Calibrating Spectra

PGOPHER can be used to calibrate an experimental spectrum from anything displayed in the simulation window; a line list or a simulation of a known spectrum are likely to be the most useful sources. The following built in calibration sources are available (see File, New, Calibration):
  1. The visible B-X absorption spectra of I2. The line positions for this are calculated from the constants given in F. Martin, R. Bacis, S. Churassy and J. Vergès, J. Molec. Spectrosc. 116, 71 (1986) with the Franck-Condon factors estimated from RKR curves generated from these constants. Checks against high accuracy measurements in H. Knockel, B. Bodermann, and E. Tiemann, Eur. Phys. J. D 28 199 (2004) indicates a maximum error of 0.043 cm-1, but < 0.02 cm-1 for the v" < 11 transitions typically used for calibration.
  2. Ne and Fe atomic lines with positions and intensities taken from the NIST Atomic Spectra Database (version 3.0.3), Yu. Ralchenko, F.-C. Jou, D.E. Kelleher, A.E. Kramida, A. Musgrove, J. Reader, W.L. Wiese, and K. Olsen http://physics.nist.gov/asd3 [2006, June 18]. National Institute of Standards and Technology, Gaithersburg, MD.
  3. A set of line positions for use with Ne optogalvanic spectra, commonly used for calibrating pulsed dye lasers. The lines are taken from "An atlas of optogalvanic transitions in Neon" RAL report, RAL-91-069 (1991) by S.H. Ashworth and J.M. Brown, with Ne lines from the NIST database (see above) and a few points added from our own measurements.

1. Load Experimental data and Calibration source

First load the experimental spectrum and set up the reference source for the calibration, so the simulation window looks something like the picture below; see Overlaying Files for how to do this. Note that both spectra should have upward pointing peaks; use Overlays,Invert if necessary to invert your spectra

In this case the spectrum is atomic lines, and the upper trace is an atomic line list.

2. Initial Alignment

The traces need to be roughly aligned to start with. If you have an approximate start and end point for the experiment, or know the assignment of some of the peaks already, go directly to the next step. Alternatively, it is possible to manually edit the "FrequencyOffset" and "FrequencyScale" of the Experiment overlay.

3. Assigning Peaks

Use Overlays, Calibrate (or right click on the experimental spectrum and select calibrate) to bring up the calibration window, and make sure the experimental spectrum to be calibrated is selected in the box at the top of the dialog:

Important: when this dialog is open, the behavior of the simulation window changes significantly; Alt+drag will move the experimental spectrum rather than the simulation, and peak measurement will affect the calibration peaks. Make sure the calibration window is closed when you have finished calibrating.

To set an approximate plot range (if you are not using another method for initial placement):
  1. Select "Other", "Set Range". This will add two measured "peaks" at the very start and end of the spectrum, and they will appear in the calibration window. (They are set with a large weight of 1000, implying a large uncertainty in their values, so any subsequent assignment of calibration peaks will essentially ignore these points)
  2. Enter the corresponding frequencies in the "Actual" column for these two points.
  3. Ensure the polynomial value is 1, and press "Fit".
To use specific peaks in the spectrum for calibration:
  1. Right click and drag across an experimental peak; the peak position is measured and appears in the first column of the "Calibrating" form.
  2. The "Actual" box next to it will turn red to indicate the actual position to be filled in.
  3. Right click and drag across the corresponding peak in the calibration spectrum; the position of this will be filled in the square indicated above.
  4. Repeat as required - you will only need a few peaks in the initial stages.
To correct mistakes:

4. Fitting

Given some assignments, press the "fit" button. The residuals will be filled in and the experimental plot will be adjusted to reflect the newly fitted frequency scale. The residuals will be plotted in a separate window.
You will probably want to add more peaks - go back to step 3.

5. Transferring the Calibration

Once you have a suitable calibration, you can transfer the calibration to another spectrum using one of the following entries on the "Other" menu:
In each case your are prompted to select the spectrum to apply the calibration to; select "all" the default to apply it to all but the source spectrum.