Function plots in TOPCAT
S. Erard
| Version | Author | Notes |
|---|---|---|
| 1.0 | S. Erard / M. Taylor | 15/11/2023 |
| 1.1 | S. Erard | 30/12/2024 |
Spectroscopy Bandlist
This tutorial describes how to work with spectral bandlists in the VESPA environment.
Spectral properties of materials are shared in the VO in various data services, using several formats — these include complete spectra but also bandlists. The SSHADE service in particular provides both type of data measured or collected for materials of planetary interest in solid phase.
The use of SSHADE spectra is covered here: http://www.europlanet-vespa.eu/tutos/CASSIS_VESPA_tutorial.pdf
The SSHADE bandlist service provide a description of the individual spectral bands identified in such spectra - it is available from its own web site, or via EPN-TAP from the VESPA portal or other interfaces (schema name = sshade_bandlist).
From the VESPA portal you can query the sample_classification parameter for species name (use upper case initial) :
SELECT * FROM sshade_bandlist.epn_core WHERE "sample_classification" LIKE '%Siderite%'
The data associated to each row is a table of bands with their characteristics. The external_link parameter opens a dedicated page on the SSHADE bandlist site, where detailed information is available.
In the VESPA portal, select one or several rows from the result table and click the Data selection > Send tables button. This will send the data tables to TOPCAT.
Using TOPCAT Plane plot window, you can easily plot peak intensity (peak_rel) versus peak position (pos_peak) — see Fig. 1. In addition:
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In Axes > Coords, check the Ylog box for a more convenient display
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Add an XYerror form and enter the error parameters in the Form tab
Fig. 1: Basic plot of band parameters in TOPCAT
You can run this from the Unix shell with the corresponding stilts command:
topcat -stilts plot2plane \
xpix=662 ypix=432 \
ylog=true xlabel=10000./pos_peak ylabel=peak_rel \
xmin=-0.3 xmax=109.9 ymin=4.0E-11 ymax=21976 \
legend=true \
auxvisible=false \
in=Vespa:BANDLIST_RAMAN_Siderite.data.vot x=10000./pos_peak \
y=peak_rel shading=auto leglabel='20: All' \
layer_1=Mark \
size_1=2 \
layer_2=XYError \
xerrhi_2=pos_peak_err xerrlo_2=pos_peak_err \
yerrhi_2=peak_rel_err yerrlo_2=peak_rel_err
What we really want is to reproduce the thumbnail image from the data service, i.e. to plot individual bands with Gaussian profiles (Fig. 2)
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Display the bandlist table in TOPCAT, click the header and select New synthetic column.
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In the dialogue, type Name = xgrid; Expression = sequence(100,-5,0.1). This will create a column containing a normalized vector of indices for each row / band.
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Add a new XYArray Layer to the stack
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In the Position tab select the bandlist table
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type Xvalues = add(pos_peak,multiply(width,xgrid)) - this will provide a scaled wavenumber vector around each band center.
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type Yvalues = multiply(peak_rel,arrayFunc("exp(-x*x)",xgrid)) - this will provide the corresponding Gaussian.
=> For each row of the bandlist, the two vectors are plotted against each other
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In Axes > Coords, check the Ylog box and set the scale to reproduce the thumbnail
Fig. 2: plotting the individual bands in TOPCAT
To plot the data as a function of wavelength in µm (Fig. 3):
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In the positional layer: set x = 10000./pos_peak
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In the XYLine layer: set x = divide(10000.,add(pos_peak,multiply(width,xgrid)))
You can superpose observational spectra on this plot, in order to check a possible match with the current laboratory data.
Fig. 3: Same plot as a function of wavelength in µm (band profiles are Gaussian in energy)
• All TOPCAT plots can be produced from the command line via the stilts script language, which can be incorporated in a processing pipeline. Such plots can be manipulated with the mouse in the same way as in TOPCAT.
• Use TOPCAT XYarray Layer control to work with sub-arrays and functions associated to row parameters — see: XYArray Layer Control