boris-behav-obs 8.16.6__py3-none-any.whl → 9.7.2__py3-none-any.whl

boris/time_budget_widget.py

@@ -1,7 +1,7 @@
 """
 BORIS
 Behavioral Observation Research Interactive Software
-Copyright 2012-2023 Olivier Friard
+Copyright 2012-2025 Olivier Friard
 
 This file is part of BORIS.
 
@@ -26,6 +26,7 @@ import pathlib as pl
 from decimal import Decimal as dec
 from io import StringIO
 import pandas as pd
+import time
 
 try:
     import pyreadr
@@ -36,8 +37,8 @@ except ModuleNotFoundError:
 
 
 import tablib
-from PyQt5.QtCore import Qt
-from PyQt5.QtWidgets import (
+from PySide6.QtCore import Qt
+from PySide6.QtWidgets import (
     QFileDialog,
     QHBoxLayout,
     QInputDialog,
@@ -51,6 +52,7 @@ from PyQt5.QtWidgets import (
     QTableWidgetItem,
     QVBoxLayout,
     QWidget,
+    QApplication,
 )
 
 from . import config as cfg
@@ -110,7 +112,7 @@ class timeBudgetResults(QWidget):
         spacerItem = QSpacerItem(241, 20, QSizePolicy.Expanding, QSizePolicy.Minimum)
         hbox2.addItem(spacerItem)
 
-        self.pbClose = QPushButton("Close", clicked=self.close_clicked)
+        self.pbClose = QPushButton(cfg.CLOSE, clicked=self.close_clicked)
         hbox2.addWidget(self.pbClose)
 
         hbox.addLayout(hbox2)
@@ -148,9 +150,7 @@ class timeBudgetResults(QWidget):
 
         file_formats = (cfg.TSV, cfg.CSV, cfg.ODS, cfg.XLSX, cfg.XLS, cfg.HTML, cfg.TEXT_FILE, cfg.PANDAS_DF, cfg.RDS)
 
-        file_name, filter_ = QFileDialog().getSaveFileName(
-            self, "Save Time budget analysis", "", ";;".join(file_formats)
-        )
+        file_name, filter_ = QFileDialog().getSaveFileName(self, "Save Time budget analysis", "", ";;".join(file_formats))
 
         if not file_name:
             return
@@ -164,9 +164,7 @@ class timeBudgetResults(QWidget):
             # check if file with new extension already exists
             if pl.Path(file_name).is_file():
                 if (
-                    dialog.MessageDialog(
-                        cfg.programName, f"The file {file_name} already exists.", [cfg.CANCEL, cfg.OVERWRITE]
-                    )
+                    dialog.MessageDialog(cfg.programName, f"The file {file_name} already exists.", [cfg.CANCEL, cfg.OVERWRITE])
                     == cfg.CANCEL
                 ):
                     return
@@ -206,9 +204,9 @@ class timeBudgetResults(QWidget):
         for idx in self.pj.get(cfg.INDEPENDENT_VARIABLES, []):
             if self.lw.count() == 1:
                 # var has value in obs?
-                if self.pj[cfg.INDEPENDENT_VARIABLES][idx]["label"] in self.pj[cfg.OBSERVATIONS][
-                    self.lw.item(0).text()
-                ].get(cfg.INDEPENDENT_VARIABLES, []):
+                if self.pj[cfg.INDEPENDENT_VARIABLES][idx]["label"] in self.pj[cfg.OBSERVATIONS][self.lw.item(0).text()].get(
+                    cfg.INDEPENDENT_VARIABLES, []
+                ):
                     col1.append(
                         self.pj[cfg.OBSERVATIONS][self.lw.item(0).text()][cfg.INDEPENDENT_VARIABLES][
                             self.pj[cfg.INDEPENDENT_VARIABLES][idx]["label"]
@@ -392,6 +390,7 @@ def time_budget(self, mode: str, mode2: str = "list"):
     Args:
         mode (str): ["by_behavior", "by_category"]
         mode2 (str): must be in ["list", "current"]
+                     "current" time budget of current observation
     """
 
     if mode2 == "current":
@@ -418,9 +417,7 @@ def time_budget(self, mode: str, mode2: str = "list"):
     flagGroup: bool = False
     if len(selected_observations) > 1:
         flagGroup = (
-            dialog.MessageDialog(
-                cfg.programName, "Group the selected observations in a single time budget analysis?", [cfg.YES, cfg.NO]
-            )
+            dialog.MessageDialog(cfg.programName, "Group the selected observations in a single time budget analysis?", [cfg.YES, cfg.NO])
             == cfg.YES
         )
 
@@ -428,20 +425,25 @@ def time_budget(self, mode: str, mode2: str = "list"):
         self.pj[cfg.OBSERVATIONS], selected_observations
     )
 
-    logging.debug(
-        f"max_media_duration_all_obs: {max_media_duration_all_obs}, total_media_duration_all_obs={total_media_duration_all_obs}"
-    )
+    logging.debug(f"max_media_duration_all_obs: {max_media_duration_all_obs}, total_media_duration_all_obs={total_media_duration_all_obs}")
 
     start_coding, end_coding, _ = observation_operations.coding_time(self.pj[cfg.OBSERVATIONS], selected_observations)
 
-    parameters = select_subj_behav.choose_obs_subj_behav_category(
+    start_interval, end_interval = observation_operations.time_intervals_range(self.pj[cfg.OBSERVATIONS], selected_observations)
+
+    parameters: dict = 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,
+        start_interval=None,
+        end_interval=None,
         maxTime=max_media_duration_all_obs,
         by_category=(mode == "by_category"),
         n_observations=len(selected_observations),
+        show_exclude_non_coded_modifiers=True,
     )
     if parameters == {}:
         return
@@ -450,21 +452,28 @@ def time_budget(self, mode: str, mode2: str = "list"):
         QMessageBox.warning(None, cfg.programName, "Select subject(s) and behavior(s) to analyze")
         return
 
+    logging.debug(f"{parameters=}")
+
     # ask for excluding behaviors durations from total time
-    if not start_coding.is_nan():
+    if start_coding is not None and not start_coding.is_nan():
         cancel_pressed, parameters[cfg.EXCLUDED_BEHAVIORS] = self.filter_behaviors(
             title="Select behaviors to exclude from the total time",
-            text=("The duration of the selected behaviors will " "be subtracted from the total time"),
+            text=("The duration of the selected behaviors will be subtracted from the total time"),
             table="",
-            behavior_type=[cfg.STATE_EVENT],
+            behavior_type=cfg.STATE_EVENT_TYPES,
         )
         if cancel_pressed:
             return
     else:
         parameters[cfg.EXCLUDED_BEHAVIORS] = []
 
+    self.statusbar.showMessage(f"Generating time budget for {len(selected_observations)} observation(s)")
+    QApplication.processEvents()
+
     # check if time_budget window must be used
     if flagGroup or len(selected_observations) == 1:
+        t0 = time.time()
+
         cursor = db_functions.load_events_in_db(
             self.pj,
             parameters[cfg.SELECTED_SUBJECTS],
@@ -483,7 +492,7 @@ def time_budget(self, mode: str, mode2: str = "list"):
             if obs_length == dec(-2):  # images obs without time
                 parameters[cfg.TIME_INTERVAL] = cfg.TIME_EVENTS
 
-            if parameters[cfg.TIME_INTERVAL] == cfg.TIME_FULL_OBS:
+            if parameters[cfg.TIME_INTERVAL] == cfg.TIME_FULL_OBS:  # media file duration
                 min_time = float(0)
                 # check if the last event is recorded after media file length
                 try:
@@ -494,7 +503,14 @@ def time_budget(self, mode: str, mode2: str = "list"):
                 except Exception:
                     max_time = float(obs_length)
 
-            if parameters[cfg.TIME_INTERVAL] == cfg.TIME_EVENTS:
+            if parameters[cfg.TIME_INTERVAL] == cfg.TIME_OBS_INTERVAL:
+                obs_interval = self.pj[cfg.OBSERVATIONS][obsId].get(cfg.OBSERVATION_TIME_INTERVAL, [0, 0])
+                offset = float(self.pj[cfg.OBSERVATIONS][obsId][cfg.TIME_OFFSET])
+                min_time = float(obs_interval[0]) + offset
+                # Use max media duration for max time if no interval is defined (=0)
+                max_time = float(obs_interval[1]) + offset if obs_interval[1] != 0 else float(obs_length)
+
+            if parameters[cfg.TIME_INTERVAL] == cfg.TIME_EVENTS:  # events duration
                 try:
                     min_time = float(self.pj[cfg.OBSERVATIONS][obsId][cfg.EVENTS][0][0])  # first event
                 except Exception:
@@ -512,8 +528,10 @@ def time_budget(self, mode: str, mode2: str = "list"):
                 # check intervals
                 for subj in parameters[cfg.SELECTED_SUBJECTS]:
                     for behav in parameters[cfg.SELECTED_BEHAVIORS]:
-                        if cfg.POINT in self.eventType(behav).upper():
+                        # if cfg.POINT in self.eventType(behav).upper():
+                        if project_functions.event_type(behav, self.pj[cfg.ETHOGRAM]) in cfg.POINT_EVENT_TYPES:
                             continue
+
                         # extract modifiers
 
                         cursor.execute(
@@ -542,10 +560,7 @@ def time_budget(self, mode: str, mode2: str = "list"):
                                 % 2
                             ):
                                 cursor.execute(
-                                    (
-                                        "INSERT INTO events (observation, subject, code, type, modifiers, occurence) "
-                                        "VALUES (?,?,?,?,?,?)"
-                                    ),
+                                    ("INSERT INTO events (observation, subject, code, type, modifiers, occurence) VALUES (?,?,?,?,?,?)"),
                                     (obsId, subj, behav, "STATE", modifier[0], min_time),
                                 )
 
@@ -562,10 +577,7 @@ def time_budget(self, mode: str, mode2: str = "list"):
                                 % 2
                             ):
                                 cursor.execute(
-                                    (
-                                        "INSERT INTO events (observation, subject, code, type, modifiers, occurence) "
-                                        "VALUES (?,?,?,?,?,?)"
-                                    ),
+                                    ("INSERT INTO events (observation, subject, code, type, modifiers, occurence) VALUES (?,?,?,?,?,?)"),
                                     (obsId, subj, behav, "STATE", modifier[0], max_time),
                                 )
                         try:
@@ -580,6 +592,10 @@ def time_budget(self, mode: str, mode2: str = "list"):
                 "DELETE FROM events WHERE observation = ? AND (occurence < ? OR occurence > ?)",
                 (obsId, min_time, max_time),
             )
+            try:
+                cursor.execute("COMMIT")
+            except Exception:
+                pass
 
         out, categories = time_budget_functions.time_budget_analysis(
             self.pj[cfg.ETHOGRAM], cursor, selected_observations, parameters, by_category=(mode == "by_category")
@@ -591,9 +607,7 @@ def time_budget(self, mode: str, mode2: str = "list"):
             if element["subject"] not in excl_behaviors_total_time:
                 excl_behaviors_total_time[element["subject"]] = 0
             if element["behavior"] in parameters[cfg.EXCLUDED_BEHAVIORS]:
-                excl_behaviors_total_time[element["subject"]] += (
-                    element["duration"] if not isinstance(element["duration"], str) else 0
-                )
+                excl_behaviors_total_time[element["subject"]] += element["duration"] if not isinstance(element["duration"], str) else 0
 
         # widget for results visualization
         self.tb = timeBudgetResults(self.pj, self.config_param)
@@ -613,20 +627,14 @@ def time_budget(self, mode: str, mode2: str = "list"):
         if len(selected_observations) > 1:
             if total_observation_time:
                 if self.timeFormat == cfg.HHMMSS:
-                    self.tb.lbTotalObservedTime.setText(
-                        f"Total observation length: {util.seconds2time(total_observation_time)}"
-                    )
+                    self.tb.lbTotalObservedTime.setText(f"Total observation length: {util.seconds2time(total_observation_time)}")
                 if self.timeFormat == cfg.S:
-                    self.tb.lbTotalObservedTime.setText(
-                        f"Total observation length: {float(total_observation_time):0.3f}"
-                    )
+                    self.tb.lbTotalObservedTime.setText(f"Total observation length: {float(total_observation_time):0.3f}")
             else:
                 self.tb.lbTotalObservedTime.setText("Total observation length: not available")
         else:
             if self.timeFormat == cfg.HHMMSS:
-                self.tb.lbTotalObservedTime.setText(
-                    f"Analysis from {util.seconds2time(min_time)} to {util.seconds2time(max_time)}"
-                )
+                self.tb.lbTotalObservedTime.setText(f"Analysis from {util.seconds2time(min_time)} to {util.seconds2time(max_time)}")
             if self.timeFormat == cfg.S:
                 self.tb.lbTotalObservedTime.setText(f"Analysis from {float(min_time):0.3f} to {float(max_time):0.3f} s")
 
@@ -638,6 +646,9 @@ def time_budget(self, mode: str, mode2: str = "list"):
         else:
             self.tb.excluded_behaviors_list.setVisible(False)
 
+        self.statusbar.showMessage(f"Time budget generated in {round(time.time() - t0, 3)} s", 5000)
+        logging.debug("Time budget generated")
+
         if mode == "by_behavior":
             tb_fields = [
                 "Subject",
@@ -685,10 +696,7 @@ def time_budget(self, mode: str, mode2: str = "list"):
                 elif row["duration"] not in ("-", cfg.UNPAIRED) and not start_coding.is_nan():
                     tot_time = float(total_observation_time)
                     # substract time of excluded behaviors from the total for the subject
-                    if (
-                        row["subject"] in excl_behaviors_total_time
-                        and row["behavior"] not in parameters[cfg.EXCLUDED_BEHAVIORS]
-                    ):
+                    if row["subject"] in excl_behaviors_total_time and row["behavior"] not in parameters[cfg.EXCLUDED_BEHAVIORS]:
                         tot_time -= excl_behaviors_total_time[row["subject"]]
                     item = QTableWidgetItem(f"{row['duration'] / tot_time * 100:.1f}" if tot_time > 0 else cfg.NA)
 
@@ -738,7 +746,7 @@ def time_budget(self, mode: str, mode2: str = "list"):
 
         self.tb.twTB.resizeColumnsToContents()
 
-        gui_utilities.restore_geometry(self.tb, "time budget", (0, 0))
+        gui_utilities.restore_geometry(self.tb, "time budget", (800, 600))
 
         self.tb.show()
 
@@ -768,9 +776,7 @@ def time_budget(self, mode: str, mode2: str = "list"):
         if output_format in (cfg.ODS_WB, cfg.XLSX_WB):
             workbook = tablib.Databook()
 
-            wb_file_name, filter_ = QFileDialog(self).getSaveFileName(
-                self, "Save Time budget analysis", "", output_format
-            )
+            wb_file_name, filter_ = QFileDialog(self).getSaveFileName(self, "Save Time budget analysis", "", output_format)
             if not wb_file_name:
                 return
 
@@ -779,9 +785,7 @@ def time_budget(self, mode: str, mode2: str = "list"):
                 # check if file with new extension already exists
                 if pl.Path(wb_file_name).is_file():
                     if (
-                        dialog.MessageDialog(
-                            cfg.programName, f"The file {wb_file_name} already exists.", [cfg.CANCEL, cfg.OVERWRITE]
-                        )
+                        dialog.MessageDialog(cfg.programName, f"The file {wb_file_name} already exists.", [cfg.CANCEL, cfg.OVERWRITE])
                         == cfg.CANCEL
                     ):
                         return
@@ -827,16 +831,14 @@ def time_budget(self, mode: str, mode2: str = "list"):
 
         mem_command = ""
         for obsId in selected_observations:
-            cursor = db_functions.load_events_in_db(
-                self.pj, parameters[cfg.SELECTED_SUBJECTS], [obsId], parameters[cfg.SELECTED_BEHAVIORS]
-            )
+            cursor = db_functions.load_events_in_db(self.pj, parameters[cfg.SELECTED_SUBJECTS], [obsId], parameters[cfg.SELECTED_BEHAVIORS])
 
             obs_length = observation_operations.observation_total_length(self.pj[cfg.OBSERVATIONS][obsId])
 
             if obs_length == -1:
                 obs_length = 0
 
-            if parameters["time"] == cfg.TIME_FULL_OBS:
+            if parameters[cfg.TIME_INTERVAL] == cfg.TIME_FULL_OBS:
                 min_time = float(0)
                 # check if the last event is recorded after media file length
                 try:
@@ -847,7 +849,7 @@ def time_budget(self, mode: str, mode2: str = "list"):
                 except Exception:
                     max_time = float(obs_length)
 
-            if parameters["time"] == cfg.TIME_EVENTS:
+            if parameters[cfg.TIME_INTERVAL] == cfg.TIME_EVENTS:
                 try:
                     min_time = float(self.pj[cfg.OBSERVATIONS][obsId][cfg.EVENTS][0][0])
                 except Exception:
@@ -857,19 +859,15 @@ def time_budget(self, mode: str, mode2: str = "list"):
                 except Exception:
                     max_time = float(obs_length)
 
-            if parameters["time"] == cfg.TIME_ARBITRARY_INTERVAL:
+            if parameters[cfg.TIME_INTERVAL] == cfg.TIME_ARBITRARY_INTERVAL:
                 min_time = float(parameters[cfg.START_TIME])
                 max_time = float(parameters[cfg.END_TIME])
 
                 # check intervals
                 for subj in parameters[cfg.SELECTED_SUBJECTS]:
                     for behav in parameters[cfg.SELECTED_BEHAVIORS]:
-                        if cfg.POINT in project_functions.event_type(
-                            behav, self.pj[cfg.ETHOGRAM]
-                        ):  # self.eventType(behav).upper():
+                        if project_functions.event_type(behav, self.pj[cfg.ETHOGRAM]) in cfg.POINT_EVENT_TYPES:
                             continue
-                        # extract modifiers
-                        # if plot_parameters["include modifiers"]:
 
                         cursor.execute(
                             "SELECT distinct modifiers FROM events WHERE observation = ? AND subject = ? AND code = ?",
@@ -892,10 +890,7 @@ def time_budget(self, mode: str, mode2: str = "list"):
                                 % 2
                             ):
                                 cursor.execute(
-                                    (
-                                        "INSERT INTO events (observation, subject, code, type, modifiers, occurence) "
-                                        "VALUES (?,?,?,?,?,?)"
-                                    ),
+                                    ("INSERT INTO events (observation, subject, code, type, modifiers, occurence) VALUES (?,?,?,?,?,?)"),
                                     (obsId, subj, behav, "STATE", modifier[0], min_time),
                                 )
                             if (
@@ -911,10 +906,7 @@ def time_budget(self, mode: str, mode2: str = "list"):
                                 % 2
                             ):
                                 cursor.execute(
-                                    (
-                                        "INSERT INTO events (observation, subject, code, type, modifiers, occurence) "
-                                        "VALUES (?,?,?,?,?,?)"
-                                    ),
+                                    ("INSERT INTO events (observation, subject, code, type, modifiers, occurence) VALUES (?,?,?,?,?,?)"),
                                     (obsId, subj, behav, cfg.STATE, modifier[0], max_time),
                                 )
                         try:
@@ -937,9 +929,7 @@ def time_budget(self, mode: str, mode2: str = "list"):
                 if element["subject"] not in excl_behaviors_total_time:
                     excl_behaviors_total_time[element["subject"]] = 0
                 if element["behavior"] in parameters[cfg.EXCLUDED_BEHAVIORS]:
-                    excl_behaviors_total_time[element["subject"]] += (
-                        element["duration"] if element["duration"] != "NA" else 0
-                    )
+                    excl_behaviors_total_time[element["subject"]] += element["duration"] if element["duration"] != "NA" else 0
 
             rows: list = []
             col1: list = []
@@ -953,9 +943,7 @@ def time_budget(self, mode: str, mode2: str = "list"):
             indep_var_values: list = []
             for _, v in self.pj.get(cfg.INDEPENDENT_VARIABLES, {}).items():
                 indep_var_label.append(v["label"])
-                indep_var_values.append(
-                    self.pj[cfg.OBSERVATIONS][obsId].get(cfg.INDEPENDENT_VARIABLES, {}).get(v["label"], "")
-                )
+                indep_var_values.append(self.pj[cfg.OBSERVATIONS][obsId].get(cfg.INDEPENDENT_VARIABLES, {}).get(v["label"], ""))
 
             header.extend(indep_var_label)
             col1.extend(indep_var_values)
@@ -981,10 +969,7 @@ def time_budget(self, mode: str, mode2: str = "list"):
                     elif row["duration"] not in ("-", cfg.UNPAIRED) and not start_coding.is_nan():
                         tot_time = float(max_time - min_time)
                         # substract duration of excluded behaviors from total time for each subject
-                        if (
-                            row["subject"] in excl_behaviors_total_time
-                            and row["behavior"] not in parameters[cfg.EXCLUDED_BEHAVIORS]
-                        ):
+                        if row["subject"] in excl_behaviors_total_time and row["behavior"] not in parameters[cfg.EXCLUDED_BEHAVIORS]:
                             tot_time -= excl_behaviors_total_time[row["subject"]]
                         # % of tot time
                         values.append(round(row["duration"] / tot_time * 100, 1) if tot_time > 0 else cfg.NA)

boris/transitions.py

@@ -1,7 +1,7 @@
 """
 BORIS
 Behavioral Observation Research Interactive Software
-Copyright 2012-2023 Olivier Friard
+Copyright 2012-2025 Olivier Friard
 
 This file is part of BORIS.
 
@@ -24,8 +24,9 @@ import logging
 import os
 import subprocess
 import tempfile
+from pathlib import Path
 
-from PyQt5.QtWidgets import QFileDialog, QMessageBox
+from PySide6.QtWidgets import QFileDialog, QMessageBox
 
 from . import config as cfg
 from . import dialog, export_observation, select_subj_behav
@@ -134,7 +135,7 @@ def create_transitions_gv_from_matrix(matrix, cutoff_all=0, cutoff_behavior=0, e
             else:
                 transitions[row.split("\t")[0]][behaviours[idx]] = int(r)
 
-    '''transitions_total_number = sum([sum(transitions[x].values()) for x in transitions])'''
+    """transitions_total_number = sum([sum(transitions[x].values()) for x in transitions])"""
 
     out = "digraph G { \n"
 
@@ -170,6 +171,8 @@ def transitions_matrix(self, mode):
     * number
     * frequencies_after_behaviors
     """
+    logging.debug("flag transitions_matrix function")
+
     # ask user observations to analyze
     _, selected_observations = select_observations.select_observations2(
         self, cfg.MULTIPLE, windows_title="Select observations for transitions matrix"
@@ -181,8 +184,8 @@ def transitions_matrix(self, mode):
     parameters = select_subj_behav.choose_obs_subj_behav_category(
         self,
         selected_observations,
-        flagShowIncludeModifiers=True,
-        flagShowExcludeBehaviorsWoEvents=False,
+        show_include_modifiers=True,
+        show_exclude_non_coded_behaviors=False,
         n_observations=len(selected_observations),
     )
 
@@ -194,20 +197,20 @@ def transitions_matrix(self, mode):
 
     flagMulti = False
     if len(parameters[cfg.SELECTED_SUBJECTS]) == 1:
-        fn = QFileDialog().getSaveFileName(
+        file_name, _ = QFileDialog().getSaveFileName(
             None,
             "Create matrix of transitions " + mode,
             "",
             "Transitions matrix files (*.txt *.tsv);;All files (*)",
         )
-        fileName = fn[0] if type(fn) is tuple else fn  # PyQt4/5
-
+        if not file_name:
+            return
     else:
-        exportDir = QFileDialog(self).getExistingDirectory(
+        exportDir = QFileDialog.getExistingDirectory(
             self,
             "Choose a directory to save the transitions matrices",
-            os.path.expanduser("~"),
-            options=QFileDialog(self).ShowDirsOnly,
+            str(Path.home()),
+            options=QFileDialog.ShowDirsOnly,
         )
         if not exportDir:
             return
@@ -220,9 +223,7 @@ def transitions_matrix(self, mode):
         strings_list = []
         for obs_id in selected_observations:
             strings_list.append(
-                export_observation.events_to_behavioral_sequences(
-                    self.pj, obs_id, subject, parameters, self.behav_seq_separator
-                )
+                export_observation.events_to_behavioral_sequences(self.pj, obs_id, subject, parameters, self.behav_seq_separator)
             )
 
         sequences, observed_behaviors = behavioral_strings_analysis(strings_list, self.behav_seq_separator)
@@ -258,11 +259,11 @@ def transitions_matrix(self, mode):
                 QMessageBox.critical(self, cfg.programName, f"The file {nf} can not be saved")
         else:
             try:
-                with open(fileName, "w") as outfile:
+                with open(file_name, "w") as outfile:
                     outfile.write(observed_matrix)
 
             except Exception:
-                QMessageBox.critical(self, cfg.programName, f"The file {fileName} can not be saved")
+                QMessageBox.critical(self, cfg.programName, f"The file {file_name} can not be saved")
 
 
 def transitions_dot_script():
@@ -270,21 +271,18 @@ def transitions_dot_script():
     create dot script (graphviz language) from transitions frequencies matrix
     """
 
-    fn = QFileDialog().getOpenFileNames(
+    file_names, _ = QFileDialog().getOpenFileNames(
         None,
         "Select one or more transitions matrix files",
         "",
         "Transitions matrix files (*.txt *.tsv);;All files (*)",
     )
-    fileNames = fn[0] if type(fn) is tuple else fn
 
     out = ""
 
-    for fileName in fileNames:
-        with open(fileName, "r") as infile:
-            result, gv = create_transitions_gv_from_matrix(
-                infile.read(), cutoff_all=0, cutoff_behavior=0, edge_label="percent_node"
-            )
+    for file_name in file_names:
+        with open(file_name, "r") as infile:
+            result, gv = create_transitions_gv_from_matrix(infile.read(), cutoff_all=0, cutoff_behavior=0, edge_label="percent_node")
             if result:
                 QMessageBox.critical(
                     None,
@@ -293,16 +291,24 @@ def transitions_dot_script():
                 )
                 return
 
-            with open(fileName + ".gv", "w") as f:
-                f.write(gv)
+            try:
+                with open(file_name + ".gv", "w") as file_out:
+                    file_out.write(gv)
+            except Exception:
+                QMessageBox.critical(
+                    None,
+                    cfg.programName,
+                    ("Error saving the file"),
+                )
+                return
 
-            out += f"<b>{fileName}.gv</b> created<br>"
+            out += f"<b>{file_name}.gv</b> created<br>"
 
     if out:
         QMessageBox.information(
             None,
             cfg.programName,
-            (f"{out}<br><br>The DOT scripts can be used with Graphviz or WebGraphviz " "to generate diagram"),
+            (f"{out}<br><br>The DOT scripts can be used with the Graphviz package or WebGraphviz to generate diagram"),
         )
 
 
@@ -326,20 +332,17 @@ def transitions_flow_diagram():
         )
         return
 
-    fn = QFileDialog().getOpenFileNames(
+    file_names, _ = QFileDialog().getOpenFileNames(
         None,
         "Select one or more transitions matrix files",
         "",
         "Transitions matrix files (*.txt *.tsv);;All files (*)",
     )
-    fileNames = fn[0] if type(fn) is tuple else fn
 
     out = ""
-    for fileName in fileNames:
-        with open(fileName, "r") as infile:
-            result, gv = create_transitions_gv_from_matrix(
-                infile.read(), cutoff_all=0, cutoff_behavior=0, edge_label="percent_node"
-            )
+    for file_name in file_names:
+        with open(file_name, "r") as infile:
+            result, gv = create_transitions_gv_from_matrix(infile.read(), cutoff_all=0, cutoff_behavior=0, edge_label="percent_node")
             if result:
                 QMessageBox.critical(
                     None,
@@ -348,18 +351,15 @@ def transitions_flow_diagram():
                 )
                 return
 
-            with open(tempfile.gettempdir() + os.sep + os.path.basename(fileName) + ".tmp.gv", "w") as f:
+            with open(tempfile.gettempdir() + os.sep + os.path.basename(file_name) + ".tmp.gv", "w") as f:
                 f.write(gv)
             result = subprocess.getoutput(
-                (
-                    f'dot -Tpng -o "{fileName}.png" '
-                    f'"{tempfile.gettempdir() + os.sep + os.path.basename(fileName)}.tmp.gv"'
-                )
+                (f'dot -Tpng -o "{file_name}.png" "{tempfile.gettempdir() + os.sep + os.path.basename(file_name)}.tmp.gv"')
             )
             if not result:
-                out += f"<b>{fileName}.png</b> created<br>"
+                out += f"<b>{file_name}.png</b> created<br>"
             else:
-                out += f"Problem with <b>{fileName}</b><br>"
+                out += f"Problem with <b>{file_name}</b><br>"
 
     if out:
         QMessageBox.information(None, cfg.programName, out)