time noise and depth noise variable are used instead of time and depth to avoid size incompatibility #9

Model/create_table_for_save_as.py

@@ -20,16 +20,20 @@
 
 # -*- coding: utf-8 -*-
 
+import os
+import time
+import sqlite3
+import logging
 
 import numpy as np
-from PyQt5.QtWidgets import QFileDialog, QApplication, QMessageBox
-import sqlite3
-import settings as stg
-from os import chdir
-import time
 
+from PyQt5.QtWidgets import QFileDialog, QApplication, QMessageBox
+
+import settings as stg
 from settings import ABS_name
 
+logger = logging.getLogger()
+
 class CreateTableForSaveAs:
 
     def __init__(self):
@@ -165,23 +169,32 @@ class CreateTableForSaveAs:
 
 
     def open_file_dialog(self):
-        options = QFileDialog.Options()
-        name = QFileDialog.getSaveFileName(
-            caption="Save As", directory="", filter="AcouSed Files (*.acd)", options=QFileDialog.DontUseNativeDialog)
+        name, _ = QFileDialog.getSaveFileName(
+            caption="Save As",
+            directory="",
+            filter="AcouSed Files (*.acd)",
+            options=QFileDialog.DontUseNativeDialog
+        )
 
-        if name[0]:
+        if name != "":
+            filename = os.path.basename(name)
+            if os.path.splitext(filename)[1] != ".acd":
+                filename += ".acd"
 
-            stg.dirname_save_as = "/".join(name[0].split("/")[:-1]) + "/"
-            stg.filename_save_as = name[0].split("/")[-1]
+            logger.debug(f"selected save file: '{filename}'")
 
-            chdir(stg.dirname_save_as)
+            stg.dirname_save_as = os.path.dirname(name)
+            stg.filename_save_as = filename
+
+            try:
+                os.chdir(stg.dirname_save_as)
+            except OSError as e:
+                logger.warning(f"chdir: {str(e)}")
 
             start = time.time()
             self.create_table()
             print(f"end : {time.time() - start} sec")
-
         else:
-
             msgBox = QMessageBox()
             msgBox.setWindowTitle("Save Error")
             msgBox.setIcon(QMessageBox.Warning)
@@ -192,7 +205,7 @@ class CreateTableForSaveAs:
     def create_table(self):
 
         # Create a new database and open a database connection to allow sqlite3 to work with it.
-        cnx = sqlite3.connect(stg.filename_save_as + '.acd')
+        cnx = sqlite3.connect(stg.filename_save_as)
 
         # Create database cursor to execute SQL statements and fetch results from SQL queries.
         cur = cnx.cursor()
@@ -459,6 +472,3 @@ class CreateTableForSaveAs:
 
         # Close database connection
         cnx.close()
-
-
-

Model/read_table_for_open.py

@@ -20,37 +20,50 @@
 
 # -*- coding: utf-8 -*-
 
-
+import os
 import sys
-import numpy as np
-from PyQt5.QtWidgets import QFileDialog, QApplication, QWidget, QTabWidget
 import sqlite3
-from os import path, chdir
+import logging
+import numpy as np
+
+from PyQt5.QtWidgets import QFileDialog, QApplication, QWidget, QTabWidget
+
 import settings as stg
 from settings import BS_raw_data, acoustic_data
 
 from View.acoustic_data_tab import AcousticDataTab
 
+
+logger = logging.getLogger()
+
 class ReadTableForOpen:
 
     def __init__(self):
+        self.opened = False
 
-        pass
+        self.open_file_dialog()
 
     def open_file_dialog(self):
+        name, _ = QFileDialog.getOpenFileName(
+            caption="Open Acoused file",
+            directory="",
+            filter="Acoused file (*.acd)",
+            options=QFileDialog.DontUseNativeDialog
+        )
 
-        name = QFileDialog.getOpenFileName(caption="Open Acoused file", directory="", filter="Acoused file (*.acd)",
-                                           options=QFileDialog.DontUseNativeDialog)
+        if name != "":
+            stg.dirname_open = os.path.dirname(name)
+            stg.filename_open = os.path.basename(name)
 
-        if name:
+            try:
+                os.chdir(stg.dirname_open)
+            except OSError as e:
+                logger.warning(f"chdir: {str(e)}")
 
-            stg.dirname_open = path.dirname(name[0])
-            stg.filename_open = path.basename(name[0])
-
-            chdir(stg.dirname_open)
             self.sql_file_to_open = open(stg.filename_open)
-
             self.read_table()
+            self.opened = True
+
 
     def read_table(self):
 
@@ -428,4 +441,3 @@ class ReadTableForOpen:
 
             stg.BS_raw_data.append(np.reshape(stg.BS_raw_data_reshape[i],
                                               (len(stg.freq[i]), stg.depth[i].shape[1], stg.time[i].shape[1])))
-

Model/update_table_for_save.py

@@ -51,7 +51,7 @@ class UpdateTableForSave:
     def update_table(self):
 
         # Create a new database and open a database connection to allow sqlite3 to work with it.
-        cnx = sqlite3.connect(stg.filename_save_as + '.acd')
+        cnx = sqlite3.connect(stg.filename_save_as)
 
         # Create database cursor to execute SQL statements and fetch results from SQL queries.
         cur = cnx.cursor()
@@ -104,7 +104,10 @@ class UpdateTableForSave:
         # Drop Table if exists
         cur.execute("DROP TABLE if exists Measure")
 
-        cur.execute("""CREATE TABLE Measure(ID INTEGER PRIMARY KEY AUTOINCREMENT,
+        cur.execute(
+            """
+            CREATE TABLE Measure(
+              ID INTEGER PRIMARY KEY AUTOINCREMENT,
               acoustic_data INTEGER,
               Date STRING,
               Hour STRING,
@@ -121,25 +124,52 @@ class UpdateTableForSave:
               NbPingsAveragedPerProfile FLOAT,
               GainRx FLOAT,
               GainTx FLOAT
+            )"""
         )
-                                            """)
 
         # Fill the table Measure
         for i in stg.acoustic_data:
-
             for j in range(stg.freq[i].shape[0]):
-                cur.execute(''' INSERT into Measure(acoustic_data, Date, Hour, frequency, sound_attenuation, kt_read, kt_corrected, NbProfiles, 
-                                                                NbProfilesPerSeconds, NbCells, CellSize, PulseLength, 
-                                                                NbPingsPerSeconds, NbPingsAveragedPerProfile, GainRx, GainTx, 
+                cur.execute(
+                    '''
+                    INSERT into Measure(
+                      acoustic_data,
+                      Date, Hour,
+                      frequency,
+                      sound_attenuation,
+                      kt_read, kt_corrected,
+                      NbProfiles, NbProfilesPerSeconds,
+                      NbCells, CellSize,
+                      PulseLength,
+                      NbPingsPerSeconds,
+                      NbPingsAveragedPerProfile,
+                      GainRx, GainTx
+                    ) VALUES(?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)''',
+                    (
+                        stg.acoustic_data[i],
+                        (
+                            str(stg.date[i].year) + str('-') +
+                            str(stg.date[i].month) + str('-') +
+                            str(stg.date[i].day)
+                        ),
+                        (
+                            str(stg.hour[i].hour) + str(':') +
+                            str(stg.hour[i].minute)
+                        ),
+                        stg.freq[i][j],
+                        stg.water_attenuation[i][j],
+                        stg.kt_read[j],
+                        stg.kt_corrected[j],
+                        stg.nb_profiles[i][j],
+                        stg.nb_profiles_per_sec[i][j],
+                        stg.nb_cells[i][j],
+                        stg.cell_size[i][j],
+                        stg.pulse_length[i][j],
+                        stg.nb_pings_per_sec[i][j],
+                        stg.nb_pings_averaged_per_profile[i][j],
+                        stg.gain_rx[i][j], stg.gain_tx[i][j]
+                    )
                 )
-                                            VALUES(?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)''',
-                            (stg.acoustic_data[i], stg.freq[i][j], stg.water_attenuation[i][j], stg.kt_read[j], stg.kt_corrected[j],
-                             stg.nb_profiles[i][j], stg.nb_profiles_per_sec[i][j], stg.nb_cells[i][j],
-                             stg.cell_size[i][j], stg.pulse_length[i][j], stg.nb_pings_per_sec[i][j],
-                             stg.nb_pings_averaged_per_profile[i][j], stg.gain_rx[i][j], stg.gain_tx[i][j],
-                             str(stg.date[i].year) + str('-') + str(stg.date[i].month) + str('-') + str(stg.date[i].day),
-                             str(stg.hour[i].hour) + str(':') + str(stg.hour[i].minute)
-                             ))
 
         # Commit the transaction after executing INSERT.
         cnx.commit()
@@ -417,6 +447,3 @@ class UpdateTableForSave:
 
         # Close database connection
         cnx.close()
-
-
-

README.md

@@ -11,85 +11,43 @@ It is divided in six tabs:
 - Calibration : calibration parameter are computed
 - Inversion : inversion method is calculated to provide fine and sand sediments fields
 
+## Software documentation
 
+### Installation
 
-## User Manual
+Acoused is developped for Linux and Windows on Python version 3.8 or
+greater. By default, Acoused is developped with Pypi package
+dependencies, but is also possible to use Guix package manager to run
+Acoused.
 
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
+## Development documentation
 
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
+### **TODO** Windows
 
+### Linux
 
+You can use Pypi to get correct software environment and run the
+program.
 
-## Support files
+```shell
+  python3 -m venv venv
+  source ./venv/bin/activate
+  python3 -m pip install -r requirement.txt
+  python3 main.py
+```
 
-- [ ] [Acoustic inversion method diagram](https://forgemia.inra.fr/theophile.terraz/acoused/-/blob/main/Acoustic_Inversion_theory.pdf?ref_type=heads) 
-- [ ] [Tutorial AQUAscat software : AQUAtalk](https://forgemia.inra.fr/theophile.terraz/acoused/-/blob/main/Tutorial_AQUAscat_software.pdf?ref_type=heads) 
+### Linux with Guix
 
-## Integrate with your tools
+To run Acoused within a [GNU Guix](https://guix.gnu.org/) software
+environment, you need Guix installed on your computer and run the
+script `guix.sh` to run the program.
 
-- [ ] [Set up project integrations](https://gitlab.irstea.fr/brahim/acoused/-/settings/integrations)
+```shell
+  ./guix.sh
 
-## Collaborate with your team
-
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Automatically merge when pipeline succeeds](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
-
-## Test and Deploy
-
-Use the built-in continuous integration in GitLab.
-
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
-
-***
-
-# Editing this README
-
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template.
-
-## Suggestions for a good README
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
-
-## Name
-Choose a self-explaining name for your project.
-
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
-
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
-
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
-
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
-
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
-
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
-
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
-
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
-
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
-
-## Acknowledgment
-This study was conducted within the [Rhône Sediment Observatory](https://observatoire-sediments-rhone.fr/) (OSR), a multi-partner research program funded through the Plan Rhône by the European Regional Development Fund (ERDF), Agence de l’Eau RMC, CNR, EDF and three regional councils (Auvergne-Rhône-Alpes, PACA and Occitanie). It was then also support by CNR. 
+  # If you need sqlitebrowser, use this command
+  guix shell sqlitebrowser -- ./guix.sh
+```
 
 ## License
 
@@ -102,11 +60,21 @@ This program is distributed in the hope that it will be useful, but WITHOUT ANY
 
 You should have received a copy of the GNU General Public License along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
-## Contacts
+## Authors & Contacts
+
+- Brahim MOUDJED  2022-2025 ([INRAE](https://www.inrae.fr/))
+- Pierre-Antoine ROUBY  2025 ([TECC](https://parouby.fr))
 
 If you have any questions or suggestions, please contact us to celine.berni@inrae.fr and/or jerome.lecoz@inrae.fr.
 
-## References
+## Acknowledgment (Funding)
+This study was conducted within the [Rhône Sediment Observatory](https://observatoire-sediments-rhone.fr/) (OSR), a multi-partner research program funded through the Plan Rhône by the European Regional Development Fund (ERDF), Agence de l’Eau RMC, CNR, EDF and three regional councils (Auvergne-Rhône-Alpes, PACA and Occitanie). It was also support by CNR. 
+
+## Support files & References 
+
+- [ ] [Acoustic inversion method diagram](https://forgemia.inra.fr/theophile.terraz/acoused/-/blob/main/Acoustic_Inversion_theory.pdf?ref_type=heads) 
+- [ ] [Tutorial AQUAscat software : AQUAtalk](https://forgemia.inra.fr/theophile.terraz/acoused/-/blob/main/Tutorial_AQUAscat_software.pdf?ref_type=heads)
+
 
 - [ ] [Adrien Vergne thesis (2018)](https://theses.fr/2018GREAU046)
 - [ ] [Vergne A., Le Coz J., Berni C., & Pierrefeu G. (2020), Water Resources Research, 56(2)](https://doi.org/10.1029/2019WR024877)

View/acoustic_data_tab.py

@@ -21,11 +21,18 @@
 # -*- coding: utf-8 -*-
 
 
-from PyQt5.QtWidgets import (QWidget, QVBoxLayout, QHBoxLayout, QGroupBox, QPushButton, QComboBox, QLineEdit, QLabel,
-                             QGridLayout, QTableView, QSpacerItem, QSizePolicy, QFileDialog, QMessageBox, QScrollArea,
-                             QSlider, QMenu, QCheckBox)
+from PyQt5.QtWidgets import (
+    QWidget, QVBoxLayout, QHBoxLayout, QGroupBox,
+    QPushButton, QComboBox, QLineEdit, QLabel,
+    QGridLayout, QTableView, QSpacerItem, QSizePolicy,
+    QFileDialog, QMessageBox, QScrollArea,
+    QSlider, QMenu, QCheckBox
+)
 from PyQt5.QtGui import QPixmap, QIcon
-from PyQt5.QtCore import Qt, QCoreApplication, pyqtSignal, QEvent, QSize, QPropertyAnimation
+from PyQt5.QtCore import (
+    Qt, QCoreApplication, pyqtSignal, QEvent, QSize,
+    QPropertyAnimation
+)
 
 import numpy as np
 import pandas as pd
@@ -35,7 +42,7 @@ from matplotlib.colors import LogNorm, CSS4_COLORS, BoundaryNorm
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolBar
 
-from os import path
+import os
 from copy import deepcopy
 import locale
 
@@ -1232,71 +1239,76 @@ class AcousticDataTab(QWidget):
                               self.combobox_frequency_information.currentIndex()]))
 
     def open_dialog_box(self):
+        abs_params = [
+            (None, None),
+            ("AQUAscat file", "Aquascat file (*.aqa)"),
+            ("UBSediFlow file", "UBSediFlow file (*.udt)"),
+        ]
 
-        # --- Open dialog box + choice directory and select file ---
-        if self.combobox_ABS_system_choice.currentIndex() == 0:
+
+        system = self.combobox_ABS_system_choice.currentIndex()
+
+        if system == 0:
             msgBox = QMessageBox()
             msgBox.setWindowTitle("Download Error")
             msgBox.setIcon(QMessageBox.Warning)
             msgBox.setText("Choose ABS system before download acoustic files")
             msgBox.setStandardButtons(QMessageBox.Ok)
             msgBox.exec()
-        elif self.combobox_ABS_system_choice.currentIndex() == 1:
+        else:
+            abs_name, abs_file_type = abs_params[system]
 
-            filename = QFileDialog.getOpenFileNames(self, "AQUAscat file",
-                                                   [stg.path_BS_raw_data[-1] if self.fileListWidget.count() > 0 else ""][0],
-                                                   "Aquascat file (*.aqa)",
-                                                    options=QFileDialog.DontUseNativeDialog)
+            filenames, _ = QFileDialog.getOpenFileNames(
+                self, abs_name,
+                [
+                    stg.path_BS_raw_data[-1]
+                    if self.fileListWidget.count() > 0
+                    else ""
+                ][0],
+                abs_file_type,
+                options=QFileDialog.DontUseNativeDialog
+            )
 
-            for n in filename[0]:
+            if len(filenames) == 0:
+                return
 
-                stg.path_BS_raw_data.append(path.dirname(n))
-                stg.filename_BS_raw_data.append(path.basename(n))
-                stg.data_preprocessed.append(path.basename(n))
+            for n in filenames:
+                stg.path_BS_raw_data.append(os.path.dirname(n))
+                stg.filename_BS_raw_data.append(os.path.basename(n))
+                stg.data_preprocessed.append(os.path.basename(n))
 
-        elif self.combobox_ABS_system_choice.currentIndex() == 2:
-            filename = QFileDialog.getOpenFileNames(self, "UBSediFlow file",
-                                                   [stg.path_BS_raw_data[-1] if self.fileListWidget.count() > 0 else ""][0],
-                                                   "UBSediFlow file (*.udt)",
-                                                   options=QFileDialog.DontUseNativeDialog)
-
-            for n in filename[0]:
-
-                stg.path_BS_raw_data.append(path.dirname(n))
-                stg.filename_BS_raw_data.append(path.basename(n))
-                stg.data_preprocessed.append(path.basename(n))
+            self.open_acoustic_data()
 
+    def open_acoustic_data(self):
         # --- Fill lineEdit with path and file names + load acoustic data ---
         # --- fill date, hour and measurements information + fill frequency combobox for bottom detection ---
-        if self.combobox_ABS_system_choice.currentIndex() != 0:
-
+        system = self.combobox_ABS_system_choice.currentIndex()
+        if system != 0:
             try:
-
                 self.load_BS_acoustic_raw_data()
-
             except ValueError as e:
-
                 msgBox = QMessageBox()
                 msgBox.setWindowTitle("Download Error")
                 msgBox.setIcon(QMessageBox.Warning)
                 msgBox.setText("Please select a file")
                 msgBox.setStandardButtons(QMessageBox.Ok)
                 msgBox.exec()
-
             else:
-
                 if self.fileListWidget.count() == 0:
-
-                    for p, f in zip(stg.path_BS_raw_data, stg.filename_BS_raw_data):
+                    for p, f in zip(stg.path_BS_raw_data,
+                                    stg.filename_BS_raw_data):
                         self.fileListWidget.addFilenames([f])
                         self.fileListWidget.setToolTip(p)
-
                 else:
-
-                    for k in range(self.fileListWidget.count(), len(stg.filename_BS_raw_data), 1):
-                        self.fileListWidget.addFilenames([stg.filename_BS_raw_data[k]])
-                        self.fileListWidget.setToolTip(stg.path_BS_raw_data[k])
-
+                    for k in range(self.fileListWidget.count(),
+                                   len(stg.filename_BS_raw_data),
+                                   1):
+                        self.fileListWidget.addFilenames(
+                            [stg.filename_BS_raw_data[k]]
+                        )
+                        self.fileListWidget.setToolTip(
+                            stg.path_BS_raw_data[k]
+                        )
 
                 self.fill_measurements_information_groupbox()
                 self.fill_table()
@@ -1304,7 +1316,11 @@ class AcousticDataTab(QWidget):
                 self.update_frequency_combobox()
                 self.water_attenuation()
 
-                stg.acoustic_data = list(range(self.fileListWidget.count()))
+                stg.acoustic_data = list(
+                    range(
+                        self.fileListWidget.count()
+                    )
+                )
 
     def rename_file_in_ListWidget(self, event):
 
@@ -2719,4 +2735,3 @@ class AcousticDataTab(QWidget):
                         self.update_plot_profile()
 
                     self.fig_BS.canvas.draw_idle()
-

View/mainwindow.py

@@ -39,7 +39,7 @@ from View.about_window import AboutWindow
 import settings as stg
 
 import numpy as np
-from subprocess import check_call, run
+from subprocess import Popen
 
 import time
 
@@ -262,37 +262,62 @@ class Ui_MainWindow(object):
 
     def save_as(self):
         CreateTableForSaveAs()
-        self.mainwindow.setWindowTitle("AcouSed - " + stg.filename_save_as + ".acd")
+        self.mainwindow.setWindowTitle(
+            "AcouSed - " +
+            stg.filename_save_as
+        )
 
     def save(self):
         UpdateTableForSave()
 
     def open(self):
-        ReadTableForOpen()
+        reader = ReadTableForOpen()
+        if reader.opened:
+            self.mainwindow.open_study_update_tabs()
 
     def load_calibration_constant_values(self):
         cc_kt = CalibrationConstantKt()
         cc_kt.exec()
 
     def db_browser_for_sqlite(self):
-        check_call("/usr/bin/sqlitebrowser")
+        try:
+            Popen("sqlitebrowser")
+        except OSError as e:
+            msg_box = QtWidgets.QMessageBox()
+            msg_box.setWindowTitle("DB Browser for SQLite Error")
+            msg_box.setIcon(QtWidgets.QMessageBox.Critical)
+            msg_box.setText(f"DB Browser for SQLite Error:\n  {str(e)}")
+            msg_box.setStandardButtons(QtWidgets.QMessageBox.Ok)
+            msg_box.exec()
 
     def about_window(self):
         print("about")
         aw = AboutWindow()
         aw.exec()
 
+    def current_file_path(self, filename):
+        return os.path.abspath(
+            os.path.join(
+                os.path.dirname(__file__),
+                "..", filename
+            )
+        )
+
+    def open_doc_file(self, filename):
+        QtGui.QDesktopServices.openUrl(
+            QtCore.QUrl(
+                f"file://{self.current_file_path(filename)}"
+            )
+        )
+
     def user_manual(self):
-        open('AcouSed_UserManual.pdf')
-        run(["open", 'AcouSed_UserManual.pdf'])
+        self.open_doc_file('AcouSed_UserManual.pdf')
 
     def inversion_acoustic_theory(self):
-        open('Acoustic_Inversion_theory.pdf')
-        run(["open", 'Acoustic_Inversion_theory.pdf'])
+        self.open_doc_file('Acoustic_Inversion_theory.pdf')
 
     def tutorial_AQUAscat_software(self):
-        open('Tutorial_AQUAscat_software.pdf')
-        run(["open", 'Tutorial_AQUAscat_software.pdf'])
+        self.open_doc_file('Tutorial_AQUAscat_software.pdf')
 
     def export_table_of_acoustic_BS_values_to_excel_or_libreOfficeCalc_file(self):
 

View/note_tab.py

@@ -1,7 +1,8 @@
-import sys
-
-from PyQt5.QtWidgets import QApplication, QWidget, QVBoxLayout, QHBoxLayout, QTextEdit, QPushButton, QSpacerItem, \
-                            QSpinBox, QSizePolicy, QFontComboBox, QColorDialog
+from PyQt5.QtWidgets import (
+    QApplication, QWidget, QVBoxLayout, QHBoxLayout,
+    QTextEdit, QPushButton, QSpacerItem, QSpinBox,
+    QSizePolicy, QFontComboBox, QColorDialog
+)
 from PyQt5.QtGui import QPixmap, QIcon, QFont
 from PyQt5.QtCore import Qt
 
@@ -189,27 +190,21 @@ class NoteTab(QWidget):
         self.textEdit.setAlignment(Qt.AlignJustify)
 
     def print_settings(self):
-
-        self.textEdit.setText("Acoustic data: \n\n"
+        self.textEdit.setText(
+            "Acoustic data: \n\n"
             f"   ABS raw data file: {stg.path_BS_raw_data}/{stg.filename_BS_raw_data} \n"
             f"   ABS noise data file: {stg.path_BS_noise_data}/{stg.filename_BS_noise_data} \n"
             "\n\n"
             "------------------------------------------------------------------------- \n\n\n"
 
             "Particle size data: \n"
-                              f"   Fine sediments data file: {stg.fine_sediment_path}/{stg.fine_sediment_filename} \n"
-                              f"   Sand sediments data file: {stg.sand_sediment_path}/{stg.sand_sediment_filename} \n"
+            f"   Fine sediments data file: {stg.path_fine}/{stg.filename_fine} \n"
+            f"   Sand sediments data file: {stg.path_sand}/{stg.filename_sand} \n"
             "\n\n"
-                              "------------------------------------------------------------------------- \n\n\n")
+            "------------------------------------------------------------------------- \n\n\n"
+        )
 
         # "Acoustic Inversion parameters: \n"
         # f"   frequencies to compute VBI: {stg.freq_text[int(stg.frequencies_to_compute_VBI[0, 0])]}, "
         # f"{stg.freq_text[int(stg.frequencies_to_compute_VBI[1, 0])]} \n"
         # f"   frequency to compute SSC: {stg.freq_text[int(stg.frequency_to_compute_SSC[0])]}")
-
-
-# if __name__ == "__main__":
-#     app = QApplication(sys.argv)
-#     window = NoteTab()
-#     window.show()
-#     sys.exit(app.exec_())

View/plot_noise_window.py

@@ -1,8 +1,7 @@
 
 from PyQt5.QtGui import QIcon, QPixmap
 from PyQt5.QtWidgets import (QWidget, QLabel, QHBoxLayout, QVBoxLayout, QApplication, QMainWindow, QGridLayout,
-                             QDialog, QDialogButtonBox, QPushButton, QTextEdit, QFrame, QTabWidget, QScrollArea)
-from PyQt5.QtCore import Qt
+                             QDialog, QFrame, QTabWidget, QScrollArea)
 
 import numpy as np
 
@@ -11,13 +10,8 @@ from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolBar
 from matplotlib.colors import LogNorm, BoundaryNorm
 
-import datetime
-
 import settings as stg
 
-from Translation.constant_string import HORIZONTAL
-from settings import depth_cross_section
-
 
 class PlotNoiseWindow(QDialog):
 
@@ -55,12 +49,10 @@ class PlotNoiseWindow(QDialog):
                     val_min = np.nanmin(stg.BS_noise_raw_data[i][freq_ind, :, :])
                     val_max = np.nanmax(stg.BS_noise_raw_data[i][freq_ind, :, :])
 
-                    print("val_min = ", val_min, "val_max = ", val_max)
-
                     if val_min == val_max:
                         exec("pcm = self.ax" + str(i) + "[" + str(freq_ind) + "]" + ".pcolormesh(" +
-                             "stg.time[" + str(i) + "][" + str(freq_ind) + ", :]," +
-                             "-stg.depth[" + str(i) + "][" + str(freq_ind) + ", :]," +
+                             "stg.time_noise[" + str(i) + "][" + str(freq_ind) + ", :]," +
+                             "-stg.depth_noise[" + str(i) + "][" + str(freq_ind) + ", :]," +
                              "stg.BS_noise_raw_data[" + str(i) + "][" + str(freq_ind) + ", :, :]," +
                              "cmap='hsv')")
                     else:

View/signal_processing_tab.py

@@ -1084,21 +1084,18 @@ class SignalProcessingTab(QWidget):
                         val_max = np.nanmax(stg.SNR_stream_bed[self.combobox_acoustic_data_choice.currentIndex()][f, :, :])
                         if val_min == val_max:
                             levels = np.array([00.1, 1, 2, 10, 100, 1000, 1e6])
-                            bounds = [00.1, 1, 2, 10, 100, 1000, val_max, val_max * 1.2]
+                            bounds = [00.1, 1, 2, 10, 100, 1000, val_max * 1.2]
                             norm = BoundaryNorm(boundaries=bounds, ncolors=300)
                         else:
                             if val_min == 0:
                                 val_min = 1e-5
                             if val_max > 1000:
                                 levels = np.array([00.1, 1, 2, 10, 100, 1000, 1e6])
-                                bounds = [00.1, 1, 2, 10, 100, 1000, val_max, val_max * 1.2]
+                                bounds = [00.1, 1, 2, 10, 100, 1000, val_max * 1.2]
                                 norm = BoundaryNorm(boundaries=bounds, ncolors=300)
                             else:
-                                levels = np.array([00.1, 1, 2, 10, 100, val_max])
-                                bounds = [00.1, 1, 2, 10, 100, 1000, val_max * 1000]
-                                norm = BoundaryNorm(boundaries=bounds, ncolors=300)
-
-                        bounds = [00.1, 1, 2, 10, 100, 1000, val_max, val_max * 1.2]
+                                levels = np.array([00.1, 1, 2, 10, 100, 1000, val_max * 1000 + 1])
+                                bounds = [00.1, 1, 2, 10, 100, 1000, val_max * 1000 + 1]
                                 norm = BoundaryNorm(boundaries=bounds, ncolors=300)
 
                         cf = (self.axis_SNR[f].contourf(x, -y,
@@ -1140,22 +1137,19 @@ class SignalProcessingTab(QWidget):
                         val_max = np.nanmax(stg.SNR_cross_section[self.combobox_acoustic_data_choice.currentIndex()][f, :, :])
                         if val_min == val_max:
                             levels = np.array([00.1, 1, 2, 10, 100, 1000, 1e6])
-                            bounds = [00.1, 1, 2, 10, 100, 1000, val_max, val_max * 1.2]
+                            bounds = [00.1, 1, 2, 10, 100, 1000, val_max * 1.2]
                             norm = BoundaryNorm(boundaries=bounds, ncolors=300)
                         else:
                             if val_min == 0:
                                 val_min = 1e-5
                             if val_max > 1000:
                                 levels = np.array([00.1, 1, 2, 10, 100, 1000, 1e6])
-                                bounds = [00.1, 1, 2, 10, 100, 1000, val_max, val_max * 1.2]
+                                bounds = [00.1, 1, 2, 10, 100, 1000, val_max * 1.2]
                                 norm = BoundaryNorm(boundaries=bounds, ncolors=300)
 
                             else:
-                                levels = np.array([00.1, 1, 2, 10, 100, val_max])
-                                bounds = [00.1, 1, 2, 10, 100, 1000, val_max * 1000]
-                                norm = BoundaryNorm(boundaries=bounds, ncolors=300)
-
-                        bounds = [00.1, 1, 2, 10, 100, 1000, val_max, val_max * 1.2]
+                                levels = np.array([00.1, 1, 2, 10, 100, 1000, val_max * 1000 + 1])
+                                bounds = [00.1, 1, 2, 10, 100, 1000, val_max * 1000 + 1]
                                 norm = BoundaryNorm(boundaries=bounds, ncolors=300)
 
                         cf = (self.axis_SNR[f].contourf(x, -y,
@@ -1172,18 +1166,18 @@ class SignalProcessingTab(QWidget):
                         val_max = np.nanmax(stg.SNR_raw_data[self.combobox_acoustic_data_choice.currentIndex()][f, :, :])
                         if val_min == val_max:
                             levels = np.array([00.1, 1, 2, 10, 100, 1000, 1e6])
-                            bounds = [00.1, 1, 2, 10, 100, 1000, val_max, val_max * 1.2]
+                            bounds = [00.1, 1, 2, 10, 100, 1000, val_max * 1.2]
                             norm = BoundaryNorm(boundaries=bounds, ncolors=300)
                         else:
                             if val_min == 0:
                                 val_min = 1e-5
                             if val_max > 1000:
                                 levels = np.array([00.1, 1, 2, 10, 100, 1000, 1e6])
-                                bounds = [00.1, 1, 2, 10, 100, 1000, val_max, val_max * 1.2]
+                                bounds = [00.1, 1, 2, 10, 100, 1000, val_max * 1.2]
                                 norm = BoundaryNorm(boundaries=bounds, ncolors=300)
                             else:
-                                levels = np.array([00.1, 1, 2, 10, 100, val_max])
-                                bounds = [00.1, 1, 2, 10, 100, 1000, val_max * 1000]
+                                levels = np.array([00.1, 1, 2, 10, 100, 1000, val_max*1000 + 1])
+                                bounds = [00.1, 1, 2, 10, 100, 1000, val_max * 1000 + 1]
                                 norm = BoundaryNorm(boundaries=bounds, ncolors=300)
 
                         cf = (self.axis_SNR[f].contourf(x, -y,

main.py

@@ -1,4 +1,5 @@
 import sys
+import logging
 import traceback
 
 from PyQt5.QtWidgets import QApplication, QMainWindow
@@ -26,6 +27,13 @@ import matplotlib.pyplot as plt
 PERCENT_SCREEN_SIZE = 0.85
 _translate = QCoreApplication.translate
 
+logging.basicConfig(
+    level=logging.DEBUG,
+    format=('[AcouSed][%(levelname)s] %(message)s')
+)
+
+logger = logging.getLogger()
+logger.setLevel(logging.DEBUG)
 
 class MainApplication(QMainWindow):
 
@@ -41,15 +49,18 @@ class MainApplication(QMainWindow):
         height = size.height()
         self.resize(int(PERCENT_SCREEN_SIZE*width), int(PERCENT_SCREEN_SIZE*height))
         try:
-            self.read_table_open = ReadTableForOpen()
             # **************************************************
             # -------------- Acoustic data tab ---------------
 
             self.acoustic_data_tab = AcousticDataTab(self.ui_mainwindow.tab1)
             print("0 AcousticDataTab ", id(AcousticDataTab))
 
-            self.acoustic_data_tab.combobox_ABS_system_choice.editTextChanged.connect(
-                self.acoustic_data_tab.ABS_system_choice)
+            self.acoustic_data_tab\
+                .combobox_ABS_system_choice\
+                .editTextChanged\
+                .connect(
+                    self.acoustic_data_tab.ABS_system_choice
+                )
 
             # **************************************************
             # --------- Signal pre-processing data tab ----------
@@ -84,20 +95,19 @@ class MainApplication(QMainWindow):
 
             # self.user_manual_tab = UserManualTab(self.ui_mainwindow.tab7)
 
-            self.ui_mainwindow.actionOpen.triggered.connect(self.trig_open)
-
         # **************************************************
         # ---------------- Text File Error -----------------
 
         except Exception as e:
+            logger.error(str(e))
+            logger.error(traceback.format_exc())
+
             with open("Error_file.txt", "w", encoding="utf-8") as sortie:
                 sortie.write(str(e))
                 sortie.write(traceback.format_exc())
                 # traceback.TracebackException.from_exception(e).print(file=sortie)
 
-    def trig_open(self):
-        self.read_table_open.open_file_dialog()
-
+    def open_study_update_tabs(self):
         self.acoustic_data_tab.combobox_ABS_system_choice.setCurrentText(stg.ABS_name[0])
         self.acoustic_data_tab.fileListWidget.addFilenames(stg.filename_BS_raw_data)
 
@@ -108,7 +118,6 @@ class MainApplication(QMainWindow):
         self.sample_data_tab.lineEdit_fine_sediment.setToolTip(stg.path_fine)
         # self.sample_data_tab.fill_table_fine()
 
-
 if __name__ == '__main__':
     # print("sys.argv:", [arg for arg in sys.argv])
     # app = MainApplication(sys.argv)

manifest.scm

@@ -210,4 +210,4 @@ user-defined extensions).")
               "python-scipy" "python-scikit-learn"
               "python-pyqt@5" "python-pyqt5-sip"
               "python-numpy@1" "python-pandas@1.5"
-              "python-matplotlib"))))
+              "python-matplotlib" "python-odfpy"))))

requirements.txt

@@ -0,0 +1,13 @@
+matplotlib==3.6.3
+numpy==1.23.5
+pandas==1.5.3
+PyQt5==5.15.9
+PyQt5-Qt5==5.15.2
+PyQt5-sip==12.11.0
+python-dateutil==2.8.2
+scikit-learn==1.2.1
+scipy==1.10.0
+pyqt-file-list-widget==0.0.1
+qtrangeslider==0.1.5
+astropy==6.1.7
+odfpy==1.4.1