boris-behav-obs 9.7.12__py3-none-any.whl → 9.8.2__py3-none-any.whl

boris/__init__.py

@@ -2,7 +2,7 @@
 BORIS
 Behavioral Observation Research Interactive Software
 
-Copyright 2012-2025 Olivier Friard
+Copyright 2012-2026 Olivier Friard
 
 This file is part of BORIS.
 

boris/__main__.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/about.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
   it under the terms of the GNU General Public License as published by
@@ -80,7 +80,8 @@ def actionAbout_activated(self):
     programs_versions.extend(["\nGraphViz", gv_result if "graphviz" in gv_result else "not installed", "https://www.graphviz.org/"])
 
     about_dialog: QMessageBox = QMessageBox()
-    about_dialog.setIconPixmap(QPixmap(":/boris_unito"))
+    # about_dialog.setIconPixmap(QPixmap(":/boris_unito"))
+    about_dialog.setIconPixmap(QPixmap(":/dbios_unito"))
 
     about_dialog.setWindowTitle(f"About {cfg.programName}")
     about_dialog.setStandardButtons(QMessageBox.Ok)
@@ -90,7 +91,7 @@ def actionAbout_activated(self):
     about_dialog.setInformativeText(
         (
             f"<b>{cfg.programName}</b> v. {version.__version__} - {version.__version_date__}"
-            "<p>Copyright &copy; 2012-2025 Olivier Friard - Marco Gamba<br>"
+            "<p>Copyright &copy; 2012-2026 Olivier Friard - Marco Gamba<br>"
             "Department of Life Sciences and Systems Biology<br>"
             "University of Torino - Italy<br>"
             "<br>"

boris/add_modifier.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/advanced_event_filtering.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
   it under the terms of the GNU General Public License as published by

boris/analysis_plugins/export_to_feral.py

@@ -0,0 +1,336 @@
+"""
+BORIS plugin
+
+Export observations to FERAL (getferal.ai)
+"""
+
+import json
+from pathlib import Path
+
+import pandas as pd
+from PySide6.QtCore import Qt
+from PySide6.QtWidgets import (
+    QDialog,
+    QFileDialog,
+    QHBoxLayout,
+    QLabel,
+    QListWidget,
+    QListWidgetItem,
+    QPushButton,
+    QVBoxLayout,
+)
+
+__version__ = "0.3.2"
+__version_date__ = "2025-12-19"
+__plugin_name__ = "Export observations to FERAL"
+__author__ = "Jacopo Razzauti - The Rockefeller University; Olivier Friard - University of Torino - Italy"
+
+
+# ---------------------------
+# Dialog: choose behaviors
+# ---------------------------
+class BehaviorSelectDialog(QDialog):
+    """Select which BORIS behavior codes should become FERAL classes.
+
+    Class 0 is reserved for "other". Any behavior not selected is mapped to 0.
+    """
+
+    def __init__(self, behavior_codes, parent=None):
+        super().__init__(parent)
+
+        self.setWindowTitle("Select behaviors to export (0 is 'other')")
+        self.setModal(True)
+
+        main_layout = QVBoxLayout(self)
+
+        info = QLabel("Select behaviors to export.\nClass 0 is reserved for 'other'.\nUnselected behaviors are mapped to 0.")
+        info.setWordWrap(True)
+        main_layout.addWidget(info)
+
+        self.list_behaviors = QListWidget()
+        self.list_behaviors.setSelectionMode(QListWidget.ExtendedSelection)
+
+        for code in sorted(behavior_codes):
+            item = QListWidgetItem(code)
+            item.setSelected(True)  # default: select all
+            self.list_behaviors.addItem(item)
+
+        main_layout.addWidget(self.list_behaviors)
+
+        buttons_layout = QHBoxLayout()
+        btn_all = QPushButton("Select all")
+        btn_none = QPushButton("Select none")
+        btn_ok = QPushButton("OK")
+        btn_cancel = QPushButton("Cancel")
+
+        btn_all.clicked.connect(self._select_all)
+        btn_none.clicked.connect(self._select_none)
+        btn_ok.clicked.connect(self.accept)
+        btn_cancel.clicked.connect(self.reject)
+
+        buttons_layout.addWidget(btn_all)
+        buttons_layout.addWidget(btn_none)
+        buttons_layout.addStretch()
+        buttons_layout.addWidget(btn_ok)
+        buttons_layout.addWidget(btn_cancel)
+
+        main_layout.addLayout(buttons_layout)
+
+    def _select_all(self):
+        for i in range(self.list_behaviors.count()):
+            self.list_behaviors.item(i).setSelected(True)
+
+    def _select_none(self):
+        for i in range(self.list_behaviors.count()):
+            self.list_behaviors.item(i).setSelected(False)
+
+    def selected_codes(self):
+        return [it.text() for it in self.list_behaviors.selectedItems()]
+
+
+# ---------------------------
+# Dialog: split videos
+# ---------------------------
+class CategoryDialog(QDialog):
+    def __init__(self, items, parent=None):
+        super().__init__(parent)
+
+        self.setWindowTitle("Organize the videos in categories")
+        self.setModal(True)
+
+        main_layout = QVBoxLayout(self)
+        lists_layout = QHBoxLayout()
+
+        self.list_unclassified = self._make_list_widget()
+        self.list_train = self._make_list_widget()
+        self.list_val = self._make_list_widget()
+        self.list_test = self._make_list_widget()
+        self.list_inference = self._make_list_widget()
+
+        lists_layout.addLayout(self._make_column("All videos", self.list_unclassified))
+        lists_layout.addLayout(self._make_column("train", self.list_train))
+        lists_layout.addLayout(self._make_column("val", self.list_val))
+        lists_layout.addLayout(self._make_column("test", self.list_test))
+        lists_layout.addLayout(self._make_column("inference", self.list_inference))
+
+        main_layout.addLayout(lists_layout)
+
+        buttons_layout = QHBoxLayout()
+        btn_ok = QPushButton("OK")
+        btn_cancel = QPushButton("Cancel")
+        btn_ok.clicked.connect(self.accept)
+        btn_cancel.clicked.connect(self.reject)
+
+        buttons_layout.addStretch()
+        buttons_layout.addWidget(btn_ok)
+        buttons_layout.addWidget(btn_cancel)
+        main_layout.addLayout(buttons_layout)
+
+        for text in items:
+            QListWidgetItem(text, self.list_unclassified)
+
+    @staticmethod
+    def _make_column(title, widget):
+        col = QVBoxLayout()
+        col.addWidget(QLabel(title))
+        col.addWidget(widget)
+        return col
+
+    @staticmethod
+    def _make_list_widget():
+        lw = QListWidget()
+        lw.setSelectionMode(QListWidget.ExtendedSelection)
+        lw.setDragEnabled(True)
+        lw.setAcceptDrops(True)
+        lw.setDropIndicatorShown(True)
+        lw.setDragDropMode(QListWidget.DragDrop)
+        lw.setDefaultDropAction(Qt.MoveAction)
+        return lw
+
+    @staticmethod
+    def _collect(widget):
+        # "*" is used to mark videos with at least one event
+        return [widget.item(i).text().rstrip("*") for i in range(widget.count())]
+
+    def categories(self):
+        return {
+            "unclassified": self._collect(self.list_unclassified),
+            "train": self._collect(self.list_train),
+            "val": self._collect(self.list_val),
+            "test": self._collect(self.list_test),
+            "inference": self._collect(self.list_inference),
+        }
+
+
+def run(df: pd.DataFrame, project: dict):
+    """Export BORIS observations/events to a FERAL-compatible JSON.
+
+    See https://www.getferal.ai/ > Label Preparation
+    """
+
+    def log(msg):
+        messages.append(str(msg))
+
+    def safe_float(d, key):
+        try:
+            return float(d[key])
+        except Exception:
+            return None
+
+    messages = []
+
+    out = {
+        "is_multilabel": False,
+        "splits": {"train": [], "val": [], "test": [], "inference": []},
+    }
+
+    # ---- Behaviors (FERAL classes) ----
+    behavior_conf = project.get("behaviors_conf", {})
+    boris_codes = [behavior_conf[k].get("code") for k in behavior_conf]
+    boris_codes = [c for c in boris_codes if c]  # drop None/empty
+
+    # Reserve 0 for background. If BORIS has a behavior literally named "other",
+    # treat it as background and do not include as a class.
+    boris_codes_no_other = [c for c in boris_codes if c != "other"]
+
+    dlg = BehaviorSelectDialog(boris_codes_no_other)
+    if not dlg.exec():
+        return "Behavior selection canceled; export aborted."
+
+    selected = sorted(set(dlg.selected_codes()))
+    if not selected:
+        log("No behaviors selected: everything will be mapped to class 0 ('other').")
+
+    class_names = {"0": "other"}
+    for i, code in enumerate(selected, start=1):
+        class_names[str(i)] = code
+
+    out["class_names"] = class_names
+    behavior_to_idx = {code: i for i, code in enumerate(selected, start=1)}
+
+    if selected:
+        log(f"Selected behaviors: {', '.join(selected)}")
+    log(f"Classes: {class_names}")
+
+    # ---- Iterate observations/videos ----
+    labels = {}
+    video_list = []
+
+    # df dataframe cannot have a "Media file" column
+    # has_media_file_col = "Media file" in df.columns
+    has_subject_col = "Subject" in df.columns
+
+    observations = sorted(project.get("observations", {}).keys())
+    if not observations:
+        return "No observations found in project; nothing to export."
+
+    for obs_id in observations:
+        log("---")
+        log(obs_id)
+
+        obs = project["observations"][obs_id]
+        media_files = obs.get("file", {}).get("1", [])
+        if not media_files:
+            log(f"Observation {obs_id} has no video in player 1.")
+            continue
+
+        media_info = obs.get("media_info", {})
+        fps_dict = media_info.get("fps", {})
+        length_dict = media_info.get("length", {})
+        frames_dict = media_info.get("frames", {}) or {}
+
+        for media_path in media_files:
+            video_name = Path(media_path).name
+
+            if video_name in labels:
+                log(f"Duplicate video name '{video_name}' encountered; skipping (obs {obs_id}).")
+                continue
+
+            # df dataframe cannot have a "Media file" column
+            # Filter events for this observation + this media file when possible
+            # if has_media_file_col:
+            #     df_video = df[(df["Observation id"] == obs_id) & (df["Media file"] == media_path)]
+            # else:
+            #     df_video = df[df["Observation id"] == obs_id]
+            #     log("Warning: df has no 'Media file' column; using all events from observation.")
+
+            df_video = df[df["Observation id"] == obs_id]
+
+            # Enforce single-subject labeling when Subject column exists
+            if has_subject_col and not df_video.empty:
+                subjects = df_video["Subject"].dropna().unique().tolist()
+                if len(subjects) > 1:
+                    log(f"More than one subject in {video_name}: {subjects}. Skipping.")
+                    continue
+
+            # Mark videos that contain at least one event with "*"
+            video_list.append(video_name + ("*" if not df_video.empty else ""))
+
+            fps = safe_float(fps_dict, media_path)
+            duration = safe_float(length_dict, media_path)
+            if fps is None:
+                log(f"Missing/invalid FPS for {video_name}. Skipping.")
+                continue
+            if duration is None:
+                log(f"Missing/invalid duration for {video_name}. Skipping.")
+                continue
+
+            if media_path in frames_dict:
+                n_frames = int(frames_dict[media_path])
+                log(f"{video_name}: fps={fps} duration={duration} frames={n_frames} (BORIS)")
+            else:
+                n_frames = int(round(duration * fps))
+                log(f"{video_name}: fps={fps} duration={duration} frames={n_frames} (rounded)")
+
+            if n_frames <= 0:
+                log(f"Non-positive frame count for {video_name}. Skipping.")
+                continue
+
+            frame_dt = 1.0 / fps
+            labels[video_name] = [0] * n_frames  # default: "other"
+
+            # Fill per-frame labels
+            for frame_idx in range(n_frames):
+                t = frame_idx * frame_dt
+                behaviors = df_video[(df_video["Start (s)"] <= t) & (df_video["Stop (s)"] >= t)]["Behavior"].unique().tolist()
+
+                if len(behaviors) > 1:
+                    log(
+                        f"{video_name}: overlapping behaviors at frame {frame_idx} (t={t:.6f}s): "
+                        f"{behaviors}. Removing video (is_multilabel=False)."
+                    )
+                    del labels[video_name]
+                    break
+
+                if not behaviors:
+                    continue
+
+                labels[video_name][frame_idx] = behavior_to_idx.get(behaviors[0], 0)
+
+    out["labels"] = labels
+
+    # ---- Splits dialog ----
+    split_dlg = CategoryDialog(video_list)
+    if not split_dlg.exec():
+        log("Export canceled at split assignment stage.")
+        return "\n".join(messages)
+
+    splits = split_dlg.categories()
+    splits.pop("unclassified", None)
+    out["splits"] = splits
+
+    filename, _ = QFileDialog.getSaveFileName(
+        None,
+        "Choose a file to save",
+        "",
+        "JSON files (*.json);;All files (*.*)",
+    )
+    if not filename:
+        log("No output file selected; nothing written.")
+        return "\n".join(messages)
+
+    with open(filename, "w", encoding="utf-8") as f_out:
+        json.dump(out, f_out, indent=2)
+
+    log(f"Saved: {filename}")
+    return "\n".join(messages)

boris/analysis_plugins/irr_weighted_cohen_kappa.py

@@ -4,9 +4,9 @@ BORIS plugin
 Inter Rater Reliability (IRR) Weighted Cohen's Kappa
 """
 
-import pandas as pd
-from typing import List, Tuple, Dict, Optional
+from typing import Dict, List, Optional, Tuple
 
+import pandas as pd
 from PySide6.QtWidgets import QInputDialog
 
 __version__ = "0.0.3"

boris/behav_coding_map_creator.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/behavior_binary_table.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
   it under the terms of the GNU General Public License as published by

boris/behaviors_coding_map.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/boris_cli.py

@@ -3,7 +3,7 @@ BORIS CLI
 
 Behavioral Observation Research Interactive Software Command Line Interface
 
-Copyright 2012-2025 Olivier Friard
+Copyright 2012-2026 Olivier Friard
 
   This program is free software; you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by

boris/cmd_arguments.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/coding_pad.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
   it under the terms of the GNU General Public License as published by

boris/config.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.
 
@@ -165,6 +165,7 @@ REMOVE = "Remove"
 SAVE = "Save"
 DISCARD = "Discard"
 OK = "OK"
+ABORT = "Abort"
 OVERWRITE = "Overwrite"
 OVERWRITE_ALL = "Overwrite all"
 SKIP = "Skip"
@@ -493,6 +494,13 @@ FRAME_DEFAULT_CACHE_SIZE = 1
 
 EXCLUDED = "excluded"
 
+# codes for Input_dialog class
+CHECKBOX = "cb"
+LINE_EDIT = "le"
+SPINBOX = "sb"
+DOUBLE_SPINBOX = "dsb"
+ITEMS_LIST = "il"
+
 # modifiers
 MODIFIERS = "modifiers"
 SINGLE_SELECTION = 0
@@ -539,10 +547,13 @@ 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_DEFAULT_NFFT = "256"
 SPECTROGRAM_NOVERLAP = "SPECTROGRAM_NOVERLAP"
-SPECTROGRAM_DEFAULT_NOVERLAP = 900
+SPECTROGRAM_DEFAULT_NOVERLAP = 128
 SPECTROGRAM_VMIN = "SPECTROGRAM_VMIN"
+
+SPECTROGRAM_USE_VMIN_VMAX = "SPECTROGRAM_USE_VMIN_VMAX"
+SPECTROGRAM_USE_VMIN_VMAX_DEFAULT = False
 SPECTROGRAM_DEFAULT_VMIN = -100
 SPECTROGRAM_VMAX = "SPECTROGRAM_VMAX"
 SPECTROGRAM_DEFAULT_VMAX = -20
@@ -737,6 +748,7 @@ INIT_PARAM = {
     PROJECT_FILE_INDENTATION: PROJECT_FILE_INDENTATION_DEFAULT_VALUE,
     f"{MEDIA} tw fields": MEDIA_TW_EVENTS_FIELDS_DEFAULT,
     # FRAME_STEP_SIZE: FRAME_STEP_SIZE_DEFAULT_VALUE,
+    TOOLBAR_ICON_SIZE: DEFAULT_TOOLBAR_ICON_SIZE_VALUE,
 }
 
 SDIS_EXT = "sds"

boris/config_file.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.
 
@@ -21,27 +21,27 @@ This file is part of BORIS.
 Read and write the BORIS config file
 """
 
-import pathlib as pl
 import logging
+import pathlib as pl
 import time
 
+from PySide6.QtCore import QByteArray, QSettings
+
 from . import config as cfg
 from . import dialog
 
-from PySide6.QtCore import QByteArray, QSettings
-
 
-def read(self):
+def read(self) -> None:
     """
     read config file
     """
 
-    ini_fil_p_pe_p_path = pl.Path.home() / pl.Path(".boris")
+    ini_file_path = pl.Path.home() / pl.Path(".boris")
 
-    logging.debug(f"read config file: {ini_fil_p_pe_p_path}")
+    logging.debug(f"read config file: {ini_file_path}")
 
-    if ini_fil_p_pe_p_path.is_file():
-        settings = QSettings(str(ini_fil_p_pe_p_path), QSettings.IniFormat)
+    if ini_file_path.is_file():
+        settings = QSettings(str(ini_file_path), QSettings.Format.IniFormat)
 
         try:
             self.config_param = settings.value("config")
@@ -180,7 +180,7 @@ def read(self):
                                 "(An internet connection is required)\n"
                                 "You can change this option in the Preferences (File > Preferences)"
                             ),
-                            [cfg.YES, cfg.NO],
+                            (cfg.YES, cfg.NO),
                         )
                         == cfg.YES
                     )
@@ -244,7 +244,7 @@ def read(self):
                 dialog.MessageDialog(
                     cfg.programName,
                     ("The colors list contain colors that are very light.\nDo you want to reload the default colors list?"),
-                    [cfg.NO, cfg.YES],
+                    (cfg.NO, cfg.YES),
                 )
                 == cfg.YES
             ):
@@ -261,7 +261,7 @@ def read(self):
                 dialog.MessageDialog(
                     cfg.programName,
                     ("The colors list contain colors that are very light.\nDo you want to reload the default colors list?"),
-                    [cfg.NO, cfg.YES],
+                    (cfg.NO, cfg.YES),
                 )
                 == cfg.YES
             ):
@@ -280,7 +280,7 @@ def read(self):
                         "You can change this option in the"
                         " Preferences (File > Preferences)"
                     ),
-                    [cfg.NO, cfg.YES],
+                    (cfg.NO, cfg.YES),
                 )
                 == cfg.YES
             )
@@ -289,18 +289,17 @@ def read(self):
 
     # recent projects
     logging.debug("read recent projects")
+    self.recent_projects: list = []
     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)
+        settings = QSettings(str(recent_projects_file_path), QSettings.Format.IniFormat)
         try:
             self.recent_projects = settings.value("recent_projects").split("|||")
             while "" in self.recent_projects:
                 self.recent_projects.remove("")
             self.set_recent_projects_menu()
         except Exception:
-            self.recent_projects = []
-    else:
-        self.recent_projects = []
+            pass
 
 
 def save(self, lastCheckForNewVersion=0):
@@ -312,7 +311,7 @@ def save(self, lastCheckForNewVersion=0):
 
     logging.debug(f"save config file: {file_path}")
 
-    settings = QSettings(str(file_path), QSettings.IniFormat)
+    settings = QSettings(str(file_path), QSettings.Format.IniFormat)
 
     settings.setValue("config", self.config_param)
 
@@ -352,5 +351,5 @@ def save(self, lastCheckForNewVersion=0):
     # recent projects
     logging.debug("Save recent projects")
 
-    settings = QSettings(str(pl.Path.home() / ".boris_recent_projects"), QSettings.IniFormat)
+    settings = QSettings(str(pl.Path.home() / ".boris_recent_projects"), QSettings.Format.IniFormat)
     settings.setValue("recent_projects", "|||".join(self.recent_projects))