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

boris/config.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.
 
@@ -22,8 +22,23 @@ This file is part of BORIS.
 
 programName: str = "BORIS"
 
+# socket for MPV IPC mode
+MPV_SOCKET = "/tmp/mpvsocket"
+
+
+ETHOGRAM_REPOSITORY_URL = "https://www.boris.unito.it/static/ethograms"
+
 project_format_version: str = "7.0"
 
+SECONDS_PER_DAY: int = 86_400
+
+# cutoff value for displaying HH:MM:SS.zzz or YYYY-mm-DD HH:MM:SS:ZZZ
+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
 IMAGES_OBS_PROJECT_MIN_VERSION: tuple = (8, 6)
 
@@ -37,11 +52,12 @@ MAX_UNDO_QUEUE: int = 25
 
 NA: str = "NA"
 
-REALTIME_PLOT_CURSOR_COLOR = "red"
+REALTIME_PLOT_CURSOR_COLOR: str = "red"
 
-DYNAMIC_TIME_CUTOFF_DEFAULT = 300
+DARKER_DIFFERENCE = 5
 
 CTRL_KEY: str = "Ctrl"
+ALT_KEY: str = "Alt"
 
 SPECTRO_TIMER: int = 500
 
@@ -72,6 +88,7 @@ EVENTS = "events"
 TIME_OFFSET = "time offset"
 
 CODING_MAP = "coding_map"
+CODING_MAP_sp = "coding map"  # space between words (no underscore)
 BEHAVIORS_CODING_MAP = "behaviors_coding_map"
 SUBJECTS = "subjects_conf"
 ETHOGRAM = "behaviors_conf"
@@ -118,17 +135,29 @@ CHAR_FORBIDDEN_IN_MODIFIERS = "(|),`~"
 ADAPT_FAST_JUMP = "adapt_fast_jump"
 ADAPT_FAST_JUMP_DEFAULT = False
 
+TIME = "time"
+BEHAVIOR_CODE = "code"
+SUBJECT = "subject"
+MODIFIER = "modifier"
+COMMENT = "comment"
+BEHAVIOR_KEY = "key"
+SUBJECT_KEY = "key"
+BEHAVIOR_CATEGORY = "category"
+
 
-subjectsFields = ["key", SUBJECT_NAME, DESCRIPTION]
+subjectsFields = [SUBJECT_KEY, SUBJECT_NAME, DESCRIPTION]
 
 UNPAIRED = "UNPAIRED"
 DISPLAY_SUBTITLES = "display_subtitles"
+CHECK_PROJECT_INTEGRITY = "check_project_integrity"
 
 
 YES = "Yes"
 NO = "No"
 CANCEL = "Cancel"
+IGNORE = "Ignore"
 APPEND = "Append"
+CLOSE = "Close"
 REPLACE = "Replace"
 REMOVE = "Remove"
 SAVE = "Save"
@@ -173,13 +202,6 @@ DATA_PLOT_FIELDS = {
 }
 DATA_PLOT_STYLES = ["b-", "r-", "g-", "bo", "ro", "go"]
 
-TIME = "time"
-BEHAVIOR_CODE = "code"
-SUBJECT = "subject"
-MODIFIER = "modifier"
-COMMENT = "comment"
-BEHAVIOR_KEY = "key"
-BEHAVIOR_CATEGORY = "category"
 
 FILE_PATH = "file_path"
 
@@ -188,27 +210,19 @@ IMAGE_PATH = "image path"
 FRAME_INDEX = "frame index"
 
 ZOOM_LEVEL = "zoom level"
+PAN_X = "pan-x"
+PAN_Y = "pan-y"
 ROTATION_ANGLE = "rotation angle"
 DISPLAY_MEDIA_SUBTITLES = "display subtitles"
 OVERLAY = "video overlay"
 
 
 USE_EXIF_DATE = "use_exif_date"
+SUBSTRACT_FIRST_EXIF_DATE = "substract_first_exif_date"
 TIME_LAPSE = "time_lapse_delay"
 
 
 # fields for event configuration
-"""
-fields = {
-    "type": 0,
-    "key": 1,
-    "code": 2,
-    "description": 3,
-    "modifiers": 4,
-    "excluded": 5,
-    "coding map": 6,
-}
-"""
 
 ETHOGRAM_TABLE_COLUMNS: dict = {
     0: "key",
@@ -233,18 +247,6 @@ behavioursFields: dict = {
     "excluded": 7,
     "coding map": 8,
 }
-"""
-ETHOGRAM_FIELDS = [
-    "type",
-    "key",
-    "code",
-    "description",
-    "category",
-    "modifiers",
-    "excluded",
-    "coding map",
-]
-"""
 ETHOGRAM_EDITABLE_FIELDS: tuple = ("key", "code", "description")
 
 PROJECT_BEHAVIORS_KEY_FIELD_IDX = 1
@@ -254,13 +256,20 @@ MEDIA_FILE_PATH_IDX = 2
 HAS_AUDIO_IDX = 6
 
 STATE_EVENT = "State event"
+STATE_EVENT_WITH_CODING_MAP = "State event with coding map"
+
+STATE_EVENT_TYPES = [STATE_EVENT, STATE_EVENT_WITH_CODING_MAP]
+
 POINT_EVENT = "Point event"
+POINT_EVENT_WITH_CODING_MAP = "Point event with coding map"
+
+POINT_EVENT_TYPES = [POINT_EVENT, POINT_EVENT_WITH_CODING_MAP]
 
 BEHAVIOR_TYPES = [
-    "Point event",
-    "State event",
-    "Point event with coding map",
-    "State event with coding map",
+    POINT_EVENT,
+    STATE_EVENT,
+    POINT_EVENT_WITH_CODING_MAP,
+    STATE_EVENT_WITH_CODING_MAP,
 ]
 
 DEFAULT_BEHAVIOR_TYPE = "Point event"
@@ -272,7 +281,7 @@ MEDIA_TW_EVENTS_FIELDS_DEFAULT = ("time", FRAME_INDEX, "subject", "code", "type"
 MEDIA_TW_EVENTS_FIELDS = ("time", FRAME_INDEX, "subject", "code", "type", "modifier", "comment")
 # MEDIA_TW_EVENTS_FIELDS = ("time", "subject", "code", "type", "modifier", "comment")
 LIVE_TW_EVENTS_FIELDS = ("time", "subject", "code", "type", "modifier", "comment")
-IMAGES_TW_EVENTS_FIELDS = ("time", "subject", "code", "type", "modifier", "comment", IMAGE_INDEX, "image path")
+IMAGES_TW_EVENTS_FIELDS = ("time", "subject", "code", "type", "modifier", "comment", IMAGE_INDEX, IMAGE_PATH)
 
 TW_EVENTS_FIELDS = {
     MEDIA: MEDIA_TW_EVENTS_FIELDS,
@@ -294,7 +303,7 @@ for observation_type in TW_EVENTS_FIELDS:
 # fields for project events list
 MEDIA_PJ_EVENTS_FIELDS = (TIME, "subject", "code", "modifier", "comment", FRAME_INDEX)
 LIVE_PJ_EVENTS_FIELDS = (TIME, "subject", "code", "modifier", "comment")
-IMAGES_PJ_EVENTS_FIELDS = (TIME, "subject", "code", "modifier", "comment", "image index", "image path")
+IMAGES_PJ_EVENTS_FIELDS = (TIME, "subject", "code", "modifier", "comment", IMAGE_INDEX, IMAGE_PATH)
 
 PJ_EVENTS_FIELDS = {
     MEDIA: MEDIA_PJ_EVENTS_FIELDS,
@@ -305,9 +314,6 @@ PJ_EVENTS_FIELDS = {
     VIEWER_IMAGES: IMAGES_PJ_EVENTS_FIELDS,
 }
 
-# fields for independent variable definition
-tw_indVarFields = ["label", "description", "type", "default value", "possible values"]
-
 
 PJ_OBS_FIELDS = {}
 for observation_type in PJ_EVENTS_FIELDS:
@@ -315,12 +321,17 @@ for observation_type in PJ_EVENTS_FIELDS:
     for idx, field in enumerate(PJ_EVENTS_FIELDS[observation_type]):
         PJ_OBS_FIELDS[observation_type][field] = idx
 
+
+# fields for independent variable definition
+tw_indVarFields = ["label", "description", "type", "default value", "possible values"]
+
+
 EVENT_TIME_FIELD_IDX = 0
 EVENT_SUBJECT_FIELD_IDX = 1
 EVENT_BEHAVIOR_FIELD_IDX = 2
 EVENT_MODIFIER_FIELD_IDX = 3
 EVENT_COMMENT_FIELD_IDX = 4
-EVENT_STATUS_FIELD_IDX = 5
+EVENT_STATUS_FIELD_IDX = -1
 # EVENT_IMAGEIDX_FIELD_IDX = 6
 # EVENT_IMAGEPATH_FIELD_IDX = 7
 
@@ -345,6 +356,14 @@ START_FROM_CURRENT_EPOCH_TIME = "start_from_current_epoch_time"
 
 SCAN_SAMPLING_TIME = "scan_sampling_time"
 
+POINT_OBJECT = "Point"
+SEGMENT_OBJECT = "Segment"
+ANGLE_OBJECT = "Angle"
+ORIENTED_ANGLE_OBJECT = "Oriented angle"
+POLYGON_OBJECT = "Polygon"
+POLYLINE_OBJECT = "Polyline"
+
+
 NEW = "new"
 LIST = "list"
 EDIT = "edit"
@@ -364,6 +383,7 @@ SELECTED_BEHAVIORS = "selected behaviors"
 SELECTED_SUBJECTS = "selected subjects"
 INCLUDE_MODIFIERS = "include modifiers"
 EXCLUDE_BEHAVIORS = "exclude behaviors"
+EXCLUDE_NON_CODED_MODIFIERS = "exclude_non_coded_modifiers"
 EXCLUDED_BEHAVIORS = "excluded behaviors"
 TIME_INTERVAL = "time"
 START_TIME = "start time"
@@ -381,6 +401,7 @@ TIMESTAMP_idx = 3
 
 TIME_FULL_OBS = "full obs"
 TIME_EVENTS = "limit to events"
+TIME_OBS_INTERVAL = "interval of observation"
 TIME_ARBITRARY_INTERVAL = "time interval"
 
 AVAILABLE_INDEP_VAR_TYPES = [NUMERIC, TEXT, SET_OF_VALUES, TIMESTAMP]
@@ -390,16 +411,27 @@ OBSERVATIONS = "observations"
 
 CLOSE_BEHAVIORS_BETWEEN_VIDEOS = "close_behaviors_between_videos"
 
-MPV_HWDEC_OPTIONS = ("auto", "auto-safe", "no")
-MPV_HWDEC_DEFAULT_VALUE = "auto"
+# MPV hardware decode
 MPV_HWDEC = "mpv_hwdec"
+MPV_HWDEC_NO = "no"
+MPV_HWDEC_AUTO = "auto"
+MPV_HWDEC_AUTOSAFE = "auto-safe"
+MPV_HWDEC_OPTIONS = (MPV_HWDEC_AUTO, MPV_HWDEC_AUTOSAFE, MPV_HWDEC_NO)
+MPV_HWDEC_DEFAULT_VALUE = MPV_HWDEC_AUTO
 
+ANALYSIS_PLUGINS = "analysis_plugins"
+EXCLUDED_PLUGINS = "excluded_plugins"
+PERSONAL_PLUGINS_DIR = "personal_plugins_dir"
 
 PROJECT_FILE_INDENTATION = "project file indentation"
 PROJECT_FILE_INDENTATION_COMBO_OPTIONS = ("None", "Newline", "Tab", "2 spaces", "4 spaces")
 PROJECT_FILE_INDENTATION_OPTIONS = (None, 0, "\t", 2, 4)
 PROJECT_FILE_INDENTATION_DEFAULT_VALUE = None
 
+TOOLBAR_ICON_SIZE = "toolbar icon size"
+DEFAULT_TOOLBAR_ICON_SIZE_VALUE = 24
+
+
 VIDEO_VIEWER = 0
 PICTURE_VIEWER = 1
 
@@ -416,6 +448,7 @@ LENGTH = "length"
 FPS = "fps"
 HAS_AUDIO = "hasAudio"
 HAS_VIDEO = "hasVideo"
+MEDIA_CREATION_TIME = "media_creation_time"
 
 STATE = "STATE"
 POINT = "POINT"
@@ -423,12 +456,15 @@ POINT = "POINT"
 START = "START"
 STOP = "STOP"
 
-PLAYER1, PLAYER2 = "1", "2"
+PLAYER1 = "1"
+PLAYER2 = "2"
 ALL_PLAYERS = [str(x + 1) for x in range(N_PLAYER)]
 
 VISUALIZE_SPECTROGRAM = "visualize_spectrogram"
 VISUALIZE_WAVEFORM = "visualize_waveform"
+MEDIA_CREATION_DATE_AS_OFFSET = "media_creation_date_as_offset"
 
+MEDIA_SCAN_SAMPLING_DURATION = "media_scan_sampling_duration"
 IMAGE_DISPLAY_DURATION = "image_display_duration"
 
 # plot type
@@ -436,6 +472,9 @@ WAVEFORM_PLOT = "waveform"
 SPECTROGRAM_PLOT = "spectrogram"
 EVENTS_PLOT = "plot_events"
 
+PLAYING = "playing"
+PAUSED = "paused"
+STOPPED = "stopped"
 
 POINT_EVENT_ST_DURATION = 0.5
 
@@ -446,6 +485,8 @@ SLIDER_MAXIMUM = 1000
 
 FRAME_DEFAULT_CACHE_SIZE = 1
 
+EXCLUDED = "excluded"
+
 # modifiers
 MODIFIERS = "modifiers"
 SINGLE_SELECTION = 0
@@ -489,6 +530,16 @@ NO_COLOR_CODING_PAD = "#777777"
 SPECTROGRAM_COLOR_MAPS = ["viridis", "inferno", "plasma", "magma", "gray", "YlOrRd"]
 SPECTROGRAM_DEFAULT_COLOR_MAP = "viridis"
 SPECTROGRAM_DEFAULT_TIME_INTERVAL = 10
+SPECTROGRAM_WINDOW_TYPE = "SPECTROGRAM_WINDOW_TYPE"
+SPECTROGRAM_DEFAULT_WINDOW_TYPE = "hanning"
+SPECTROGRAM_NFFT = "SPECTROGRAM_NFFT"
+SPECTROGRAM_DEFAULT_NFFT = "1024"
+SPECTROGRAM_NOVERLAP = "SPECTROGRAM_NOVERLAP"
+SPECTROGRAM_DEFAULT_NOVERLAP = 900
+SPECTROGRAM_VMIN = "SPECTROGRAM_VMIN"
+SPECTROGRAM_DEFAULT_VMIN = -100
+SPECTROGRAM_VMAX = "SPECTROGRAM_VMAX"
+SPECTROGRAM_DEFAULT_VMAX = -20
 
 # see matplotlib.colors.cnames.keys()
 # https://xkcd.com/color/rgb/
@@ -663,6 +714,7 @@ EMPTY_PROJECT = {
     ETHOGRAM: {},
     OBSERVATIONS: {},
     BEHAVIORAL_CATEGORIES: [],
+    BEHAVIORAL_CATEGORIES_CONF: {},
     INDEPENDENT_VARIABLES: {},
     CODING_MAP: {},
     BEHAVIORS_CODING_MAP: [],
@@ -683,10 +735,10 @@ INIT_PARAM = {
 SDIS_EXT = "sds"
 TBS_EXT = "tbs"
 TSV_EXT = "tsv"
-CSV_EXT = "cvs"
+CSV_EXT = "csv"
 RDS_EXT = "rds"
 PANDAS_DF_EXT = "pkl"
-HMTL_EXT = "html"
+HTML_EXT = "html"
 SQL_EXT = "sql"
 ODS_EXT = "ods"
 XLS_EXT = "xls"
@@ -716,7 +768,7 @@ FILE_NAME_SUFFIX = {
     XLSX: XLSX_EXT,
     XLSX_WB: XLSX_EXT,
     XLS: XLS_EXT,
-    HTML: HMTL_EXT,
+    HTML: HTML_EXT,
     PANDAS_DF: PANDAS_DF_EXT,
     RDS: RDS_EXT,
     SQL: SQL_EXT,

boris/config_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.
 
@@ -18,21 +18,17 @@ This file is part of BORIS.
   You should have received a copy of the GNU General Public License
   along with this program; if not see <http://www.gnu.org/licenses/>.
 
-"""
-
-"""
 Read and write the BORIS config file
 """
 
 import pathlib as pl
 import logging
 import time
-import os
 
 from . import config as cfg
 from . import dialog
 
-from PyQt5.QtCore import QByteArray, QSettings
+from PySide6.QtCore import QByteArray, QSettings
 
 
 def read(self):
@@ -40,19 +36,19 @@ def read(self):
     read config file
     """
 
-    iniFilePath = pl.Path.home() / pl.Path(".boris")
+    ini_fil_p_pe_p_path = pl.Path.home() / pl.Path(".boris")
 
-    logging.debug(f"read config file: {iniFilePath}")
+    logging.debug(f"read config file: {ini_fil_p_pe_p_path}")
 
-    if iniFilePath.is_file():
-        settings = QSettings(str(iniFilePath), QSettings.IniFormat)
+    if ini_fil_p_pe_p_path.is_file():
+        settings = QSettings(str(ini_fil_p_pe_p_path), QSettings.IniFormat)
 
         try:
             self.config_param = settings.value("config")
         except Exception:
-            self.config_param = None
-            pass
-        if self.config_param is None:
+            self.config_param = {}
+
+        if self.config_param == {}:
             self.config_param = cfg.INIT_PARAM
 
             # for back compatibility
@@ -76,7 +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:
@@ -172,25 +168,27 @@ def read(self):
 
         # check for new version
         self.checkForNewVersion = False
-        try:
-            if settings.value("check_for_new_version") is None:
-                self.checkForNewVersion = (
-                    dialog.MessageDialog(
-                        cfg.programName,
-                        (
-                            "Allow BORIS to automatically check for new version and news?\n"
-                            "(An internet connection is required)\n"
-                            "You can change this option in the Preferences (File > Preferences)"
-                        ),
-                        [cfg.YES, cfg.NO],
+
+        if not self.no_first_launch_dialog:
+            try:
+                if settings.value("check_for_new_version") is None:
+                    self.checkForNewVersion = (
+                        dialog.MessageDialog(
+                            cfg.programName,
+                            (
+                                "Allow BORIS to automatically check for new version and news?\n"
+                                "(An internet connection is required)\n"
+                                "You can change this option in the Preferences (File > Preferences)"
+                            ),
+                            [cfg.YES, cfg.NO],
+                        )
+                        == cfg.YES
                     )
-                    == cfg.YES
-                )
-            else:
-                self.checkForNewVersion = settings.value("check_for_new_version") == "true"
-        except Exception:
-            self.checkForNewVersion = False
-        logging.debug(f"check_for_new_version: {self.checkForNewVersion}")
+                else:
+                    self.checkForNewVersion = settings.value("check_for_new_version") == "true"
+            except Exception:
+                self.checkForNewVersion = False
+        logging.debug(f"Automatic check for new version: {self.checkForNewVersion}")
 
         # pause before add event
         self.pause_before_addevent = False
@@ -203,11 +201,11 @@ def read(self):
 
         if self.checkForNewVersion:
             if settings.value("last_check_for_new_version") and (
-                int(time.mktime(time.localtime())) - int(settings.value("last_check_for_new_version"))
-                > cfg.CHECK_NEW_VERSION_DELAY
+                int(time.mktime(time.localtime())) - int(settings.value("last_check_for_new_version")) > cfg.CHECK_NEW_VERSION_DELAY
             ):
                 self.actionCheckUpdate_activated(flagMsgOnlyIfNew=True)
-        logging.debug(f"last_check_for_new_version: {settings.value('last_check_for_new_version')}")
+
+        logging.debug(f"last check for new version: {settings.value('last_check_for_new_version')}")
 
         self.ffmpeg_cache_dir = ""
         try:
@@ -245,10 +243,7 @@ def read(self):
             if (
                 dialog.MessageDialog(
                     cfg.programName,
-                    (
-                        "The colors list contain colors that are very light.\n"
-                        "Do you want to reload the default colors list?"
-                    ),
+                    ("The colors list contain colors that are very light.\nDo you want to reload the default colors list?"),
                     [cfg.NO, cfg.YES],
                 )
                 == cfg.YES
@@ -261,18 +256,11 @@ def read(self):
         except Exception:
             self.behav_category_colors = cfg.CATEGORY_COLORS_LIST
 
-        if (
-            "white" in self.behav_category_colors
-            or "azure" in self.behav_category_colors
-            or "snow" in self.behav_category_colors
-        ):
+        if "white" in self.behav_category_colors or "azure" in self.behav_category_colors or "snow" in self.behav_category_colors:
             if (
                 dialog.MessageDialog(
                     cfg.programName,
-                    (
-                        "The colors list contain colors that are very light.\n"
-                        "Do you want to reload the default colors list?"
-                    ),
+                    ("The colors list contain colors that are very light.\nDo you want to reload the default colors list?"),
                     [cfg.NO, cfg.YES],
                 )
                 == cfg.YES
@@ -282,25 +270,28 @@ def read(self):
     else:  # no .boris file found
         logging.info("No config file found")
         # ask user for checking for new version
-        self.checkForNewVersion = (
-            dialog.MessageDialog(
-                cfg.programName,
-                (
-                    "Allow BORIS to automatically check for new version?\n"
-                    "(An internet connection is required)\n"
-                    "You can change this option in the"
-                    " Preferences (File > Preferences)"
-                ),
-                [cfg.NO, cfg.YES],
+        if not self.no_first_launch_dialog:
+            self.checkForNewVersion = (
+                dialog.MessageDialog(
+                    cfg.programName,
+                    (
+                        "Allow BORIS to automatically check for new version?\n"
+                        "(An internet connection is required)\n"
+                        "You can change this option in the"
+                        " Preferences (File > Preferences)"
+                    ),
+                    [cfg.NO, cfg.YES],
+                )
+                == cfg.YES
             )
-            == cfg.YES
-        )
+        else:
+            self.checkForNewVersion = False
 
     # recent projects
-    logging.info("read recent projects")
-    iniFilePath = str(pl.Path.home() / ".boris_recent_projects")
-    if os.path.isfile(iniFilePath):
-        settings = QSettings(iniFilePath, QSettings.IniFormat)
+    logging.debug("read recent projects")
+    recent_projects_file_path = pl.Path.home() / ".boris_recent_projects"
+    if recent_projects_file_path.is_file():
+        settings = QSettings(str(recent_projects_file_path), QSettings.IniFormat)
         try:
             self.recent_projects = settings.value("recent_projects").split("|||")
             while "" in self.recent_projects: