boris-behav-obs 9.3.4__tar.gz → 9.4__tar.gz

{boris_behav_obs-9.3.4/boris_behav_obs.egg-info → boris_behav_obs-9.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boris-behav-obs
-Version: 9.3.4
+Version: 9.4
 Summary: BORIS - Behavioral Observation Research Interactive Software
 Author-email: Olivier Friard <olivier.friard@unito.it>
 License-Expression: GPL-3.0-only

boris_behav_obs-9.4/boris/1.py

@@ -0,0 +1,45 @@
+import time
+from PIL import Image, ImageDraw, ImageFont
+import mpv
+
+player = mpv.MPV()
+
+player.loop = True
+player.play('/home/olivier/gdrive_sync/src/python/generate_video_test/video1.mp4')
+player.wait_until_playing()
+
+font = ImageFont.truetype('DejaVuSans.ttf', 40)
+
+overlay = player.create_image_overlay()
+
+img = Image.new('RGBA', (400, 150),  (255, 255, 255, 0))
+d = ImageDraw.Draw(img)
+d.text((10, 10), 'Hello World', font=font, fill=(0, 255, 255, 128))
+#d.text((10, 60), f't={ts:.3f}', font=font, fill=(255, 0, 255, 255))
+
+pos = 100
+
+overlay.update(img, pos=(2*pos, pos))
+
+
+while not player.core_idle:
+    pass
+
+
+    '''
+    for pos in range(0, 500, 5):
+        ts = player.time_pos
+        if ts is None:
+            break
+
+        img = Image.new('RGBA', (400, 150),  (255, 255, 255, 0))
+        d = ImageDraw.Draw(img)
+        d.text((10, 10), 'Hello World', font=font, fill=(0, 255, 255, 128))
+        d.text((10, 60), f't={ts:.3f}', font=font, fill=(255, 0, 255, 255))
+
+        overlay.update(img, pos=(2*pos, pos))
+        time.sleep(0.05)
+
+
+    overlay.remove()
+    '''

{boris_behav_obs-9.3.4 → boris_behav_obs-9.4}/boris/about.py

@@ -31,7 +31,6 @@ from . import config as cfg
 from . import utilities as util
 
 
-from PySide6.QtCore import qVersion
 from PySide6.QtGui import QPixmap
 from PySide6.QtWidgets import QMessageBox
 
@@ -41,8 +40,6 @@ def actionAbout_activated(self):
     About dialog
     """
 
-    import PySide6
-
     programs_versions: list = ["MPV media player"]
 
     mpv_lib_version, mpv_lib_file_path, mpv_api_version = util.mpv_lib_version()
@@ -108,6 +105,7 @@ def actionAbout_activated(self):
             '<a href="https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12584">DOI:10.1111/2041-210X.12584</a>'
         )
     )
+    """
     n = "\n"
     current_system = platform.uname()
     details = (
@@ -123,8 +121,11 @@ def actionAbout_activated(self):
             f"Memory (RAM)  Total: {memory.get('total_memory', 'Not available'):.2f} Mb  "
             f"Free: {memory.get('free_memory', 'Not available'):.2f} Mb\n\n"
         )
+    """
+
+    details = util.get_systeminfo()
 
-    details += n.join(programs_versions)
+    details += "\n".join(programs_versions)
     """
     memory_in_use = f"{utilities.rss_memory_used(self.pid)} Mb" if utilities.rss_memory_used(self.pid) != -1 else "Not available"
     percent_memory_in_use = (f"({utilities.rss_memory_percent_used(self.pid):.1f} % of total memory)"

{boris_behav_obs-9.3.4 → boris_behav_obs-9.4}/boris/config.py

@@ -37,6 +37,7 @@ SECONDS_PER_DAY: int = 86_400
 HOUR_CUTOFF: int = 7 * 24
 DATE_CUTOFF: int = HOUR_CUTOFF * 60 * 60  # 1 week
 
+# cutoff for displaying time in HH:MM:SS.zzz format
 SMART_TIME_CUTOFF_DEFAULT: int = 300
 
 # minimal project version for handling observations from images
@@ -218,6 +219,7 @@ OVERLAY = "video overlay"
 
 
 USE_EXIF_DATE = "use_exif_date"
+SUBSTRACT_FIRST_EXIF_DATE = "substract_first_exif_date"
 TIME_LAPSE = "time_lapse_delay"
 
 

{boris_behav_obs-9.3.4 → boris_behav_obs-9.4}/boris/config_file.py

@@ -72,7 +72,7 @@ def read(self):
         if not isinstance(self.saved_state, QByteArray):
             self.saved_state = None
 
-        logging.debug(f"saved state: {self.saved_state}")
+        # logging.debug(f"saved state: {self.saved_state}")
 
         self.timeFormat = cfg.HHMMSS
         try:

{boris_behav_obs-9.3.4 → boris_behav_obs-9.4}/boris/converters.py

@@ -22,8 +22,6 @@ This file is part of BORIS.
 
 import sys
 import json
-import urllib.error
-import urllib.parse
 import urllib.request
 
 
@@ -314,7 +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)

{boris_behav_obs-9.3.4 → boris_behav_obs-9.4}/boris/core.py

@@ -19,34 +19,31 @@ This file is part of BORIS.
   along with this program; if not see <http://www.gnu.org/licenses/>.
 
 """
+# ruff: noqa: E402
 
 import os
 import sys
+import pathlib as pl
 
-os.environ["PATH"] = os.path.dirname(__file__) + os.sep + "misc" + os.pathsep + os.environ["PATH"]
+# os.environ["PATH"] = os.path.dirname(__file__) + os.sep + "misc" + os.pathsep + os.environ["PATH"]
 
+os.environ["PATH"] = str(pl.Path(__file__).parent / "misc") + os.pathsep + os.environ["PATH"]
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), ".")))
 
-
 import datetime
-
 import json
 import logging
-import pathlib as pl
 import platform
 import re
 import PIL.Image
 import PIL.ImageEnhance
+from PIL.ImageQt import Image
 import subprocess
-
 import locale
 import tempfile
 import time
-import urllib.error
-import urllib.parse
 import urllib.request
 from typing import Union, Tuple
-
 from decimal import Decimal as dec
 from decimal import ROUND_DOWN
 import gzip
@@ -57,7 +54,6 @@ import shutil
 
 matplotlib.use("QtAgg")
 
-import PySide6
 from PySide6.QtCore import (
     Qt,
     QPoint,
@@ -66,7 +62,6 @@ from PySide6.QtCore import (
     QDateTime,
     QUrl,
     QAbstractTableModel,
-    qVersion,
     QElapsedTimer,
     QSettings,
 )
@@ -88,7 +83,28 @@ from PySide6.QtWidgets import (
     QStyledItemDelegate,
     QTableWidgetItem,
 )
-from PIL.ImageQt import Image
+
+
+from . import cmd_arguments
+
+# parse command line arguments
+(options, args) = cmd_arguments.parse_arguments()
+
+# set logging parameters
+if options.debug:
+    logging.basicConfig(
+        format="%(asctime)s,%(msecs)d  %(module)s l.%(lineno)d %(levelname)s %(message)s",
+        datefmt="%H:%M:%S",
+        level=logging.DEBUG,
+    )
+else:
+    logging.basicConfig(
+        format="%(asctime)s,%(msecs)d  %(message)s",
+        datefmt="%H:%M:%S",
+        level=logging.INFO,
+    )
+
+from . import utilities as util
 
 from . import dialog
 from . import gui_utilities
@@ -105,21 +121,15 @@ from . import plot_waveform_rt
 from . import plot_events_rt
 from . import plugins
 from . import project_functions
-
 from . import select_observations
 from . import subjects_pad
 from . import version
 from . import event_operations
-from . import cmd_arguments
-
 from . import core_qrc
 from .core_ui import Ui_MainWindow
 from . import config as cfg
 from . import video_operations
-
 from . import project
-from . import utilities as util
-
 from . import menu_options as menu_options
 from . import connections as connections
 from . import config_file
@@ -128,7 +138,7 @@ from . import observation_operations
 from . import write_event
 
 
-# matplotlib.pyplot.switch_backend("Qt5Agg")
+logging.debug("test")
 
 __version__ = version.__version__
 __version_date__ = version.__version_date__
@@ -143,44 +153,13 @@ if util.versiontuple(platform.python_version()) < util.versiontuple(MIN_PYTHON_V
 if sys.platform == "darwin":  # for MacOS
     os.environ["LC_ALL"] = "en_US.UTF-8"
 
-# parse command line arguments
-(options, args) = cmd_arguments.parse_arguments()
-
-# set logging parameters
-if options.debug:
-    logging.basicConfig(
-        format="%(asctime)s,%(msecs)d  %(module)s l.%(lineno)d %(levelname)s %(message)s",
-        datefmt="%H:%M:%S",
-        level=logging.DEBUG,
-    )
-else:
-    logging.basicConfig(
-        format="%(asctime)s,%(msecs)d  %(message)s",
-        datefmt="%H:%M:%S",
-        level=logging.INFO,
-    )
 
 if options.version:
     print(f"version {__version__} release date: {__version_date__}")
     sys.exit(0)
 
-
 logging.debug("BORIS started")
-logging.info(f"BORIS version {__version__} release date: {__version_date__}")
-logging.info(f"Operating system: {platform.uname().system} {platform.uname().release} {platform.uname().version}")
-logging.info(f"CPU: {platform.uname().machine} {platform.uname().processor}")
-logging.info(f"Python {platform.python_version()} ({'64-bit' if sys.maxsize > 2**32 else '32-bit'})")
-logging.info(f"Qt {qVersion()} - PySide {PySide6.__version__}")
-
-
-(r, memory) = util.mem_info()
-if not r:
-    logging.info(
-        (
-            f"Memory (RAM)  Total: {memory.get('total_memory', 'Not available'):.2f} Mb  "
-            f"Free: {memory.get('free_memory', 'Not available'):.2f} Mb"
-        )
-    )
+logging.info(util.get_systeminfo())
 
 
 def excepthook(exception_type, exception_value, traceback_object):
@@ -308,9 +287,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
     play_rate_step: float = 0.1
     currentSubject: str = ""  # contains the current subject of observation
 
-    # FFmpeg
-    memx = -1
-    memy = -1
+    # geometric measurements
     mem_player = -1
 
     # path for ffmpeg/ffmpeg.exe program
@@ -339,6 +316,10 @@ class MainWindow(QMainWindow, Ui_MainWindow):
 
     mem_hash_obs: int = 0
 
+    # variables for list of observations
+    data: list = []
+    not_paired: list = []
+
     '''
     def add_button_menu(self, data, menu_obj):
         """
@@ -1342,21 +1323,6 @@ class MainWindow(QMainWindow, Ui_MainWindow):
             self.pj[cfg.BEHAVIORS_CODING_MAP][idx] = dict(behav_coding_map)
             return
 
-            """
-            QMessageBox.critical(
-                None,
-                cfg.programName,
-                (
-                    "The current project already contains a behaviors coding map "
-                    f"with the same name (<b>{behav_coding_map['name']}</b>)"
-                ),
-                QMessageBox.Ok | QMessageBox.Default,
-                QMessageBox.NoButton,
-            )
-
-            return
-            """
-
         self.pj[cfg.BEHAVIORS_CODING_MAP].append(behav_coding_map)
         QMessageBox.information(
             self,
@@ -1375,7 +1341,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
         try:
             last_version = urllib.request.urlopen(version_URL).read().strip().decode("utf-8")
         except Exception:
-            QMessageBox.warning(self, cfg.programName, "Can not check for updates...")
+            QMessageBox.warning(self, cfg.programName, "Can not check for updates. Check your connection.")
             return
 
         # record check timestamp
@@ -1526,7 +1492,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
         jt.setWindowTitle("Jump to specific time")
         jt.label.setText("Set the time")
 
-        if jt.exec_():
+        if jt.exec():
             new_time = jt.time_widget.get_time()
             if new_time < 0:
                 return
@@ -1704,7 +1670,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
                 QMessageBox.critical(
                     None,
                     cfg.programName,
-                    ("The picture directory was changed since the creation of observation."),
+                    ("The picture directory has changed since the creation of observation."),
                     QMessageBox.Ok | QMessageBox.Default,
                     QMessageBox.NoButton,
                 )
@@ -1718,15 +1684,13 @@ class MainWindow(QMainWindow, Ui_MainWindow):
             # extract EXIF tag
             if self.pj[cfg.OBSERVATIONS][self.observationId].get(cfg.USE_EXIF_DATE, False):
                 date_time_original = util.extract_exif_DateTimeOriginal(self.images_list[self.image_idx])
+
                 if date_time_original != -1:
                     msg += f"<br>EXIF Date/Time Original: <b>{datetime.datetime.fromtimestamp(date_time_original):%Y-%m-%d %H:%M:%S}</b>"
-                else:
-                    msg += "<br>EXIF Date/Time Original: <b>NA</b>"
 
-                if self.image_idx == 0 and date_time_original != -1:
-                    self.image_time_ref = date_time_original
+                    if self.image_idx == 0:
+                        self.image_time_ref = date_time_original
 
-                if date_time_original != -1:
                     if self.image_time_ref is not None:
                         seconds_from_1st = date_time_original - self.image_time_ref
 
@@ -1736,6 +1700,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
                         seconds_from_1st_formated = seconds_from_1st
 
                 else:
+                    msg += "<br>EXIF Date/Time Original: <b>NA</b>"
                     seconds_from_1st_formated = cfg.NA
 
                 msg += f"<br>Time from 1st image: <b>{seconds_from_1st_formated}</b>"
@@ -2311,11 +2276,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
         self.tv_events.setModel(model)
 
         # column width
-        # https://doc.qt.io/qtforpython-5/PySide2/QtWidgets/QHeaderView.html#more
-        self.tv_events.horizontalHeader().setSectionResizeMode(QHeaderView.ResizeToContents)
-
-        # self.table.setSortingEnabled(True)
-        # self.table.sortByColumn(0, Qt.AscendingOrder)
+        self.tv_events.horizontalHeader().setSectionResizeMode(QHeaderView.Interactive)
 
     def load_tw_events(self, obs_id) -> None:
         """
@@ -2343,76 +2304,6 @@ class MainWindow(QMainWindow, Ui_MainWindow):
 
         return
 
-        """
-        DISABLED tableview component is used
-        
-        logging.debug(f"begin load events from obs in tablewidget: {obs_id}")
-
-        t1 = time.time()
-
-        self.twEvents.clear()
-
-        self.twEvents.setColumnCount(len(cfg.TW_EVENTS_FIELDS[self.playerType]))
-        self.twEvents.setHorizontalHeaderLabels([s.capitalize() for s in cfg.TW_EVENTS_FIELDS[self.playerType]])
-
-        for idx, field in enumerate(cfg.TW_EVENTS_FIELDS[self.playerType]):
-            if field not in self.config_param.get(f"{self.playerType} tw fields", cfg.TW_EVENTS_FIELDS[self.playerType]):
-                self.twEvents.horizontalHeader().hideSection(idx)
-            else:
-                self.twEvents.horizontalHeader().showSection(idx)
-
-        self.twEvents.setRowCount(len(self.pj[cfg.OBSERVATIONS][obs_id][cfg.EVENTS]))
-        if self.filtered_behaviors or self.filtered_subjects:
-            self.twEvents.setRowCount(0)
-        row = 0
-
-        for event_idx, event in enumerate(self.pj[cfg.OBSERVATIONS][obs_id][cfg.EVENTS]):
-            if self.filtered_behaviors and event[cfg.PJ_OBS_FIELDS[self.playerType][cfg.BEHAVIOR_CODE]] not in self.filtered_behaviors:
-                continue
-
-            if self.filtered_subjects and event[cfg.PJ_OBS_FIELDS[self.playerType][cfg.SUBJECT]] not in self.filtered_subjects:
-                continue
-
-            if self.filtered_behaviors or self.filtered_subjects:
-                self.twEvents.insertRow(self.twEvents.rowCount())
-
-            for field_type in cfg.TW_EVENTS_FIELDS[self.playerType]:
-                if field_type in cfg.PJ_EVENTS_FIELDS[self.playerType]:
-                    field = event_operations.read_event_field(event, self.playerType, field_type)
-
-                    if field_type == cfg.TIME:
-                        item = QTableWidgetItem(str(util.convertTime(self.timeFormat, field)))
-
-                        # add index of project events
-                        item.setData(Qt.UserRole, event_idx)
-                        self.twEvents.setItem(row, cfg.TW_OBS_FIELD[self.playerType][field_type], item)
-                        continue
-
-                    if field_type in (cfg.IMAGE_INDEX, cfg.FRAME_INDEX):
-                        field = str(field)
-
-                    self.twEvents.setItem(
-                        row,
-                        cfg.TW_OBS_FIELD[self.playerType][field_type],
-                        QTableWidgetItem(field),
-                    )
-
-                else:
-                    self.twEvents.setItem(
-                        row,
-                        cfg.TW_OBS_FIELD[self.playerType][field_type],
-                        QTableWidgetItem(""),
-                    )
-
-            row += 1
-
-        self.update_events_start_stop()
-
-        print("load twevent:", time.time() - t1)
-
-        logging.debug("end load events from obs")
-        """
-
     def close_tool_windows(self):
         """
         close tool windows:
@@ -3493,7 +3384,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
             return
 
         logging.debug(
-            f"{self.config_param[cfg.CHECK_PROJECT_INTEGRITY] if cfg.CHECK_PROJECT_INTEGRITY in self.config_param else "Check project integrity config NOT FOUND"=}"
+            f"{self.config_param[cfg.CHECK_PROJECT_INTEGRITY] if cfg.CHECK_PROJECT_INTEGRITY in self.config_param else 'Check project integrity config NOT FOUND'=}"
         )
 
         if self.config_param.get(cfg.CHECK_PROJECT_INTEGRITY, True):
@@ -4707,7 +4598,10 @@ class MainWindow(QMainWindow, Ui_MainWindow):
                     self.pj[cfg.OBSERVATIONS][self.observationId].get(cfg.USE_EXIF_DATE, False)
                     and util.extract_exif_DateTimeOriginal(self.images_list[self.image_idx]) != -1
                 ):
-                    time_ = util.extract_exif_DateTimeOriginal(self.images_list[self.image_idx]) - self.image_time_ref
+                    time_ = util.extract_exif_DateTimeOriginal(self.images_list[self.image_idx])
+                    # check if first value must be substracted
+                    if self.pj[cfg.OBSERVATIONS][self.observationId].get(cfg.SUBSTRACT_FIRST_EXIF_DATE, True):
+                        time_ -= self.image_time_ref
 
                 elif self.pj[cfg.OBSERVATIONS][self.observationId].get(cfg.TIME_LAPSE, 0):
                     time_ = (self.image_idx + 1) * self.pj[cfg.OBSERVATIONS][self.observationId].get(cfg.TIME_LAPSE, 0)
@@ -4765,7 +4659,10 @@ class MainWindow(QMainWindow, Ui_MainWindow):
                     self.pj[cfg.OBSERVATIONS][self.observationId].get(cfg.USE_EXIF_DATE, False)
                     and util.extract_exif_DateTimeOriginal(self.images_list[self.image_idx]) != -1
                 ):
-                    time_ = util.extract_exif_DateTimeOriginal(self.images_list[self.image_idx]) - self.image_time_ref
+                    time_ = util.extract_exif_DateTimeOriginal(self.images_list[self.image_idx])
+                    # check if first value must be substracte
+                    if self.pj[cfg.OBSERVATIONS][self.observationId].get(cfg.SUBSTRACT_FIRST_EXIF_DATE, True):
+                        time_ -= self.image_time_ref
 
                 elif self.pj[cfg.OBSERVATIONS][self.observationId].get(cfg.TIME_LAPSE, 0):
                     time_ = (self.image_idx + 1) * self.pj[cfg.OBSERVATIONS][self.observationId].get(cfg.TIME_LAPSE, 0)
@@ -5791,21 +5688,54 @@ def main():
 
     locale.setlocale(locale.LC_NUMERIC, "C")
 
-    # splashscreen
-    # no splashscreen for Mac because it can mask the first use dialog box
-
-    if (not options.nosplashscreen) and (sys.platform != "darwin"):
-        start = time.time()
-        splash = QSplashScreen(QPixmap(":/splash"))
-        splash.show()
-        splash.raise_()
-        app.processEvents()
-        while time.time() - start < 1:
-            time.sleep(0.001)
-
     # check FFmpeg
     ret, msg = util.check_ffmpeg_path()
     if not ret:
+        if sys.platform.startswith("win"):
+            QMessageBox.warning(
+                None,
+                cfg.programName,
+                "FFmpeg is not available.<br>It will be downloaded",
+                QMessageBox.Ok | QMessageBox.Default,
+                QMessageBox.NoButton,
+            )
+
+            # download ffmpeg and ffprobe from https://github.com/boris-behav-obs/boris-behav-obs.github.io/releases/download/files/
+            url = "https://github.com/boris-behav-obs/boris-behav-obs.github.io/releases/download/files/"
+
+            # search where to download ffmpeg
+            ffmpeg_dir = pl.Path(__file__).parent / "misc"
+
+            logging.debug(f"{ffmpeg_dir=}")
+
+            if not ffmpeg_dir.is_dir():
+                logging.info(f"Creating {ffmpeg_dir} directory")
+                ffmpeg_dir.mkdir(parents=True, exist_ok=True)
+
+            for file_ in ("ffmpeg.exe", "ffprobe.exe"):
+                local_filename = ffmpeg_dir / file_
+                logging.info(f"Downloading {file_}...")
+                try:
+                    urllib.request.urlretrieve(url + file_, local_filename)
+                except Exception:
+                    logging.critical("The FFmpeg program can not be downloaded! Check your connection.")
+                    QMessageBox.warning(
+                        None,
+                        cfg.programName,
+                        "The FFmpeg program can not be downloaded!\nCheck your connection.",
+                        QMessageBox.Ok | QMessageBox.Default,
+                        QMessageBox.NoButton,
+                    )
+                    sys.exit(3)
+
+                logging.info(f"File downloaded as {local_filename}")
+
+            # re-test for ffmpeg
+            ret, msg = util.check_ffmpeg_path()
+
+    if ret:
+        ffmpeg_bin = msg
+    else:
         QMessageBox.critical(
             None,
             cfg.programName,
@@ -5814,8 +5744,17 @@ def main():
             QMessageBox.NoButton,
         )
         sys.exit(3)
-    else:
-        ffmpeg_bin = msg
+
+    # splashscreen
+    # no splashscreen for Mac because it can mask the first use dialog box
+    if (not options.nosplashscreen) and (sys.platform != "darwin"):
+        start = time.time()
+        splash = QSplashScreen(QPixmap(":/splash"))
+        splash.show()
+        splash.raise_()
+        app.processEvents()
+        while time.time() - start < 1:
+            time.sleep(0.001)
 
     app.setApplicationName(cfg.programName)