Guide for GILDAS-CLASS users

Reading Files

PySpecKit can read many file types including CLASS .cls files.

For example, a typical single-dish observing file will consist of a large number of individual spectra. These may be on-the-fly spectra or multiple integrations on a single source; either way the pointing and spectral information for each individual data point should be incorporated in the data file.

The spectra are recorded from the data file into an pyspeckit.classes.ObsBlock object. An ObsBlock (Observation Block) is simply a container for many spectra; in most regards it behaves the same way as a pyspeckit.Spectrum object, but it has a few extra attributes built-in (e.g., spectral averaging).

A file can be loaded as a named object. The data is filtered as it is read in. The following line will ensure that the spectra in the n2hp ObsBlock contain only data from the F1M spectrometer with lines labeled ‘N2HP(3-2)’ or ‘N2H+(3-2)’:

from pyspeckit.spectrum.readers.read_class import class_to_obsblocks
n2hp = class_to_obsblocks(filename,
    telescope=['SMT-F1M-HU','SMT-F1M-VU'],
    line=['N2HP(3-2)','N2H+(3-2)'])

Working with the data

You can treat an ObsBlock like any other pyspeckit.Spectrum object, but there are a few unique features.

The ‘smooth’ function will smooth each individual spectrum in the ObsBlock, which can be useful if you want to smooth before averaging.

The ‘average’ function averages spectra. Weights for the averaging can be specified. The error is also computed either by taking the RMS of the averaged spectra or by averaging the error spectra.

You can plot each spectrum in an individual window with the ploteach function, or all overlaid simultaneously with the ‘plotter’ function. If you want to loop through each spectrum, waiting for user input after displaying, you can do something like:

ax = pylab.gca()
for sp in n2hp:
    sp.plotter(axis=ax)
    input("Waiting for input...")

You can also fit a line profile to each spectrum in the observation block using the fiteach command.

Selecting Spectra

There are 3 keywords that can be used to select spectra when reading in a file. The line and telescope keywords are required in order to make an observation block, otherwise the spectral axes will not be common to all spectra:

n2hp = class_to_obsblocks(filename,
    telescope=['SMT-F1M-HU','SMT-F1M-VU'],
    line=['N2HP(3-2)','N2H+(3-2)'])

If you want to read in all of the data and don’t care about the line or telescope, you can instead use:

all_data = class_to_spectra(filename)

You can select data after they are read in by matching header keywords:

g10 = pyspeckit.ObsBlock([sp for sp in all_data if sp.specname == 'g10'])

Fitting Data

In CLASS, you would specify the data range with individual commands on the command line, e.g.:

[this isn't quite right]
xrange 5 25

In pyspeckit, you can specify the range in multiple ways, but the default is to use the plotted window. For example:

sp.plotter(xmin=5, xmax=25)
sp.baseline()
sp.specfit()

will perform a baseline fit and spectrum fit over the range 5-25 km/s (the units of xmin, xmax are the plotted units). More intricate specifications are possible:

sp.plotter()
# Fit a baseline over the region 5-25 km/s, excluding 7-10 km/s and 15-18 km/s
sp.baseline.selectregion(xmin=5,xmax=25,exclude=[7,10,15,18])
sp.baseline()
sp.specfit()