[AstroPy] Gaussian models fitter non-functional?

[John Wainwright]

Thanks Erik, and sorry, I should have found those.  I realize now I was asking relative to the detect_sources() and segment_properties() functions in the photutils <http://photutils.readthedocs.org/en/latest/index.html> affiliate package, which I think use a 2D Gaussian fit to generate the basic morphological properties I've been getting.   Presumably, I could use the centroids from that data as peak seeds for a Moffat2D model fit.

Thanks again,
John.

> On Oct 20, 2015, at 7:01 AM, Erik Bray <embray at stsci.edu> wrote:
> 
> On 10/19/2015 05:56 PM, John Wainwright wrote:
>> Just on the topic of PSF fitting, is there any plan to implement Moffat PSF
>> models?  I'm trying to replicate some of the PSF fitting
>> <http://pixinsight.com/doc/tools/DynamicPSF/DynamicPSF.html> capabilities found
>> in PixInsight <http://pixinsight.com/> which provides excellent Moffat modeling
>> support.
> 
> Well, there are are already these implementations:
> 
> http://docs.astropy.org/en/latest/api/astropy.modeling.functional_models.Moffat1D.html#astropy.modeling.functional_models.Moffat1D
> 
> http://docs.astropy.org/en/latest/api/astropy.modeling.functional_models.Moffat2D.html#astropy.modeling.functional_models.Moffat2D
> 
> So you can check how they compare.  You can also always add your own version:
> 
> http://docs.astropy.org/en/latest/modeling/new.html
> 
> 
> 
>>> On Oct 19, 2015, at 11:45 AM, Jeff Mangum <jmangum at nrao.edu
>>> <mailto:jmangum at nrao.edu>> wrote:
>>> 
>>> Thanks for the responses.  Adam Ginsburg and I iterated a bit on this problem
>>> and found that the issue was the fact that the image I was fitting contained
>>> nans.  Once I removed the nans the gaussian fit routine works.  Note that if
>>> the fitter in astropy.models is not able to handle images with nans, then
>>> perhaps it should issue a warning.
>>> 
>>> -- Jeff
>>> 
>>> On 10/19/15 11:00 AM, Erik Bray wrote:
>>>> On 10/16/2015 09:47 AM, Giuliano Iorio wrote:
>>>>> 
>>>>> Hi Jeff,
>>>>> this is the kind of staff that usually happens if the position of the
>>>>> initial guess is too far away the right one. Did you plot the contour of the
>>>>> fitted gaussian on the image?
>>>>> It can be also that the image is too noisy around the target to fit. I
>>>>> usually use only a little subarray around the target, then I search the
>>>>> position of the maximum and I set the initial guess of xo and yo to its
>>>>> position. After I normalize all the subarray to the value of the maximum and
>>>>> cut all the signal below a certain threshold (usually 0.1).
>>>>> In this way I am able to obtain a robust fit also in very noisy map.
>>>> 
>>>> I agree pretty much with all of Giuliano's advice.  And again it might help
>>>> to exclude data outside a smaller subarray.  Without actually seeing the data
>>>> it's hard to provide much other advice.
>>>> 
>>>> Have you tried a different optimizer?  There are a couple other non-linear
>>>> fitters in the package and some have different sensitivities to initial
>>>> conditions.  But it's certainly not "non-functional".
>>>> 
>>>> Erik
>>>> 
>>>>>> Hi Jeff--
>>>>>> 
>>>>>> The fitted model will not be in g_init (this remains unchanged), but in g.
>>>>>>  If you take a look in g, you should be able to see the fitted results.
>>>>>> 
>>>>>> Cheers
>>>>>> Steve
>>>>>> 
>>>>>> ----- Original Message -----
>>>>>> From: "Jeff Mangum" <jmangum at nrao.edu <mailto:jmangum at nrao.edu>>
>>>>>> To: astropy at scipy.org <mailto:astropy at scipy.org>
>>>>>> Sent: Friday, October 16, 2015 3:11:56 PM
>>>>>> Subject: [AstroPy] Gaussian models fitter non-functional?
>>>>>> 
>>>>>> Hello,
>>>>>> 
>>>>>> Long-time listener but first-time caller.  Have been trying to use the
>>>>>> 2D Gaussian fitting capabilities within astropy.models to fit a 2D
>>>>>> Gaussian to an image (in FITS format).  Here is my script:
>>>>>> 
>>>>>> import numpy as np
>>>>>> import radio_beam
>>>>>> from astropy.modeling import models, fitting
>>>>>> from astropy import units as u
>>>>>> from astropy.io import fits
>>>>>> import astropy.coordinates as coord
>>>>>> import astropy.wcs as wcs
>>>>>> import matplotlib
>>>>>> import pylab as pl
>>>>>> 
>>>>>> # The following is the position of the peak in both J1 and J2, so use
>>>>>> # it as the starting guess
>>>>>> ra0 = '13h15m03.50s'
>>>>>> dec0 = '24d37m08.2s'
>>>>>> 
>>>>>> radeg = coord.Angle(ra0, unit=u.hour).degree
>>>>>> decdeg = coord.Angle(dec0, unit=u.degree)
>>>>>> 
>>>>>> # Now open the image
>>>>>> hdulist = fits.open('IC860CbandCarrayH2COJ1_moment0.fits')
>>>>>> #hdulist = fits.open('IC860KubandDarrayH2COJ2_moment0.fits')
>>>>>> w = wcs.WCS(hdulist[0].header, hdulist)
>>>>>> 
>>>>>> yy,xx = np.indices(hdulist[0].data.shape)
>>>>>> 
>>>>>> x0,y0 = w.wcs_world2pix(radeg, decdeg, 1)
>>>>>> 
>>>>>> # Now fit 2D gaussian
>>>>>> g_init = models.Gaussian2D(amplitude=1., x_mean=x0, y_mean=y0,
>>>>>> x_stddev=1, y_stddev=1)
>>>>>> fit_g = fitting.LevMarLSQFitter()
>>>>>> g = fit_g(g_init, xx, yy, hdulist[0].data)
>>>>>> 
>>>>>> 
>>>>>> When I look at g_init (which is where I believe the fit results should
>>>>>> be), I see that the fit has not moved from its initial settings.  It
>>>>>> appears that the fitter just did not run.  With Adam Ginsburg's help I
>>>>>> have a workaround using gaussfitter, but would certainly like to make
>>>>>> this work with astropy.models.  Thanks!
>>>>>> 
>>>>>> -- Jeff
> 
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