2.1. The main window¶

The main window provides an overview of the state of ARTEMIS as well as of your current fitting project. This window is divided into 7 areas.

Fig. 2.2 The main window.

At the top is a menu bar. We will examine the contents of each menu below.
At the bottom is the status bar. This area is used to convey messages to you during the course of operating the program.
On the left is a stack of buttons used to show and hide various parts of ARTEMIS. Each of these will be described in detail later in the document.
To the right is the listing of data groups. The Add button is used to import a new data set into ARTEMIS. As data are imported, they will listed as a stack of buttons below the Add button.
Next comes the listing of FEFF calculations. The Add button is used to import new structural data set into ARTEMIS. This may be input data for FEFF, an atoms.inp file, or a CIF file containing crystal structure data. As FEFF calculations are started, they will listed as a stack of buttons below the Add button.
The wide area to the right of the FEFF calculations contains several controls for the current fitting project. The Name and Description boxes are used to describe the current state of your fitting project. The name should be a concise description of the current fit and is used as a label identifying a specific fit. The description is a lengthier, free-form bit of text describing the current fit in more detail. This text will be written to log files. ARTEMIS does a decent job of automatically generating text for both of these boxes, but providing your own text will help you to document the progression of your fitting project. This section also has controls for selecting the space in which your fit is evaluated and for saving a project file in a single click.
On the far right is the Fit button. As you might imagine, this button is clicked to initiate a fit. The color of this button will change to provide a heuristic evaluation of the quality of each fit. Below the Fit button is Show log button, used to show or hide a window containing the results from the most recent fit.

2.1.1. File drag and drop¶

The data set and FEFF calculation area on the main window, areas 4 and 5 above, are drop targets for files drag dragged from your computer's file manager.

You can drop ATHENA project files (.prj) onto the data set area. To import data from some other source, you are required to use the File menu.
You can drop CIF, ATOMS input, or FEFF input files onto the FEFF calculation area.
You can drop an ARTEMIS project file (.fpj) onto either of the data set and FEFF calculation areas. To import old-style artemis project files or DEMETER serializations, you are required to use the File menu.

You can only drag drag and drop one file at a time. If you try to drag more than one of any file type, a warning will be issued in the status bar and no import will happen. Similarly, you may not drop a folder.

2.1.2. The File menu¶

Clicking on File displays this menu, which is mostly used for various kinds of input and output. Note that some menu items that have keyboard shortcuts attached and that these shortcuts are shown in the menu.

Fig. 2.3 The File menu.

The first option is used to import any kind of data into ARTEMIS, including ARTEMIS or ATHENA project files, ASCII files containing χ(k) data, FEFF or ATOMS input files, CIF files, or a few other things. ARTEMIS is usually good about properly identifying the type of input file and doing the right thing with it. In the rare situation where this doesn't work, try the import submenu.
The second option provides a submenu of recently imported files broken down by file type, including ARTEMIS projects, ATHENA projects, structure data for ATOMS or FEFF, and a couple of other more obscure file types.
The next three items are used to save ARTEMIS project files. Save project saves the current state of the project to its current, prompting for a name if it does not yet have one. Save project as will prompt for the name to which to save the current state of the project. Save current fit will save a project file containing only the current fit, without any of the history. These project files are the sort that can be dragged from your computer's file manager onto the data or FEFF list.
The import submenu is used to specify the file type to import. Typically, this is not necessary and is only provided for the rare situation when ARTEMIS fails to recognize one of its standard input data types.
The export submenu is used to generate files in the format of an IFEFFIT script or a perl script using DEMETER. These files attempt to capture the current state of your fitting project. It is unlikely that the output of either of these export options will be immediately useful without some editing. The purpose of these export options is to allow you to use ARTEMIS to develop a fitting model, then use the exported file in some other way, for instance as part of a script for automated batch processing.
The next menu item displays a window used to set program preferences.
Finally, there are menu items for closing the current fitting project and for exiting the program. Each of these will prompt you to save your fitting option if you have not recently done so.

2.1.3. The Monitor menu¶

This menu provides several options for monitoring the state of ARTEMIS, IFEFFIT, and the plotting backend (usually Gnuplot).

Fig. 2.4 The Monitor menu.

The command buffer contains a record of every data processing command sent to IFEFFIT or LARCH and every plotting command sent to the plotting backend. Bruce uses these buffers to debug the prgram as he implements new features. You may want to use these buffers to learn the details of interacting directly with IFEFFIT, LARCH, or the plotting backend.
The status bar buffer contains a record of nearly every message sent the status bar in the main window as well as those messages displayed in the status bars of other windows in ARTEMIS. All messages are time stamped.
The Show Ifeffit menu will cause IFEFFIT to display detailed information in the command buffer about the internal state of different kind of data. This is another thing Bruce uses to debug program issues.
The Debug options menu contains several items used to display technical information about the current state of ARTEMIS. Again, this is a tool Bruce uses when developing the program. After reporting a bug to the IFEFFIT mailing list, Bruce may ask for information obtained using these menu items. This submenu is only displayed if the ♦Artemis→debug_menus configuration parameter is set to a true value.
Show Ifeffit's memory use item displays a crude, somewhat unreliable calculation of the resources still available to IFEFFIT.

2.1.4. The Plot menu¶

Fig. 2.5 The Plot menu.

When using Gnuplot as the plotting backend, you have an option to direct plots to multiple windows, thus allowing you to plot something new without removing an existing plot. This menu controls which of four such plot displays is active.

The top two options are used to export the most recent plot to a PNG or PDF file. You will be prompted for a filename.

The bottom two options tick on or off the Plot after fit buttons for each data set, which may be useful for a multiple data set fit.

ARTEMIS can make plots in a style that resembles the famous XKCD comic. To make use of this most essential feature, you should first download and install the Humor-Sans font onto your computer. Once you have installed the font, simply check the Plot ‣ Plot XKCD style button. Enjoy!

2.1.6. Status bar¶

This area in the main window is used to display various kinds of messages, including updates on long-running tasks, hints about controls underneath the mouse, and other announcements.

On some platforms, the status bar is able to display color. If you are one one of those platforms, the status bar will display with a green background during a long running task and with a red background when an error has occured or when something needs your immediate attention.

Many controls in the main window and elsewhere have hints attached to them which will be displayed in this status bar when the mouse passes over. These hints are intended to teach about the functionality of the control beheath the mouse. Hints are not recorded in the status bar buffer.

Many short and long running tasks display updates of various kinds. Many of these are recorded in the status bar buffer. Messages displayed in the status bar with a green or red background are recorded in the status bar buffer with green or red text. Messages which only indicate the progress of a long running task are not recorded in the buffer.

2.1.7. The Data list¶

The data list starts off with a single control, which is used to import data into your fitting project. Clicking the Add button will open the standard file selection dialog for your platform. That is, on Windows, the standard Windows file selection dialog is used; on Linux, the standard Gnome file selection dialog is used; and so on.

Fig. 2.7 The data list.

The standard manner of importing data into ARTEMIS is to use an ATHENA project file. Thus the file selection dialog will, by default, look for files with the .prj extension. You may also drag drag .prj files from your computer's file manager and drop them onto the data list.

As you import data, a stack of buttons – one for each data group – is made. These buttons are used to show or hide the windows associated with each data group. In this example, a multiple data set fit (i.e. one in which models for more than one data set are co-refined) is shown. One of the associated data windows is displayed on screen, as indicated by the depressed state of the button labeled Dimethyltin dichloride. The other data window is hidden. See the Data window chapter.

Caution

ARTEMIS has a very different relationship to your data than ATHENA. The very purpose of ATHENA is to process large quantities of data, thus a typical ATHENA project will contain many – perhaps dozens – of data groups. ARTEMIS expects that you will import only that data whose EXAFS you intend to analyze. If you are doing a single-data-set analysis, the Data list will contain only that item. If you import many data sets without actually using them in the fitting model, ARTEMIS may get confused. And so will you.

2.1.8. The Athena project selection dialog¶

When importing data from an ATHENA project file, the project selection dialog is shown. It presents you with a list of all data groups from the project file. The file listing is configured such that only one item can be selected at a time. The selected data group is also plotted. Any title lines from that data group are displayed in the text box on the upper right.

Fig. 2.8 The ATHENA project selection dialog.

The plot that is made when you select a data group is controlled by the Plot as box of radio buttons. These buttons have no impact on how the data imported into ARTEMIS. They are only used to determine how the data are displayed to you as you select the data group to import. Unlike the ATHENA project selection dialog, this one only allows you to select one data group at a time.

The next set of radio buttons selects what set of Fourier transform and fitting parameters will be used. The first choice says to use the values found in the ATHENA project file. The second choice says to use ARTEMIS's default values. The third choice is only relevant when replacing the data in a current fitting project. In that case, the values currently selected for the data being replaced will be retained.

To continue importing data, click the Import button. The Cancel button dismisses this dialog without importing data.

2.1.9. The recent data dialog¶

You can access a list of recently imported data by rightclick right clicking on the Add button. This presents a dialog with a selection list. Click on one of your recent files, then click OK or type Return. Alternately, leftclick double-click on your choice in the list of recent files.

Fig. 2.9 The recent data dialog.

2.1.10. The Feff list¶

The FEFF list starts off with a single control, which is used to import structural data into your fitting project. Clicking the Add button will open the standard file selection dialog for your platform. That is, on Windows, the standard Windows file selection dialog is used; on Linux, the standard Gnome file selection dialog is used; and so on.

Fig. 2.10 The FEFF list.

The standard manner of importing structural data into ARTEMIS is to import an input file for ATOMS or FEFF or to import a CIF file containing crystal data. Thus the file selection dialog will, by default, look for files with the .inp or .cif extension.

As you import structural data, a stack of buttons – one for each FEFF calculation – is made. These buttons are used to show or hide the windows associated with each data group. In this example, two FEFF calculations have been made. Neither is being displayed on screen. See the Atoms/Feff chapter.

rightclick Right clicking on the Add button will present the same recent file selection dialog as for the data list. In this case, the list will contain recently imported ATOMS, FEFF, or CIF files.

You may also drag drag CIF, ATOMS input, or FEFF input files from your computer's file manager and drop them onto the FEFF list.

2.1.11. Fit information¶

This section of the main window is used to specify properties of the fit. The name is a short bit of text that will be used as a label for each fit. The number will be auto-incremented unless you explicitly set it.

Fig. 2.11 The fit properties.

The description is a longer bit of text which you can use to describe the current fitting model. Here, too, the number is auto-incremented unless you explcitly set it. The text from this box is written to the log file, thus can be used to document your fitting model.

The set of radio buttons is used to select the space in which the fit will be evaluated. The default is to evaluate the fit in R space.

Finally, the Save button is used to quickly save your fitting model to a project file. If you model is already associated with a file, this is a quick one-click saving tool. If no project file is associated, the file selection dialog will prompt you for a file. The default is to use the .fpj extension.

2.1.12. Fit and log buttons¶

All the way to the right of the main window are the Fit and Show log buttons. Click the Fit button to initiate the fit. The log button is used to show and hide a window which displays the log from the most recent fit. See the chapter on the Log and Journal windows. In the event of a fit that exits abnormally, error messages explaining the problems will be show in the log window.

Fig. 2.12 The Fit and Show log buttons.

At start-up the Fit button is yellow. After each fit, the color of this button will range from red to green as a heuristic indication of the fit quality. See the happiness section for more details.

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