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):
- 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.
- 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.
- 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):
- 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)
- Enter the corresponding frequencies in the "Actual" column for
these two points.
- Ensure the polynomial value is 1, and press "Fit".
To use specific peaks in the spectrum for calibration:
- Right click and drag across an
experimental peak; the peak
position is measured and appears in the first column of the
"Calibrating" form.
- The "Actual" box next to it will turn red to indicate the actual
position to be filled in.
- Right click and drag across the
corresponding peak in the
calibration spectrum; the position of this will be filled in the square
indicated above.
- Repeat as required - you will only need a few peaks in the
initial stages.
To correct mistakes:
- To cancel or re-do an assignment click the "Assign" button; this
is for re-doing steps 2 and 3 above.
- To delete entries use the "x" button
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.
- The undo fit button will step the
function and plot back one step,
- By default a linear function is
used; to use a higher order
polynomial change the number in the spin box. The details of the
function will be displayed on pressing the button next to it; this also
allows an arbitrary function to be entered,
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:
- Copy
Frequency To: This
is for the common case of spectra with a common x axis, as when several signals are
recorded simultaneously. (This implies they have the
same number of points.)
- Apply
Calibration To:
This is for the more general case where you the spectra have
independent x axes, but the
mapping between x and
frequency is the same for both spectra. (This will typically apply to
spectra recorded independently, and also plate spectra are likely to
be
this way.) Note that the original x
scale is lost on saving in this mode.
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.