boris-behav-obs 9.6.2__py2.py3-none-any.whl → 9.6.4__py2.py3-none-any.whl

boris/1.py

@@ -0,0 +1,45 @@
+import time
+from PIL import Image, ImageDraw, ImageFont
+import mpv
+
+player = mpv.MPV()
+
+player.loop = True
+player.play('/home/olivier/gdrive_sync/src/python/generate_video_test/video1.mp4')
+player.wait_until_playing()
+
+font = ImageFont.truetype('DejaVuSans.ttf', 40)
+
+overlay = player.create_image_overlay()
+
+img = Image.new('RGBA', (400, 150),  (255, 255, 255, 0))
+d = ImageDraw.Draw(img)
+d.text((10, 10), 'Hello World', font=font, fill=(0, 255, 255, 128))
+#d.text((10, 60), f't={ts:.3f}', font=font, fill=(255, 0, 255, 255))
+
+pos = 100
+
+overlay.update(img, pos=(2*pos, pos))
+
+
+while not player.core_idle:
+    pass
+
+
+    '''
+    for pos in range(0, 500, 5):
+        ts = player.time_pos
+        if ts is None:
+            break
+
+        img = Image.new('RGBA', (400, 150),  (255, 255, 255, 0))
+        d = ImageDraw.Draw(img)
+        d.text((10, 10), 'Hello World', font=font, fill=(0, 255, 255, 128))
+        d.text((10, 60), f't={ts:.3f}', font=font, fill=(255, 0, 255, 255))
+
+        overlay.update(img, pos=(2*pos, pos))
+        time.sleep(0.05)
+
+
+    overlay.remove()
+    '''

boris/analysis_plugins/irr_cohen_kappa.py

@@ -1,35 +1,59 @@
 """
 BORIS plugin
 
-Inter Rater Reliability (IRR) Unweighted Cohen Kappa
+Inter Rater Reliability (IRR) Unweighted Cohen's Kappa
 """
 
 import pandas as pd
 from sklearn.metrics import cohen_kappa_score
+from typing import Dict, Tuple
 
-__version__ = "0.0.1"
-__version_date__ = "2025-08-25"
-__plugin_name__ = "Inter Rater Reliability - Unweighted Cohen Kappa"
+__version__ = "0.0.2"
+__version_date__ = "2025-08-29"
+__plugin_name__ = "Inter Rater Reliability - Unweighted Cohen's Kappa"
 __author__ = "Olivier Friard - University of Torino - Italy"
+__description__ = """
+This plugin calculates Cohen's Kappa to measure inter-rater reliability between two observers who code categorical behaviors over time intervals.
+Unlike the weighted version, this approach does not take into account the duration of the intervals.
+Each segment of time is treated equally, regardless of how long it lasts.
+This plugin does not take into account the modifiers.
 
+How it works:
 
-def run(df: pd.DataFrame):
+Time segmentation
+The program identifies all the time boundaries (start and end points) used by both observers.
+These boundaries are merged into a common timeline, which is then divided into a set of non-overlapping elementary intervals.
+
+Assigning codes
+For each elementary interval, the program determines which behavior was coded by each observer.
+
+Comparison of codes
+The program builds two parallel lists of behavior codes, one for each observer.
+Each elementary interval is counted as one unit of observation, no matter how long the interval actually lasts.
+
+Cohen's Kappa calculation
+Using these two lists, the program computes Cohen's Kappa using the cohen_kappa_score function of the sklearn package.
+(see https://scikit-learn.org/stable/modules/generated/sklearn.metrics.cohen_kappa_score.html for details)
+This coefficient measures how much the observers agree on their coding, adjusted for the amount of agreement that would be expected by chance.
+
+"""
+
+
+def run(df: pd.DataFrame) -> pd.DataFrame:
     """
-    Calculate the Inter Rater Reliability - Unweighted Cohen Kappa
+    Calculate the Inter Rater Reliability - Unweighted Cohen's Kappa
     """
 
-    # attribute a code for each interval
+    # Attribute all active codes for each interval
     def get_code(t_start, obs):
-        for seg in obs:
-            if t_start >= seg[0] and t_start < seg[1]:
-                return seg[2]
-        return ""
-
-    # Get unique values as a numpy array
-    unique_obs = df["Observation id"].unique()
+        active_codes = [seg[2] for seg in obs if seg[0] <= t_start < seg[1]]
+        if not active_codes:
+            return ""
+        # Sort to ensure deterministic representation (e.g., "A+B" instead of "B+A")
+        return "+".join(sorted(active_codes))
 
-    # Convert to a list
-    unique_obs_list = unique_obs.tolist()
+    # Get unique values
+    unique_obs_list = df["Observation id"].unique().tolist()
 
     # Convert to tuples grouped by observation
     grouped = {
@@ -40,10 +64,11 @@ def run(df: pd.DataFrame):
         for obs, group in df.groupby("Observation id")
     }
 
-    ck_results: dict = {}
+    ck_results: Dict[Tuple[str, str], str] = {}
     for idx1, obs_id1 in enumerate(unique_obs_list):
         obs1 = grouped[obs_id1]
 
+        # Perfect agreement with itself
         ck_results[(obs_id1, obs_id1)] = "1.000"
 
         for obs_id2 in unique_obs_list[idx1 + 1 :]:

boris/analysis_plugins/irr_cohen_kappa_with_modifiers.py

@@ -1,35 +1,59 @@
 """
 BORIS plugin
 
-Inter Rater Reliability (IRR) Unweighted Cohen Kappa with modifiers
+Inter Rater Reliability (IRR) Unweighted Cohen's Kappa with modifiers
 """
 
 import pandas as pd
 from sklearn.metrics import cohen_kappa_score
 
-__version__ = "0.0.1"
-__version_date__ = "2025-08-25"
-__plugin_name__ = "Inter Rater Reliability - Unweighted Cohen Kappa with modifiers"
+__version__ = "0.0.2"
+__version_date__ = "2025-08-29"
+__plugin_name__ = "Inter Rater Reliability - Unweighted Cohen's Kappa with modifiers"
 __author__ = "Olivier Friard - University of Torino - Italy"
+__description__ = """
+This plugin calculates Cohen's Kappa to measure inter-rater reliability between two observers who code categorical behaviors over time intervals.
+Unlike the weighted version, this approach does not take into account the duration of the intervals.
+Each segment of time is treated equally, regardless of how long it lasts.
+This plugin takes into account the modifiers.
+
+
+How it works:
+
+Time segmentation
+The program identifies all the time boundaries (start and end points) used by both observers.
+These boundaries are merged into a common timeline, which is then divided into a set of non-overlapping elementary intervals.
+
+Assigning codes
+For each elementary interval, the program determines which behavior was coded by each observer.
+
+Comparison of codes
+The program builds two parallel lists of behavior codes, one for each observer.
+Each elementary interval is counted as one unit of observation, no matter how long the interval actually lasts.
+
+Cohen's Kappa calculation
+Using these two lists, the program computes Cohen's Kappa using the cohen_kappa_score function of the sklearn package.
+(see https://scikit-learn.org/stable/modules/generated/sklearn.metrics.cohen_kappa_score.html for details)
+This coefficient measures how much the observers agree on their coding, adjusted for the amount of agreement that would be expected by chance.
+
+"""
 
 
 def run(df: pd.DataFrame):
     """
-    Calculate the Inter Rater Reliability - Unweighted Cohen Kappa with modifiers
+    Calculate the Inter Rater Reliability - Unweighted Cohen's Kappa with modifiers
     """
 
-    # attribute a code for each interval
+    # Attribute all active codes for each interval
     def get_code(t_start, obs):
-        for seg in obs:
-            if t_start >= seg[0] and t_start < seg[1]:
-                return seg[2]
-        return ""
-
-    # Get unique values as a numpy array
-    unique_obs = df["Observation id"].unique()
-
-    # Convert to a list
-    unique_obs_list = unique_obs.tolist()
+        active_codes = [seg[2] for seg in obs if seg[0] <= t_start < seg[1]]
+        if not active_codes:
+            return ""
+        # Sort to ensure deterministic representation (e.g., "A+B" instead of "B+A")
+        return "+".join(sorted(active_codes))
+
+    # Get unique values
+    unique_obs_list = df["Observation id"].unique().tolist()
 
     # Convert to tuples grouped by observation
     grouped: dict = {}

boris/analysis_plugins/irr_weighted_cohen_kappa.py

@@ -1,21 +1,47 @@
 """
 BORIS plugin
 
-Inter Rater Reliability (IRR) Weighted Cohen Kappa
+Inter Rater Reliability (IRR) Weighted Cohen's Kappa
 """
 
 import pandas as pd
 from typing import List, Tuple, Dict, Optional
 
-__version__ = "0.0.1"
-__version_date__ = "2025-08-25"
-__plugin_name__ = "Inter Rater Reliability - Weighted Cohen Kappa"
+__version__ = "0.0.2"
+__version_date__ = "2025-08-29"
+__plugin_name__ = "Inter Rater Reliability - Weighted Cohen's Kappa"
 __author__ = "Olivier Friard - University of Torino - Italy"
+__description__ = """
+This plugin calculates Cohen's Kappa to measure inter-rater reliability between two observers who code categorical behaviors over time intervals.
+Unlike the unweighted version, this approach takes into account the duration of each coded interval, giving more weight to longer intervals in the agreement calculation.
+This plugin does not take into account the modifiers.
+
+How it works:
+
+Time segmentation
+The program collects all the time boundaries from both observers and merges them into a unified set of time points.
+These define a set of non-overlapping elementary intervals covering the entire observed period.
+
+Assigning codes
+For each elementary interval, the program identifies the behavior category assigned by each observer.
+
+Weighted contingency table
+Instead of treating each interval equally, the program assigns a weight equal to the duration of the interval.
+These durations are accumulated in a contingency table that records how much time was spent in each combination of categories across the two observers.
+
+Agreement calculation
+
+Observed agreement (po): The proportion of total time where both observers assigned the same category.
+
+Expected agreement (pe): The proportion of agreement expected by chance, based on the time-weighted marginal distributions of each observer's coding.
+
+Cohen's Kappa (κ): Computed from the weighted observed and expected agreements.
+"""
 
 
 def run(df: pd.DataFrame):
     """
-    Calculate the Inter Rater Reliability - Weighted Cohen Kappa
+    Calculate the Inter Rater Reliability - Weighted Cohen's Kappa
     """
 
     def cohen_kappa_weighted_by_time(
@@ -41,12 +67,12 @@ def run(df: pd.DataFrame):
         # 2. Build elementary intervals (non-overlapping time bins)
         elementary_intervals = [(time_points[i], time_points[i + 1]) for i in range(len(time_points) - 1)]
 
-        # 3. Helper: get the active code for an observer at a given time
+        # 3. # Attribute all active codes for each interval
         def get_code(t: float, obs: List[Tuple[float, float, str]]) -> Optional[str]:
-            for seg in obs:
-                if seg[0] <= t < seg[1]:
-                    return seg[2]
-            return None  # in case no segment covers this time
+            active_codes = [seg[2] for seg in obs if seg[0] <= t < seg[1]]
+            if not active_codes:
+                return None
+            return "+".join(sorted(active_codes))  # rappresentazione deterministica
 
         # 4. Build weighted contingency table (durations instead of counts)
         contingency: Dict[Tuple[Optional[str], Optional[str]], float] = {}

boris/analysis_plugins/irr_weighted_cohen_kappa_with_modifiers.py

@@ -1,21 +1,47 @@
 """
 BORIS plugin
 
-Inter Rater Reliability (IRR) Weighted Cohen Kappa with modifiers
+Inter Rater Reliability (IRR) Weighted Cohen's Kappa with modifiers
 """
 
 import pandas as pd
 from typing import List, Tuple, Dict, Optional
 
-__version__ = "0.0.1"
-__version_date__ = "2025-08-25"
-__plugin_name__ = "Inter Rater Reliability - Weighted Cohen Kappa with modifiers"
+__version__ = "0.0.2"
+__version_date__ = "2025-08-29"
+__plugin_name__ = "Inter Rater Reliability - Weighted Cohen's Kappa with modifiers"
 __author__ = "Olivier Friard - University of Torino - Italy"
+__description__ = """
+This plugin calculates Cohen's Kappa to measure inter-rater reliability between two observers who code categorical behaviors over time intervals.
+Unlike the unweighted version, this approach takes into account the duration of each coded interval, giving more weight to longer intervals in the agreement calculation.
+This plugin takes into account the modifiers.
+
+How it works:
+
+Time segmentation
+The program collects all the time boundaries from both observers and merges them into a unified set of time points.
+These define a set of non-overlapping elementary intervals covering the entire observed period.
+
+Assigning codes
+For each elementary interval, the program identifies the behavior category assigned by each observer.
+
+Weighted contingency table
+Instead of treating each interval equally, the program assigns a weight equal to the duration of the interval.
+These durations are accumulated in a contingency table that records how much time was spent in each combination of categories across the two observers.
+
+Agreement calculation
+
+Observed agreement (po): The proportion of total time where both observers assigned the same category.
+
+Expected agreement (pe): The proportion of agreement expected by chance, based on the time-weighted marginal distributions of each observer's coding.
+
+Cohen's Kappa (κ): Computed from the weighted observed and expected agreements.
+"""
 
 
 def run(df: pd.DataFrame):
     """
-    Calculate the Inter Rater Reliability - Weighted Cohen Kappa with modifiers
+    Calculate the Inter Rater Reliability - Weighted Cohen's Kappa with modifiers
     """
 
     def cohen_kappa_weighted_by_time(
@@ -41,12 +67,12 @@ def run(df: pd.DataFrame):
         # 2. Build elementary intervals (non-overlapping time bins)
         elementary_intervals = [(time_points[i], time_points[i + 1]) for i in range(len(time_points) - 1)]
 
-        # 3. Helper: get the active code for an observer at a given time
+        # 3. Attribute all active codes for each interval
         def get_code(t: float, obs: List[Tuple[float, float, str]]) -> Optional[str]:
-            for seg in obs:
-                if seg[0] <= t < seg[1]:
-                    return seg[2]
-            return None  # in case no segment covers this time
+            active_codes = [seg[2] for seg in obs if seg[0] <= t < seg[1]]
+            if not active_codes:
+                return None
+            return "+".join(sorted(active_codes))  # rappresentazione deterministica
 
         # 4. Build weighted contingency table (durations instead of counts)
         contingency: Dict[Tuple[Optional[str], Optional[str]], float] = {}

boris/analysis_plugins/time_budget.py

@@ -26,10 +26,6 @@ def run(df: pd.DataFrame):
     - % of total subject observation duration
     """
 
-    print("running time budget plugin")
-
-    print(df)
-
     group_by = ["Subject", "Behavior"]
 
     dfs = [

boris/behav_coding_map_creator.py

@@ -431,7 +431,6 @@ class BehaviorsMapCreatorWindow(QMainWindow):
                 self.selectedPolygon = None
                 self.selectedPolygonMemBrush = None
 
-            print(self.polygonsList2)
             idx = 0
             for areaCode, pg in self.polygonsList2:
                 if pg.contains(test):

boris/coding_pad.py

@@ -261,8 +261,6 @@ def show_coding_pad(self):
         self.codingpad.setWindowFlags(Qt.WindowStaysOnTopHint)
         self.codingpad.sendEventSignal.connect(self.signal_from_widget)
 
-        print(f"{self.signal_from_widget=}")
-
         self.codingpad.clickSignal.connect(self.click_signal_from_coding_pad)
         self.codingpad.close_signal.connect(self.close_signal_from_coding_pad)
         self.codingpad.show()

boris/config_file.py

@@ -169,8 +169,6 @@ def read(self):
         # check for new version
         self.checkForNewVersion = False
 
-        # print(f"{self.no_first_launch_dialog=}")
-
         if not self.no_first_launch_dialog:
             try:
                 if settings.value("check_for_new_version") is None:

boris/core.py

@@ -205,7 +205,6 @@ class TableModel(QAbstractTableModel):
             if 0 <= row < self.rowCount():
                 column = index.column()
 
-                # print(self._data[:3])
                 if cfg.TW_EVENTS_FIELDS[self.observation_type][column] == "type":
                     return self._data[row][-1]
                 else:
@@ -2137,39 +2136,47 @@ class MainWindow(QMainWindow, Ui_MainWindow):
             set_and_update_pan_and_zoom(new_pan_x, new_pan_y, new_zoom)
 
         if cmd == "MBTN_LEFT_DBL":
-            print("left dbl")
+            logging.debug("MBTN_LEFT_DBL")
             # ZOOM IN x2
             do_zoom_in_clicked_coords(zoom_increment=1)
             return
         if cmd == "MBTN_RIGHT_DBL":
+            logging.debug("MBTN_RIGHT_DBL")
             # ZOOM OUT x2
             do_zoom_in_clicked_coords(zoom_increment=-1)
             return
         if cmd == "Ctrl+WHEEL_UP":
+            logging.debug("Ctrl+WHEEL_UP")
             # ZOOM IN (3 wheel steps to zoom X2)
             do_zoom_in_clicked_coords(zoom_increment=1.0 / 3.0)
             return
         if cmd == "Ctrl+WHEEL_DOWN":
+            logging.debug("Ctrl+WHEEL_DOWN")
             # ZOOM OUT (3 wheel steps to zoom X2)
             do_zoom_in_clicked_coords(zoom_increment=-1.0 / 3.0)
             return
         if cmd == "WHEEL_UP":
+            logging.debug("WHEEL_UP")
             # PAN UP (VIDEO MOVES DOWN)
             do_pan_in_clicked_coords(pan_x_increment=0, pan_y_increment=+0.01)
             return
         if cmd == "WHEEL_DOWN":
+            logging.debug("WHEEL_DOWN")
             # PAN DOWN (VIDEO MOVES UP)
             do_pan_in_clicked_coords(pan_x_increment=0, pan_y_increment=-0.01)
             return
         if cmd == "Shift+WHEEL_UP":
+            logging.debug("Shift+WHEEL_UP")
             # PAN LEFT (VIDEO MOVES TO THE RIGHT)
             do_pan_in_clicked_coords(pan_x_increment=+0.01, pan_y_increment=0)
             return
         if cmd == "Shift+WHEEL_DOWN":
+            logging.debug("Shift+WHEEL_DOWN")
             # PAN RIGHT (VIDEO MOVES TO THE LEFT)
             do_pan_in_clicked_coords(pan_x_increment=-0.01, pan_y_increment=0)
             return
         if cmd == "Shift+MBTN_LEFT":
+            logging.debug("Shift+MBTN_LEFT")
             # RESET PAN AND ZOOM TO DEFAULT
             set_and_update_pan_and_zoom(pan_x=0, pan_y=0, zoom=0)
             return
@@ -3745,21 +3752,10 @@ class MainWindow(QMainWindow, Ui_MainWindow):
 
             # calculate time for current media file in case of many queued media files
 
-            print(mediaFileIdx_s)
-            print(type(eventtime_s))
-            print(durations)
-
             eventtime_onmedia_s = round(eventtime_s - util.float2decimal(sum(durations[0:mediaFileIdx_s])), 3)
             eventtime_onmedia_e = round(eventtime_e - util.float2decimal(sum(durations[0:mediaFileIdx_e])), 3)
 
-            print(row_s, media_path_s, eventtime_s, eventtime_onmedia_s)
-            print(self.pj[cfg.OBSERVATIONS][self.observationId][cfg.EVENTS][row_s])
-
-            print(row_e, media_path_e, eventtime_e, eventtime_onmedia_e)
-            print(self.pj[cfg.OBSERVATIONS][self.observationId][cfg.EVENTS][row_e])
-
             if media_path_s != media_path_e:
-                print("events are located on 2 different media files")
                 return
 
             media_path = media_path_s
@@ -3770,7 +3766,6 @@ class MainWindow(QMainWindow, Ui_MainWindow):
             if "BORISEXTERNAL" in os.environ:
                 external_command_template = os.environ["BORISEXTERNAL"]
             else:
-                print("BORISEXTERNAL env var not defined")
                 return
 
             external_command = external_command_template.format(
@@ -3853,11 +3848,6 @@ class MainWindow(QMainWindow, Ui_MainWindow):
 
             time_, cumulative_time = self.get_obs_time()
 
-            """
-            print(time_)
-            print(cumulative_time)
-            """
-
             if self.pj[cfg.OBSERVATIONS][self.observationId].get(cfg.MEDIA_CREATION_DATE_AS_OFFSET, False):
                 write_event.write_event(self, event, time_)
             else:
@@ -5222,25 +5212,20 @@ class MainWindow(QMainWindow, Ui_MainWindow):
             if (not self.find_dialog.cbFindInSelectedEvents.isChecked()) or (
                 self.find_dialog.cbFindInSelectedEvents.isChecked() and event_idx in self.find_dialog.rowsToFind
             ):
-                print(f"{event=}")
-
                 # search only on filtered events
                 if event_idx not in self.tv_idx2events_idx:
                     continue
 
                 for idx in fields_list:
-                    print(f"{idx=}")
                     if (self.find_dialog.cb_case_sensitive.isChecked() and self.find_dialog.findText.text() in event[idx]) or (
                         not self.find_dialog.cb_case_sensitive.isChecked()
                         and self.find_dialog.findText.text().upper() in event[idx].upper()
                     ):
                         self.find_dialog.currentIdx = event_idx
 
-                        # self.twEvents.scrollToItem(self.twEvents.item(event_idx, 0))
                         index = self.tv_events.model().index(event_idx, 0)
                         self.tv_events.scrollTo(index, QAbstractItemView.EnsureVisible)
                         self.tv_events.selectRow(event_idx)
-                        # self.twEvents.selectRow(event_idx)
                         return
 
         if msg != "FIND_FROM_BEGINING":

boris/db_functions.py

@@ -188,7 +188,7 @@ def load_aggregated_events_in_db(
         selected_behaviors = sorted([pj[cfg.ETHOGRAM][x][cfg.BEHAVIOR_CODE] for x in pj[cfg.ETHOGRAM]])
 
     # check if state events are paired
-    out = ""
+    out: str = ""
     for obs_id in selected_observations:
         r, msg = project_functions.check_state_events_obs(obs_id, pj[cfg.ETHOGRAM], pj[cfg.OBSERVATIONS][obs_id], cfg.HHMMSS)
         if not r:
@@ -212,11 +212,11 @@ def load_aggregated_events_in_db(
 
     db = sqlite3.connect(":memory:")
 
-    """
     # only for debugging
+    """
     import os
-    os.system("rm /tmp/ramdisk/aggreg.sqlite")
-    db = sqlite3.connect("/tmp/ramdisk/aggreg.sqlite", isolation_level=None)
+    os.system("rm /tmp/ramdisk/aggregated_events.sqlite")
+    db = sqlite3.connect("/tmp/ramdisk/aggregated_events.sqlite", isolation_level=None)
     """
 
     db.row_factory = sqlite3.Row

boris/edit_event.py

@@ -128,8 +128,6 @@ class DlgEditEvent(QDialog, Ui_Form):
         set time to current media time
         """
 
-        print(f"{self.current_time=}")
-
         if self.observation_type in (cfg.LIVE, cfg.MEDIA):
             self.time_widget.set_time(dec(float(self.current_time)))
 
@@ -137,13 +135,6 @@ class DlgEditEvent(QDialog, Ui_Form):
             if self.exif_date_time is not None:
                 self.time_widget.set_time(dec(self.exif_date_time))
 
-    # def frame_idx_na(self):
-    #     """
-    #     set/unset frame index NA
-    #     """
-    #     self.lb_frame_idx.setEnabled(not self.cb_set_frame_idx_na.isChecked())
-    #     self.sb_frame_idx.setEnabled(not self.cb_set_frame_idx_na.isChecked())
-
     def time_na(self):
         """
         set/unset time to NA