Plotting data

You have already been introduced to the basic functionality of the Plot window. In this chapter, all the details of ARTEMIS' plotting system will be explained. While ARTEMIS does not provide all the plotting capabilities offered by real plotting tools like Gnuplot, Origin, Excel, Kaleidagraph, and others, it does provide enough options to create interesting and instructive visualization of your EXAFS fitting project.

Let's briefly go over the basic features of the Plot window. The buttons at the top are used to make plots of data and paths in one of the three spaces. The data listed in the plotting list at the bottom of the Plot window will be included in the plots made with those three buttons.

The part of the complex χ(R) or χ(q) functions is controled by the two sets of radiobuttons at the top of the “limits” tab. Additional traces – the fit, the window, and so on – can be included by clicking on their check buttons. Finally, the plotting range along the x-axis can be set for each of the three spaces. At the top of the Plot window are a series of radio buttons used to set the k-weighting used in plots. A plot of χ(k) will be weighted by the specified factor of k. Plots of χ(R) or χ(q) will use that valule of k-weighting for the forward Fourier transform.

The “kw” option for k-weighting will use the user-specified value of k-weight for each data set included in the plot. That value will also be used for any paths associated with that data set.

Please note that the value of k-weight selected for plotting has no bearing on how the fit is performed. The k-weighting specified on the Data window is used to evaluate the fit. Fit evaluation and visualization are different tasks, each with their own value of k-weight.

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The plotting list

The contents of the plotting list are included in a plot made from the Plot window. There are a number of ways of populating the plotting list manually and there are tools for repopulating the list upon completion of a fit.

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Populating the plotting list manually

The most basic way of moving a data set or a path to the plotting list is to click on a plot transfer button. These are the light blue buttons, , at the top of the Data window. There is one to the left of the name of the data set. Clicking on this button inserts that data at the end of the plotting list. There is also a transfer button on each Path page to the left of the path's name.

Clicking on any of the path transfer buttons inserts that path at the end of the plotting list.

In this way, the plotting list can be built up item by item. The order in which items are inserted into the plotting list is the order in which they are displayed in the plot. An item can be removed from a plot without removing it from the plotting list by unchecking its check box.

Of course, adding a number of paths to the plotting list by checking on their individual transfer buttons can be quite tedious. Transfering of items into the plotting list is another of the many chores that use the set of marked paths. Marking a path is done is by checking its check box in the Path list or by using one of the handy options in the Marks menu. Once a set of paths is marked, selecting “Transfer marked” from the Actions menu will move that set in order to the end of the plotting list. By learning to use path marks effectively, you can quickly build interesting plots which include data along with many paths. Note that keyboard shortcuts exist for everything in the Mark and Actions menus. These are shown in the menus themselves. Learning these shortcuts makes setting up interesting plots much faster and easier.

The “Clear” button at the bottom of the Plot window is used to remove all content from the plotting list.

Items in the list can be reordered by dragging and dropping while holding down the control key. Note that an item will be placed after the item on which it is dropped.

Right clicking on an item will post a pop-up button for removing that item from the list. Selecting more than one path then right-clicking will post a menu with options for removing the selected paths or for altering their check buttons.

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Refreshing the plotting list after a fit

After a fit finishes, the plotting list will be populated with all of the data sets and paths which have their “Plot after fit” button checked. On the Data window, this checkbutton is found in the “Other parameters” section at the bottom of the page. On the Path page, this checkbutton is directly below the name of the path at the top of the page.

Upon completion of the fit, the plotting list is cleared the repopulated with all the items selected for plotting after the fit. The data are inserted in the order they appear in the Data sets list in the Main window. Paths associated with that data set are inserted after their data set in the order they appear in that data set's path list.

The refreshing of the plotting list can be turned off by checking the “Freeze” button below the plotting list. This will preserve the state of the plotting list as it appeared before starting the fit.

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Plotting a sum of paths without performing a fit

There are several ways to do this, but the easiest is to select “Make sum of all paths and plot in R” from the Actions menu on the Data page. This will create a VPath out of all the paths included in the fitting model for the data. The VPath will be placed in the plotting list in the Plot window and the plot will be made in R. You can then plot in other spaces using the plotting buttons.