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Re: [bug-gnuastro] Error: interpolate_close_neighbors_on_thread

From: Mohammad Akhlaghi
Subject: Re: [bug-gnuastro] Error: interpolate_close_neighbors_on_thread
Date: Thu, 19 Oct 2017 22:07:01 +0200
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:52.0) Gecko/20100101 Thunderbird/52.4.0

Hi Alejandro,

Thank you very much for the message. I am very happy that Gnuastro is being useful for your work. Besides bugs/crashes, please continue to share your thoughts (for example suggested improvements) on its programs so we can implement them and make it more useful for your work and others in the next versions.

This particular crash is due to the fact that NoiseChisel is not able to find enough blank regions in the dataset to calculate the quantile threshold. With the default settings, it needs at least 9 tiles over the dataset where there is no significant signal in the smoothed/convolved image (see P.S.). However, as the error message says, with this dataset and NoiseChisel configuration, only 4 tiles could be found. You can see the successful (non-NaN) tiles with the following command (note the `--checkqthresh' option). After running it, a new multi-extension FITS image will be created which shows the tiles that are be used):

$ astnoisechisel -h0 ib5x2byrq_00i_single_ext.fits --checkqthresh

The main reason that NoiseChisel can only find 4 tiles is that this image has a lot of cosmic rays and the threshold is defined and applied on the smoothed image. As you see in the smoothed image (first image extension in the output of the command above), these cosmic rays get smoothed (and thus cover/remove the regions of good noise).

Since cosmic rays are essentially random, the best way to avoid them, in estimating the quantile threshold, is to slightly decrease the tile size with this command:

$ astnoisechisel -h0 ib5x2byrq_00i_single_ext.fits --tilesize=40,40

With this command, my NoiseChisel (version 0.4.32) successfully completed on this image. The changes in NoiseChisel since your version (0.3.53) do not concern this particular problem, so this fix should also work on your system too. However, please see P.Ss.

By decreasing the tile size, we are increasing the number of tiles and thus decrease the chances that cosmic rays fall in them. But we don't want to decrease the tile size too much because their area (number of pixels) will decrease significantly and thus the scatter in measuring the different parameters (quantile threshold, Sky value and etc) will increase, thus degrading the final result. You can see the tiles over the input image with the `--checktiles' option.

Another way to fix the problem would be to mask (set to NaN) the cosmic rays, but that involves major pre-processing before NoiseChisel with other exposures.

I hope this helps,


To better understand this, please see the description of `--qthresh' in the Gnuastro book:

(or this command: $ info gnuastro "Detection options" )

In particular, the "Quantifying signal in a tile" section fully describes how the tiles with no major signal are found:

(or this command: $ info gnuastro Quantifying )


Gnuastro version 0.4 was released in September with many bug fixes and additions. I recommend subscribing to the info-gnuastro mailing list to be informed on every release:


If you want an even more recent version of Gnuastro, you can always use this link to download the most recent un-official version (0.4.32 currently, the version will be updated in the future):


In any case, please consult the `NEWS' file before starting to use Gnuastro. In particular as you will see there, since version 0.4, NoiseChisel has undergone significant updates (improvements!).

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