boris-behav-obs 9.0.8__tar.gz → 9.1.1__tar.gz

{boris_behav_obs-9.0.8 → boris_behav_obs-9.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: boris-behav-obs
-Version: 9.0.8
+Version: 9.1.1
 Summary: BORIS - Behavioral Observation Research Interactive Software
 Author-email: Olivier Friard <olivier.friard@unito.it>
 License:                     GNU GENERAL PUBLIC LICENSE

{boris_behav_obs-9.0.8 → boris_behav_obs-9.1.1}/boris/advanced_event_filtering.py

@@ -235,7 +235,7 @@ class Advanced_event_filtering_dialog(QDialog):
         self.tw.clear()
 
         if flag_error or self.rb_details.isChecked():
-            self.lb_results.setText(f"Results ({len(self.out)} event{'s'*(len(self.out) > 1)})")
+            self.lb_results.setText(f"Results ({len(self.out)} event{'s' * (len(self.out) > 1)})")
 
             self.tw.setRowCount(len(self.out))
             self.tw.setColumnCount(len(self.details_header))  # obs_id, comment, start, stop, duration
@@ -261,7 +261,7 @@ class Advanced_event_filtering_dialog(QDialog):
                     ]
                 )
 
-            self.lb_results.setText(f"Results ({len(summary)} observation{'s'*(len(summary) > 1)})")
+            self.lb_results.setText(f"Results ({len(summary)} observation{'s' * (len(summary) > 1)})")
             self.tw.setRowCount(len(summary))
             self.tw.setColumnCount(len(self.summary_header))  # obs_id, mean, stdev
             self.tw.setHorizontalHeaderLabels(self.summary_header)
@@ -352,17 +352,22 @@ def event_filtering(self):
 
     max_media_duration_all_obs, _ = observation_operations.media_duration(self.pj[cfg.OBSERVATIONS], selected_observations)
 
+    start_interval, end_interval = observation_operations.time_intervals_range(self.pj[cfg.OBSERVATIONS], selected_observations)
+
     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,
         maxTime=max_media_duration_all_obs,
         show_include_modifiers=False,
         show_exclude_non_coded_behaviors=False,
         by_category=False,
         n_observations=len(selected_observations),
     )
+
     if parameters == {}:
         return
 
@@ -380,7 +385,7 @@ def event_filtering(self):
         cursor.execute("SELECT MIN(start), MAX(stop) FROM aggregated_events")
         min_time, max_time = cursor.fetchone()
 
-    if parameters[cfg.TIME_INTERVAL] == cfg.TIME_ARBITRARY_INTERVAL:
+    if parameters[cfg.TIME_INTERVAL] in (cfg.TIME_ARBITRARY_INTERVAL, cfg.TIME_OBS_INTERVAL):
         min_time = float(parameters[cfg.START_TIME])
         max_time = float(parameters[cfg.END_TIME])
 
@@ -443,6 +448,6 @@ def event_filtering(self):
 
     w = Advanced_event_filtering_dialog(events)
     w.lb_time_interval.setText(
-        ("Time interval: " f"{util.smart_time_format(min_time, self.timeFormat)} - " f"{util.smart_time_format(max_time, self.timeFormat)}")
+        (f"Time interval: {util.smart_time_format(min_time, self.timeFormat)} - {util.smart_time_format(max_time, self.timeFormat)}")
     )
     w.exec_()

{boris_behav_obs-9.0.8 → boris_behav_obs-9.1.1}/boris/analysis_plugins/number_of_occurences.py

@@ -17,10 +17,9 @@ def run(df: pd.DataFrame):
     Calculate the number of occurrences of behaviors by subject.
     """
 
-    string_results: str = ""
     df_results: pd.DataFrame = df.groupby(["Subject", "Behavior"])["Behavior"].count().reset_index(name="number of occurences")
 
-    return df_results, string_results
+    return df_results
 
 
 def main(df: pd.DataFrame, observations_list: list = [], parameters: dict = {}) -> pd.DataFrame:

{boris_behav_obs-9.0.8 → boris_behav_obs-9.1.1}/boris/analysis_plugins/time_budget.py

@@ -26,8 +26,6 @@ def run(df: pd.DataFrame):
     - % of total subject observation duration
     """
 
-    string_results: str = "test\ntest1"
-
     group_by = ["Subject", "Behavior"]
 
     dfs = [
@@ -60,7 +58,7 @@ def run(df: pd.DataFrame):
     for df in dfs[1:]:
         merged_df = pd.merge(merged_df, df, on=group_by)
 
-    return merged_df, string_results
+    return merged_df
 
 
 def main(df: pd.DataFrame, observations_list: list = [], parameters: dict = {}) -> pd.DataFrame:

{boris_behav_obs-9.0.8 → boris_behav_obs-9.1.1}/boris/behavior_binary_table.py

@@ -79,6 +79,14 @@ def create_behavior_binary_table(pj: dict, selected_observations: list, paramete
                 max_obs_length, _ = observation_operations.observation_length(pj, [obs_id])
                 end_time = dec(max_obs_length)
 
+        if parameters_obs["time"] == cfg.TIME_OBS_INTERVAL:
+            obs_interval = pj[cfg.OBSERVATIONS][obs_id][cfg.OBSERVATION_TIME_INTERVAL]
+            offset = pj[cfg.OBSERVATIONS][obs_id][cfg.TIME_OFFSET]
+            start_time = dec(obs_interval[0]) + offset
+            # Use max observation length for end time if no interval is defined (=0)
+            max_obs_length, _ = observation_operations.observation_length(pj, [obs_id])
+            end_time = dec(obs_interval[1]) + offset if obs_interval[1] != 0 else dec(max_obs_length)
+
         if obs_id not in results_df:
             results_df[obs_id] = {}
 
@@ -201,11 +209,15 @@ def behavior_binary_table(self):
 
     start_coding, end_coding, _ = observation_operations.coding_time(self.pj[cfg.OBSERVATIONS], selected_observations)
 
+    start_interval, end_interval = observation_operations.time_intervals_range(self.pj[cfg.OBSERVATIONS], selected_observations)
+
     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,
         maxTime=max_media_duration_all_obs,
         show_include_modifiers=True,
         show_exclude_non_coded_behaviors=True,

{boris_behav_obs-9.0.8 → boris_behav_obs-9.1.1}/boris/config.py

@@ -256,9 +256,13 @@ HAS_AUDIO_IDX = 6
 STATE_EVENT = "State event"
 STATE_EVENT_WITH_CODING_MAP = "State event with coding map"
 
+STATE_EVENT_TYPES = [STATE_EVENT, STATE_EVENT_WITH_CODING_MAP]
+
 POINT_EVENT = "Point event"
 POINT_EVENT_WITH_CODING_MAP = "Point event with coding map"
 
+POINT_EVENT_TYPES = [POINT_EVENT, POINT_EVENT_WITH_CODING_MAP]
+
 BEHAVIOR_TYPES = [
     POINT_EVENT,
     STATE_EVENT,
@@ -395,6 +399,7 @@ TIMESTAMP_idx = 3
 
 TIME_FULL_OBS = "full obs"
 TIME_EVENTS = "limit to events"
+TIME_OBS_INTERVAL = "interval of observation"
 TIME_ARBITRARY_INTERVAL = "time interval"
 
 AVAILABLE_INDEP_VAR_TYPES = [NUMERIC, TEXT, SET_OF_VALUES, TIMESTAMP]

{boris_behav_obs-9.0.8 → boris_behav_obs-9.1.1}/boris/config_file.py

@@ -36,19 +36,19 @@ def read(self):
     read config file
     """
 
-    iniFilePath = pl.Path.home() / pl.Path(".boris")
+    ini_fil_p_pe_p_path = pl.Path.home() / pl.Path(".boris")
 
-    logging.debug(f"read config file: {iniFilePath}")
+    logging.debug(f"read config file: {ini_fil_p_pe_p_path}")
 
-    if iniFilePath.is_file():
-        settings = QSettings(str(iniFilePath), QSettings.IniFormat)
+    if ini_fil_p_pe_p_path.is_file():
+        settings = QSettings(str(ini_fil_p_pe_p_path), QSettings.IniFormat)
 
         try:
             self.config_param = settings.value("config")
         except Exception:
-            self.config_param = None
+            self.config_param = {}
 
-        if self.config_param is None:
+        if self.config_param == {}:
             self.config_param = cfg.INIT_PARAM
 
             # for back compatibility
@@ -245,7 +245,7 @@ def read(self):
             if (
                 dialog.MessageDialog(
                     cfg.programName,
-                    ("The colors list contain colors that are very light.\n" "Do you want to reload the default colors list?"),
+                    ("The colors list contain colors that are very light.\nDo you want to reload the default colors list?"),
                     [cfg.NO, cfg.YES],
                 )
                 == cfg.YES
@@ -262,7 +262,7 @@ def read(self):
             if (
                 dialog.MessageDialog(
                     cfg.programName,
-                    ("The colors list contain colors that are very light.\n" "Do you want to reload the default colors list?"),
+                    ("The colors list contain colors that are very light.\nDo you want to reload the default colors list?"),
                     [cfg.NO, cfg.YES],
                 )
                 == cfg.YES

{boris_behav_obs-9.0.8 → boris_behav_obs-9.1.1}/boris/connections.py

@@ -160,7 +160,9 @@ def connections(self):
     self.actionAll_transitions.triggered.connect(lambda: transitions.transitions_matrix(self, "frequency"))
     self.actionNumber_of_transitions.triggered.connect(lambda: transitions.transitions_matrix(self, "number"))
 
-    self.actionFrequencies_of_transitions_after_behaviors.triggered.connect(lambda: self.transitions_matrix("frequencies_after_behaviors"))
+    self.actionFrequencies_of_transitions_after_behaviors.triggered.connect(
+        lambda: transitions.transitions_matrix(self, "frequencies_after_behaviors")
+    )
 
     # menu playback
     self.actionJumpTo.triggered.connect(self.jump_to)

{boris_behav_obs-9.0.8 → boris_behav_obs-9.1.1}/boris/cooccurence.py

@@ -82,6 +82,8 @@ def get_cooccurence(self):
     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():
@@ -94,12 +96,18 @@ def get_cooccurence(self):
         )
         return
 
+    start_interval, end_interval = observation_operations.time_intervals_range(self.pj[cfg.OBSERVATIONS], selected_observations)
+
     while True:
         flag_ok: bool = True
         parameters = select_subj_behav.choose_obs_subj_behav_category(
             self,
             selected_observations,
-            window_title="Select the behaviors",
+            start_coding=start_coding,
+            end_coding=end_coding,
+            start_interval=start_interval,
+            end_interval=end_interval,
+            maxTime=max_media_duration_all_obs,
             n_observations=len(selected_observations),
             show_include_modifiers=False,
             show_exclude_non_coded_behaviors=True,