boris-behav-obs 9.7.7__py3-none-any.whl

boris/select_subj_behav.py

@@ -0,0 +1,286 @@
+"""
+BORIS
+Behavioral Observation Research Interactive Software
+Copyright 2012-2025 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/>.
+
+"""
+
+import logging
+from decimal import Decimal as dec
+from typing import Optional
+
+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
+from . import utilities as util
+
+
+def choose_obs_subj_behav_category(
+    self,
+    selected_observations: list,
+    start_coding: Optional[dec] = dec("NaN"),  #  Union[..., None]
+    end_coding: Optional[dec] = dec("NaN"),
+    start_interval: Optional[dec] = dec("NaN"),
+    end_interval: Optional[dec] = dec("NaN"),
+    maxTime: Optional[dec] = None,
+    show_include_modifiers: bool = True,
+    show_exclude_non_coded_behaviors: bool = True,
+    by_category: bool = False,
+    n_observations: int = 1,
+    show_time_bin_size: bool = False,
+    window_title: str = "Select subjects and behaviors",
+    show_exclude_non_coded_modifiers: bool = False,
+) -> dict:
+    """
+    show window for:
+    - selection of subjects
+    - selection of behaviors (based on selected subjects)
+    - selection of time interval
+    - inclusion/exclusion of modifiers
+    - inclusion/exclusion of behaviors without events (show_exclude_non_coded_behaviors == True)
+    - selection of time bin size (show_time_bin_size == True)
+
+    Args:
+        selected_observations (list): List of selected observations
+        ...
+        show_exclude_non_coded_modifiers (bool): display the Exclude non coded modifiers checkbox
+
+    Returns:
+        dict: {"selected subjects": selectedSubjects,
+            "selected behaviors": selectedBehaviors,
+            "include modifiers": True/False,
+            "exclude behaviors": True/False,
+            "time": TIME_FULL_OBS / TIME_EVENTS / TIME_ARBITRARY_INTERVAL / TIME_OBS_INTERVAL
+            "start time": startTime,
+            "end time": endTime
+            }
+
+    """
+
+    paramPanelWindow = param_panel.Param_panel()
+    paramPanelWindow.resize(400, 400)
+    paramPanelWindow.setWindowTitle(window_title)
+    paramPanelWindow.selectedObservations = selected_observations
+    paramPanelWindow.pj = self.pj
+    paramPanelWindow.extract_observed_behaviors = self.extract_observed_behaviors
+
+    paramPanelWindow.cbIncludeModifiers.setVisible(show_include_modifiers)
+    paramPanelWindow.cb_exclude_non_coded_modifiers.setVisible(show_exclude_non_coded_modifiers)
+    paramPanelWindow.cbExcludeBehaviors.setVisible(show_exclude_non_coded_behaviors)
+    # show_time_bin_size:
+    paramPanelWindow.frm_time_bin_size.setVisible(show_time_bin_size)
+
+    if by_category:
+        paramPanelWindow.cbIncludeModifiers.setVisible(False)
+        paramPanelWindow.cbExcludeBehaviors.setVisible(False)
+        paramPanelWindow.cb_exclude_non_coded_modifiers.setVisible(False)
+
+    # set state of cb_exclude_non_coded_modifiers
+    paramPanelWindow.cb_exclude_non_coded_modifiers.setEnabled(paramPanelWindow.cbIncludeModifiers.isChecked())
+
+    paramPanelWindow.media_duration = maxTime
+    paramPanelWindow.start_coding = start_coding
+    paramPanelWindow.end_coding = end_coding
+    paramPanelWindow.start_interval = start_interval
+    paramPanelWindow.end_interval = end_interval
+
+    if self.timeFormat == cfg.S:
+        paramPanelWindow.start_time.rb_seconds.setChecked(True)
+        paramPanelWindow.end_time.rb_seconds.setChecked(True)
+    if self.timeFormat == cfg.HHMMSS:
+        paramPanelWindow.start_time.rb_time.setChecked(True)
+        paramPanelWindow.end_time.rb_time.setChecked(True)
+
+    if n_observations > 1:
+        paramPanelWindow.frm_time_interval.setVisible(False)
+    else:
+        if (start_coding is None) or (start_coding.is_nan()):
+            paramPanelWindow.rb_observed_events.setEnabled(False)
+            paramPanelWindow.frm_time_interval.setVisible(False)
+            paramPanelWindow.rb_user_defined.setVisible(False)
+            paramPanelWindow.rb_obs_interval.setVisible(False)
+            paramPanelWindow.rb_media_duration.setVisible(False)
+        else:
+            paramPanelWindow.frm_time_interval.setEnabled(False)
+            paramPanelWindow.start_time.set_time(start_coding)
+            paramPanelWindow.end_time.set_time(end_coding)
+
+    # check observation time interval
+    if start_interval is None or start_interval.is_nan() or end_interval is None or end_interval.is_nan():
+        paramPanelWindow.rb_obs_interval.setEnabled(False)
+
+    if selected_observations:
+        observedSubjects = project_functions.extract_observed_subjects(self.pj, selected_observations)
+    else:
+        # load all subjects and "No focal subject"
+        observedSubjects = [self.pj[cfg.SUBJECTS][x][cfg.SUBJECT_NAME] for x in self.pj[cfg.SUBJECTS]] + [""]
+    selectedSubjects = []
+
+    # add 'No focal subject'
+    if "" in observedSubjects:
+        selectedSubjects.append(cfg.NO_FOCAL_SUBJECT)
+        paramPanelWindow.item = QListWidgetItem(paramPanelWindow.lwSubjects)
+        paramPanelWindow.ch = QCheckBox()
+        paramPanelWindow.ch.setText(cfg.NO_FOCAL_SUBJECT)
+        paramPanelWindow.ch.stateChanged.connect(paramPanelWindow.cb_changed)
+        paramPanelWindow.ch.setChecked(True)
+        paramPanelWindow.lwSubjects.setItemWidget(paramPanelWindow.item, paramPanelWindow.ch)
+
+    all_subjects = [self.pj[cfg.SUBJECTS][x][cfg.SUBJECT_NAME] for x in util.sorted_keys(self.pj[cfg.SUBJECTS])]
+
+    for subject in all_subjects:
+        paramPanelWindow.item = QListWidgetItem(paramPanelWindow.lwSubjects)
+        paramPanelWindow.ch = QCheckBox()
+        paramPanelWindow.ch.setText(subject)
+        paramPanelWindow.ch.stateChanged.connect(paramPanelWindow.cb_changed)
+        if subject in observedSubjects:
+            selectedSubjects.append(subject)
+            paramPanelWindow.ch.setChecked(True)
+
+        paramPanelWindow.lwSubjects.setItemWidget(paramPanelWindow.item, paramPanelWindow.ch)
+
+    logging.debug(f"selected subjects: {selectedSubjects}")
+
+    if selected_observations:
+        observedBehaviors = self.extract_observed_behaviors(selected_observations, selectedSubjects)  # not sorted
+    else:
+        # load all behaviors
+        observedBehaviors = [self.pj[cfg.ETHOGRAM][x][cfg.BEHAVIOR_CODE] for x in self.pj[cfg.ETHOGRAM]]
+
+    logging.debug(f"observed behaviors: {observedBehaviors}")
+
+    if cfg.BEHAVIORAL_CATEGORIES in self.pj:
+        categories = self.pj[cfg.BEHAVIORAL_CATEGORIES][:]
+        # check if behavior not included in a category
+        try:
+            if "" in [
+                self.pj[cfg.ETHOGRAM][idx][cfg.BEHAVIOR_CATEGORY]
+                for idx in self.pj[cfg.ETHOGRAM]
+                if cfg.BEHAVIOR_CATEGORY in self.pj[cfg.ETHOGRAM][idx]
+            ]:
+                categories += [""]
+        except Exception:
+            categories = ["###no category###"]
+
+    else:
+        categories = ["###no category###"]
+
+    for category in categories:
+        if category != "###no category###":
+            if category == "":
+                paramPanelWindow.item = QListWidgetItem("No category")
+                paramPanelWindow.item.setData(34, "No category")
+            else:
+                paramPanelWindow.item = QListWidgetItem(category)
+                paramPanelWindow.item.setData(34, category)
+
+            font = QFont()
+            font.setBold(True)
+            paramPanelWindow.item.setFont(font)
+            paramPanelWindow.item.setData(33, "category")
+            paramPanelWindow.item.setData(35, False)
+
+            paramPanelWindow.lwBehaviors.addItem(paramPanelWindow.item)
+
+        for behavior in [self.pj[cfg.ETHOGRAM][x][cfg.BEHAVIOR_CODE] for x in util.sorted_keys(self.pj[cfg.ETHOGRAM])]:
+            if (categories == ["###no category###"]) or (
+                behavior
+                in [
+                    self.pj[cfg.ETHOGRAM][x][cfg.BEHAVIOR_CODE]
+                    for x in self.pj[cfg.ETHOGRAM]
+                    if cfg.BEHAVIOR_CATEGORY in self.pj[cfg.ETHOGRAM][x] and self.pj[cfg.ETHOGRAM][x][cfg.BEHAVIOR_CATEGORY] == category
+                ]
+            ):
+                paramPanelWindow.item = QListWidgetItem(behavior)
+                if behavior in observedBehaviors:
+                    paramPanelWindow.item.setCheckState(Qt.Checked)
+                else:
+                    paramPanelWindow.item.setCheckState(Qt.Unchecked)
+
+                if category != "###no category###":
+                    paramPanelWindow.item.setData(33, "behavior")
+                    if category == "":
+                        paramPanelWindow.item.setData(34, "No category")
+                    else:
+                        paramPanelWindow.item.setData(34, category)
+
+                paramPanelWindow.lwBehaviors.addItem(paramPanelWindow.item)
+
+    gui_utilities.restore_geometry(paramPanelWindow, "param panel", (600, 500))
+
+    if not paramPanelWindow.exec_():
+        return {}
+
+    gui_utilities.save_geometry(paramPanelWindow, "param panel")
+
+    selectedSubjects = paramPanelWindow.selectedSubjects
+    selectedBehaviors = paramPanelWindow.selectedBehaviors
+
+    logging.debug(f"selected subjects: {selectedSubjects}")
+    logging.debug(f"selected behaviors: {selectedBehaviors}")
+
+    if paramPanelWindow.rb_user_defined.isChecked():
+        startTime = paramPanelWindow.start_time.get_time()
+        endTime = paramPanelWindow.end_time.get_time()
+
+        if startTime > endTime:
+            QMessageBox.warning(
+                None,
+                cfg.programName,
+                "The start time is after the end time",
+                QMessageBox.Ok | QMessageBox.Default,
+                QMessageBox.NoButton,
+            )
+            return {cfg.SELECTED_SUBJECTS: [], cfg.SELECTED_BEHAVIORS: []}
+
+    elif paramPanelWindow.rb_obs_interval.isChecked() and not ((start_interval is None) or start_interval.is_nan()):
+        startTime = paramPanelWindow.start_time.get_time()
+        endTime = paramPanelWindow.end_time.get_time()
+
+    else:
+        startTime = None
+        endTime = None
+
+    # if startTime is None:
+    #    startTime = dec("NaN")
+    # if endTime is None:
+    #    endTime = dec("NaN")
+
+    if paramPanelWindow.rb_media_duration.isChecked():
+        time_param = cfg.TIME_FULL_OBS
+    if paramPanelWindow.rb_observed_events.isChecked():
+        time_param = cfg.TIME_EVENTS
+    if paramPanelWindow.rb_obs_interval.isChecked():
+        time_param = cfg.TIME_OBS_INTERVAL
+    if paramPanelWindow.rb_user_defined.isChecked():
+        time_param = cfg.TIME_ARBITRARY_INTERVAL
+
+    return {
+        cfg.SELECTED_SUBJECTS: selectedSubjects,
+        cfg.SELECTED_BEHAVIORS: selectedBehaviors,
+        cfg.INCLUDE_MODIFIERS: paramPanelWindow.cbIncludeModifiers.isChecked(),
+        cfg.EXCLUDE_BEHAVIORS: paramPanelWindow.cbExcludeBehaviors.isChecked(),
+        cfg.EXCLUDE_NON_CODED_MODIFIERS: paramPanelWindow.cb_exclude_non_coded_modifiers.isChecked(),
+        "time": time_param,
+        cfg.START_TIME: startTime,
+        cfg.END_TIME: endTime,
+        cfg.TIME_BIN_SIZE: paramPanelWindow.sb_time_bin_size.value(),
+    }

boris/state_events.py

@@ -0,0 +1,197 @@
+"""
+BORIS
+Behavioral Observation Research Interactive Software
+Copyright 2012-2025 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
+  the Free Software Foundation; either version 2 of the License, or
+  (at your option) any later version.
+
+  This program 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.
+
+Module containing functions for state events
+
+"""
+
+import time
+from decimal import Decimal as dec
+
+from PySide6.QtWidgets import QMessageBox, QAbstractItemView
+
+from . import config as cfg
+from . import dialog, project_functions, select_observations
+
+
+def check_state_events(self, mode: str = "all") -> None:
+    """
+    check state events for each subject
+    use check_state_events_obs function in project_functions.py
+
+    Args:
+        mode (str): current: check current observation / all: ask user to select observations
+    """
+
+    tot_out = ""
+    if mode == "current":
+        if self.observationId:
+            _, msg = project_functions.check_state_events_obs(
+                self.observationId,
+                self.pj[cfg.ETHOGRAM],
+                self.pj[cfg.OBSERVATIONS][self.observationId],
+                self.timeFormat,
+            )
+            tot_out = f"Observation: <strong>{self.observationId}</strong><br>{msg}<br><br>"
+
+    if mode == "all":
+        if not self.pj[cfg.OBSERVATIONS]:
+            QMessageBox.warning(
+                self,
+                cfg.programName,
+                "The project does not contain any observation",
+                QMessageBox.Ok | QMessageBox.Default,
+                QMessageBox.NoButton,
+            )
+            return
+
+        # ask user observations to analyze
+        _, selectedObservations = select_observations.select_observations2(self, mode=cfg.MULTIPLE, windows_title="")
+        if not selectedObservations:
+            return
+
+        for obsId in sorted(selectedObservations):
+            r, msg = project_functions.check_state_events_obs(
+                obsId, self.pj[cfg.ETHOGRAM], self.pj[cfg.OBSERVATIONS][obsId], self.timeFormat
+            )
+
+            tot_out += f"<strong>{obsId}</strong><br>{msg}<br>"
+
+    results = dialog.Results_dialog()
+    results.setWindowTitle("Check state events")
+    results.ptText.clear()
+    results.ptText.setReadOnly(True)
+    results.ptText.appendHtml(tot_out)
+    results.exec_()
+
+
+def fix_unpaired_events(self, silent_mode: bool = False):
+    """
+    fix unpaired state events
+    """
+
+    if self.observationId:
+        r, msg = project_functions.check_state_events_obs(
+            self.observationId, self.pj[cfg.ETHOGRAM], self.pj[cfg.OBSERVATIONS][self.observationId]
+        )
+        if not silent_mode and "not PAIRED" not in msg:
+            QMessageBox.information(
+                None,
+                cfg.programName,
+                "All state events are already paired",
+                QMessageBox.Ok | QMessageBox.Default,
+                QMessageBox.NoButton,
+            )
+            return
+
+        w = dialog.Ask_time(0)
+        w.setWindowTitle("Fix UNPAIRED state events")
+        w.label.setText("Fix UNPAIRED events at time:")
+
+        if not w.exec_():
+            return
+
+        fix_at_time = w.time_widget.get_time()
+        if fix_at_time.is_nan():
+            QMessageBox.warning(
+                self,
+                cfg.programName,
+                ("Select a time format"),
+            )
+            return
+
+        events_to_add = project_functions.fix_unpaired_state_events(
+            self.pj[cfg.ETHOGRAM],
+            self.pj[cfg.OBSERVATIONS][self.observationId],
+            fix_at_time - dec("0.001"),
+        )
+
+        if events_to_add:
+            # determine the new frame index
+            if (self.pj[cfg.OBSERVATIONS][self.observationId][cfg.TYPE] == cfg.MEDIA) and self.playerType == cfg.MEDIA:
+                mem_time = self.getLaps()
+                for event in events_to_add:
+                    if not self.seek_mediaplayer(event[0]):
+                        time.sleep(0.1)
+                        frame_idx = self.get_frame_index()
+                        event[cfg.PJ_OBS_FIELDS[cfg.MEDIA][cfg.FRAME_INDEX]] = frame_idx
+                self.seek_mediaplayer(mem_time)
+
+            self.pj[cfg.OBSERVATIONS][self.observationId][cfg.EVENTS].extend(events_to_add)
+            self.project_changed()
+            self.pj[cfg.OBSERVATIONS][self.observationId][cfg.EVENTS].sort(key=lambda x: x[:3])
+            self.load_tw_events(self.observationId)
+
+            index = self.tv_events.model().index(
+                [
+                    event_idx
+                    for event_idx, event in enumerate(self.pj[cfg.OBSERVATIONS][self.observationId][cfg.EVENTS])
+                    if event[cfg.PJ_OBS_FIELDS[self.playerType][cfg.TIME]] == fix_at_time
+                ][0],
+                0,
+            )
+            self.tv_events.scrollTo(index, QAbstractItemView.EnsureVisible)
+
+    # selected observations
+    else:
+        _, selected_observations = select_observations.select_observations2(self, mode=cfg.MULTIPLE, windows_title="")
+        if not selected_observations:
+            return
+
+        # check if state events are paired
+        out: str = ""
+        for obs_id in selected_observations:
+            r, msg = project_functions.check_state_events_obs(obs_id, self.pj[cfg.ETHOGRAM], self.pj[cfg.OBSERVATIONS][obs_id])
+            if "NOT PAIRED" in msg.upper():
+                # determine max time of events
+                fix_at_time = max(x[0] for x in self.pj[cfg.OBSERVATIONS][obs_id][cfg.EVENTS])
+                # list of events to add to fix unpaired events
+                events_to_add = project_functions.fix_unpaired_state_events(
+                    self.pj[cfg.ETHOGRAM], self.pj[cfg.OBSERVATIONS][obs_id], fix_at_time
+                )
+                if events_to_add:
+                    events_backup = self.pj[cfg.OBSERVATIONS][obs_id][cfg.EVENTS][:]
+                    self.pj[cfg.OBSERVATIONS][obs_id][cfg.EVENTS].extend(events_to_add)
+
+                    # check if modified obs if fixed
+                    r, msg = project_functions.check_state_events_obs(obs_id, self.pj[cfg.ETHOGRAM], self.pj[cfg.OBSERVATIONS][obs_id])
+                    if "NOT PAIRED" in msg.upper():
+                        out += f"The observation <b>{obs_id}</b> can not be automatically fixed.<br><br>"
+                        self.pj[cfg.OBSERVATIONS][obs_id][cfg.EVENTS] = events_backup
+                    else:
+                        out += f"<b>{obs_id}</b><br>"
+                        self.project_changed()
+        if out:
+            out = "The following observations were modified to fix the unpaired state events:<br><br>" + out
+            self.results = dialog.Results_dialog()
+            self.results.setWindowTitle(cfg.programName + " - Fixed observations")
+            self.results.ptText.setReadOnly(True)
+            self.results.ptText.appendHtml(out)
+            self.results.pbSave.setVisible(False)
+            self.results.pbCancel.setVisible(True)
+            self.results.exec_()
+        else:
+            QMessageBox.information(
+                None,
+                cfg.programName,
+                "All state events are already paired",
+                QMessageBox.Ok | QMessageBox.Default,
+                QMessageBox.NoButton,
+            )

boris/subjects_pad.py

@@ -0,0 +1,106 @@
+"""
+BORIS
+Behavioral Observation Research Interactive Software
+Copyright 2012-2025 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
+  the Free Software Foundation; either version 2 of the License, or
+  (at your option) any later version.
+
+  This program 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.
+"""
+
+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 = Signal(str)
+    sendEventSignal = Signal(QEvent)
+    close_signal = Signal(QRect)
+
+    def __init__(self, pj, filtered_subjects, parent=None):
+        super(SubjectsPad, self).__init__(parent)
+        self.pj = pj
+        self.filtered_subjects = filtered_subjects
+
+        self.setWindowTitle("Subjects pad")
+        self.grid = QGridLayout(self)
+        self.installEventFilter(self)
+        self.compose()
+
+    def compose(self):
+        for i in reversed(range(self.grid.count())):
+            self.grid.itemAt(i).widget().setParent(None)
+
+        subjects_list = [
+            ["", self.pj[cfg.SUBJECTS][x]["name"]]
+            for x in util.sorted_keys(self.pj[cfg.SUBJECTS])
+            if self.pj[cfg.SUBJECTS][x]["name"] in self.filtered_subjects
+        ]
+        dim = int(len(subjects_list) ** 0.5 + 0.999)
+
+        c = 0
+        for i in range(1, dim + 1):
+            for j in range(1, dim + 1):
+                if c >= len(subjects_list):
+                    break
+                self.addWidget(subjects_list[c][1], i, j)
+                c += 1
+
+    def addWidget(self, subject, i, j):
+        self.grid.addWidget(Button(), i, j)
+        index = self.grid.count() - 1
+        widget = self.grid.itemAt(index).widget()
+
+        if widget is not None:
+            widget.pushButton.setText(subject)
+            color = "cyan"
+            widget.pushButton.setStyleSheet(
+                (
+                    "background-color: {}; border-radius: 0px; min-width: 50px; max-width: 200px;"
+                    " min-height:50px; max-height:200px; font-weight: bold;"
+                ).format(color)
+            )
+            widget.pushButton.clicked.connect(lambda: self.click(subject))
+
+    def click(self, subject):
+        self.clickSignal.emit(subject)
+
+    def eventFilter(self, receiver, event):
+        """
+        send event (if keypress) to main window
+        """
+        if event.type() == QEvent.KeyPress:
+            self.sendEventSignal.emit(event)
+            return True
+        else:
+            return False
+
+    def closeEvent(self, event):
+        """
+        send event for widget geometry memory
+        """
+        self.close_signal.emit(self.geometry())
+
+
+class Button(QWidget):
+    def __init__(self, parent=None):
+        super(Button, self).__init__(parent)
+        self.pushButton = QPushButton()
+        self.pushButton.setFocusPolicy(Qt.NoFocus)
+        layout = QHBoxLayout()
+        layout.addWidget(self.pushButton)
+        self.setLayout(layout)