Re: Checking GSL for Spectroscopy

[Fritz Sonnichsen]

Thank you Mohammad. I looked at your web page and you do exciting stuff!
Your assessment of GSL is what I needed. I think the manual is well written
and tells me what I can do with it--as you mention the higher level details
applied to a specific area of science probably require another
added package- or at least writing the software "in house". I probably will
proceed that way. One difficulty is that this code will probably eventually
get handed off to a biologist and a software engineer--so I need to try to
keep it on terms that they can maintain.
     I also need to be sure that a language (e.g. GSL) will stay around
long term---seems like that is a problem these days.  In addition I find
that a lot of the "post C" languages can get very cluttered in the wrong
hands and tend so stick with C as a science language especially for code
destined to other people (perhaps I am showing my age!).
   Regarding AI and Machine Learning it is rather new to me and I probably
will not be involved other than using openCV for image processing. I just
want to track if any of it has been accommodated by existing routines, but
I guess it is rather broad and subject to its own packages-

Cheers
Fritz


On Tue, Mar 16, 2021 at 9:55 AM Mohammad Akhlaghi <mohammad@akhlaghi.org>
wrote:

> Hi Fritz,
>
> GSL is a low-level/fundamental/core numeric analysis library providing
> the low-level tools for numeric operations that are common in many
> different science applications.
>
> So for example in GNU Astronomy Utilities (that I am maintaining), we
> heavily rely on many of GSL's low-level tools and use them extensively
> for astronomical data analysis. It is the same for many other scientific
> software (they use GSL for low-level computationally hard operations).
>
> So if you want to write a high-level spectral analysis library/program
> many of the computational tools you'll need are in GSL (for example for
> fitting emission lines or the continuum, or convolving/smoothing data
> and many more things), but you have to write the wrapper functions to
> use them in the special context you need in your spectral analysis.
>
> About AI, I think its out of GSL's scope (similar to the logic above:
> GSL is a low-level/fundamental library)! I am not a GSL maintainer, but
> this is just what I feel given the current set of tools it provides.
>
> Cheers,
> Mohammad
>
>
> On 3/16/21 1:25 PM, Mike Marchywka wrote:
> > Can you comment on how you compare spectra? Just for my own
> > personal interest, not sure if will further the thread here however..
> > Not sure a "dot product" in the conventional sense would help much.
> > You could imagine comparing peak positions and relative heights
> > or a fit to a continuum for example.  Peaks plus black body in some
> > vector comparison?
> >
> > note new address
> >   Mike Marchywka 306 Charles Cox Drive Canton, GA 30115
> >   2295 Collinworth  Drive Marietta GA 30062.  formerly 487 Salem Woods
> Drive Marietta GA 30067 404-788-1216 (C)<- leave message 989-348-4796 (P)<-
> emergency
> >
> >
> > ________________________________________
> > From: Help-gsl <help-gsl-bounces+marchywka=hotmail.com@gnu.org> on
> behalf of Fritz Sonnichsen <sonnichs@gmail.com>
> > Sent: Tuesday, March 16, 2021 9:15 AM
> > To: help-gsl@gnu.org
> > Subject: Checking GSL for Spectroscopy
> >
> > I am preparing to convert MATLAB code to something more general. The new
> > code will run on LInux and ARM processors.
> >     For a lot of reasons I am not going to use Python. We also want to
> > keep this project "close" to scientists and do not want to turn it into a
> > full time computer programming job. So the final word is that I am
> looking
> > for something that can be called by (and hopefully is written) in C.
> Worse
> > case I will just write the code myself but would prefer to start
> > integrating our systems into something with a lot of pre-written and
> vetted
> > routines.
> >
> > GSL looks like a good choice. Maybe R comes next. We have a mix of needs
> > but I will point out a few:
> > 1) Baselining a spectrum
> > 2) Finding peaks in that spectrum
> > 3) using Pearson correlation to compare the spectrum QUICKLY to
> > about 50,000 recorded examples.
> >
> > We also have some uses with basic statistics and we do some image
> > processing.
> >
> > So my question is--does GSL position itself in these areas? MATLAB (with
> > packages) does them all.
> >       I am not sure how active GSL, if it is keeping up with AI, imaging
> and
> > spectroscopy--or is it fading or giving way to popular languages for
> > example. I was surprised that the 600+ page manual did not seem to show
> > anything relating to the simple spectral analysis described above for
> > example. Certainly I can search the web for others' code but at some
> point
> > if I cannot attach to a well established product I will just write it
> > myself.
> >
> > Any comments appreciated
> > thanks
> > Fritz
> >
>