boris-behav-obs 8.16.5__py3-none-any.whl → 9.7.1__py3-none-any.whl

boris/events_cursor.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
@@ -21,14 +21,14 @@ Copyright 2012-2023 Olivier Friard
 
 """
 
-from PyQt5.QtCore import QPoint, Qt
-from PyQt5.QtGui import QPolygon, QPen, QColor, QBrush
-from PyQt5.QtWidgets import QStyledItemDelegate
+from PySide6.QtCore import QPoint, Qt
+from PySide6.QtGui import QPolygon, QPen, QColor, QBrush, QPainter
+from PySide6.QtWidgets import QStyledItemDelegate
 
 
 class StyledItemDelegateTriangle(QStyledItemDelegate):
     """
-    painter for twEvents with current time highlighting
+    painter for tv_events with current time highlighting
     """
 
     def __init__(self, row, parent=None):
@@ -36,18 +36,26 @@ class StyledItemDelegateTriangle(QStyledItemDelegate):
         self.row = row
 
     def paint(self, painter, option, index):
+        """
+        draw a red triangle on ceel corresponfing to current event
+        """
 
         super(StyledItemDelegateTriangle, self).paint(painter, option, index)
 
-        if self.row != -1:
-            if index.row() == self.row:
-                polygonTriangle = QPolygon(3)
-                polygonTriangle.setPoint(0, QPoint(option.rect.x() + 15, option.rect.y()))
-                polygonTriangle.setPoint(1, QPoint(option.rect.x(), option.rect.y() - 5))
-                polygonTriangle.setPoint(2, QPoint(option.rect.x(), option.rect.y() + 5))
-                painter.save()
-                painter.setRenderHint(painter.Antialiasing)
-                painter.setBrush(QBrush(QColor(Qt.red)))
-                painter.setPen(QPen(QColor(Qt.red)))
-                painter.drawPolygon(polygonTriangle)
-                painter.restore()
+        if self.row == -1:
+            return
+        if index.row() == self.row:
+            triangle = QPolygon(
+                [
+                    QPoint(option.rect.x() + 15, option.rect.y()),
+                    QPoint(option.rect.x(), option.rect.y() - 5),
+                    QPoint(option.rect.x(), option.rect.y() + 5),
+                ]
+            )
+
+            painter.save()
+            painter.setRenderHint(QPainter.RenderHint.Antialiasing)
+            painter.setBrush(QBrush(QColor(Qt.red)))
+            painter.setPen(QPen(QColor(Qt.red)))
+            painter.drawPolygon(triangle)
+            painter.restore()

boris/events_snapshots.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
@@ -21,14 +21,13 @@ Copyright 2012-2023 Olivier Friard
 
 """
 
-
 import logging
 import os
 import pathlib as pl
 import subprocess
 from decimal import Decimal as dec
 
-from PyQt5.QtWidgets import QFileDialog, QInputDialog, QMessageBox
+from PySide6.QtWidgets import QApplication, QFileDialog, QInputDialog, QMessageBox
 
 from . import config as cfg
 from . import db_functions, dialog, project_functions, select_observations, select_subj_behav
@@ -80,8 +79,8 @@ def events_snapshots(self):
         selected_observations,
         start_coding=dec("NaN"),
         end_coding=dec("NaN"),
-        flagShowIncludeModifiers=False,
-        flagShowExcludeBehaviorsWoEvents=False,
+        show_include_modifiers=False,
+        show_exclude_non_coded_behaviors=False,
         n_observations=len(selected_observations),
     )
 
@@ -110,11 +109,11 @@ def events_snapshots(self):
         return
 
     # directory for saving frames
-    export_dir = QFileDialog().getExistingDirectory(
+    export_dir = QFileDialog.getExistingDirectory(
         self,
         "Choose a directory to extract events",
         os.path.expanduser("~"),
-        options=QFileDialog(self).ShowDirsOnly,
+        options=QFileDialog.ShowDirsOnly,
     )
     if not export_dir:
         return
@@ -128,9 +127,7 @@ def events_snapshots(self):
     )
 
     for obs_id in selected_observations:
-
         for nplayer in self.pj[cfg.OBSERVATIONS][obs_id][cfg.FILE]:
-
             if not self.pj[cfg.OBSERVATIONS][obs_id][cfg.FILE][nplayer]:
                 continue
             duration1 = []  # in seconds
@@ -138,9 +135,7 @@ def events_snapshots(self):
                 duration1.append(self.pj[cfg.OBSERVATIONS][obs_id][cfg.MEDIA_INFO][cfg.LENGTH][mediaFile])
 
             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 = ?",
                         (obs_id, subject, behavior),
@@ -150,10 +145,7 @@ def events_snapshots(self):
                     behavior_state = project_functions.event_type(behavior, self.pj[cfg.ETHOGRAM])
 
                     for idx, row in enumerate(rows):
-
-                        mediaFileIdx = [
-                            idx1 for idx1, x in enumerate(duration1) if row["occurence"] >= sum(duration1[0:idx1])
-                        ][-1]
+                        mediaFileIdx = [idx1 for idx1, x in enumerate(duration1) if row["occurence"] >= sum(duration1[0:idx1])][-1]
 
                         # check if media has video
                         flag_no_video = False
@@ -165,9 +157,7 @@ def events_snapshots(self):
                             flag_no_video = True
 
                         if flag_no_video:
-                            logging.debug(
-                                f"Media {self.pj[cfg.OBSERVATIONS][obs_id][cfg.FILE][nplayer][mediaFileIdx]} does not have video"
-                            )
+                            logging.debug(f"Media {self.pj[cfg.OBSERVATIONS][obs_id][cfg.FILE][nplayer][mediaFileIdx]} does not have video")
                             flag_no_video = True
                             response = dialog.MessageDialog(
                                 cfg.programName,
@@ -197,9 +187,7 @@ def events_snapshots(self):
                             mediafile_fps = 0
 
                         if not mediafile_fps:
-                            logging.debug(
-                                f"FPS not found for {self.pj[cfg.OBSERVATIONS][obs_id][cfg.FILE][nplayer][mediaFileIdx]}"
-                            )
+                            logging.debug(f"FPS not found for {self.pj[cfg.OBSERVATIONS][obs_id][cfg.FILE][nplayer][mediaFileIdx]}")
                             response = dialog.MessageDialog(
                                 cfg.programName,
                                 (
@@ -213,11 +201,7 @@ def events_snapshots(self):
                             if response == "Abort":
                                 return
 
-                        global_start = (
-                            dec("0.000")
-                            if row["occurence"] < time_interval
-                            else round(row["occurence"] - time_interval, 3)
-                        )
+                        global_start = dec("0.000") if row["occurence"] < time_interval else round(row["occurence"] - time_interval, 3)
                         start = round(
                             row["occurence"]
                             - time_interval
@@ -228,8 +212,7 @@ def events_snapshots(self):
                         if start < time_interval:
                             start = dec("0.000")
 
-                        if cfg.POINT in behavior_state:
-
+                        if behavior_state in cfg.POINT_EVENT_TYPES:
                             media_path = project_functions.full_path(
                                 self.pj[cfg.OBSERVATIONS][obs_id][cfg.FILE][nplayer][mediaFileIdx],
                                 self.projectFileName,
@@ -239,17 +222,14 @@ def events_snapshots(self):
                             if vframes == 0:
                                 vframes = 1
 
-                        if cfg.STATE in behavior_state:
+                        if behavior_state in cfg.STATE_EVENT_TYPES:
                             if idx % 2 == 0:
-
                                 # check if stop is on same media file
                                 if (
                                     mediaFileIdx
-                                    != [
-                                        idx1
-                                        for idx1, x in enumerate(duration1)
-                                        if rows[idx + 1]["occurence"] >= sum(duration1[0:idx1])
-                                    ][-1]
+                                    != [idx1 for idx1, x in enumerate(duration1) if rows[idx + 1]["occurence"] >= sum(duration1[0:idx1])][
+                                        -1
+                                    ]
                                 ):
                                     response = dialog.MessageDialog(
                                         cfg.programName,
@@ -365,8 +345,8 @@ def extract_events(self):
         selected_observations,
         start_coding=dec("NaN"),
         end_coding=dec("NaN"),
-        flagShowIncludeModifiers=False,
-        flagShowExcludeBehaviorsWoEvents=False,
+        show_include_modifiers=False,
+        show_exclude_non_coded_behaviors=False,
     )
     if parameters == {}:
         return
@@ -377,9 +357,7 @@ def extract_events(self):
 
     # Ask for time interval around the event
     while True:
-        text, ok = QInputDialog.getDouble(
-            self, "Time interval around the events", "Time (in seconds):", 0.0, 0.0, 86400, 1
-        )
+        text, ok = QInputDialog.getDouble(self, "Time interval around the events", "Time (in seconds):", 0.0, 0.0, 86400, 1)
         if not ok:
             return
         try:
@@ -395,11 +373,11 @@ def extract_events(self):
     if not ok:
         return
 
-    export_dir = QFileDialog().getExistingDirectory(
+    export_dir = QFileDialog.getExistingDirectory(
         self,
         "Choose a directory to extract events",
         os.path.expanduser("~"),
-        options=QFileDialog(self).ShowDirsOnly,
+        options=QFileDialog.ShowDirsOnly,
     )
     if not export_dir:
         return
@@ -412,19 +390,13 @@ def extract_events(self):
         time_interval=cfg.TIME_FULL_OBS,
     )
 
-    """
-    ffmpeg_extract_command = (
-        '"{ffmpeg_bin}" -i "{input_}" -y -ss {start} -to {stop} {codecs} '
-        ' "{dir_}{sep}{obsId}_{player}_{subject}_{behavior}_{globalStart}'
-        '-{globalStop}{extension}" '
-    )
-    """
+    self.statusBar().showMessage("Extracting sequences from media files")
+    QApplication.processEvents()
+
     ffmpeg_extract_command: str = '"{ffmpeg_bin}" -ss {start} -i "{input_}" -y -t {duration} {codecs} '
     mem_command: str = ""
     for obs_id in selected_observations:
-
         for nplayer in self.pj[cfg.OBSERVATIONS][obs_id][cfg.FILE]:
-
             if not self.pj[cfg.OBSERVATIONS][obs_id][cfg.FILE][nplayer]:
                 continue
 
@@ -433,9 +405,7 @@ def extract_events(self):
                 duration1.append(self.pj[cfg.OBSERVATIONS][obs_id][cfg.MEDIA_INFO][cfg.LENGTH][mediaFile])
 
             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 = ?",
                         (obs_id, subject, behavior),
@@ -443,14 +413,11 @@ def extract_events(self):
                     rows = [{"occurence": util.float2decimal(r["occurence"])} for r in cursor.fetchall()]
 
                     behavior_state = project_functions.event_type(behavior, self.pj[cfg.ETHOGRAM])
-                    if cfg.STATE in behavior_state and len(rows) % 2:  # unpaired events
+                    if behavior_state in cfg.STATE_EVENT_TYPES and len(rows) % 2:  # unpaired events
                         continue
 
                     for idx, row in enumerate(rows):
-
-                        mediaFileIdx = [
-                            idx1 for idx1, x in enumerate(duration1) if row["occurence"] >= sum(duration1[0:idx1])
-                        ][-1]
+                        mediaFileIdx = [idx1 for idx1, x in enumerate(duration1) if row["occurence"] >= sum(duration1[0:idx1])][-1]
 
                         if "VIDEO" in items_to_extract.upper():
                             # check if media has video
@@ -459,7 +426,7 @@ def extract_events(self):
                                 has_video = self.pj[cfg.OBSERVATIONS][obs_id][cfg.MEDIA_INFO][cfg.HAS_VIDEO][
                                     self.pj[cfg.OBSERVATIONS][obs_id][cfg.FILE][nplayer][mediaFileIdx]
                                 ]
-                            except:
+                            except Exception:
                                 has_video = False
                             if not has_video:
                                 if (
@@ -487,10 +454,9 @@ def extract_events(self):
                                 has_audio = self.pj[cfg.OBSERVATIONS][obs_id][cfg.MEDIA_INFO][cfg.HAS_AUDIO][
                                     self.pj[cfg.OBSERVATIONS][obs_id][cfg.FILE][nplayer][mediaFileIdx]
                                 ]
-                            except:
+                            except Exception:
                                 has_audio = False
                             if not has_audio:
-
                                 if (
                                     dialog.MessageDialog(
                                         cfg.programName,
@@ -506,13 +472,8 @@ def extract_events(self):
                             new_extension = ".wav"
                             codecs = "-vn"
 
-                        if cfg.POINT in behavior_state:
-
-                            globalStart = (
-                                dec("0.000")
-                                if row["occurence"] < timeOffset
-                                else round(row["occurence"] - timeOffset, 3)
-                            )
+                        if behavior_state in cfg.POINT_EVENT_TYPES:
+                            globalStart = dec("0.000") if row["occurence"] < timeOffset else round(row["occurence"] - timeOffset, 3)
                             start = round(
                                 row["occurence"]
                                 - (timeOffset if timeOffset else 1)  # if time offset is not set default = 1 s
@@ -533,17 +494,14 @@ def extract_events(self):
                                 3,
                             )
 
-                        if cfg.STATE in behavior_state:
-
+                        if behavior_state in cfg.STATE_EVENT_TYPES:
                             if idx % 2 == 0:
                                 # check if stop is on same media file
                                 if (
                                     mediaFileIdx
-                                    != [
-                                        idx1
-                                        for idx1, x in enumerate(duration1)
-                                        if rows[idx + 1]["occurence"] >= sum(duration1[0:idx1])
-                                    ][-1]
+                                    != [idx1 for idx1, x in enumerate(duration1) if rows[idx + 1]["occurence"] >= sum(duration1[0:idx1])][
+                                        -1
+                                    ]
                                 ):
                                     response = dialog.MessageDialog(
                                         cfg.programName,
@@ -558,11 +516,7 @@ def extract_events(self):
                                     if response == "Abort":
                                         return
 
-                                globalStart = (
-                                    dec("0.000")
-                                    if row["occurence"] < timeOffset
-                                    else round(row["occurence"] - timeOffset, 3)
-                                )
+                                globalStart = dec("0.000") if row["occurence"] < timeOffset else round(row["occurence"] - timeOffset, 3)
                                 start = round(
                                     row["occurence"]
                                     - timeOffset
@@ -629,10 +583,10 @@ def extract_events(self):
                             codecs=codecs,
                         )
 
-                        logging.debug(f"ffmpeg command: {ffmpeg_command} '{new_file_name}'")
+                        logging.debug(f'ffmpeg command: {ffmpeg_command} "{new_file_name}"')
 
                         p = subprocess.Popen(
-                            f"{ffmpeg_command} '{new_file_name}'",
+                            f'{ffmpeg_command} "{new_file_name}"',
                             stdout=subprocess.PIPE,
                             stderr=subprocess.PIPE,
                             shell=True,

boris/exclusion_matrix.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.
 
@@ -21,7 +21,7 @@ This file is part of BORIS.
 """
 
 import logging
-from PyQt5.QtWidgets import (
+from PySide6.QtWidgets import (
     QDialog,
     QVBoxLayout,
     QHBoxLayout,
@@ -42,10 +42,7 @@ class ExclusionMatrix(QDialog):
 
         self.label = QLabel()
         self.label.setText(
-            (
-                "Check if behaviors are mutually exclusive.\n"
-                "The Point events (displayed on blue background) cannot be excluded)"
-            )
+            ("Check if behaviors are mutually exclusive.\nThe Point events (displayed on blue background) cannot be excluded)")
         )
         hbox.addWidget(self.label)
 
@@ -139,8 +136,6 @@ class ExclusionMatrix(QDialog):
                 if c_name != r_name:
                     try:
                         if f"{c_name}|{r_name}" in self.checkboxes:
-                            self.checkboxes[f"{c_name}|{r_name}"].setChecked(
-                                self.checkboxes[f"{r_name}|{c_name}"].isChecked()
-                            )
+                            self.checkboxes[f"{c_name}|{r_name}"].setChecked(self.checkboxes[f"{r_name}|{c_name}"].isChecked())
                     except Exception:
                         logging.warning(f"Error during checking/unchecking for {r_name}/{c_name} in exclusion matrix")