boris-behav-obs 9.7.8__tar.gz → 9.7.12__tar.gz

{boris_behav_obs-9.7.8 → boris_behav_obs-9.7.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boris-behav-obs
-Version: 9.7.8
+Version: 9.7.12
 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 2442 citations in peer-reviewed scientific publications.
+The BORIS paper has more than 2472 citations in peer-reviewed scientific publications.
 
 
 

{boris_behav_obs-9.7.8 → boris_behav_obs-9.7.12}/README.md

@@ -13,7 +13,7 @@ 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 2442 citations in peer-reviewed scientific publications.
+The BORIS paper has more than 2472 citations in peer-reviewed scientific publications.
 
 
 

boris_behav_obs-9.7.12/boris/analysis_plugins/_export_to_feral.py

@@ -0,0 +1,225 @@
+"""
+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)

{boris_behav_obs-9.7.8 → boris_behav_obs-9.7.12}/boris/behav_coding_map_creator.py

@@ -119,12 +119,12 @@ class BehaviorsMapCreatorWindow(QMainWindow):
         self.saveMapAction.setShortcut("Ctrl+S")
         self.saveMapAction.setStatusTip("Save the behavior coding map")
         self.saveMapAction.setEnabled(False)
-        self.saveMapAction.triggered.connect(self.saveMap_clicked)
+        self.saveMapAction.triggered.connect(self.save_map_clicked)
 
         self.saveAsMapAction = QAction(QIcon(), "Save the behavior coding map as ...", self)
         self.saveAsMapAction.setStatusTip("Save the behavior coding map as ...")
         self.saveAsMapAction.setEnabled(False)
-        self.saveAsMapAction.triggered.connect(self.saveAsMap_clicked)
+        self.saveAsMapAction.triggered.connect(self.save_as_map_clicked)
 
         self.mapNameAction = QAction(QIcon(), "&Edit name of behaviors coding map", self)
         self.mapNameAction.setShortcut("Ctrl+M")
@@ -389,7 +389,7 @@ class BehaviorsMapCreatorWindow(QMainWindow):
             )
 
             if response == cfg.SAVE:
-                if not self.saveMap_clicked():
+                if not self.save_map_clicked():
                     event.ignore()
 
             if response == cfg.CANCEL:
@@ -615,7 +615,7 @@ class BehaviorsMapCreatorWindow(QMainWindow):
             )
 
             if response == cfg.SAVE:
-                if not self.saveMap_clicked():
+                if not self.save_map_clicked():
                     return
 
             if response == cfg.CANCEL:
@@ -659,7 +659,7 @@ class BehaviorsMapCreatorWindow(QMainWindow):
                 ["Save", "Discard", "Cancel"],
             )
 
-            if (response == "Save" and not self.saveMap_clicked()) or (response == "Cancel"):
+            if (response == "Save" and not self.save_map_clicked()) or (response == "Cancel"):
                 return
 
         fileName, _ = QFileDialog(self).getOpenFileName(
@@ -783,7 +783,7 @@ class BehaviorsMapCreatorWindow(QMainWindow):
         else:
             return False
 
-    def saveAsMap_clicked(self):
+    def save_as_map_clicked(self):
         filters = "Behaviors coding map (*.behav_coding_map);;All files (*)"
 
         self.fileName, _ = QFileDialog.getSaveFileName(self, "Save behaviors coding map as", "", filters)
@@ -794,7 +794,7 @@ class BehaviorsMapCreatorWindow(QMainWindow):
             self.fileName += ".behav_coding_map"
         self.saveMap()
 
-    def saveMap_clicked(self):
+    def save_map_clicked(self):
         if not self.fileName:
             self.fileName, _ = QFileDialog().getSaveFileName(
                 self,

{boris_behav_obs-9.7.8 → boris_behav_obs-9.7.12}/boris/coding_pad.py

@@ -38,7 +38,7 @@ class Button(QWidget):
 
 
 class CodingPad(QWidget):
-    clickSignal = Signal(str)
+    click_signal = Signal(str)
     sendEventSignal = Signal(QEvent)
     close_signal = Signal(QRect, dict)
 
@@ -208,7 +208,8 @@ class CodingPad(QWidget):
         """
         Button clicked
         """
-        self.clickSignal.emit(behavior_code)
+        print(f"{behavior_code=}")
+        self.click_signal.emit(behavior_code)
 
     def eventFilter(self, receiver, event) -> bool:
         """
@@ -261,7 +262,7 @@ def show_coding_pad(self):
         self.codingpad.setWindowFlags(Qt.WindowStaysOnTopHint)
         self.codingpad.sendEventSignal.connect(self.signal_from_widget)
 
-        self.codingpad.clickSignal.connect(self.click_signal_from_coding_pad)
+        self.codingpad.click_signal.connect(self.click_signal_from_coding_pad)
         self.codingpad.close_signal.connect(self.close_signal_from_coding_pad)
         self.codingpad.show()
 

{boris_behav_obs-9.7.8 → boris_behav_obs-9.7.12}/boris/core.py

@@ -630,7 +630,8 @@ class MainWindow(QMainWindow, Ui_MainWindow):
         """
         handle click received from coding pad
         """
-        q = QKeyEvent(QEvent.KeyPress, Qt.Key_Enter, Qt.NoModifier, text=behaviorCode)
+        q = QKeyEvent(QEvent.Type.KeyPress, Qt.Key.Key_Enter, Qt.KeyboardModifier.NoModifier, text=behaviorCode)
+
         self.keyPressEvent(q)
 
     def close_signal_from_coding_pad(self, geometry, preferences):
@@ -644,7 +645,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
         """
         handle click received from subjects pad
         """
-        q = QKeyEvent(QEvent.KeyPress, Qt.Key_Enter, Qt.NoModifier, text="#subject#" + subject)
+        q = QKeyEvent(QEvent.Type.KeyPress, Qt.Key.Key_Enter, Qt.KeyboardModifier.NoModifier, text="#subject#" + subject)
         self.keyPressEvent(q)
 
     def signal_from_subjects_pad(self, event):
@@ -698,7 +699,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
             self.subjects_pad = subjects_pad.SubjectsPad(self.pj, filtered_subjects)
             self.subjects_pad.setWindowFlags(Qt.WindowStaysOnTopHint)
             self.subjects_pad.sendEventSignal.connect(self.signal_from_subjects_pad)
-            self.subjects_pad.clickSignal.connect(self.click_signal_from_subjects_pad)
+            self.subjects_pad.click_signal.connect(self.click_signal_from_subjects_pad)
             self.subjects_pad.close_signal.connect(self.close_signal_from_subjects_pad)
             self.subjects_pad.show()
 
@@ -1500,7 +1501,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
         logging.debug("previous media file")
 
         if self.playerType == cfg.MEDIA:
-            #if len(self.pj[cfg.OBSERVATIONS][self.observationId][cfg.FILE][cfg.PLAYER1]) == 1:
+            # if len(self.pj[cfg.OBSERVATIONS][self.observationId][cfg.FILE][cfg.PLAYER1]) == 1:
             #    self.seek_mediaplayer(dec(0))
             #    return
 
@@ -1510,7 +1511,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
 
             elif self.dw_player[0].player.playlist_count == 1:
                 self.seek_mediaplayer(dec(0))
-                #self.statusbar.showMessage("There is only one media file", 5000)
+                # self.statusbar.showMessage("There is only one media file", 5000)
 
             if hasattr(self, "spectro"):
                 self.spectro.memChunk = -1
@@ -4151,8 +4152,8 @@ class MainWindow(QMainWindow, Ui_MainWindow):
         called only in IPC mode
         """
         # check if eof reached
-        #print(f"{self.dw_player[0].player.playlist_pos=}")
-        #print(f"{self.dw_player[0].player.playlist_count=}")
+        # print(f"{self.dw_player[0].player.playlist_pos=}")
+        # print(f"{self.dw_player[0].player.playlist_count=}")
         if self.dw_player[0].player.eof_reached and self.dw_player[0].player.core_idle:
             logging.debug("end of playlist reached")
             if self.dw_player[0].player.playlist_pos is not None and self.dw_player[0].player.playlist_count is not None:
@@ -4220,8 +4221,11 @@ class MainWindow(QMainWindow, Ui_MainWindow):
 
                 # sync players 2..8 if time diff >= 1 s
                 if not math.isnan(ct) and not math.isnan(ct0):
-                    if abs(ct0 - (ct + dec(self.pj[cfg.OBSERVATIONS][self.observationId][cfg.MEDIA_INFO][cfg.OFFSET][str(n_player + 1)]))) >= 1:
-                        self.sync_time(n_player, ct0)  # self.seek_mediaplayer(ct0, n_player)
+                    if (
+                        abs(ct0 - (ct + dec(self.pj[cfg.OBSERVATIONS][self.observationId][cfg.MEDIA_INFO][cfg.OFFSET][str(n_player + 1)])))
+                        >= 1
+                    ):
+                        self.sync_time(n_player, float(ct0))  # self.seek_mediaplayer(ct0, n_player)
 
         currentTimeOffset = dec(cumulative_time_pos + self.pj[cfg.OBSERVATIONS][self.observationId][cfg.TIME_OFFSET])
 
@@ -4254,7 +4258,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
         # current media name
         playlist = self.dw_player[0].player.playlist
         playlist_pos = self.dw_player[0].player.playlist_pos
-        if playlist is not None and playlist_pos is not None:
+        if playlist is not None and playlist_pos is not None and playlist:
             current_media_name = Path(playlist[playlist_pos]["filename"]).name
             current_playlist_index = playlist_pos
         else:
@@ -4335,7 +4339,8 @@ class MainWindow(QMainWindow, Ui_MainWindow):
             # set video scroll bar
 
             if scroll_slider and not self.user_move_slider:
-                self.video_slider.setValue(round(current_media_time_pos / current_media_duration * (cfg.SLIDER_MAXIMUM - 1)))
+                if current_media_time_pos is not None and current_media_duration is not None:
+                    self.video_slider.setValue(round(current_media_time_pos / current_media_duration * (cfg.SLIDER_MAXIMUM - 1)))
 
     def mpv_eof_reached(self):
         """
@@ -4842,7 +4847,8 @@ class MainWindow(QMainWindow, Ui_MainWindow):
 
         # play / pause with space bar
         if self.pj[cfg.OBSERVATIONS][self.observationId][cfg.TYPE] == cfg.LIVE:
-            if ek in (Qt.Key_Space, Qt.Key_Enter, Qt.Key_Return):
+            # if ek in (Qt.Key_Space, Qt.Key_Enter, Qt.Key_Return):
+            if ek == Qt.Key_Space:
                 if self.liveObservationStarted:
                     if (
                         dialog.MessageDialog(cfg.programName, "Are you sure to stop the current live observation?", [cfg.YES, cfg.NO])
@@ -5485,7 +5491,6 @@ class MainWindow(QMainWindow, Ui_MainWindow):
                 if self.dw_player[0].player.playlist_pos == self.dw_player[0].player.playlist_count - 1:
                     self.seek_mediaplayer(dec(0))
 
-
         # check if player 1 is ended
         for i, dw in enumerate(self.dw_player):
             if (
@@ -5867,7 +5872,7 @@ def main():
             QMessageBox.warning(
                 None,
                 cfg.programName,
-                (f"This version of BORIS for macOS is still EXPERIMENTAL and should be used at your own risk."),
+                ("This version of BORIS for macOS is still EXPERIMENTAL and should be used at your own risk."),
                 QMessageBox.Ok | QMessageBox.Default,
                 QMessageBox.NoButton,
             )
@@ -5898,4 +5903,3 @@ def main():
     del window
 
     sys.exit(return_code)
-

{boris_behav_obs-9.7.8 → boris_behav_obs-9.7.12}/boris/modifier_coding_map_creator.py

@@ -134,7 +134,7 @@ class ModifiersMapCreatorWindow(QMainWindow):
         self.saveMapAction.setShortcut("Ctrl+S")
         self.saveMapAction.setStatusTip("Save modifiers map")
         self.saveMapAction.setEnabled(False)
-        self.saveMapAction.triggered.connect(self.saveMap_clicked)
+        self.saveMapAction.triggered.connect(self.save_map_clicked)
 
         self.saveAsMapAction = QAction(QIcon(), "Save modifiers map as", self)
         self.saveAsMapAction.setStatusTip("Save modifiers map as")
@@ -343,7 +343,7 @@ class ModifiersMapCreatorWindow(QMainWindow):
             )
 
             if response == cfg.SAVE:
-                if not self.saveMap_clicked():
+                if not self.save_map_clicked():
                     event.ignore()
 
             if response == cfg.CANCEL:
@@ -567,7 +567,7 @@ class ModifiersMapCreatorWindow(QMainWindow):
             )
 
             if response == "Save":
-                if not self.saveMap_clicked():
+                if not self.save_map_clicked():
                     return
 
             if response == "Cancel":
@@ -606,7 +606,7 @@ class ModifiersMapCreatorWindow(QMainWindow):
             )
 
             if response == cfg.SAVE:
-                if not self.saveMap_clicked():
+                if not self.save_map_clicked():
                     return
 
             if response == cfg.CANCEL:
@@ -733,7 +733,7 @@ class ModifiersMapCreatorWindow(QMainWindow):
                 self.fileName += ".boris_map"
             self.saveMap()
 
-    def saveMap_clicked(self):
+    def save_map_clicked(self):
         if not self.fileName:
             fn = QFileDialog(self).getSaveFileName(
                 self,
@@ -746,7 +746,7 @@ class ModifiersMapCreatorWindow(QMainWindow):
             else:
                 self.fileName = fn
 
-            if self.fileName and Path(self.fileName).suffix() != ".boris_map":
+            if self.fileName and Path(self.fileName).suffix != ".boris_map":
                 self.fileName += ".boris_map"
 
         if self.fileName: