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can not parse the fits header with more than 2 axis #66
Description
It can not work with the fits file which has more than 2 axis, like in radio data.
For example, a header as below :
SIMPLE = T /Standard FITS
BITPIX = -32 /Floating point (32 bit)
NAXIS = 4
NAXIS1 = 1600
NAXIS2 = 1600
NAXIS3 = 1
NAXIS4 = 1
EXTEND = T
EQUINOX = 2.000000000000E+03
RADESYS = 'FK5 '
LONPOLE = 1.800000000000E+02
LATPOLE = -3.529166667528E+00
CTYPE1 = 'RA---SIN'
CRVAL1 = 4.201666666401E+01
CDELT1 = -8.333333333333E-05
CRPIX1 = 8.010000000000E+02
CUNIT1 = 'deg '
CTYPE2 = 'DEC--SIN'
CRVAL2 = -3.529166667528E+00
CDELT2 = 8.333333333333E-05
CRPIX2 = 8.010000000000E+02
CUNIT2 = 'deg '
CTYPE3 = 'STOKES '
CRVAL3 = 1.000000000000E+00
CDELT3 = 1.000000000000E+00
CRPIX3 = 1.000000000000E+00
CUNIT3 = ' '
CTYPE4 = 'FREQ '
CRVAL4 = 1.519499768816E+09
CDELT4 = 1.024001037953E+09
CRPIX4 = 1.000000000000E+00
CUNIT4 = 'Hz '
PV2_1 = 0.000000000000E+00
PV2_2 = 0.000000000000E+00
It will cause the error:
File "build/bdist.linux-x86_64/egg/pyregion/__init__.py", line 57, in as_imagecoord
File "build/bdist.linux-x86_64/egg/pyregion/ds9_region_parser.py", line 184, in sky_to_image
File "build/bdist.linux-x86_64/egg/pyregion/wcs_helper.py", line 231, in _get_radesys
ValueError: too many values to unpack
Activity
mhardcastle commentedon Jul 27, 2016
This is true, but in a sense ds9's fault: as ds9 does not put Stokes or frequency values into its regions even when applied to a cube, pyregion is necessarily going to have trouble applying them to images.
In my ds9 radio flux measurement plugin http://github.com/mhardcastle/radioflux I go to a lot of trouble to 'flatten' radio maps down to the 2D form expected to allow pyregion to apply regions to them. I'm not sure this is logic that wants to be in pyregion itself -- e.g. what should you do if you actually have a cube, as opposed to the (1,1,y,x) shape of many radio maps?
bsipocz commentedon Jul 28, 2016
@henrysting @mhardcastle - There are plans to deprecate pyregions when the replacement package, regions, is mature enough. You may want to take a look at it, and raise feature requests there rather than here.
Regarding the original issue, maybe the spectral-cube package is more relevant place for it.
leejjoon commentedon Aug 1, 2016
I have been knowing this issue, but was not quite sure what the right way to fix is.
As a workaournd, I recommend you to read the header as a wcs object and its 'sub' method to retrieve space part of the axes. Maybe we can safely do this within the pyregion,
keflavich commentedon Aug 1, 2016
wcs.sub([wcs.WCSSUB_CELESTIAL])is probably the 'best' way to do thisEDIT: the shortcut for that is just
wcs.celestialcdeil commentedon Aug 1, 2016
Does anyone here have time to make a pull request adding this example to the docs?
mhardcastle commentedon Aug 1, 2016
I will try to test this and document it. But it might be even better if this were the default behaviour in pyregion, since ds9 regions are always spatial, and so always need to be applied to the celestial subset of wcs?
mhardcastle commentedon Aug 1, 2016
Documented, pull request raised.
cdeil commentedon Aug 2, 2016
@mhardcastle documented this in #81 .
I don't know. To me both options seem reasonable:
wcs.sub([wcs.WCSSUB_CELESTIAL])before passing it topyregionwcs.sub([wcs.WCSSUB_CELESTIAL])on input in pyregion methods to automatically do this for users as a convenienceAnother option would be to check the
wcson input and give a better errror message.@leejjoon @keflavich @astrofrog - Thoughts?
leejjoon commentedon Aug 2, 2016
My inclination is option 2, but only when fits header is given as an argument. I would suggest that no automatic call is made If wcs object is given. Just in case of any odd cases.
keflavich commentedon Aug 2, 2016
I also favor option 2. I think it should be applied even if a
wcsargument is passed.However, if you prefer not to do this for the
wcsinput option, we should check thatwcs.naxis==2or do atry/exceptfor coordinate conversion, and catch the failure with a suggestion that the user usewcs.celestialinstead.leejjoon commentedon Aug 2, 2016
I was just wondering if there is any corner cases where a user does not want to have the 'sub' method called. After a second thought, I think we can have 'sub' called only when the naxis is larger than 2.
Document that astropy#66 is fixed and Headers are required
cdeil commentedon May 15, 2017
Reading through this issue and #87 and stuff linked to from there, I'm confused.
Can someone involved here please comment on status in
pyregionmaster and is possible also whether this is now covered by a test and mentioned in the docs correctly?leejjoon commentedon May 15, 2017
I believe the issue itself was fixed, but I don't think the test case is added (I have opened a new PR #113 with a simple test case). This also needs to be documented I believe.
cdeil commentedon May 17, 2017
@leejjoon - Can you also update the docs if needed in #113 to clear this issue out for the upcoming 2.0 release?