boris-behav-obs 8.27.10__py2.py3-none-any.whl → 9.0.2__py2.py3-none-any.whl

boris/qrc_boris.py

@@ -2,11 +2,11 @@
 
 # Resource object code
 #
-# Created by: The Resource Compiler for PyQt5 (Qt v5.13.0)
+# Created by: The Resource Compiler for PySide6 (Qt v5.13.0)
 #
 # WARNING! All changes made in this file will be lost!
 
-from PyQt5 import QtCore
+from PySide6 import QtCore
 
 qt_resource_data = b"\
 \x00\x00\x04\xba\
@@ -10369,7 +10369,7 @@ qt_resource_struct_v2 = b"\
 \x00\x00\x01\x70\xe3\xd1\xd7\xb0\
 "
 
-qt_version = [int(v) for v in QtCore.qVersion().split('.')]
+qt_version = [int(v) for v in QtCore.qVersion().split(".")]
 if qt_version < [5, 8, 0]:
     rcc_version = 1
     qt_resource_struct = qt_resource_struct_v1
@@ -10377,10 +10377,13 @@ else:
     rcc_version = 2
     qt_resource_struct = qt_resource_struct_v2
 
+
 def qInitResources():
     QtCore.qRegisterResourceData(rcc_version, qt_resource_struct, qt_resource_name, qt_resource_data)
 
+
 def qCleanupResources():
     QtCore.qUnregisterResourceData(rcc_version, qt_resource_struct, qt_resource_name, qt_resource_data)
 
+
 qInitResources()

boris/qrc_boris5.py

@@ -2,11 +2,11 @@
 
 # Resource object code
 #
-# Created by: The Resource Compiler for PyQt5 (Qt v5.11.2)
+# Created by: The Resource Compiler for PySide6 (Qt v5.11.2)
 #
 # WARNING! All changes made in this file will be lost!
 
-from PyQt5 import QtCore
+from PySide6 import QtCore
 
 qt_resource_data = b"\
 \x00\x00\x04\xa6\
@@ -2559,7 +2559,7 @@ qt_resource_struct_v2 = b"\
 \x00\x00\x01\x68\x32\x38\xb4\xfd\
 "
 
-qt_version = [int(v) for v in QtCore.qVersion().split('.')]
+qt_version = [int(v) for v in QtCore.qVersion().split(".")]
 if qt_version < [5, 8, 0]:
     rcc_version = 1
     qt_resource_struct = qt_resource_struct_v1
@@ -2567,10 +2567,13 @@ else:
     rcc_version = 2
     qt_resource_struct = qt_resource_struct_v2
 
+
 def qInitResources():
     QtCore.qRegisterResourceData(rcc_version, qt_resource_struct, qt_resource_name, qt_resource_data)
 
+
 def qCleanupResources():
     QtCore.qUnregisterResourceData(rcc_version, qt_resource_struct, qt_resource_name, qt_resource_data)
 
+
 qInitResources()

boris/select_modifiers.py

@@ -22,8 +22,8 @@ This file is part of BORIS.
 
 import re
 
-from PyQt5.QtCore import Qt, QEvent
-from PyQt5.QtWidgets import (
+from PySide6.QtCore import Qt, QEvent
+from PySide6.QtWidgets import (
     QDialog,
     QVBoxLayout,
     QLabel,

boris/select_observations.py

@@ -22,8 +22,8 @@ Copyright 2012-2024 Olivier Friard
 """
 
 from typing import Tuple
-from PyQt5.QtCore import Qt
-from PyQt5.QtWidgets import QAbstractItemView
+from PySide6.QtCore import Qt
+from PySide6.QtWidgets import QAbstractItemView
 
 from . import config as cfg
 from . import gui_utilities, observations_list, project_functions

boris/select_subj_behav.py

@@ -24,9 +24,9 @@ import logging
 from decimal import Decimal as dec
 from typing import Optional
 
-from PyQt5.QtCore import Qt
-from PyQt5.QtGui import QFont
-from PyQt5.QtWidgets import QCheckBox, QListWidgetItem, QMessageBox
+from PySide6.QtCore import Qt
+from PySide6.QtGui import QFont
+from PySide6.QtWidgets import QCheckBox, QListWidgetItem, QMessageBox
 
 from . import config as cfg
 from . import gui_utilities, param_panel, project_functions

boris/state_events.py

@@ -25,7 +25,7 @@ Module containing functions for state events
 import time
 from decimal import Decimal as dec
 
-from PyQt5.QtWidgets import QMessageBox, QAbstractItemView
+from PySide6.QtWidgets import QMessageBox, QAbstractItemView
 
 from . import config as cfg
 from . import dialog, project_functions, select_observations

boris/subjects_pad.py

@@ -19,17 +19,17 @@ Copyright 2012-2024 Olivier Friard
   MA 02110-1301, USA.
 """
 
-from PyQt5.QtCore import pyqtSignal, QRect, QEvent, Qt
-from PyQt5.QtWidgets import QGridLayout, QPushButton, QHBoxLayout, QWidget
+from PySide6.QtCore import Signal, QRect, QEvent, Qt
+from PySide6.QtWidgets import QGridLayout, QPushButton, QHBoxLayout, QWidget
 
 from . import config as cfg
 from . import utilities as util
 
 
 class SubjectsPad(QWidget):
-    clickSignal = pyqtSignal(str)
-    sendEventSignal = pyqtSignal(QEvent)
-    close_signal = pyqtSignal(QRect)
+    clickSignal = Signal(str)
+    sendEventSignal = Signal(QEvent)
+    close_signal = Signal(QRect)
 
     def __init__(self, pj, filtered_subjects, parent=None):
         super(SubjectsPad, self).__init__(parent)

boris/synthetic_time_budget.py

@@ -23,8 +23,8 @@ This file is part of BORIS.
 import logging
 import pathlib as pl
 
-from PyQt5.QtWidgets import QFileDialog, QMessageBox
-from PyQt5.QtGui import QFont, QTextOption, QTextCursor
+from PySide6.QtWidgets import QFileDialog, QMessageBox
+from PySide6.QtGui import QFont, QTextOption, QTextCursor
 
 from . import config as cfg
 from . import (

boris/time_budget_functions.py

@@ -671,10 +671,14 @@ def time_budget_analysis(
     categories: dict = {}
     out: list = []
     for subject in parameters[cfg.SELECTED_SUBJECTS]:
+        logging.debug(f"{subject=}")
+
         out_cat: list = []
         categories[subject] = {}
 
         for behavior in parameters[cfg.SELECTED_BEHAVIORS]:
+            logging.debug(f"{behavior=}")
+
             if parameters[cfg.INCLUDE_MODIFIERS]:  # with modifiers
                 if parameters[cfg.EXCLUDE_NON_CODED_MODIFIERS]:
                     # get coded modifiers
@@ -1012,6 +1016,15 @@ def time_budget_analysis(
                         continue
 
                     if len(rows) % 2:  # unpaired events
+                        """
+                        print()
+                        print(f"{subject=}")
+                        print(f"{behavior=}")
+                        print()
+                        for row in rows:
+                            print(f"{row['observation']=}  {row['occurence']=}")
+                        print()
+                        """
                         out_cat.append(
                             {
                                 "subject": subject,
@@ -1108,6 +1121,8 @@ def time_budget_analysis(
                         "-",
                         cfg.NA,
                     ):
+                        # print(f"{categories[subject][category]["duration"]=}")
+                        # print(f"{behav["duration"]=}")
                         categories[subject][category]["duration"] += behav["duration"]
                     else:
                         categories[subject][category]["duration"] = cfg.NA

boris/time_budget_widget.py

@@ -37,8 +37,8 @@ except ModuleNotFoundError:
 
 
 import tablib
-from PyQt5.QtCore import Qt
-from PyQt5.QtWidgets import (
+from PySide6.QtCore import Qt
+from PySide6.QtWidgets import (
     QFileDialog,
     QHBoxLayout,
     QInputDialog,
@@ -631,8 +631,8 @@ def time_budget(self, mode: str, mode2: str = "list"):
         else:
             self.tb.excluded_behaviors_list.setVisible(False)
 
-        self.statusbar.showMessage(f"Time budget generated in {round(time.time() - t0, 3)} s")
-        logging.debug("Time budget generated", 5000)
+        self.statusbar.showMessage(f"Time budget generated in {round(time.time() - t0, 3)} s", 5000)
+        logging.debug("Time budget generated")
 
         if mode == "by_behavior":
             tb_fields = [

boris/transitions.py

@@ -24,8 +24,9 @@ import logging
 import os
 import subprocess
 import tempfile
+from pathlib import Path
 
-from PyQt5.QtWidgets import QFileDialog, QMessageBox
+from PySide6.QtWidgets import QFileDialog, QMessageBox
 
 from . import config as cfg
 from . import dialog, export_observation, select_subj_behav
@@ -170,6 +171,8 @@ def transitions_matrix(self, mode):
     * number
     * frequencies_after_behaviors
     """
+    logging.debug("flag transitions_matrix function")
+
     # ask user observations to analyze
     _, selected_observations = select_observations.select_observations2(
         self, cfg.MULTIPLE, windows_title="Select observations for transitions matrix"
@@ -194,20 +197,20 @@ def transitions_matrix(self, mode):
 
     flagMulti = False
     if len(parameters[cfg.SELECTED_SUBJECTS]) == 1:
-        fn = QFileDialog().getSaveFileName(
+        file_name, _ = QFileDialog().getSaveFileName(
             None,
             "Create matrix of transitions " + mode,
             "",
             "Transitions matrix files (*.txt *.tsv);;All files (*)",
         )
-        fileName = fn[0] if type(fn) is tuple else fn  # PyQt4/5
-
+        if not file_name:
+            return
     else:
-        exportDir = QFileDialog(self).getExistingDirectory(
+        exportDir = QFileDialog.getExistingDirectory(
             self,
             "Choose a directory to save the transitions matrices",
-            os.path.expanduser("~"),
-            options=QFileDialog(self).ShowDirsOnly,
+            str(Path.home()),
+            options=QFileDialog.ShowDirsOnly,
         )
         if not exportDir:
             return
@@ -256,11 +259,11 @@ def transitions_matrix(self, mode):
                 QMessageBox.critical(self, cfg.programName, f"The file {nf} can not be saved")
         else:
             try:
-                with open(fileName, "w") as outfile:
+                with open(file_name, "w") as outfile:
                     outfile.write(observed_matrix)
 
             except Exception:
-                QMessageBox.critical(self, cfg.programName, f"The file {fileName} can not be saved")
+                QMessageBox.critical(self, cfg.programName, f"The file {file_name} can not be saved")
 
 
 def transitions_dot_script():
@@ -268,18 +271,17 @@ def transitions_dot_script():
     create dot script (graphviz language) from transitions frequencies matrix
     """
 
-    fn = QFileDialog().getOpenFileNames(
+    file_names, _ = QFileDialog().getOpenFileNames(
         None,
         "Select one or more transitions matrix files",
         "",
         "Transitions matrix files (*.txt *.tsv);;All files (*)",
     )
-    fileNames = fn[0] if type(fn) is tuple else fn
 
     out = ""
 
-    for fileName in fileNames:
-        with open(fileName, "r") as infile:
+    for file_name in file_names:
+        with open(file_name, "r") as infile:
             result, gv = create_transitions_gv_from_matrix(infile.read(), cutoff_all=0, cutoff_behavior=0, edge_label="percent_node")
             if result:
                 QMessageBox.critical(
@@ -289,16 +291,24 @@ def transitions_dot_script():
                 )
                 return
 
-            with open(fileName + ".gv", "w") as f:
-                f.write(gv)
+            try:
+                with open(file_name + ".gv", "w") as file_out:
+                    file_out.write(gv)
+            except Exception:
+                QMessageBox.critical(
+                    None,
+                    cfg.programName,
+                    ("Error saving the file"),
+                )
+                return
 
-            out += f"<b>{fileName}.gv</b> created<br>"
+            out += f"<b>{file_name}.gv</b> created<br>"
 
     if out:
         QMessageBox.information(
             None,
             cfg.programName,
-            (f"{out}<br><br>The DOT scripts can be used with Graphviz or WebGraphviz " "to generate diagram"),
+            (f"{out}<br><br>The DOT scripts can be used with the Graphviz package or WebGraphviz to generate diagram"),
         )
 
 
@@ -322,17 +332,16 @@ def transitions_flow_diagram():
         )
         return
 
-    fn = QFileDialog().getOpenFileNames(
+    file_names, _ = QFileDialog().getOpenFileNames(
         None,
         "Select one or more transitions matrix files",
         "",
         "Transitions matrix files (*.txt *.tsv);;All files (*)",
     )
-    fileNames = fn[0] if type(fn) is tuple else fn
 
     out = ""
-    for fileName in fileNames:
-        with open(fileName, "r") as infile:
+    for file_name in file_names:
+        with open(file_name, "r") as infile:
             result, gv = create_transitions_gv_from_matrix(infile.read(), cutoff_all=0, cutoff_behavior=0, edge_label="percent_node")
             if result:
                 QMessageBox.critical(
@@ -342,15 +351,15 @@ def transitions_flow_diagram():
                 )
                 return
 
-            with open(tempfile.gettempdir() + os.sep + os.path.basename(fileName) + ".tmp.gv", "w") as f:
+            with open(tempfile.gettempdir() + os.sep + os.path.basename(file_name) + ".tmp.gv", "w") as f:
                 f.write(gv)
             result = subprocess.getoutput(
-                (f'dot -Tpng -o "{fileName}.png" ' f'"{tempfile.gettempdir() + os.sep + os.path.basename(fileName)}.tmp.gv"')
+                (f'dot -Tpng -o "{file_name}.png" ' f'"{tempfile.gettempdir() + os.sep + os.path.basename(file_name)}.tmp.gv"')
             )
             if not result:
-                out += f"<b>{fileName}.png</b> created<br>"
+                out += f"<b>{file_name}.png</b> created<br>"
             else:
-                out += f"Problem with <b>{fileName}</b><br>"
+                out += f"Problem with <b>{file_name}</b><br>"
 
     if out:
         QMessageBox.information(None, cfg.programName, out)

boris/utilities.py

@@ -33,13 +33,19 @@ import subprocess
 import sys
 import urllib.parse
 import wave
+import exifread
+import datetime
 from decimal import Decimal as dec
 from decimal import getcontext, ROUND_DOWN
 from shutil import copyfile
 from typing import Union, Tuple
 
+from hachoir.parser import createParser
+from hachoir.metadata import extractMetadata
+
+
 import numpy as np
-from PyQt5.QtGui import QPixmap, QImage
+from PySide6.QtGui import QPixmap, QImage
 
 from PIL.ImageQt import Image
 
@@ -65,6 +71,93 @@ except RuntimeError:  # libmpv found but version too old
 """
 
 
+def extract_exif_DateTimeOriginal(file_path: str) -> int:
+    """
+    extract the EXIF DateTimeOriginal tag
+    return epoch time
+    if the tag is not available return -1
+
+    Args:
+        file_path (str): path of the media file
+
+    Returns:
+        int: timestamp
+
+    """
+    try:
+        with open(file_path, "rb") as f_in:
+            tags = exifread.process_file(f_in, details=False, stop_tag="EXIF DateTimeOriginal")
+            if "EXIF DateTimeOriginal" in tags:
+                date_time_original = (
+                    f"{tags['EXIF DateTimeOriginal'].values[:4]}-"
+                    f"{tags['EXIF DateTimeOriginal'].values[5:7]}-"
+                    f"{tags['EXIF DateTimeOriginal'].values[8:10]} "
+                    f"{tags['EXIF DateTimeOriginal'].values.split(' ')[-1]}"
+                )
+                return int(datetime.datetime.strptime(date_time_original, "%Y-%m-%d %H:%M:%S").timestamp())
+            else:
+                try:
+                    # read from file name (YYYY-MM-DD_HHMMSS)
+                    return int(datetime.datetime.strptime(pl.Path(file_path).stem, "%Y-%m-%d_%H%M%S").timestamp())
+                except Exception:
+                    # read from file name (YYYY-MM-DD_HH:MM:SS)
+                    return int(datetime.datetime.strptime(pl.Path(file_path).stem, "%Y-%m-%d_%H:%M:%S").timestamp())
+
+    except Exception:
+        return -1
+
+
+def extract_video_creation_date(file_path: str) -> int | None:
+    """
+    returns the timestamp of the media creation date time with Hachoir
+    """
+
+    logging.debug(f"extract_video_creation_date for {file_path}")
+
+    if not pl.Path(file_path).is_file():
+        logging.debug(f"{file_path} not found")
+        return None
+    try:
+        parser = createParser(file_path)
+        metadata = extractMetadata(parser)
+    except Exception:
+        return None
+
+    if metadata.has("creation_date"):
+        if metadata.get("creation_date") == datetime.datetime(1904, 1, 1, 0, 0):
+            return None
+        return metadata.get("creation_date").timestamp()
+    else:
+        return None
+
+
+def extract_date_time_from_file_name(file_path: str) -> int:
+    """
+    extract YYYY-MM-DD_HHMMSS or YYYY-MM-DD_HH:MM:SS from file name
+    """
+
+    patterns = (r"\d{4}-\d{2}-\d{2}_\d{6}", r"\d{4}-\d{2}-\d{2}_\d{2}:\d{2}:\d{2}")
+    for pattern in patterns:
+        matches = re.findall(pattern, file_path)
+
+        if matches:
+            if pattern == r"\d{4}-\d{2}-\d{2}_\d{6}":
+                logging.debug(
+                    f"extract_date_time_from_file_name timestamp from {file_path}: {int(datetime.datetime.strptime(matches[0], '%Y-%m-%d_%H%M%S').timestamp())}"
+                )
+
+                return int(datetime.datetime.strptime(matches[0], "%Y-%m-%d_%H%M%S").timestamp())
+
+            if pattern == r"\d{4}-\d{2}-\d{2}_\d{2}:\d{2}:\d{2}":
+                logging.debug(
+                    f"extract_date_time_from_file_name timestamp from {file_path}: {int(datetime.datetime.strptime(matches[0], '%Y-%m-%d_%H:%M:%S').timestamp())}"
+                )
+
+                return int(datetime.datetime.strptime(matches[0], "%Y-%m-%d_%H:%M:%S").timestamp())
+
+    return None
+
+
 def mpv_lib_version() -> Tuple[str, str, str]:
     """
     Version of MPV library
@@ -438,7 +531,7 @@ def state_behavior_codes(ethogram: dict) -> list:
         list: list of behavior codes defined as STATE event
 
     """
-    return [ethogram[x][cfg.BEHAVIOR_CODE] for x in ethogram if cfg.STATE in ethogram[x][cfg.TYPE].upper()]
+    return [ethogram[x][cfg.BEHAVIOR_CODE] for x in ethogram if ethogram[x][cfg.TYPE] == cfg.STATE_EVENT]
 
 
 def point_behavior_codes(ethogram: dict) -> list:
@@ -1524,7 +1617,7 @@ def has_coding_map(ethogram: dict, behavior_idx: str) -> bool:
         return False
     if not ethogram[behavior_idx].get("coding map", False):
         return False
-    return False
+    return True
 
 
 def dir_images_number(dir_path_str: str) -> dict:

boris/version.py

@@ -20,5 +20,5 @@ This file is part of BORIS.
 
 """
 
-__version__ = "8.27.10"
-__version_date__ = "2024-10-07"
+__version__ = "9.0.2"
+__version_date__ = "2025-01-15"

boris/video_equalizer.py

@@ -20,8 +20,8 @@ This file is part of BORIS.
 
 """
 
-from PyQt5.QtWidgets import QDialog
-from PyQt5.QtCore import pyqtSignal, QEvent
+from PySide6.QtWidgets import QDialog
+from PySide6.QtCore import Signal, QEvent
 from .video_equalizer_ui import Ui_Equalizer
 
 
@@ -30,8 +30,8 @@ class Video_equalizer(QDialog, Ui_Equalizer):
     management of video equalizer: brightness, saturation, contrast, gamma and hue
     """
 
-    sendEventSignal = pyqtSignal(int, str, int)
-    sendKeyPressSignal = pyqtSignal(QEvent)
+    sendEventSignal = Signal(int, str, int)
+    sendKeyPressSignal = Signal(QEvent)
 
     def __init__(self, equalizer, parent=None):
         super().__init__(parent)