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

boris/cooccurence.py

@@ -0,0 +1,250 @@
+"""
+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 for analyzing the co-occurence of behaviors
+
+"""
+
+from . import config as cfg
+from . import select_subj_behav
+from . import dialog
+from . import utilities as util
+from . import select_observations
+
+from . import project_functions, observation_operations
+
+from PySide6.QtWidgets import QMessageBox
+from PySide6.QtGui import QFont, QTextOption
+from . import portion as I
+import itertools
+import logging
+from decimal import Decimal as dec
+
+
+def get_cooccurence(self):
+    """
+    get co-occurence of selected behaviors
+    """
+
+    QMessageBox.warning(
+        None,
+        cfg.programName,
+        (
+            "This function is experimental. Please test it and report any bug and suggestions at <br>"
+            '<a href="https://github.com/olivierfriard/BORIS/issues">'
+            "https://github.com/olivierfriard/BORIS/issues</a><br>"
+            "Thank you for your collaboration!"
+        ),
+        QMessageBox.Ok | QMessageBox.Default,
+        QMessageBox.NoButton,
+    )
+
+    def interval_len(interval: I) -> dec:
+        """ "
+        returns duration of an interval or a set of intervals
+        """
+        if interval.empty:
+            return dec(0)
+        else:
+            return dec(sum([x.upper - x.lower for x in interval]))
+
+    _, selected_observations = select_observations.select_observations2(
+        self, cfg.MULTIPLE, windows_title="Select the observations for behaviors co-occurence analysis"
+    )
+
+    if not selected_observations:
+        return
+
+    # check if coded behaviors are defined in ethogram
+    if project_functions.check_coded_behaviors_in_obs_list(self.pj, selected_observations):
+        return
+
+    # check if state events are paired
+    not_ok, selected_observations = project_functions.check_state_events(self.pj, selected_observations)
+    if not_ok or not selected_observations:
+        return
+
+    max_media_duration_all_obs, _ = observation_operations.media_duration(self.pj[cfg.OBSERVATIONS], selected_observations)
+
+    start_coding, end_coding, _ = observation_operations.coding_time(self.pj[cfg.OBSERVATIONS], selected_observations)
+    # exit with message if events do not have timestamp
+    if start_coding.is_nan():
+        QMessageBox.critical(
+            None,
+            cfg.programName,
+            ("This function is not available for observations with events that do not have timestamp"),
+            QMessageBox.Ok | QMessageBox.Default,
+            QMessageBox.NoButton,
+        )
+        return
+
+    start_interval, end_interval = observation_operations.time_intervals_range(self.pj[cfg.OBSERVATIONS], selected_observations)
+
+    # loop on choose subjects /behaviors until parameters are OK
+    while True:
+        flag_ok: bool = True
+        parameters = select_subj_behav.choose_obs_subj_behav_category(
+            self,
+            selected_observations,
+            start_coding=start_coding,
+            end_coding=end_coding,
+            # start_interval=start_interval,
+            # end_interval=end_interval,
+            start_interval=None,
+            end_interval=None,
+            maxTime=max_media_duration_all_obs,
+            n_observations=len(selected_observations),
+            show_include_modifiers=False,
+            show_exclude_non_coded_behaviors=True,
+        )
+
+        if not parameters:  # cancel button pressed
+            return
+
+        if not parameters[cfg.SELECTED_SUBJECTS]:
+            QMessageBox.warning(None, cfg.programName, "Select the subject(s) to analyze")
+            flag_ok = False
+
+        # check number of behaviors (must be <=4)
+        if flag_ok and len(parameters[cfg.SELECTED_BEHAVIORS]) > 4:
+            QMessageBox.warning(None, cfg.programName, "You cannot select more than 4 behaviors")
+            flag_ok = False
+
+        # check number of behaviors (must be > 1)
+        if flag_ok and len(parameters[cfg.SELECTED_BEHAVIORS]) < 2:
+            QMessageBox.warning(None, cfg.programName, "You must select almost 2 behaviors")
+            flag_ok = False
+
+        if flag_ok:
+            break
+
+    logging.debug(f"{parameters[cfg.SELECTED_BEHAVIORS]}")
+
+    state_events_list = util.state_behavior_codes(self.pj[cfg.ETHOGRAM])
+
+    events_interval: dict = {}
+    mem_events_interval: dict = {}
+
+    for obs_id in selected_observations:
+        events_interval[obs_id] = {}
+        mem_events_interval[obs_id] = {}
+
+        for event in self.pj[cfg.OBSERVATIONS][obs_id][cfg.EVENTS]:
+            if event[cfg.EVENT_SUBJECT_FIELD_IDX] not in events_interval[obs_id]:
+                events_interval[obs_id][event[cfg.EVENT_SUBJECT_FIELD_IDX]] = {}
+                mem_events_interval[obs_id][event[cfg.EVENT_SUBJECT_FIELD_IDX]] = {}
+
+            if event[cfg.EVENT_BEHAVIOR_FIELD_IDX] not in events_interval[obs_id][event[cfg.EVENT_SUBJECT_FIELD_IDX]]:
+                events_interval[obs_id][event[cfg.EVENT_SUBJECT_FIELD_IDX]][event[cfg.EVENT_BEHAVIOR_FIELD_IDX]] = I.empty()
+                mem_events_interval[obs_id][event[cfg.EVENT_SUBJECT_FIELD_IDX]][event[cfg.EVENT_BEHAVIOR_FIELD_IDX]] = []
+
+            # state event
+            if event[cfg.EVENT_BEHAVIOR_FIELD_IDX] in state_events_list:
+                mem_events_interval[obs_id][event[cfg.EVENT_SUBJECT_FIELD_IDX]][event[cfg.EVENT_BEHAVIOR_FIELD_IDX]].append(
+                    event[cfg.EVENT_TIME_FIELD_IDX]
+                )
+                if len(mem_events_interval[obs_id][event[cfg.EVENT_SUBJECT_FIELD_IDX]][event[cfg.EVENT_BEHAVIOR_FIELD_IDX]]) == 2:
+                    events_interval[obs_id][event[cfg.EVENT_SUBJECT_FIELD_IDX]][event[cfg.EVENT_BEHAVIOR_FIELD_IDX]] |= I.closedopen(
+                        mem_events_interval[obs_id][event[cfg.EVENT_SUBJECT_FIELD_IDX]][event[cfg.EVENT_BEHAVIOR_FIELD_IDX]][0],
+                        mem_events_interval[obs_id][event[cfg.EVENT_SUBJECT_FIELD_IDX]][event[cfg.EVENT_BEHAVIOR_FIELD_IDX]][1],
+                    )
+                    mem_events_interval[obs_id][event[cfg.EVENT_SUBJECT_FIELD_IDX]][event[cfg.EVENT_BEHAVIOR_FIELD_IDX]] = []
+            # point event
+            else:
+                events_interval[obs_id][event[cfg.EVENT_SUBJECT_FIELD_IDX]][event[cfg.EVENT_BEHAVIOR_FIELD_IDX]] |= I.singleton(
+                    event[cfg.EVENT_TIME_FIELD_IDX]
+                )
+
+    logging.debug(f"events_interval: {events_interval}")
+
+    cooccurence_results: dict = {}
+
+    for obs_id in selected_observations:
+        logging.debug(f"obs_id: {obs_id}")
+
+        for subject in parameters[cfg.SELECTED_SUBJECTS]:
+            if subject == "No focal subject":
+                subj = ""
+            else:
+                subj = subject
+
+            if subject not in cooccurence_results:
+                cooccurence_results[subject] = {}
+
+            logging.debug(f"subject {subject}")
+
+            for n_combinations in range(2, len(parameters[cfg.SELECTED_BEHAVIORS]) + 1):
+                union = I.empty()
+
+                logging.debug(f"{n_combinations=}")
+
+                for combination in itertools.combinations(parameters[cfg.SELECTED_BEHAVIORS], n_combinations):
+                    logging.debug(f"{combination=}")
+                    if subj in events_interval[obs_id]:
+                        # init
+                        if combination[0] in events_interval[obs_id][subj]:
+                            union = events_interval[obs_id][subj][combination[0]]
+                        else:
+                            union = I.empty()
+
+                        logging.debug(f"{combination[0]=} {union=}")
+
+                        for combination2 in combination[1:]:
+                            if combination2 in events_interval[obs_id][subj]:
+                                inter2 = events_interval[obs_id][subj][combination2]
+                            else:
+                                inter2 = I.empty()
+
+                            logging.debug(f"{combination2=} {inter2=}")
+
+                            union &= inter2
+
+                        if combination not in cooccurence_results[subject]:
+                            cooccurence_results[subject][combination] = 0
+
+                        logging.debug(f"{combination=} {union=}")
+                        cooccurence_results[subject][combination] += interval_len(union)
+                    else:
+                        if combination not in cooccurence_results[subject]:
+                            cooccurence_results[subject][combination] = 0
+                        cooccurence_results[subject][combination] += 0
+
+                    logging.debug(f"{cooccurence_results[subject][combination]=}")
+
+    logging.debug(cooccurence_results)
+
+    out = f"<b>Co-occurence of behaviors: {','.join(parameters[cfg.SELECTED_BEHAVIORS])}</b><br><br>"
+    for subject in parameters[cfg.SELECTED_SUBJECTS]:
+        out += f"<br>Subject <b>{subject}</b><br><br>"
+        for combination in cooccurence_results[subject]:
+            if parameters[cfg.EXCLUDE_BEHAVIORS] and not cooccurence_results[subject][combination]:
+                continue
+            duration = f"<b>{cooccurence_results[subject][combination]}</b>" if cooccurence_results[subject][combination] else "0"
+            out += f"<b>{'</b> and <b>'.join(combination)}</b>: {duration} s<br>"
+
+    self.results = dialog.Results_dialog()
+    self.results.setWindowTitle("Behaviors co-occurence")
+    self.results.ptText.setFont(QFont("Courier", 12))
+    self.results.ptText.setWordWrapMode(QTextOption.NoWrap)
+    self.results.ptText.setReadOnly(True)
+    self.results.ptText.clear()
+    self.results.ptText.appendHtml(out)
+    self.results.show()