Pierre PHILIPPE contributed to the project by researching and documenting the morphological analysis calculations. This commit adds him to the list of contributors in the README.md file.

 fix(data_processing.py): fix formula for R_V_scan to include parentheses for correct order of operations
 fix(output.py): add delta_z parameter to generate_headers function to correctly display the delta_z value in the output file
 feat(output.py): add delta_z value to output file headers if add_headers setting is enabled
 feat(MainWindow.py): add delta_z value to output file headers if add_headers setting is enabled
 feat(DiscreteDataWorker.py): add delta_z value to output file headers if add_headers setting is enabled
 feat(RawDataWorker.py): add delta_z value to output file headers if add_headers setting is enabled

The changes in data_processing.py fix a variable name and a formula to correctly calculate the R_max and R_V_scan values.

The version number in SettingManager.py has been updated to 1.2.2. This is a chore commit as it does not introduce any new features or bug fixes, but rather updates the version number to reflect the current state of the code.

 feat(data_processing.py): add raw_data parameter to get_advanced_data function to improve flexibility
The L variable was not being computed in the get_advanced_data function, which is necessary for the calculation of the tortuosity. The raw_data parameter was added to the get_advanced_data function to improve flexibility and allow for more advanced calculations to be performed.

 fix(input.py): add filename attribute to ScannedObject class
The filename attribute was not being set in the ScannedObject class, which is necessary for generating the output file headers.

 feat(output.py): add function to generate headers for output file
The generate_headers function was added to generate the headers for the output file. The headers include the filename, date, version, discretisation method, and whether the data was verticalised.

 chore(MainWindow.py): enable process_advanced_data function

 style(MainWindow.ui, UI_MainWindow.py): adjust GUI layout and label text for better user experience
The GUI layout has been adjusted to improve the user experience. The window width has been reduced from 1419 to 1336 pixels to better fit the screen. The minimum and maximum sizes of the MainSettings widget have been increased from 518 to 600 pixels to allow for more space for the labels. The labels have been updated to include the units of measurement to improve clarity.

 fix(AdvancedDataWorker.py): add raw_data parameter to __init__ method
 feat(AdvancedDataWorker.py): add support for raw data processing in get_advanced_data method
The AdvancedDataWorker class now has a raw_data parameter in its __init__ method, which is used in the get_advanced_data method. This allows for raw data processing in addition to the existing discrete data processing.

 fix(DiscreteDataWorker.py): generate headers before formatting data
 feat(DiscreteDataWorker.py): add support for generating headers in output file
The DiscreteDataWorker class now generates headers for the output file if the add_headers setting is enabled. The headers are generated before formatting the data to ensure that the headers are included in the output file.

 fix(PreProcessWorker.py): set filename of ScannedObject
The PreProcessWorker class now sets the filename of the ScannedObject to the basename

 style(UI_Settings.py): reorganize widgets in the settings UI for better readability
 fix(data_extraction.py): fix standard deviation calculation to use unbiased estimator
 chore(SettingManager.py): add "add_headers" setting with default value of True
The changes in UI_Settings.py are purely cosmetic and do not affect the functionality of the code. The fix in data_extraction.py corrects the standard deviation calculation to use the unbiased estimator. The addition of the "add_headers" setting in SettingManager.py allows for the addition of headers to output files.

 feat(README.md): add automated installation scripts for Windows, Linux, and Mac
The README file now includes instructions for both manual and automated installation of the program. Automated installation scripts have been added for Windows, Linux, and Mac to simplify the installation process. The scripts install the required dependencies using pip.

Added instructions for generating documentation using Sphinx and the readthedocs theme. The documentation can be found in the `docs/build` directory and can be opened by launching the `index.html` file in a web browser. The instructions include installing the readthedocs theme and running the `make html` command in the `docs` directory to generate the documentation.

The Sphinx documentation has been added to the project. This includes a Makefile, a make.bat file, and a conf.py file in the docs directory. The source directory contains the documentation files in reStructuredText format. The documentation includes an installation guide and an API reference. The utils package has been reorganized to be more modular and easier to document. The documentation can be built using the `make html` command in the docs directory.

 feat(utils): add new modules and packages to the project
New modules and packages have been added to the project. The following packages have been added:
- utils.gui.pyqt.about
- utils.gui.pyqt.error_popup
- utils.gui.pyqt.main_window
- utils.gui.pyqt.settings
- utils.math
- utils.settings

The new packages contain modules that provide additional functionality to the project.

The variable names σ_〈R〉 and σ_〈R〉^tot were corrected to σ_<R> and σ_<R>^tot respectively to improve consistency with the naming conventions used in the rest of the code.

This commit adds missing variables to the documentation of the `get_advanced_data` function in `data_processing.py`. The added variables are `H`, `L`, `l`, `MI_mR`, `MI_mH`, `MI_mr_in`, `V_scan`, `R_V_scan`, `S_V_scan`, and `HI`. This improves the documentation of the function and makes it easier for developers to understand the function's behavior.

 fix(data_processing.py): fix typo in advanced data keys and add R_max to advanced data
 feat(MainWindow.py): add support for exporting advanced data to a text file
 style(MainWindow.ui, UI_MainWindow.py): change the display of advanced data labels to use <R> instead of 〈R〉 and σ<R> instead of σ〈R〉
The README.md file now reflects the fact that the tool can now read .stl files. The advanced data keys in data_processing.py have been fixed to use the correct symbols and R_max has been added to the advanced data. The MainWindow.py now allows the user to export the advanced data to a text file. The display of advanced data labels in MainWindow.ui and UI_MainWindow.py has been changed to use <R> instead of 〈

 feat(input.py): add support for binary and ascii STL files to ScannedObject class
The ScannedObject class now has a static variable called authorised_extensions which contains a list of file extensions that are supported by the class. This improves the readability of the code and makes it easier to maintain. The ScannedObject class now also supports binary and ascii STL files, which increases the flexibility of the class and allows it to handle more file formats.

 feat(MainWindow.py, PreProcessWorker.py, Settings.py, UI_Settings.py, settings.ui): add support for verticalising scanned objects
 feat(Settings.py, UI_Settings.py, settings.ui): add checkbox to enable/disable verticalisation of scanned objects
The changes add support for verticalising scanned objects before processing them. A new checkbox has been added to the settings UI to enable/disable this feature.

 refactor(SettingManager.py): add default settings dictionary and refactor createInitialSettings method
 feat(SettingManager.py): add new settings to the config file if they are not present
The `default_settings` dictionary is added to the `SettingManager` class to store the default values for the settings. The `createInitialSettings` method is refactored to use the `default_settings` dictionary to set the initial values of the settings. If new settings are added to the `default_settings` dictionary, they are added to the config file if they are not already present. The `remove_changed` method is added to remove the `has_changed` flag.

The first letter of the title "Analyse morphologique" was not capitalized, which is inconsistent with the usual capitalization rules for titles.

 chore(README.md): update image and fix typo in rotation instructions
The image in the README.md file was updated to reflect the correct rotation instructions. A typo in the rotation instructions was also fixed.

 chore(README.md): fix typo in contributor's role
A typo in the role of one of the contributors was fixed.

 fix(data_processing.py): add missing half discretisation values to L calculation
The calculation of L in the get_advanced_data function of data_processing.py was missing half the discretisation values at the beginning and end of the object.

 fix(input.py): remove print statement
A print statement was accidentally left in the from_xyz_file method of the ScannedObject class in input

 feat(input.py): add support for reading .xyz files and raise InvalidFileFormat exception if file format is not supported
 chore(gui): add warning popup when trying to use Mesh3D graph with .xyz file
 chore(gui): refactor MainWindow.check_input_file method to handle .xyz files
 chore(gui): refactor PreProcessWorker to use ScannedObject.from_file method
 chore(math): add check for faces in verticalise function to avoid errors when faces is None
The ScannedObject constructor now handles the case where faces is None. Support for reading .xyz files has been added, and an InvalidFileFormat exception is raised if the file format is not supported. A warning popup has been added to the MainWindow when trying to use the Mesh3D graph with a .xyz file. The MainWindow.check_input_file method

This commit improves the readability of the README.md file by fixing typos and grammatical errors. The changes include correcting the capitalization of some words, fixing the spelling of some words, and improving the formatting of the text. The commit also adds instructions for using the 2D and 3D graphs, and adds information for developers, including the variable naming convention, the use of relative imports, and the use of Qt Designer. Finally, the commit adds a contributors section to acknowledge the contributions of the developers who worked on the project.

The README file has been updated to include a more detailed description of the Analyse Morphologique tool, including its features and capabilities. Additionally, installation and usage instructions have been added to the README file to help users get started with the tool.

 refactor(SettingManager.py): reorder authors list and update description
The version number has been updated to 1.2.0 to reflect the changes made to the application. The authors list has been reordered and the description has been updated to provide a more detailed explanation of the tool's functionality.

The x_mean QDoubleSpinBox is now set to read-only to prevent the user from changing its value.

The default value of the "show_graph_checkbox" element has been changed from false to true. The "x_mean" element has been set to read-only mode. The "scrollAreaWidgetContents" element has been shifted upwards by 179 pixels to improve the layout. These changes improve the user experience and make the GUI more intuitive.

 refactor(MainWindow.py): rename process_advanced_data method to process_advanced_metrics to improve semantics
 refactor(AdvancedDataWorker.py): add V_scan parameter to constructor to improve semantics
 refactor(Settings.py): add conditional to set output_file_separator to '\t' if '\\t' is entered
The refresh_advanced_metrics button is now connected to its own method to improve readability. The process_advanced_data method has been renamed to process_advanced_metrics to better reflect its purpose. The AdvancedDataWorker constructor now takes a V_scan parameter to improve semantics. The Settings class now has a conditional to set the output_file_separator to '\t' if '\\t' is entered to improve consistency.

The function parameter `update_progress_bar` has been renamed to `progressbar_placeholder` to improve the semantics of the function. This change does not affect the functionality of the code.

 feat(data_processing.py): add new morphological indicators to the output of the `get_advanced_data` function
The `get_advanced_data` function now calculates and returns the following morphological indicators:
- MI_mR: the ratio of the maximum radius to the mean radius
- MI_mH: the ratio of the maximum radius to the height of the object
- V_scan: the volume of the scanned object
- R_V_scan: the radius of a sphere with the same volume as the scanned object
- S_V_scan: the surface area of a sphere with the same volume as the scanned object
- R_h: the hydraulic radius of the object
- HI: the hydraulic index of the object

 chore(data_processing.py): update keys in the dict returned by get_advanced_data function to be more descriptive
 feat(MainWindow.py): add functionality to export advanced data to a text file
 feat(MainWindow.py): add button to export advanced data to a text file
 feat(MainWindow.ui): update labels for Volume and Surface to include units
The keys in the dict returned by the get_advanced_data function were updated to be more descriptive. The export_advanced_data function was added to the MainWindow class to allow the user to export the advanced data to a text file. A button was added to the GUI to allow the user to export the advanced data. The labels for Volume and Surface were updated to include the units of measurement.

 style(UI_MainWindow.py): rename tab_5 to parameters and tab_6 to values for better semantics
The names of the tabs have been changed to better reflect their contents. The tab previously named tab_5 is now named parameters, and the tab previously named tab_6 is now named values. This improves the readability and maintainability of the code.

 style(UI_MainWindow.py): rename tab_6 to values and tab to graph_pane_1, tab_2 to graph_pane_2, tab_3 to graph_pane_3, and tab_4 to graph_pane_4 for better semantics
This commit only renames the tabs in the UI_MainWindow.py file to improve the semantics of the code. The tab_6 is renamed to values, and tab, tab_2, tab_3, and tab_4 are renamed to graph_pane_1, graph_pane_2, graph_pane_3, and graph_pane_4, respectively.

 refactor(UI_MainWindow.py): update labels for volume and surface to include units
The labels for volume and surface have been updated to include the units of measurement in millimeters. The tab names for the settings and graph panes have also been updated to improve readability and consistency with the naming conventions.

 refactor(AdvancedDataWorker.py): update keys in the dict returned by the function to be more explicit
 refactor(position_manipulation.py): remove unnecessary computation of the center of gravity in the verticalise function
The keys in the dict returned by the AdvancedDataWorker function have been updated to be more explicit. The keys 'Volume' and 'Surface' have been updated to 'Volume en mm3' and 'Surface en mm2' respectively to indicate the units of measurement. In the position_manipulation.py file, the computation of the center of gravity in the verticalise function was unnecessary and has been removed to improve performance.

 feat(data_processing.py): add function to calculate morphological indicators from discrete data
The variable name teta_diffs was changed to theta_diffs to improve semantics. A new function was added to calculate morphological indicators from discrete data. The function calculates Tortuosity, Volume, Surface, Mean radius, Standard deviation of radius, Sigma r tot, MI_l, and MI_p.

 refactor(input.py): remove unused result_file_path parameter from ScannedObject constructor and from_xyz_file method
 feat(input.py): add encoding parameter to open method in from_obj_file and from_xyz_file methods
The result_file_path parameter was not being used in the ScannedObject constructor and from_xyz_file method, so it was removed to simplify the code. The encoding parameter was added to the open method in the from_obj_file and from_xyz_file methods to ensure that the files are opened with the correct encoding.

 fix(output.py): add utf-8 encoding when writing to output file
 feat(output.py): remove unused import and function argument, improve code readability
The fix adds the utf-8 encoding when writing to the output file to avoid encoding issues. The feat removes the unused import and function argument to improve code readability. The function format_data now only takes the necessary arguments and the unused import is removed.

 fix(main_window.py): fix typo in function name
 feat(main_window.py): add persistence to pre-processed data
The fix corrects a typo in the function name get_true_theta_from_x_y. The feat adds persistence to the pre-processed data by storing the raw data, discrete data, and advanced data in the main window. This avoids re-computation of the data when switching between tabs.

 style(MainWindow.ui): add export_advanced_metrics button to the UI
 style(UI_MainWindow.py): add export_advanced_metrics button to the UI
 style(ressources_rc.py): update the resource file
 fix(data_extraction.py): fix typo in function name get_mean_teta to get_mean_theta
The changes add a new button to the UI named "export_advanced_metrics" which allows the user to export variables. The resource file is updated to reflect the changes. The typo in the function name get_mean_teta is fixed to get_mean_theta.

This commit adds a docstring to the run() method in the DiscreteDataWorker class. The docstring explains what the method does, what it calculates, and what it emits. It also mentions that the result is saved in a file located in the output_path. This improves the readability and maintainability of the code.

The name of the module has been changed to AdvancedDataWorker.py to better reflect its functionality. The description has been updated to include the extraction of morphological indicators. The parameters and instance variables have been updated to reflect the change in functionality. The run() method has been updated to include a description of the emitted signal and the keys of the dictionary that is emitted.

 refactor(PreProcessWorker.py): rename objpath to obj_path and discretisation_value to delta_z for better readability
This commit renames the objpath parameter to obj_path and discretisation_value to delta_z for better readability and consistency with the naming conventions. The function run() has been updated to include a more detailed description of what it does.

 fix(RawDataWorker.py): fix typo in theta key name in the output dict
 feat(RawDataWorker.py): save the result of the calculation in a file located in the output_path
The run method now has a docstring that explains what it does. The typo in the theta key name in the output dict has been fixed. The result of the calculation is now saved in a file located in the output_path. This improves the functionality of the RawDataWorker class.

 feat(MainWindow.py): add support for calculating advanced data in a separate thread
 feat(AdvancedDataWorker.py): add worker to calculate advanced data in a thread
The `get_advanced_data` function was added to calculate advanced data from the discrete data. The `process_advanced_data` function was added to the `MainWindow` class to start a thread to calculate the advanced data. The `AdvancedDataWorker` class was added to calculate the advanced data in a separate thread. This allows the application to be more responsive and not freeze while the advanced data is being calculated.

 feat(data_processing.py): remove deprecated get_discrete_vertices2 method and rename get_discrete_vertices3 to get_discrete_vertices. Simplify get_discrete_vertices method by removing the selection of the discretisation method from the settings and always using the Z0-Zi < DeltaZ method. This improves code readability and maintainability.
 feat(input.py): remove deprecated result_file_path and bruteforce_discretization_result attributes from ScannedObject class. Add old_delta, old_discrete, and old_discrete_type attributes to cache the results of the get_discrete_vertices method. This improves performance by avoiding unnecessary recomputations of the discretized vertices.
 feat(MainWindow.py): add support for selecting a layer to display discrete graphs for. Add two new graph types: "Coupe de la couche" and "Difference entre le rayon de chaque points

 fix(ui): change tab index to display the correct tab on startup
 feat(ui): add label and combobox to select layer to display
 fix(worker): add discretisation_value parameter to PreProcessWorker constructor
 feat(math): add get_true_teta_from_x_y, get_difference_from_mean_value, and get_distance_between_two_vertices functions
The UI fix changes the tab index to display the correct tab on startup. The new label and combobox allow the user to select the layer to display. The worker fix adds a discretisation_value parameter to the PreProcessWorker constructor. The new math functions are get_true_teta_from_x_y, get_difference_from_mean_value, and get_distance_between_two_vertices. These functions are useful for calculating teta, differences from mean values, and distances between vertices.

 feat(gui): add an about window to the GUI to display information about the software
The INRAE logo has been added to the GUI as a resource. An about window has been added to the GUI to display information about the software such as the description, authors, and version. The about window can be accessed via the "A propos de ce logiciel" menu item.

The authors value was previously a string with multiple authors separated by a comma. The value has been changed to a list of strings to match the expected format.

 chore(SettingManager.py): add version attribute to SettingManager class and update config.yml version if needed
The SettingManager class now has a version attribute to keep track of the version of the configuration file. If the version in the configuration file is different from the version in the SettingManager class, the version in the configuration file is updated to match the version in the SettingManager class. This ensures that the configuration file is always up-to-date with the latest version of the application.