Sometimes SIP fails to make the PVD of the mask

[paoloserra]

I'm getting this error.

	-Source 1: SoFiA J035043.00-361253.9.
	Start making spatial images.
	No SPECSYS or VELREF in header to define reference frame, checking CTYPE3.
	Found CTYPE3 spectral axis type VRAD in header.
	No SPECSYS, VELREF, or reference frame in CTYPE3, assuming data in TOPOCENT reference frame.
	Found J2000.0 equinox in header.
	The first HI contour defined at SNR = [2.5, 3.5] has level = 3.965e+01 (mom0 data units).
	No user image given. Proceeding with the download of any requested archive images.
WARNING: AstropyDeprecationWarning: The truth value of a Quantity is ambiguous. In the future this will raise a ValueError. [astropy.units.quantity]
WARNING: InputWarning: Coordinate string is being interpreted as an ICRS coordinate. [astroquery.utils.commons]
	Survey image retrieved from DSS2 Blue.
	Making DSS2 Blue overlaid with HI contours.
	Making HI grey scale map.
	Making pixel SNR map.
	Making velocity map.
	WARNING: Assuming channels are uniform width in velocity.
	WARNING: Assuming channels are uniform width in velocity.
	Making pv slice.
	Reading in mask cubelet.
Traceback (most recent call last):
  File "/home/pserra/.local/lib/python3.7/site-packages/pvextractor/utils/wcs_utils.py", line 19, in get_spatial_scale
    np.testing.assert_almost_equal(abs(scale[0,0]), abs(scale[0,1]))
  File "/home/pserra/.local/lib/python3.7/site-packages/numpy/testing/_private/utils.py", line 599, in assert_almost_equal
    raise AssertionError(_build_err_msg())
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0055558091777239815
 DESIRED: 0.00555530281073768

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/pserra/Astro/software/SoFiA-image-pipeline/image_pipeline.py", line 175, in <module>
    surveys=list(surveys), snr_range=args.snr_range, user_image=args.user_image, user_range=args.user_range)
  File "/home/pserra/Astro/software/SoFiA-image-pipeline/src/make_images.py", line 608, in main
    make_pv(source, src_basename, cube_params, opt_view=opt_view, suffix=suffix)
  File "/home/pserra/Astro/software/SoFiA-image-pipeline/src/make_images.py", line 405, in make_pv
    mask_pv = create_pv(source, src_basename + '_{}_mask.fits'.format(str(source['id'])), opt_view=opt_view[0])
  File "/home/pserra/Astro/software/SoFiA-image-pipeline/modules/functions.py", line 285, in create_pv
    mask_pv = extract_pv_slice(mask[0].data, slice, wcs=WCS(mask[0].header, fix=True, translate_units='shd'))
  File "/home/pserra/.local/lib/python3.7/site-packages/pvextractor/pvextractor.py", line 78, in extract_pv_slice
    scale = get_spatial_scale(wcs)
  File "/home/pserra/.local/lib/python3.7/site-packages/pvextractor/utils/wcs_utils.py", line 21, in get_spatial_scale
    raise ValueError("Non-square pixels.  Please resample data.")
ValueError: Non-square pixels.  Please resample data.

[kmhess]

Hi Paolo,

The masking was tricky to implement and google is not really helping me with these errors. Can you send me the sofia fits files for the source it fails on, and a *_cat.txt containing only this source? Does plotting the mask fail for all your sources or only some of them? Since it's complaining about non-square pixels...is there a certain position angle for which these fail, or sources that are weird for some other reason? (Like maybe its failing on not a real source, but an artefact SoFiA has picked up?)

[kmhess]

@paoloserra These edits are in the mask_pv branch. Can you test if this at least skips over your sources where plotting the mask fails. I'm not sure which exception to catch, so I've tried with the first one, "AssertionError", but I can't test it. (It's good to not be too broad, in catching exceptions, if possible, right?)

[paoloserra]

unfortunately AssertionError does not catch it -- which I don't really understand since that's what the error message says... that's a little beyond me frankly :(

[paoloserra]

It's good to not be too broad, in catching exceptions, if possible, right?

I agree, but I'm clearly no programmer :)

[kmhess]

If you change AssertionError to ValueError, does it work?

…

On Tue, Apr 12, 2022 at 12:14 PM paoloserra ***@***.***> wrote: It's good to not be too broad, in catching exceptions, if possible, right? I agree, but I'm clearly no programmer :) — Reply to this email directly, view it on GitHub <#35 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADRLMRTJBUZBCE4GU36FNHDVEVEILANCNFSM5SZMS3MA> . You are receiving this because you commented.Message ID: ***@***.***>

[paoloserra]

Yeah that worked, I've made the change in that branch.

[paoloserra]

Just to clarify, I think this deserves to be merged into master as it allows users with this problem to keep going.

Maybe we can open a separate issue about how to solve the problem and find a way to plot the mask contours.

[kmhess]

Branch has been merged. I'm happy to keep this as the open issue since it has your error at the top. I did a little digging into the Assertion Error, but I think that might be a feature that astropy needs to deal with, tbh.

[paoloserra]

OK, I will rename the issue though.

[kmhess]

For sample data in Galactic coordinates, the mask PVD also fails.

[kmhess]

I've noticed this issue seems to have resolved itself somehow with the #57 noregrid branch, at least for some sources!

[kmhess]

It looks like pvextractor may allow a work around for this issue now with a new PR:
radio-astro-tools/pvextractor#113
Some background:
radio-astro-tools/pvextractor#107