meafs_code package

Subpackages

• meafs_code.scripts package
  • Submodules
  • meafs_code.scripts.abundance_plot module
    • erase_emission_order()
    • erase_null_abund()
    • folders_creation()
    • get_diff()
    • get_spectrum()
    • main()
    • plot_abund_box()
    • plot_abund_hist()
    • plot_differ_hist()
    • plot_lines()
  • meafs_code.scripts.abundance_fit module
    • args_menu()
    • check_order()
    • create_basic_folder_structure()
    • cur_time()
    • fit_abundance()
    • get_sep()
    • get_specs_lims()
    • gui_call()
    • log_write()
    • main()
    • open_linelist_refer_fl()
    • open_previous()
    • open_spec_obs()
    • plot_abund_nofit()
    • plot_spec()
    • plot_spec_gui()
    • plot_spec_ui()
    • read_config()
    • save_spec()
  • meafs_code.scripts.bisec_interpol module
    • bisec()
    • chi2()
    • main()
  • meafs_code.scripts.fit_functions module
    • bisec()
    • c_init()
    • chi2()
    • cut_spec()
    • fit_continuum()
    • line_boundaries()
    • spec_operations()
  • meafs_code.scripts.turbospec_functions module
    • change_abund_configfl()
    • change_spec_range_configfl()
    • check_elem_configfl()
    • optimize_abund()
    • optimize_spec()
    • run_configfl()
  • meafs_code.scripts.unify_plots module
    • main()
    • run_pdflatex()
    • write()
  • meafs_code.scripts.voigt_functions module
    • find_func()
    • gaussian()
    • lorentzian()
    • optimize_abund()
    • optimize_spec()
    • voigt()
  • Module contents

Submodules

meafs_code.gui module

MEAFS GUI

Matheus J. Castro

This is the main file. Here it is included all MEAFS features and the GUI.

class meafs_code.gui.MEAFS(parent=None)

Bases: QMainWindow, Ui_MEAFS

Main class that define the properties of the GUI.

LineAddRemove(uiobject, add, islinelist=False)

Add new or removes lines from a QT table.

Parameters:

• uiobject – the QT table widget to change.

• add – true: add a line; false: remove a line.

• islinelist – if it is a line-list table, also calls the function to generate the checkboxes.

argument_resolve(fastcheck=False)

Resolve the arguments passed in the commandline.

Parameters:

fastcheck – if true, only check for the help and version arguments.

auto_save()

Save the session by the auto_save.plk file name or the name previously chosen by the user.

auto_set_output()

Try to find the synthetic spectrum output file name automatic by looking in the configuration file

static browse(uiobject, caption, direc=None)

Show a File Dialog to select some file.

Parameters:

• uiobject – the QT widget that shows the file path.

• caption – the caption in File Dialog.

• direc – the first directory that File Dialog should show.

static browse_dir_out(uiobject, caption, direc=None)

Show a File Dialog to select some directory.

Parameters:

• uiobject – the QT widget that shows the file path.

• caption – the caption in File Dialog.

• direc – the first directory that File Dialog should show.

centralize_child_window(wind)

Centralize child windows in respect of the main window.

Parameters:

wind – the new window widget to be centralized.

checkLinelistElements()

Check or uncheck all checkboxes in the line-list table.

checkLineliststate()

Count the number of checked checkboxes in the line-list table, update the progress total value accordingly and also check or uncheck the “Select All” element.

check_output_folder()

Check if the output folder location is written.

Returns:

true if it is present, otherwise false.

checkmethod()

Check which methods tab is selected and disable the other ones.

checktabshels()

Modify the behaviour of some UI elements to guide the user through the creation of the final plots for the abundances.

clear_scale(show_msg=True)

Resets the fixed scale to show images in the final plots area, allowing resizing the GUI into smaller sizes.

Parameters:

show_msg – Option to pop up a message saying that the scale was cleared.

clear_spectrum_plot()

Clear all plots in the Spectrum Plot tab, except the spectra themselves.

clearstd()

Clear the QT Widget that receive the stdout and stderr messages.

closeEvent(event)

Handles the close button event and trigger an “are you sure?” message.

Parameters:

event – the event itself.

datatableconfig(load=False, loaddata=None)

Configure the button to show the spectrum file name and the tooltip to show the full path in the data QT table.

Parameters:

• load – if it is to load or to clear the spectrum data.

• loaddata – the data containing the file names.

datatableselect()

Configure the data QT table with the buttons to select spectra or clear them.

dict_to_qtable(qtable, dict_table, checkboxes=None, tooltip=False)

Transform a QT Table in a dictionary.

Parameters:

• qtable – the QT Table to be written.

• dict_table – the dictionary to read the data.

• checkboxes – the index of checkboxes, if exists.

• tooltip – write the item or the tooltip (for spectrum data table)

enable_auto_save()

Enable or disable the timed auto-save and the close auto-save capability and write this setting in to the settings file.

fitparWindow()

Call and get the values of the Fit Parameters window.

full_spec_plot_range()

Apply the total maximum and minimum values of the current plot and change the range to it.

get_delimiter(error_msg=None)

Get the current set delimiter type in MEAFS GUI.

Parameters:

error_msg – Custom error message to show.

Returns:

the delimiter, None (for auto-detect) or -1 (for error).

graymethods(metharray)

Gray the tabs of the methods that are not selected.

Parameters:

metharray – the pattern that should be grayed.

gui_hold(value)

Froozen some widgets in the GUI so they can not be modified while running the fit.

Parameters:

value – if it is to hold or not the GUI

loadData()

Load the data present in the QT table and call the function to plot the spectra in the GUI.

loadLinelist()

Load a line-list file with element and wavelength in the proper QT table.

loadRefer()

Load the abundance reference file containing the elements and their abundances in the QT table.

load_session(direc=None, list_save=None, loadprev=False)

Load a previously saved session, or a list with all session-variables.

Parameters:

• direc – the directory where the File Dialog should first open.

• list_save – a list with all session-variable. If it is different from None, the prompt to choose a file will not be shown.

• loadprev – if true, the path of the file needs to be written in the self.filepath variable.

static make_jupyter_widget_with_kernel()

Create and configure the Jupyter QT Widget.

Returns:

the widget itself.

new_session()

Load a new empty session by overriding all variable to the default values.

norm_trunc_spec()

Call the Normalize and Truncate window

open_prev_results()

Open CSV files with previous runs and load the results, including the available plots (if any).

static qtable_to_dict(qtable, checkboxes=None, tooltip=False)

Transform a QT Table in a dictionary.

Parameters:

• qtable – the QT Table to be read.

• checkboxes – the index of checkboxes, if exists.

• tooltip – get the item or the tooltip (for spectrum data table)

Returns:

the dictionary

quitbtn()

Create an alias to the close button event.

results_show_tab()

Show the results of the selected line in the results table in the results tab and focus the plot in the current line.

run_check_continuum()

Call the Continuum algorithm and draw in the plot the results.

run_erase_continuum()

Erase from the plot the continuum fit line.

run_final_plots(plot_type, single=False)

Run the subroutines to create the final plots.

Parameters:

• plot_type – type of the final plot to create.

• single – create a final plot to a single line or for all of them.

run_fit()

Call the fit algorithm.

run_fit_nopars()

Call the fit algorithm only for the abundance, without fitting the Wavelength Shift, Continuum and Convolution.

run_nofit()

Call the fit algorithm without any fit at all, only to generate the plots with the selected values.

save_cur_abund()

Save the results of the fit in a CSV file.

save_session(saveas=False, direc=None, flname=None, getdill=False)

Save a session using dill.

Parameters:

• saveas – if true, ignore the self.filepath variable.

• direc – the directory where the File Dialog should first open.

• flname – file name to save the session. If present, the File Dialog will not be shown.

• getdill – if true, does not save the session and return the list to be saved.

Returns:

the list to be saved (if getdill is true), true if the session is saved or false if the self.filepath was not properly filled.

show_about()

Create a new window to show info about MEAFS.

show_error(msg)

Show a QT window for some user-input-error message.

Parameters:

msg – the message to be shown.

static show_question(parent, title, message)

Pop-up a question message.

Parameters:

• parent – the parent window.

• title – the box title.

• message – the message.

Returns:

True or False.

show_quit()

Shows the quit message “are you sure?”

Returns:

true or false, depending on the clicked button.

stop_func()

Define if the stop button was precessed during a run.

tablecheckbox(state)

Create a QT Widget with a CheckBox inside to use it in QT tables.

Parameters:

state – if it should be checked or not.

Returns:

the QT widget containing the checkbox.

tablecheckboxindividual()

Check or uncheck a unique checkbox in the line-list table.

turbospec_config_path(init=True, tp=None, onlytext=False)

Check, select and write into the settings the path to the configuration and output files of TurboSpectrum

Parameters:

• init – if it is only to look if the path in the database exists

• tp – type of file being called

class meafs_code.gui.Stdredirect(edit, color=None, out=None, showtab=None)

Bases: object

Class that redirect the stdout (outputs) and the stderr (errors) to the GUI and to the terminal, if available.

flush()

Flush function from the sys.flush()

write(text)

Write function that actually writes the output in the GUI and in the terminal (if present).

Parameters:

text – the text message to be printed.

class meafs_code.gui.VerticalNavigationToolbar2QT(canvas, parent=None, coordinates=True)

Bases: NavigationToolbar2QT

Class to create a vertical toolbar for the plot in the matplotlib package.

set_message(s)

Write the mouse pointer coordinates in the toolbar.

Parameters:

s – the message to write (coordinates)

toolitems = [('Home', 'Reset original view', 'home', 'home'), ('Back', 'Back to previous view', 'back', 'back'), ('Forward', 'Forward to next view', 'forward', 'forward'), (None, None, None, None), ('Pan', 'Left button pans, Right button zooms\nx/y fixes axis, CTRL fixes aspect', 'move', 'pan'), ('Zoom', 'Zoom to rectangle\nx/y fixes axis', 'zoom_to_rect', 'zoom'), (None, None, None, None), ('Save', 'Save the figure', 'filesave', 'save_figure')]

meafs_code.gui.exception_hook(exctype, value, traceback)

Function to redirect the errors of the modules to the main module, so the error can be verified.

meafs_code.gui.main()

Main function to run the GUI.

meafs_code.desktop_entry module

MEAFS Desktop Entry Creation

Matheus J. Castro

This file analyse and create aliases in the system to run MEAFS through an entry in the system menu.

meafs_code.desktop_entry.create()

Create the menu entry in the system to run MEAFS.

meafs_code.desktop_entry.get_curr_dir()

Get the current environment running python (like anaconda or system) and the directory where the file is located.

Returns:

the command that activates anaconda environment (if present) and the file absolute path.

meafs_code.desktop_entry.remove()

Remove the menu entry in the system that run MEAFS.