Re: R: command: astsubtractsky and astnoisechisel

[Mohammad Akhlaghi]

Thanks Gabriele,

From your email, the main error message is in [1] below.

If you run the following command in a terminal (as the error message 
suggests) you will see the list of HDUs in 'kernel.fits':

astfits /media/sf_Tesi/DatiInput/HighStellarDensity/NISP_Images/kernel.fits

You will see that this file only has a single HDU.

The default '--hdu=0' option that is suggested in the error message is 
for the main input ('input_file' in your code). To specify the HDU for 
reading the kernel, you should use '--khdu', it is described in this 
part of the book:

https://www.gnu.org/software/gnuastro/manual/html_node/NoiseChisel-input.html

So if you add '--khdu=0' to your run of NoiseChisel, this error should 
be fixed and you won't face a problem about the zero values on the edges 
(with '--hdu=3', you were changing the main input's HDU!).

It is great that you are comparing NoiseChisel! Just be careful that 
both NoiseChisel and SExtractor (as in any science software!) are highly 
customizable and it is advised to read their manuals to understand your 
results and optimize them for your science scenario. In the case of 
NoiseChisel after doing the tutorial of the previous email, read this 
tutorial to

https://www.gnu.org/software/gnuastro/manual/html_node/Detecting-large-extended-targets.html

Generally, it is easier to first test your commands on the command-line, 
and then put them in a script ;-).

Another small tip: With Gnuastro's MakeProfiles command, you can easily 
create any Gaussian kernel image. For example the output of the command 
above is a 2D Gaussian profile with a FWHM of 2 pixels and trucated at 5 
times the FWHM.

astmkprof --kernel=gaussian,2,5 --oversample=1 --output=kernel.fits

For more on this option, see:

https://www.gnu.org/software/gnuastro/manual//html_node/MakeProfiles-output-dataset.html

Cheers,
Mohammad







[1] Main error message
```
astnoisechisel: 
/media/sf_Tesi/DatiInput/HighStellarDensity/NISP_Images/kernel.fits: 
only has one HDU.

You should tell Gnuastro's command-line programs to look for data in the 
primary HDU with the '--hdu=0' option (or '-h0'). For library users, you 
can put "0" (a string literal) for the function's HDU argument. For 
more, see the FOOTNOTE below.

Pro TIP: if your desired HDU has a name (value to 'EXTNAME' keyword), it 
is best to just use that name with '--hdu' instead of relying on a 
counter. You can see the list of HDUs in a FITS file (with their data 
format, type, size and possibly HDU name) using Gnuastro's 'astfits' 
program, for example:

    astfits 
/media/sf_Tesi/DatiInput/HighStellarDensity/NISP_Images/kernel.fits

FOOTNOTE -- When writing a new FITS file, Gnuastro leaves the pimary HDU 
only for metadata. The output datasets (tables, images or cubes) are 
written after the primary HDU. In this way the keywords of the the first 
HDU can be used as metadata of the whole file (which may contain many 
extensions, this is stipulated in the FITS standard). Usually the 
primary HDU keywords contains the option names and values that the 
program was run with. Because of this, Gnuastro's default HDU to read 
data in a FITS file is the second (or '--hdu=1'). This error is commonly 
caused when the FITS file wasn't created by Gnuastro or by a program 
respecting this convention.
```