Other plotting features

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Zooming and cursor position

Zooming on a region of a plot is done using Gnuplot's own capabilities. In the plot window, a zoom is initiated by a right click. The mouse is then dragged to cover a rectangular area on the plot. Right-clicking a second time will cause the plot to be redisplayed on the zoomed region.

Gnuplot displays the position of the cursor in the bottom part of the plot window. This is continuously updated as the mouse moves over the plot window.

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Special plots for the current group

Quad plot

The quad plot is the default plot that gets made when data are first imported. Using the current set of processing parameters, the data are displayed in energy, k, R, and back-transform k all in the same plot window. This plot can also be made by right-clicking on the q button.

Normalized data and derivative

This plot type shows the normalized μ(E) spectrum along with its derivative. The derivative spectrum is scaled by an amount that makes it display nicely along with the normalized data.

Data + I0 + signal

I₀ can be plotted along with μ(E) and the signal as shown below. The I₀ and signal channel is among the data saved in a project file. This example shows μ(E) of Au chloride along with the signal and I₀ channels.This plot can also be made by right-clicking on the E button. (The norm+deriv plot can be configured for right-click use with the ♦Artemis → right_single_e configuration parameter.)

k123 plot

A k123 plot is a way of visualizing the effect of k-weighting on the χ(k) spectrum. The k¹-weighted spectrum is scaled up to be about the same size as the k²-weighted spectrum. Similarly, the k³-weighted spectrum is scaled down. This plot can also be made by right-clicking on the k button.

R123 plot

A R123 plot is a way of visualizing the effect of k-weighting on the χ(R) spectrum. The Fourier transform is made with k-weightings of 1, 2, and, 3. The FT of the k¹-weighted spectrum is scaled up to be about the same size as the FT or the k²-weighted spectrum. Similarly, the FT of the k³-weighted spectrum is scaled down. The current setting in the R tab is used to make this plot. For this figure, the magnitude setting was selected. This plot can also be made by right-clicking on the R button.

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Special plots for the marked groups

The “Marked groups” submenu offers two special kinds of plots relating to the set of groups in the group list that have been marked.

Bi-Quad plot

This special plot is like the quad plot described above, but is used to compare two marked groups. To make this plot you must have two – and only two – groups selected from the group list. It is helpful

Plot with E0 at 0

This special plot is used to visualize μ(E) spectra measured at different edges. Each spectrum, Cu and Fe in this example, is shifted so that its point of E₀ is displayed at 0 on the energy axis.

Plot I0 of marked groups

This plot allows examination of the I₀ signals of a set of marked groups. This plot can also be made by right-clicking on the E button. (The other two special marked groups plots can be configured for right-click use with the ♦Artemis → right_marked_e configuration parameter.)

Plot scaled by edge step

The marked groups can be plotted as normalized μ(E), but scaled by the size of the edge step. Without flattening, this is identical to plotting the μ(E) data with the pre-edge line subtracted. Otherwise, it is different in that the post-edge region will be flattened and will oscillate around the level of the edge step size.

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Special plots for merged groups

When data are merged, the standard deviation spectrum is also computed and saved in project files. The merged data can be plotted along with its standard deviation as shown in the merge section in a couple of interesting ways.

Merge + standard deviation

In this plot, the merged data are displayed along with the standard deviation. The standard deviation has been added to and subtracted from the merged data. This is the plot that is displayed by default when a merge is made. This behavior is controled by the ♦Athena → merge_plot configuration parameter.

Merge + variance

In this plot, the standard deviation spectrum is plotted directly. It is scaled to plot nicely with the merged data. The point of this plot is to see how the variability in the data included in the merge is distributed in energy.

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Special plotting targets

The Plot menu provides a few more ways to control how your data are displayed. The “Save last plot as” submenu allows you to send the most recent plot to a PNG or PDF file. You will be prompted for a filename, then the most recent plot will be written to that file in the format specified. Currently, only PNG and PDF are supported. Saving to a file does not work for quad plots – you'll have to rely on a screen-capture tool for that.

Finally, you have the option of directing the on-screen plot to one of four terminals. The selected terminal, number 1 by default, is updated as new plots are made. When you switch to a new terminal, other active terminals will become unchanging. This means you can save a particular plot on screen while continuing to make new plots.

Consider other file types. SVG and EPS should work. Gnuplot's GIF and JPG terminals are not sufficiently featureful to replicate all the details of ATHENA's plots.

Consider making the number of terminals a configuration parameter.

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Phase corrected plots

When the “phase correction” button is clicked on, the Fourier transform for that data group will be made by subtracting the central atom phase shift. This is an incomplete phase correction – in ATHENA we know the central atom but do not necessarily have any knowledge about the scattering atom.

Note that, when making a phase corrected plot, the window function in R is not corrected in any way, thus the window will not line up with the central atom phase corrected χ(R).

Also note that the phase correction propagates through to χ(q). While the window function will display sensibly with the central atom phase corrected χ(q), a “kq” plot will be somewhat less insightful because phase correction is not performed on the original χ(k) data.

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XKCD-style plots

ATHENA 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 XKCD style” button in the Plot menu. Enjoy!