boris-behav-obs 9.7.1__py3-none-any.whl → 9.7.12__py3-none-any.whl

boris/about.py

@@ -40,7 +40,7 @@ def actionAbout_activated(self):
     About dialog
     """
 
-    programs_versions: list = ["MPV media player"]
+    programs_versions: list[str] = ["MPV media player"]
 
     mpv_lib_version, mpv_lib_file_path, mpv_api_version = util.mpv_lib_version()
     programs_versions.append(
@@ -53,13 +53,13 @@ def actionAbout_activated(self):
 
     # ffmpeg
     if self.ffmpeg_bin == "ffmpeg" and sys.platform.startswith("linux"):
-        ffmpeg_true_path = subprocess.getoutput("which ffmpeg")
+        ffmpeg_true_path: str = subprocess.getoutput("which ffmpeg")
     else:
         ffmpeg_true_path = self.ffmpeg_bin
     programs_versions.extend(
         [
             "\nFFmpeg",
-            subprocess.getoutput(f'"{self.ffmpeg_bin}" -version').split("\n")[0],
+            subprocess.getoutput(cmd=f'"{self.ffmpeg_bin}" -version').split(sep="\n")[0],
             f"Path: {ffmpeg_true_path}",
             "https://www.ffmpeg.org",
         ]
@@ -75,11 +75,11 @@ def actionAbout_activated(self):
     programs_versions.extend(["\nPandas", f"version {pd.__version__}", "https://pandas.pydata.org"])
 
     # graphviz
-    gv_result = subprocess.getoutput("dot -V")
+    gv_result = subprocess.getoutput(cmd="dot -V")
 
     programs_versions.extend(["\nGraphViz", gv_result if "graphviz" in gv_result else "not installed", "https://www.graphviz.org/"])
 
-    about_dialog = QMessageBox()
+    about_dialog: QMessageBox = QMessageBox()
     about_dialog.setIconPixmap(QPixmap(":/boris_unito"))
 
     about_dialog.setWindowTitle(f"About {cfg.programName}")

boris/add_modifier_ui.py

@@ -3,7 +3,7 @@
 ################################################################################
 ## Form generated from reading UI file 'add_modifier.ui'
 ##
-## Created by: Qt User Interface Compiler version 6.8.0
+## Created by: Qt User Interface Compiler version 6.10.0
 ##
 ## WARNING! All changes made in this file will be lost when recompiling UI file!
 ################################################################################
@@ -24,18 +24,16 @@ class Ui_Dialog(object):
     def setupUi(self, Dialog):
         if not Dialog.objectName():
             Dialog.setObjectName(u"Dialog")
-        Dialog.resize(1088, 654)
-        self.verticalLayout_5 = QVBoxLayout(Dialog)
-        self.verticalLayout_5.setObjectName(u"verticalLayout_5")
+        Dialog.resize(1339, 789)
+        self.verticalLayout_4 = QVBoxLayout(Dialog)
+        self.verticalLayout_4.setObjectName(u"verticalLayout_4")
         self.cb_ask_at_stop = QCheckBox(Dialog)
         self.cb_ask_at_stop.setObjectName(u"cb_ask_at_stop")
 
-        self.verticalLayout_5.addWidget(self.cb_ask_at_stop)
+        self.verticalLayout_4.addWidget(self.cb_ask_at_stop)
 
-        self.verticalLayout_4 = QVBoxLayout()
-        self.verticalLayout_4.setObjectName(u"verticalLayout_4")
-        self.horizontalLayout_5 = QHBoxLayout()
-        self.horizontalLayout_5.setObjectName(u"horizontalLayout_5")
+        self.horizontalLayout_8 = QHBoxLayout()
+        self.horizontalLayout_8.setObjectName(u"horizontalLayout_8")
         self.verticalLayout_2 = QVBoxLayout()
         self.verticalLayout_2.setObjectName(u"verticalLayout_2")
         self.lbModifier = QLabel(Dialog)
@@ -69,7 +67,7 @@ class Ui_Dialog(object):
         self.verticalLayout_2.addItem(self.verticalSpacer)
 
 
-        self.horizontalLayout_5.addLayout(self.verticalLayout_2)
+        self.horizontalLayout_8.addLayout(self.verticalLayout_2)
 
         self.verticalLayout_3 = QVBoxLayout()
         self.verticalLayout_3.setObjectName(u"verticalLayout_3")
@@ -88,7 +86,7 @@ class Ui_Dialog(object):
         self.verticalLayout_3.addItem(self.verticalSpacer_2)
 
 
-        self.horizontalLayout_5.addLayout(self.verticalLayout_3)
+        self.horizontalLayout_8.addLayout(self.verticalLayout_3)
 
         self.verticalLayout = QVBoxLayout()
         self.verticalLayout.setObjectName(u"verticalLayout")
@@ -102,30 +100,42 @@ class Ui_Dialog(object):
 
         self.verticalLayout.addWidget(self.tabWidgetModifiersSets)
 
+        self.horizontalLayout_5 = QHBoxLayout()
+        self.horizontalLayout_5.setObjectName(u"horizontalLayout_5")
         self.lb_name = QLabel(Dialog)
         self.lb_name.setObjectName(u"lb_name")
 
-        self.verticalLayout.addWidget(self.lb_name)
+        self.horizontalLayout_5.addWidget(self.lb_name)
 
         self.le_name = QLineEdit(Dialog)
         self.le_name.setObjectName(u"le_name")
 
-        self.verticalLayout.addWidget(self.le_name)
+        self.horizontalLayout_5.addWidget(self.le_name)
 
+
+        self.verticalLayout.addLayout(self.horizontalLayout_5)
+
+        self.horizontalLayout_6 = QHBoxLayout()
+        self.horizontalLayout_6.setObjectName(u"horizontalLayout_6")
         self.lb_description = QLabel(Dialog)
         self.lb_description.setObjectName(u"lb_description")
 
-        self.verticalLayout.addWidget(self.lb_description)
+        self.horizontalLayout_6.addWidget(self.lb_description)
 
         self.le_description = QLineEdit(Dialog)
         self.le_description.setObjectName(u"le_description")
 
-        self.verticalLayout.addWidget(self.le_description)
+        self.horizontalLayout_6.addWidget(self.le_description)
+
 
+        self.verticalLayout.addLayout(self.horizontalLayout_6)
+
+        self.horizontalLayout_7 = QHBoxLayout()
+        self.horizontalLayout_7.setObjectName(u"horizontalLayout_7")
         self.lbType = QLabel(Dialog)
         self.lbType.setObjectName(u"lbType")
 
-        self.verticalLayout.addWidget(self.lbType)
+        self.horizontalLayout_7.addWidget(self.lbType)
 
         self.cbType = QComboBox(Dialog)
         self.cbType.addItem("")
@@ -134,7 +144,14 @@ class Ui_Dialog(object):
         self.cbType.addItem("")
         self.cbType.setObjectName(u"cbType")
 
-        self.verticalLayout.addWidget(self.cbType)
+        self.horizontalLayout_7.addWidget(self.cbType)
+
+        self.horizontalSpacer_3 = QSpacerItem(40, 20, QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Minimum)
+
+        self.horizontalLayout_7.addItem(self.horizontalSpacer_3)
+
+
+        self.verticalLayout.addLayout(self.horizontalLayout_7)
 
         self.lbValues = QLabel(Dialog)
         self.lbValues.setObjectName(u"lbValues")
@@ -198,28 +215,32 @@ class Ui_Dialog(object):
 
         self.horizontalLayout_4 = QHBoxLayout()
         self.horizontalLayout_4.setObjectName(u"horizontalLayout_4")
-
-        self.verticalLayout.addLayout(self.horizontalLayout_4)
-
         self.pb_add_subjects = QPushButton(Dialog)
         self.pb_add_subjects.setObjectName(u"pb_add_subjects")
 
-        self.verticalLayout.addWidget(self.pb_add_subjects)
+        self.horizontalLayout_4.addWidget(self.pb_add_subjects)
 
         self.pb_load_file = QPushButton(Dialog)
         self.pb_load_file.setObjectName(u"pb_load_file")
 
-        self.verticalLayout.addWidget(self.pb_load_file)
+        self.horizontalLayout_4.addWidget(self.pb_load_file)
+
+        self.horizontalSpacer_2 = QSpacerItem(40, 20, QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Minimum)
+
+        self.horizontalLayout_4.addItem(self.horizontalSpacer_2)
+
+
+        self.verticalLayout.addLayout(self.horizontalLayout_4)
 
         self.verticalSpacer_3 = QSpacerItem(20, 40, QSizePolicy.Policy.Minimum, QSizePolicy.Policy.Expanding)
 
         self.verticalLayout.addItem(self.verticalSpacer_3)
 
 
-        self.horizontalLayout_5.addLayout(self.verticalLayout)
+        self.horizontalLayout_8.addLayout(self.verticalLayout)
 
 
-        self.verticalLayout_4.addLayout(self.horizontalLayout_5)
+        self.verticalLayout_4.addLayout(self.horizontalLayout_8)
 
         self.horizontalLayout_2 = QHBoxLayout()
         self.horizontalLayout_2.setObjectName(u"horizontalLayout_2")
@@ -241,9 +262,6 @@ class Ui_Dialog(object):
         self.verticalLayout_4.addLayout(self.horizontalLayout_2)
 
 
-        self.verticalLayout_5.addLayout(self.verticalLayout_4)
-
-
         self.retranslateUi(Dialog)
 
         self.tabWidgetModifiersSets.setCurrentIndex(-1)
@@ -256,8 +274,8 @@ class Ui_Dialog(object):
         Dialog.setWindowTitle(QCoreApplication.translate("Dialog", u"Set modifiers", None))
         self.cb_ask_at_stop.setText(QCoreApplication.translate("Dialog", u"Ask for modifier(s) when behavior stops", None))
         self.lbModifier.setText(QCoreApplication.translate("Dialog", u"Modifier", None))
-        self.lbCode.setText(QCoreApplication.translate("Dialog", u"Key code", None))
-        self.lbCodeHelp.setText(QCoreApplication.translate("Dialog", u"Key code is case sensitive. Type one character or a function key (F1, F2... F12)", None))
+        self.lbCode.setText(QCoreApplication.translate("Dialog", u"Shortcut", None))
+        self.lbCodeHelp.setText(QCoreApplication.translate("Dialog", u"The shortcut is case sensitive. Type one character or a function key (F1, F2... F12)", None))
         self.pbAddModifier.setText(QCoreApplication.translate("Dialog", u"->", None))
         self.pbModifyModifier.setText(QCoreApplication.translate("Dialog", u"<-", None))
         self.lb_name.setText(QCoreApplication.translate("Dialog", u"Set name", None))

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_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/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/config.py

@@ -132,6 +132,8 @@ POINT_EVENT_PLOT_COLOR = "black"
 
 CHAR_FORBIDDEN_IN_MODIFIERS = "(|),`~"
 
+FAST_FORWARD_DEFAULT_VALUE: float = 10.0
+
 ADAPT_FAST_JUMP = "adapt_fast_jump"
 ADAPT_FAST_JUMP_DEFAULT = False
 
@@ -419,6 +421,10 @@ MPV_HWDEC_AUTOSAFE = "auto-safe"
 MPV_HWDEC_OPTIONS = (MPV_HWDEC_AUTO, MPV_HWDEC_AUTOSAFE, MPV_HWDEC_NO)
 MPV_HWDEC_DEFAULT_VALUE = MPV_HWDEC_AUTO
 
+# frame step size (disabled)
+# FRAME_STEP_SIZE: str = "frame_step_size"
+# FRAME_STEP_SIZE_DEFAULT_VALUE: int = 1
+
 ANALYSIS_PLUGINS = "analysis_plugins"
 EXCLUDED_PLUGINS = "excluded_plugins"
 PERSONAL_PLUGINS_DIR = "personal_plugins_dir"
@@ -730,6 +736,7 @@ INIT_PARAM = {
     MPV_HWDEC: MPV_HWDEC_DEFAULT_VALUE,
     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,
 }
 
 SDIS_EXT = "sds"

boris/config_file.py

@@ -82,11 +82,11 @@ def read(self):
 
         logging.debug(f"time format: {self.timeFormat}")
 
-        self.fast = 10
+        self.fast = cfg.FAST_FORWARD_DEFAULT_VALUE
         try:
-            self.fast = int(settings.value("Time/fast_forward_speed"))
+            self.fast = float(settings.value("Time/fast_forward_speed"))
         except Exception:
-            self.fast = 10
+            self.fast = cfg.FAST_FORWARD_DEFAULT_VALUE
 
         logging.debug(f"Time/fast_forward_speed: {self.fast}")