Merge branch 'all_modifiers'

.gitignore

@@ -8,3 +8,4 @@ dist
 tests/output
 boris_behav_obs.egg-info
 .venv
+uv.lock

.python-version

@@ -1 +1 @@
-3.12.3
+3.12.6

boris/advanced_event_filtering.py

@@ -358,8 +358,8 @@ def event_filtering(self):
         start_coding=start_coding,
         end_coding=end_coding,
         maxTime=max_media_duration_all_obs,
-        flagShowIncludeModifiers=False,
-        flagShowExcludeBehaviorsWoEvents=False,
+        show_include_modifiers=False,
+        show_exclude_non_coded_behaviors=False,
         by_category=False,
         n_observations=len(selected_observations),
     )

boris/behavior_binary_table.py

@@ -207,8 +207,8 @@ def behavior_binary_table(self):
         start_coding=start_coding,
         end_coding=end_coding,
         maxTime=max_media_duration_all_obs,
-        flagShowIncludeModifiers=True,
-        flagShowExcludeBehaviorsWoEvents=True,
+        show_include_modifiers=True,
+        show_exclude_non_coded_behaviors=True,
         by_category=False,
         n_observations=len(selected_observations),
     )

boris/config.py

@@ -365,6 +365,7 @@
 SELECTED_SUBJECTS = "selected subjects"
 INCLUDE_MODIFIERS = "include modifiers"
 EXCLUDE_BEHAVIORS = "exclude behaviors"
+EXCLUDE_NON_CODED_MODIFIERS = "exclude_non_coded_modifiers"
 EXCLUDED_BEHAVIORS = "excluded behaviors"
 TIME_INTERVAL = "time"
 START_TIME = "start time"

boris/cooccurence.py

@@ -101,8 +101,8 @@ def interval_len(interval: I) -> dec:
             selected_observations,
             window_title="Select the behaviors",
             n_observations=len(selected_observations),
-            flagShowIncludeModifiers=False,
-            flagShowExcludeBehaviorsWoEvents=True,
+            show_include_modifiers=False,
+            show_exclude_non_coded_behaviors=True,
         )
 
         if parameters == {}:  # cancel button pressed

boris/core.py

@@ -774,7 +774,7 @@ def filter_behaviors(
         """
 
         if not self.pj[cfg.ETHOGRAM]:
-            True, []
+            return True, []
 
         behavior_type = [x.upper() for x in behavior_type]
 
@@ -2750,7 +2750,7 @@ def plot_events_triggered(self, mode: str = "list"):
             start_coding=start_coding,
             end_coding=end_coding,
             maxTime=max_obs_length,
-            flagShowExcludeBehaviorsWoEvents=True,
+            show_exclude_non_coded_behaviors=True,
             by_category=False,
             n_observations=len(selected_observations),
         )
@@ -2849,8 +2849,8 @@ def behaviors_bar_plot(self, mode: str = "list"):
             start_coding=start_coding,
             end_coding=end_coding,
             maxTime=max_obs_length if len(selected_observations) > 1 else selectedObsTotalMediaLength,
-            flagShowIncludeModifiers=False,
-            flagShowExcludeBehaviorsWoEvents=True,
+            show_include_modifiers=False,
+            show_exclude_non_coded_behaviors=True,
             n_observations=len(selected_observations),
         )
 
@@ -3730,8 +3730,8 @@ def create_subtitles(self):
             start_coding=start_coding,
             end_coding=end_coding,
             maxTime=max_media_duration_all_obs,
-            flagShowIncludeModifiers=False,
-            flagShowExcludeBehaviorsWoEvents=False,
+            show_include_modifiers=False,
+            show_exclude_non_coded_behaviors=False,
             n_observations=len(selected_observations),
         )
         if parameters == {}:

boris/db_functions.py

@@ -70,6 +70,7 @@ def load_events_in_db(
     """
 
     db = sqlite3.connect(":memory:", isolation_level=None)
+
     """
     import os
     os.system("rm /tmp/ramdisk/events.sqlite")
@@ -212,6 +213,7 @@ 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)

boris/event_operations.py

@@ -222,8 +222,8 @@ def filter_events(self):
         start_coding=dec("NaN"),
         end_coding=dec("NaN"),
         maxTime=None,
-        flagShowIncludeModifiers=False,
-        flagShowExcludeBehaviorsWoEvents=False,
+        show_include_modifiers=False,
+        show_exclude_non_coded_behaviors=False,
         by_category=False,
     )
     if parameters == {}:
@@ -983,9 +983,9 @@ def add_frame_indexes(self):
             continue
         if not self.seek_mediaplayer(event[0]):
             time.sleep(0.1)
-            self.pj[cfg.OBSERVATIONS][self.observationId][cfg.EVENTS][idx][
-                cfg.PJ_OBS_FIELDS[cfg.MEDIA][cfg.FRAME_INDEX]
-            ] = self.get_frame_index()
+            self.pj[cfg.OBSERVATIONS][self.observationId][cfg.EVENTS][idx][cfg.PJ_OBS_FIELDS[cfg.MEDIA][cfg.FRAME_INDEX]] = (
+                self.get_frame_index()
+            )
 
     self.seek_mediaplayer(mem_time)
 

boris/events_snapshots.py

@@ -21,7 +21,6 @@
 
 """
 
-
 import logging
 import os
 import pathlib as pl
@@ -80,8 +79,8 @@ def events_snapshots(self):
         selected_observations,
         start_coding=dec("NaN"),
         end_coding=dec("NaN"),
-        flagShowIncludeModifiers=False,
-        flagShowExcludeBehaviorsWoEvents=False,
+        show_include_modifiers=False,
+        show_exclude_non_coded_behaviors=False,
         n_observations=len(selected_observations),
     )
 
@@ -346,8 +345,8 @@ def extract_events(self):
         selected_observations,
         start_coding=dec("NaN"),
         end_coding=dec("NaN"),
-        flagShowIncludeModifiers=False,
-        flagShowExcludeBehaviorsWoEvents=False,
+        show_include_modifiers=False,
+        show_exclude_non_coded_behaviors=False,
     )
     if parameters == {}:
         return

boris/export_events.py

@@ -82,8 +82,8 @@ def export_events_as_behavioral_sequences(self, separated_subjects=False, timed=
         start_coding=start_coding,
         end_coding=end_coding,
         maxTime=max_media_duration_all_obs,
-        flagShowIncludeModifiers=True,
-        flagShowExcludeBehaviorsWoEvents=False,
+        show_include_modifiers=True,
+        show_exclude_non_coded_behaviors=False,
         n_observations=len(selected_observations),
     )
 
@@ -171,8 +171,8 @@ def export_tabular_events(self, mode: str = "tabular") -> None:
         start_coding=start_coding,
         end_coding=end_coding,
         maxTime=max_media_duration_all_obs,
-        flagShowIncludeModifiers=False,
-        flagShowExcludeBehaviorsWoEvents=False,
+        show_include_modifiers=False,
+        show_exclude_non_coded_behaviors=False,
         n_observations=len(selected_observations),
     )
     if parameters == {}:
@@ -283,7 +283,7 @@ def export_aggregated_events(self):
     - select subjects and behaviors
     - export events in aggregated format
 
-    Formats can be SQL (sql), SDIS (sds) or Tabular format (tsv, csv, ods, xlsx, xls, html)
+    Formats can be SQL (sql), SDIS (sds), Tabular format (tsv, csv, ods, xlsx, xls, html) or Pandas dataframe
     """
 
     def fields_type(max_modif_number: int) -> dict:
@@ -366,14 +366,14 @@ def fields_type(max_modif_number: int) -> dict:
         start_coding=start_coding,
         end_coding=end_coding,
         maxTime=max_media_duration_all_obs,
-        flagShowIncludeModifiers=False,
-        flagShowExcludeBehaviorsWoEvents=False,
+        show_include_modifiers=False,
+        show_exclude_non_coded_behaviors=False,
         n_observations=len(selected_observations),
     )
     if parameters == {}:
         return
     if not parameters[cfg.SELECTED_SUBJECTS] or not parameters[cfg.SELECTED_BEHAVIORS]:
-        QMessageBox.warning(None, cfg.programName, "Select subject(s) and behavior(s) to analyze")
+        QMessageBox.warning(None, cfg.programName, "Select subject(s) and behavior(s) to export")
         return
 
     # check for grouping results
@@ -660,8 +660,8 @@ def export_events_as_textgrid(self) -> None:
         selected_observations,
         start_coding=start_coding,
         end_coding=end_coding,
-        flagShowIncludeModifiers=False,
-        flagShowExcludeBehaviorsWoEvents=False,
+        show_include_modifiers=False,
+        show_exclude_non_coded_behaviors=False,
         maxTime=max_obs_length,
         n_observations=len(selected_observations),
     )

boris/export_observation.py

@@ -583,7 +583,7 @@ def dataset_write(dataset: tablib.Dataset, file_name: str, output_format: str, d
     try:
         if output_format in (cfg.PANDAS_DF_EXT, cfg.RDS_EXT):
             # build pandas dataframe from the tsv export of tablib dataset
-            date_type = []
+            date_type: list = []
             for field_name in dtype:
                 if dtype[field_name] == dt.datetime:
                     date_type.append(field_name)

boris/irr.py

@@ -288,8 +288,8 @@ def irr_cohen_kappa(self):
         selected_observations,
         start_coding=dec("NaN"),
         end_coding=dec("NaN"),
-        flagShowIncludeModifiers=True,
-        flagShowExcludeBehaviorsWoEvents=False,
+        show_include_modifiers=True,
+        show_exclude_non_coded_behaviors=False,
         n_observations=len(selected_observations),
     )
     if parameters == {}:
@@ -581,8 +581,8 @@ def needleman_wunch(self):
         selected_observations,
         start_coding=dec("NaN"),
         end_coding=dec("NaN"),
-        flagShowIncludeModifiers=True,
-        flagShowExcludeBehaviorsWoEvents=False,
+        show_include_modifiers=True,
+        show_exclude_non_coded_behaviors=False,
         n_observations=len(selected_observations),
     )
 

boris/latency.py

@@ -83,7 +83,7 @@ def get_latency(self):
     parameters: dict = select_subj_behav.choose_obs_subj_behav_category(
         self,
         selected_observations,
-        flagShowExcludeBehaviorsWoEvents=False,
+        show_exclude_non_coded_behaviors=False,
         window_title="Select the marker behaviors (stimulus)",
         n_observations=len(selected_observations),
     )
@@ -102,7 +102,7 @@ def get_latency(self):
     print(f"{marker_behaviors=} {marker_subjects=} {include_marker_modifiers=}")
 
     parameters: dict = select_subj_behav.choose_obs_subj_behav_category(
-        self, selected_observations, flagShowExcludeBehaviorsWoEvents=False, window_title="Select the latency behaviors"
+        self, selected_observations, show_exclude_non_coded_behaviors=False, window_title="Select the latency behaviors"
     )
     if not parameters[cfg.SELECTED_SUBJECTS] or not parameters[cfg.SELECTED_BEHAVIORS]:
         return

boris/param_panel.py

@@ -20,7 +20,6 @@
 
 """
 
-
 from PyQt5.QtCore import Qt
 from PyQt5.QtWidgets import QDialog
 
@@ -61,6 +60,16 @@ def __init__(self, parent=None):
         self.rb_observed_events.clicked.connect(lambda: self.rb_time_interval_selection(cfg.TIME_EVENTS))
         self.rb_user_defined.clicked.connect(lambda: self.rb_time_interval_selection(cfg.TIME_ARBITRARY_INTERVAL))
 
+        self.cbIncludeModifiers.stateChanged.connect(self.cb_exclude_non_coded_modifiers_visibility)
+
+        self.cb_exclude_non_coded_modifiers.setVisible(False)
+
+    def cb_exclude_non_coded_modifiers_visibility(self):
+        """
+        set visibility of cb_exclude_non_coded_modifiers
+        """
+        self.cb_exclude_non_coded_modifiers.setEnabled(self.cbIncludeModifiers.isChecked())
+
     def rb_time_interval_selection(self, button):
         """
         select the time interval for operation

boris/param_panel.ui

@@ -121,6 +121,16 @@
          </property>
         </widget>
        </item>
+       <item>
+        <widget class="QCheckBox" name="cb_exclude_non_coded_modifiers">
+         <property name="text">
+          <string>Exclude non coded modifiers</string>
+         </property>
+         <property name="checked">
+          <bool>true</bool>
+         </property>
+        </widget>
+       </item>
        <item>
         <widget class="QCheckBox" name="cbExcludeBehaviors">
          <property name="text">

boris/param_panel_ui.py

@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'boris/param_panel.ui'
 #
-# Created by: PyQt5 UI code generator 5.15.4
+# Created by: PyQt5 UI code generator 5.15.6
 #
 # WARNING: Any manual changes made to this file will be lost when pyuic5 is
 # run again.  Do not edit this file unless you know what you are doing.
@@ -64,6 +64,10 @@ def setupUi(self, Dialog):
         self.cbIncludeModifiers = QtWidgets.QCheckBox(Dialog)
         self.cbIncludeModifiers.setObjectName("cbIncludeModifiers")
         self.horizontalLayout_9.addWidget(self.cbIncludeModifiers)
+        self.cb_exclude_non_coded_modifiers = QtWidgets.QCheckBox(Dialog)
+        self.cb_exclude_non_coded_modifiers.setChecked(True)
+        self.cb_exclude_non_coded_modifiers.setObjectName("cb_exclude_non_coded_modifiers")
+        self.horizontalLayout_9.addWidget(self.cb_exclude_non_coded_modifiers)
         self.cbExcludeBehaviors = QtWidgets.QCheckBox(Dialog)
         self.cbExcludeBehaviors.setObjectName("cbExcludeBehaviors")
         self.horizontalLayout_9.addWidget(self.cbExcludeBehaviors)
@@ -177,6 +181,7 @@ def retranslateUi(self, Dialog):
         self.pbUnselectAllBehaviors.setText(_translate("Dialog", "Unselect all"))
         self.pbReverseBehaviorsSelection.setText(_translate("Dialog", "Reverse selection"))
         self.cbIncludeModifiers.setText(_translate("Dialog", "Include modifiers"))
+        self.cb_exclude_non_coded_modifiers.setText(_translate("Dialog", "Exclude non coded modifiers"))
         self.cbExcludeBehaviors.setText(_translate("Dialog", "Exclude behaviors without events"))
         self.lb_time_bin_size.setText(_translate("Dialog", "Time bin size (s)"))
         self.lb_time_interval.setText(_translate("Dialog", "Time interval"))