[AstroPy] Fwd: Help with finding absorption lines

Thu May 28 08:22:10 EDT 2020

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> 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> 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
>> >
>> > _______________________________________________
>> > AstroPy mailing list
>> > AstroPy at python.org
>> > https://mail.python.org/mailman/listinfo/astropy
>> >
>>
>> --
>>
>> Dr. Peter Dzwig
>>
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> https://mail.python.org/mailman/listinfo/astropy
>

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