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

boris/select_observations.py

@@ -1,28 +1,26 @@
 """
 BORIS
 Behavioral Observation Research Interactive Software
-Copyright 2012-2025 Olivier Friard
+Copyright 2012-2026 Olivier Friard
 
+This file is part of BORIS.
 
-  This program is free software; you can redistribute it and/or modify
+  BORIS is free software; you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
-  the Free Software Foundation; either version 2 of the License, or
-  (at your option) any later version.
+  the Free Software Foundation; either version 3 of the License, or
+  any later version.
 
-  This program is distributed in the hope that it will be useful,
+  BORIS is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
 
   You should have received a copy of the GNU General Public License
-  along with this program; if not, write to the Free Software
-  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
-  MA 02110-1301, USA.
+  along with this program; if not see <http://www.gnu.org/licenses/>.
 
 """
 
 import logging
-from typing import Tuple
 
 from PySide6.QtCore import Qt
 from PySide6.QtWidgets import QAbstractItemView
@@ -32,7 +30,7 @@ from . import gui_utilities, observations_list, project_functions
 from . import utilities as util
 
 
-def select_observations2(self, mode: str, windows_title: str = "") -> Tuple[str, list]:
+def select_observations2(self, mode: str, windows_title: str = "") -> tuple[str, list[str]]:
     """
     allow user to select observations
     mode: accepted values: OPEN, EDIT, SINGLE, MULTIPLE, SELECT1
@@ -149,37 +147,37 @@ def select_observations2(self, mode: str, windows_title: str = "") -> Tuple[str,
     obsList.mode = mode
 
     if mode == cfg.OPEN:
-        obsList.view.setSelectionMode(QAbstractItemView.SingleSelection)
+        obsList.view.setSelectionMode(QAbstractItemView.SelectionMode.SingleSelection)
         obsList.pbOpen.setVisible(True)
 
     if mode == cfg.VIEW:
-        obsList.view.setSelectionMode(QAbstractItemView.SingleSelection)
+        obsList.view.setSelectionMode(QAbstractItemView.SelectionMode.SingleSelection)
         obsList.pbView.setVisible(True)
 
     if mode == cfg.EDIT:
-        obsList.view.setSelectionMode(QAbstractItemView.SingleSelection)
+        obsList.view.setSelectionMode(QAbstractItemView.SelectionMode.SingleSelection)
         obsList.pbEdit.setVisible(True)
 
     if mode == cfg.SINGLE:
-        obsList.view.setSelectionMode(QAbstractItemView.SingleSelection)
+        obsList.view.setSelectionMode(QAbstractItemView.SelectionMode.SingleSelection)
         obsList.pbOpen.setVisible(True)
         obsList.pbView.setVisible(True)
         obsList.pbEdit.setVisible(True)
 
     if mode == cfg.MULTIPLE:
-        obsList.view.setSelectionMode(QAbstractItemView.MultiSelection)
+        obsList.view.setSelectionMode(QAbstractItemView.SelectionMode.MultiSelection)
         obsList.pbOk.setVisible(True)
         obsList.pbSelectAll.setVisible(True)
         obsList.pbUnSelectAll.setVisible(True)
 
     if mode == cfg.SELECT1:
-        obsList.view.setSelectionMode(QAbstractItemView.SingleSelection)
+        obsList.view.setSelectionMode(QAbstractItemView.SelectionMode.SingleSelection)
         obsList.pbOk.setVisible(True)
 
     # restore window geometry
     gui_utilities.restore_geometry(obsList, "observations list", (900, 600))
 
-    obsList.view.sortItems(0, Qt.AscendingOrder)
+    obsList.view.sortItems(0, Qt.SortOrder.AscendingOrder)
     for row in range(obsList.view.rowCount()):
         obsList.view.resizeRowToContents(row)
 
@@ -196,15 +194,16 @@ def select_observations2(self, mode: str, windows_title: str = "") -> Tuple[str,
                 if idx.column() == 0:  # first column
                     selected_observations.append(idx.data())
 
+    result_str: str = ""
     if result == 0:  # cancel
-        resultStr = ""
+        result_str = ""
     if result == 1:  # select
-        resultStr = "ok"
+        result_str = "ok"
     if result == 2:  # open
-        resultStr = cfg.OPEN
+        result_str = cfg.OPEN
     if result == 3:  # edit
-        resultStr = cfg.EDIT
+        result_str = cfg.EDIT
     if result == 4:  # view
-        resultStr = cfg.VIEW
+        result_str = cfg.VIEW
 
-    return resultStr, selected_observations
+    return result_str, selected_observations

boris/select_subj_behav.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.
 
@@ -35,7 +35,7 @@ from . import utilities as util
 
 def choose_obs_subj_behav_category(
     self,
-    selected_observations: list,
+    selected_observations: list[str],
     start_coding: Optional[dec] = dec("NaN"),  #  Union[..., None]
     end_coding: Optional[dec] = dec("NaN"),
     start_interval: Optional[dec] = dec("NaN"),
@@ -246,8 +246,8 @@ def choose_obs_subj_behav_category(
                 None,
                 cfg.programName,
                 "The start time is after the end time",
-                QMessageBox.Ok | QMessageBox.Default,
-                QMessageBox.NoButton,
+                QMessageBox.StandardButton.Ok | QMessageBox.StandardButton.Default,
+                QMessageBox.StandardButton.NoButton,
             )
             return {cfg.SELECTED_SUBJECTS: [], cfg.SELECTED_BEHAVIORS: []}
 

boris/state_events.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/subjects_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/synthetic_time_budget.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/time_budget_functions.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/time_budget_widget.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/transitions.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/utilities.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/version.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.
 
@@ -20,5 +20,5 @@ This file is part of BORIS.
 
 """
 
-__version__ = "9.7.12"
-__version_date__ = "2025-12-05"
+__version__ = "9.8.2a1"
+__version_date__ = "2026-01-26"

boris/video_equalizer.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/video_operations.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/view_df.py

@@ -1,11 +1,35 @@
-from .view_df_ui import Ui_Form
-from PySide6.QtWidgets import QWidget, QFileDialog
-from PySide6.QtCore import Qt, QAbstractTableModel
+"""
+BORIS
+Behavioral Observation Research Interactive Software
+Copyright 2012-2026 Olivier Friard
+
+This file is part of BORIS.
+
+  BORIS is free software; you can redistribute it and/or modify
+  it under the terms of the GNU General Public License as published by
+  the Free Software Foundation; either version 3 of the License, or
+  any later version.
+
+  BORIS is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+
+  You should have received a copy of the GNU General Public License
+  along with this program; if not see <http://www.gnu.org/licenses/>.
+
+"""
 
-from . import config as cfg
 from pathlib import Path
+
+from PySide6.QtCore import QAbstractTableModel, Qt
+from PySide6.QtWidgets import QFileDialog, QWidget
+
+from . import config as cfg
 from . import dialog
+from .view_df_ui import Ui_Form
 
+flag_pyreadr_loaded: bool = False
 try:
     import pyreadr
 

boris/write_event.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_behav_obs-9.7.12.dist-info → boris_behav_obs-9.8.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boris-behav-obs
-Version: 9.7.12
+Version: 9.8.2
 Summary: BORIS - Behavioral Observation Research Interactive Software
 Author-email: Olivier Friard <olivier.friard@unito.it>
 License-Expression: GPL-3.0-only
@@ -51,7 +51,7 @@ It provides also some analysis tools like time budget and some plotting function
 <!-- The BO-RIS paper has more than [![BORIS citations counter](https://penelope.unito.it/friard/boris_scopus_citations.png) citations](https://www.boris.unito.it/citations) in peer-reviewed scientific publications. -->
 
 
-The BORIS paper has more than 2472 citations in peer-reviewed scientific publications.
+The BORIS paper has more than 2491 citations in peer-reviewed scientific publications.
 
 
 

boris_behav_obs-9.8.2.dist-info/RECORD

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+boris/analysis_plugins/irr_cohen_kappa_with_modifiers.py,sha256=DtzFLRToR9GdkmWYDcCmpSvxHGpguVp-_n8F-t7ND7c,4461
+boris/analysis_plugins/irr_weighted_cohen_kappa.py,sha256=RX2jI4hgLU1aBkzIWqY3owZcqpMzX8DpOsrRvaIFARg,6435
+boris/analysis_plugins/irr_weighted_cohen_kappa_with_modifiers.py,sha256=DXrvac4p3_jzakHi_hTW8ZG9rniGo4YCyUH_jJ7fz8c,6744
+boris/analysis_plugins/list_of_dataframe_columns.py,sha256=VEiVhxADtyaIKN4JrfFV02TuTAfWhQ60bf1mHVQp27I,437
+boris/analysis_plugins/number_of_occurences.py,sha256=IDyDrdezqvSKT3BlD8QWpSYk8X9nnBBLI80OUnFJ3bY,509
+boris/analysis_plugins/number_of_occurences_by_independent_variable.py,sha256=_7HTKXsyxNfyO69tP8zkQEHzT0C7qHdL1sqBjnUfRQY,1459
+boris/analysis_plugins/time_budget.py,sha256=bzOS0FUJ7P2kQ9d-TxXq2_OCpo-MngGDFeU5aKsniDQ,2188
+boris/portion/__init__.py,sha256=KmMu4q-iIFO5nrVRIP340mEzxzOlZQqaRupiDmS70es,642
+boris/portion/const.py,sha256=JSYZUktIPCekB6qSom1FPfASn-X7w0G5-aNNHKhIZnw,1715
+boris/portion/dict.py,sha256=uNM-LEY52CZ2VNMMW_C9QukoyTvPlQf8vcbGa1lQBHI,11281
+boris/portion/func.py,sha256=mSQr20YS1ug7R1fRqBg8LifjtXDRvJ6Kjc3WOeL9P34,2172
+boris/portion/interval.py,sha256=sOlj3MAGGaB-JxCkigS-n3qw0fY7TANAsXv1pavr8J4,19931
+boris/portion/io.py,sha256=kpq44pw3xnIyAlPwaR5qRHKRdZ72f8HS9YVIWs5k2pk,6367
+boris_behav_obs-9.8.2.dist-info/licenses/LICENSE.TXT,sha256=WJ7YI-moTFb-uVrFjnzzhGJrnL9P2iqQe8NuED3hutI,35141
+boris_behav_obs-9.8.2.dist-info/METADATA,sha256=q_scBBgdc6GEQy6iNiM7iNBdu9bjwpumjUH1BK127Tk,5203
+boris_behav_obs-9.8.2.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+boris_behav_obs-9.8.2.dist-info/entry_points.txt,sha256=k__8XvFi4vaA4QFvQehCZjYkKmZH34HSAJI2iYCWrMs,52
+boris_behav_obs-9.8.2.dist-info/top_level.txt,sha256=fJSgm62S7WesiwTorGbOO4nNN0yzgZ3klgfGi3Px4qI,6
+boris_behav_obs-9.8.2.dist-info/RECORD,,

{boris_behav_obs-9.7.12.dist-info → boris_behav_obs-9.8.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

boris/analysis_plugins/_export_to_feral.py

@@ -1,225 +0,0 @@
-"""
-BORIS plugin
-
-Export to FERAL (getferal.ai)
-"""
-
-import pandas as pd
-import json
-from pathlib import Path
-
-from PySide6.QtWidgets import QFileDialog
-
-# dependencies for CategoryDialog
-from PySide6.QtWidgets import QListWidget, QListWidgetItem, QLabel, QPushButton, QVBoxLayout, QHBoxLayout, QDialog
-from PySide6.QtCore import Qt
-
-
-__version__ = "0.1.1"
-__version_date__ = "2025-11-28"
-__plugin_name__ = "Export observations to FERAL"
-__author__ = "Olivier Friard - University of Torino - Italy"
-
-
-class CategoryDialog(QDialog):
-    def __init__(self, items, parent=None):
-        super().__init__(parent)
-
-        self.setWindowTitle("Organize the videos in categories")
-
-        self.setModal(True)
-
-        # Main layout
-        main_layout = QVBoxLayout(self)
-        lists_layout = QHBoxLayout()
-
-        # All videos
-        self.list_unclassified = self._create_list_widget()
-        self.label_unclassified = QLabel("All videos")
-        col0_layout = QVBoxLayout()
-        col0_layout.addWidget(self.label_unclassified)
-        col0_layout.addWidget(self.list_unclassified)
-
-        self.list_cat1 = self._create_list_widget()
-        self.label_cat1 = QLabel("train")
-        col1_layout = QVBoxLayout()
-        col1_layout.addWidget(self.label_cat1)
-        col1_layout.addWidget(self.list_cat1)
-
-        self.list_cat2 = self._create_list_widget()
-        self.label_cat2 = QLabel("val")
-        col2_layout = QVBoxLayout()
-        col2_layout.addWidget(self.label_cat2)
-        col2_layout.addWidget(self.list_cat2)
-
-        self.list_cat3 = self._create_list_widget()
-        self.label_cat3 = QLabel("test")
-        col3_layout = QVBoxLayout()
-        col3_layout.addWidget(self.label_cat3)
-        col3_layout.addWidget(self.list_cat3)
-
-        self.list_cat4 = self._create_list_widget()
-        self.label_cat4 = QLabel("inference")
-        col4_layout = QVBoxLayout()
-        col4_layout.addWidget(self.label_cat4)
-        col4_layout.addWidget(self.list_cat4)
-
-        # Add all columns to the horizontal layout
-        lists_layout.addLayout(col0_layout)
-        lists_layout.addLayout(col1_layout)
-        lists_layout.addLayout(col2_layout)
-        lists_layout.addLayout(col3_layout)
-        lists_layout.addLayout(col4_layout)
-
-        main_layout.addLayout(lists_layout)
-
-        buttons_layout = QHBoxLayout()
-        self.btn_ok = QPushButton("OK")
-        self.btn_cancel = QPushButton("Cancel")
-
-        self.btn_ok.clicked.connect(self.accept)
-        self.btn_cancel.clicked.connect(self.reject)
-
-        buttons_layout.addStretch()
-        buttons_layout.addWidget(self.btn_ok)
-        buttons_layout.addWidget(self.btn_cancel)
-
-        main_layout.addLayout(buttons_layout)
-
-        # Populate "Unclassified" with input items
-        for text in items:
-            QListWidgetItem(text, self.list_unclassified)
-
-    def _create_list_widget(self):
-        """
-        Create a QListWidget ready for drag & drop.
-        """
-        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
-
-    def get_categories(self):
-        """
-        Return the content of all categories as a dictionary of lists.
-        """
-
-        def collect(widget):
-            return [widget.item(i).text().rstrip("*") for i in range(widget.count())]
-
-        return {
-            "unclassified": collect(self.list_unclassified),
-            "train": collect(self.list_cat1),
-            "val": collect(self.list_cat2),
-            "test": collect(self.list_cat3),
-            "inference": collect(self.list_cat4),
-        }
-
-
-def run(df: pd.DataFrame, project: dict):
-    """
-    Export observations to FERAL
-    See https://www.getferal.ai/ > Label Preparation
-    """
-
-    out: dict = {
-        "is_multilabel": False,
-        "splits": {
-            "train": [],
-            "val": [],
-            "test": [],
-            "inference": [],
-        },
-    }
-
-    log: list = []
-
-    # class names
-    class_names = {x: project["behaviors_conf"][x]["code"] for x in project["behaviors_conf"]}
-    out["class_names"] = class_names
-    reversed_class_names = {project["behaviors_conf"][x]["code"]: int(x) for x in project["behaviors_conf"]}
-    log.append(f"{class_names=}")
-
-    observations: list = sorted([x for x in project["observations"]])
-    log.append(f"Selected observation: {observations}")
-
-    labels: dict = {}
-    video_list: list = []
-    for observation_id in observations:
-        log.append("---")
-        log.append(observation_id)
-
-        # check number of media file in player #1
-        if len(project["observations"][observation_id]["file"]["1"]) != 1:
-            log.append(f"The observation {observation_id} contains more than one video")
-            continue
-
-        # check number of coded subjects
-        if len(set([x[1] for x in project["observations"][observation_id]["events"]])) > 1:
-            log.append(f"The observation {observation_id} contains more than one subject")
-            continue
-
-        media_file_path: str = project["observations"][observation_id]["file"]["1"][0]
-        media_file_name = str(Path(media_file_path).name)
-
-        # skip if no events
-        if not project["observations"][observation_id]["events"]:
-            video_list.append(media_file_name)
-            log.append(f"No events for observation {observation_id}")
-            continue
-        else:
-            video_list.append(media_file_name + "*")
-
-        # extract FPS
-        FPS = project["observations"][observation_id]["media_info"]["fps"][media_file_path]
-        log.append(f"{media_file_name} {FPS=}")
-        # extract media duration
-        duration = project["observations"][observation_id]["media_info"]["length"][media_file_path]
-        log.append(f"{media_file_name} {duration=}")
-
-        number_of_frames = int(duration / (1 / FPS))
-        log.append(f"{number_of_frames=}")
-
-        labels[media_file_name] = [0] * number_of_frames
-
-        for idx in range(number_of_frames):
-            t = idx * (1 / FPS)
-            behaviors = (
-                df[(df["Observation id"] == observation_id) & (df["Start (s)"] <= t) & (df["Stop (s)"] >= t)]["Behavior"].unique().tolist()
-            )
-            if len(behaviors) > 1:
-                log.append(f"The observation {observation_id} contains more than one behavior for frame {idx}")
-                del labels[media_file_name]
-                break
-            if behaviors:
-                behaviors_idx = reversed_class_names[behaviors[0]]
-                labels[media_file_name][idx] = behaviors_idx
-
-    out["labels"] = labels
-
-    # splits
-    dlg = CategoryDialog(video_list)
-
-    if dlg.exec():  # Dialog accepted
-        result = dlg.get_categories()
-        del result["unclassified"]
-        out["splits"] = result
-
-        filename, _ = QFileDialog.getSaveFileName(
-            None,
-            "Choose a file to save",
-            "",  # start directory
-            "JSON files (*.json);;All files (*.*)",
-        )
-        if filename:
-            with open(filename, "w") as f_out:
-                f_out.write(json.dumps(out, separators=(",", ": "), indent=1))
-
-    else:
-        log.append("splits section missing")
-
-    return "\n".join(log)