Simple Radio Fitting: HCO+ example
==================================

.. include:: <isogrk3.txt>


::

    import pyspeckit

    # load a FITS-compliant spectrum
    spec = pyspeckit.Spectrum('10074-190_HCOp.fits')
    # The units are originally frequency (check this by printing spec.xarr.units).
    # I want to know the velocity.  Convert!
    # Note that this only works because the reference frequency is set in the header
    spec.xarr.frequency_to_velocity()
    # Default conversion is to m/s, but we traditionally work in km/s
    spec.xarr.convert_to_unit('km/s')
    # plot it up!
    spec.plotter()
    # Subtract a baseline (the data is only 'mostly' reduced)
    spec.baseline()
    # Fit a gaussian.  We know it will be an emission line, so we force a positive guess
    spec.specfit(negamp=False)
    # Note that the errors on the fits are larger than the fitted parameters.
    # That's because this spectrum did not have an error assigned to it.  
    # Let's use the residuals:
    spec.specfit.plotresiduals()
    # Now, refit with error determined from the residuals:
    # (we pass in guesses to save time / make sure nothing changes)
    spec.specfit(guesses=spec.specfit.modelpars)

    # Save the figures to put on the web....
    spec.plotter.figure.savefig("simple_fit_example_HCOp.png")
    spec.specfit.residualaxis.figure.savefig("simple_fit_example_HCOp_residuals.png")

    # Also, let's crop out stuff we don't want...
    spec.crop(-100,100)
    # replot after cropping (crop doesn't auto-refresh)
    spec.plotter()
    # replot the fit without re-fitting
    spec.specfit.plot_fit()
    # show the annotations again
    spec.specfit.annotate()
    spec.plotter.figure.savefig("simple_fit_example_HCOp_cropped.png")

.. figure:: images/simple_fit_example_HCOp.png
    :alt: Sample HCO+ spectrum fitted with a gaussian
    :figwidth: 800
    :width: 800

    Sample HCO+ spectrum fitted with a gaussian

.. figure:: images/simple_fit_example_HCOp_residuals.png
    :alt: Residuals of the gaussian fit from the previous figure
    :figwidth: 800
    :width: 800

    Residuals of the gaussian fit from the previous figure

.. figure:: images/simple_fit_example_HCOp_cropped.png
    :alt: A zoomed-in, cropped version of the spectrum.  With the 'crop' command, the excess data is discarded.
    :figwidth: 800
    :width: 800

    A zoomed-in, cropped version of the spectrum.  With the 'crop' command, the excess data is discarded.