[AstroPy] Fwd: Help with finding absorption lines
Peter Dzwig
pdzwig at summaventures.com
Thu May 28 10:01:33 EDT 2020
Xavier, Angela,
for absorption lines that looks like a good idea.
I still don't understand why astropy has such difficulties. Anyone any
comments on the code?
Xavier, I will look at ALIS for emission lines.
Peter
On 28/05/2020 13:22, J. Xavier Prochaska wrote:
> Consider
>
> linetools -- https://github.com/linetools/linetools
>
> and
>
> ALIS -- https://github.com/rcooke-ast/ALIS
>
> Built by scientists who study absorption lines for a living..
>
> X
>
>
> On Thu, May 28, 2020 at 2:55 AM Angela Rodrigues
> <afonsoangelarodrigues at gmail.com
> <mailto:afonsoangelarodrigues at gmail.com>> wrote:
>
> Hi Dr. Peter
>
> Thank you kindly for your reply.
>
> Here's a folder with the file (it's an hdr file):
> https://drive.google.com/file/d/1Rb25_mzAKq7ZqFI9fPyOX8TnTtspYxpF/view?usp=sharing
>
> I am looking for really small shifts that reflect chemistry, and
> therefore, I cannot just eyeball it, I need the actual values.
> Indeed it is a complicated task to do without specialized software.
> Regarding the threshold, I've changed it multiple times between 0
> and 20, and still no absorption values...
>
> Thank you so much for looking into it! :)
>
>
> Peter Dzwig <pdzwig at summaventures.com
> <mailto:pdzwig at summaventures.com>> escreveu no dia quinta,
> 28/05/2020 à(s) 19:15:
>
> Angela,
>
> first thing to be said is that I sympathize. :-) I have had similar
> issues although my datasets are very different (QSOs); the second is
> that I can't open either of your files. Perhaps you tell us what
> format
> they are in.
>
> I tried running similar code to yours (despite the different
> context). I
> found that the answers, from both thresholding and derivative, I got
> were quite sensitive to the data density per unit wavelength,
> the amount
> of noise in the data and the threshold that you set.
>
> Unless the data is sufficiently dense both thresholding and
> derivative
> will produce inaccurate or even false results.
>
> In the end I found the best solution was to make a table of all the
> lines that I was interested in and simply overplot them on my
> spectrum.
> I can then see what's where and (using a combination of astropy and
> numpy) re-plot and re-examine pertinent parts of the spectrum,
> but as
> ever the limiting factor is data density.
>
> I guess in your case the lines that you would plot would be Calcium,
> Cerium, Lanthanum, Carbon, Flourine - and Neodymium? and some
> of their
> molecular forms. Tables for most are available from NIST:
> https://www.nist.gov/pml/atomic-spectra-database
>
> There probably is a best approach - a tutorial would be a good
> idea -
> and I will watch this space to see what solutions others offer.
>
> Regards,
>
> Peter Dzwig
>
> On 28/05/2020 08:43, Angela Rodrigues wrote:
> > Hello,
> >
> > I have been trying to use astropy to extract lines of
> absorption from a
> > mineral spectrum.
> > so I have the attached hdr file with the spectral analysis
> from a mineral.
> > The code to extract the data from the file is as follows:
> >
> > import spectral.io.envi as envi
> > lib = envi.open('GFZ_HySpex_REMin.hdr')
> >
> > a=lib.metadata
> > wvl = a.get('wavelength')
> > wvl = [int(float(i)) for i in wvl]
> >
> > import matplotlib.pyplot as plt
> > plt.plot(wvl,spectra[13])
> >
> > #grab spectra for parisite
> > names = lib.names
> >
> > spectra_parisite = spectra[8]
> > plt.plot(wvl, spectra_parisite)
> >
> >
> > I wanted to extract the absorption lines as in the
> documentation example
> > here <https://specutils.readthedocs.io/en/stable/fitting.html>.
> > Here's what I've done:
> >
> >
> > w = np.array(wvl)
> >
> > import astropy.units as u
> > w = w*u.nm
> > spectra_parisite = spectra_parisite*u.Jy
> > from specutils import Spectrum1D, SpectralRegion
> > spectrum = Spectrum1D(spectral_axis = w, flux = spectra_parisite)
> >
> > from matplotlib import pyplot as plt
> > plt.plot(spectrum.spectral_axis, spectrum.flux)
> > plt.xlabel('Spectral Axis
> ({})'.format(spectrum.spectral_axis.unit))
> > plt.ylabel('Flux Axis({})'.format(spectrum.flux.unit))
> > plt.grid(True)
> >
> > from specutils.manipulation import noise_region_uncertainty
> > noise_region = SpectralRegion(450*u.nm, 2500*u.nm)
> > spectrum2 = noise_region_uncertainty(spectrum, noise_region)
> >
> > from specutils.fitting import find_lines_threshold
> > lines = find_lines_threshold(spectrum2, noise_factor=0)
> > lines[lines['line_type'] == 'absorption']
> > lines[lines['line_type'] == 'emission']
> >
> > # Derivative technique
> > from specutils.fitting import find_lines_derivative
> > lines = find_lines_derivative(spectrum2, flux_threshold=0)
> > lines[lines['line_type'] == 'absorption']
> >
> >
> > However, I get no absorption feature lines. Am I doing
> something wrong?
> > The emission zones seem to be alright, but I really need the
> absorption
> > loci.
> > Thank you so much for your help!!
> > Warm regards,
> > Angela Rodrigues
> >
> > _______________________________________________
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> > AstroPy at python.org <mailto:AstroPy at python.org>
> > https://mail.python.org/mailman/listinfo/astropy
> >
>
> --
>
> Dr. Peter Dzwig
>
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>
>
>
> --
> --
> ----------------------------------------------
> J. Xavier Prochaska
> UCO/Lick Observatory
> 1156 High St.
> UC Santa Cruz
> Santa Cruz, CA 95064
>
> Affiliate of IPMU
> Affiliate of LBNL
>
> http://www.ucolick.org/~xavier/
> https://aaii.ucsc.edu/
> http://www.ucolick.org/f-4 <https://www.ucolick.org/f-4>
>
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> 831-459-5244 (Fax)
>
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Dr. Peter Dzwig
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