.OK:
                                         continue
-                                    if response == "Abort":
+                                    if response == cfg.ABORT:
                                         return
 
                                 globalStart = dec("0.000") if row["occurence"] < timeOffset else round(row["occurence"] - timeOffset, 3)
@@ -550,22 +569,27 @@ def extract_events(self):
                                 continue
 
                         new_file_name = pl.Path(export_dir) / pl.Path(
-                            (
-                                f"{util.safeFileName(obs_id).replace(' ', '-')}_"
-                                f"PLAYER{nplayer}_"
-                                f"{util.safeFileName(subject).replace(' ', '-')}_"
-                                f"{util.safeFileName(behavior)}_"
-                                f"{globalStart}-{globalStop}"
-                                f"{new_extension}"
+                            "".join(
+                                [
+                                    f"{util.safeFileName(obs_id).replace(' ', '-')}_",
+                                    f"PLAYER{nplayer}_",
+                                    f"{util.safeFileName(subject).replace(' ', '-')}_",
+                                    f"{util.safeFileName(behavior)}_",
+                                    f"{globalStart}-{globalStop}",
+                                    f"_{util.safeFileName(row[cfg.MODIFIERS].replace('|', '+')).replace(' ', '-')}"
+                                    if parameters[cfg.INCLUDE_MODIFIERS] and row[cfg.MODIFIERS]
+                                    else "",
+                                    f"{new_extension}",
+                                ]
                             )
-                        )  # .with_suffix(new_extension)
+                        )
 
                         if new_file_name.is_file():
                             if mem_command not in (cfg.OVERWRITE_ALL, cfg.SKIP_ALL):
                                 mem_command = dialog.MessageDialog(
                                     cfg.programName,
                                     f"The file <b>{new_file_name}</b> already exists.",
-                                    [cfg.OVERWRITE, cfg.OVERWRITE_ALL, cfg.SKIP, cfg.SKIP_ALL, cfg.CANCEL],
+                                    (cfg.OVERWRITE, cfg.OVERWRITE_ALL, cfg.SKIP, cfg.SKIP_ALL, cfg.CANCEL),
                                 )
                             if mem_command == cfg.CANCEL:
                                 return

boris/exclusion_matrix.py

@@ -1,7 +1,7 @@
 """
 BORIS
 Behavioral Observation Research Interactive Software
-Copyright 2012-2025 Olivier Friard
+Copyright 2012-2026 Olivier Friard
 
 This file is part of BORIS.