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apall problems w/ coordinate system:originally a gemini fits

Paula R. T. Coelho wrote on Oct 03, 2006

hi there,

I have a set of GMOS (Gemini) longslit spectra. I reduced them using Gemini package, up to wavelength calibration (gstransform). From now on I want to use noao package to extract the apertures (apall). Because gemini fits has a specific format, i did:

imcopy gmos_image[sci,1,inherit] image

and tried to extract the spectrum from 'image'. apall works nicely, but in the end it complains

Warning: coordinate system ignored (rotated?). Using pixel coordinates.

and thus the extracted spectrum is not wavelength calibrated.
does any one know how to fix this?
i will also post to gemini helpdesk, but they usually are not quick in answering...

below follows the image header.

thx a lot, paula

ntgsN20041010S0032[3108,2304][real]: M32
No bad pixels, min=0., max=0. (old)
Line storage mode, physdim [3108,2304], length of user area 8505 s.u.
Created Tue 16:32:09 03-Oct-2006, Last modified Tue 16:32:09 03-Oct-2006
Pixel file "ntgsN20041010S0032.fits" [ok][/size]
EXTEND = F / File may contain extensions
ORIGIN = 'NOAO-IRAF FITS Image Kernel July 2003' / FITS file DATE = '2006-10-03T19:32:09' / Date FITS file was generated
IRAF-TLM= '16:32:09 (03/10/2006)' / Time of last modification
OBJECT = 'M32 ' / Name of the object observed
INSTRUME= 'GMOS-N ' / Instrument used to acquire data
OBSTYPE = 'OBJECT ' / Observation type
GEMPRGID= 'GN-2004B-Q-74' / Gemini programme ID
OBSID = 'GN-2004B-Q-74-2' / Observation ID / Data label
DATALAB = 'GN-2004B-Q-74-2-002' / DHS data label
OBSERVER= 'R.Johnson' / Observer
OBSERVAT= 'Gemini-North' / Name of telescope (Gemini-North|Gemini-South)
TELESCOP= 'Gemini-North' / Gemini-North
PARALLAX= 0. / Parallax of Target
RADVEL = 0. / Heliocentric Radial Velocity
EPOCH = 2000. / Epoch for Target coordinates
EQUINOX = 2000. / Equinox of coordinate system
TRKEQUIN= 2000. / Tracking equinox
SSA = 'J.Bodnarik' / SSA
RA = 10.67916667 / Right Ascension
DEC = 40.8525 / Declination of Target
ELEVATIO= 66.2085 / Current Elevation
AZIMUTH = 335.079754166667 / Current Azimuth
CRPA = 16.8689574716234 / Current Cass Rotator Position Angle
HA = '+00:52:03.12' / Telescope hour angle
LT = '00:39:26.1' / Local time at start of observation
TRKFRAME= ' ' / Tracking co-ordinate
DECTRACK= 0. / Differential tracking rate Dec
TRKEPOCH= 0. / Differential tracking reference epoch
RATRACK = 0. / Differential tracking rate RA
FRAME = 'FK5 ' / Target coordinate system
PMDEC = 0. / Proper Motion in Declination
PMRA = 0. / Proper Motion in RA
WAVELENG= 6800. / Effective Target Wavelength
RAWIQ = '70-percentile' / Raw Image Quality
RAWCC = '70-percentile' / Raw Cloud Cover
RAWWV = 'Any ' / Raw Water Vapour/Transparency
RAWBG = '50-percentile' / Raw Background
RAWPIREQ= 'YES ' / PI Requirements Met
RAWGEMQA= 'USABLE ' / Gemini Quality Assessment
CGUIDMOD= 'Basic ' / Carousel Mode
UT = '10:39:26.1' / UT at observation start
M2BAFFLE= 'VISIBLE ' / Position of M2 baffle
M2CENBAF= 'CLOSED ' / Position of M2 central hole baffle
ST = '01:35:02.4' / Sidereal time at the start of the exposure
XOFFSET = 1.19000000349 / Telescope offset in x in arcsec
YOFFSET = 0. / Telescope offset in y in arcsec
RAOFFSET= 1.14858717259 / Telescope offset in RA in arcsec
DECOFFSE= -0.311203334287 / Telescope offset in DEC in arcsec
PA = 165. / Sky Position Angle at start of exposure
SFRT2 = 178.766 / Science fold rotation angle (degrees)
SFTILT = 44.96 / Science fold tilt angle (degrees)
SFLINEAR= -2. / Science fold linear position (mm)
AOFOLD = 'park-pos.' / AO Pick-Off Mirror Position
OIARA = 10.75379167 / RA of OIWFS guide star
OIARV = 0. / OIWFS Heliocentric Radial Velocity
OIAWAVEL= 6500. / OIWFS Effective Target Wavelength
OIADEC = 40.82497222 / Declination of OIWFS guide star
OIAEPOCH= 2000. / Epoch for OIWFS guide star coordinates
OIAEQUIN= 2000. / Equinox for OIWFS guide star coordinates
OIAFRAME= 'FK5 ' / OIWFS Target co-ordinate system
OIAOBJEC= 'GSC0280101056' / Object Name for OIWFS, Chop A
OIAPMDEC= 0. / OIWFS Proper Motion in Declination
OIAPMRA = 0. / OIWFS Proper Motion in RA
OIAPARAL= 0. / OIWFS Parallax of Target
HUMIDITY= 10. / The Relative Humidity (fraction, 0..101).
TAMBIENT= 1.9 / The ambient temp (C).
TAMBIEN2= 35.42 / The ambient temp (F).
PRESSURE= 462.17248 / The atmospheric pressure (mm Hg).
PRESSUR2= 61600. / The atmospheric pressure (Pa).
DEWPOINT= -27.3 / The dew point (C).
DEWPOIN2= -17.14 / The dew point (F).
WINDSPEE= 2.4 / The wind speed (m/s).
WINDSPE2= 5.3688 / The wind speed (mph).
WINDDIRE= 334. / The wind direction (degrees).
INPORT = 5 / Number of ISS port where GMOS was located
GMOSCC = 'GMOS-N (V4-6)' / GMOS components controller s/w
CONID = 'GMOS v8.0' / Detector controller ID
DETECTOR= 'GMOS + Red1' / Detector name
DEWAR = 'Cryostat A' / Dewar name
DEW-TEMP= -119.906103286385 / Dewar temperature (Celsius)
DETSIZE = '[1:6144,1:4644]' / Detector size
NCCDS = 3 / Number of CCD chips
NAMPS = 1 / Number of amplifiers
SHUTTER = 'OPEN ' / Shutter state during observation
AMPINTEG= 5000 / Amplifier integration time
OBSEPOCH= 2004.77465863844 / Epoch at start of exposure
TIMESYS = 'UT1 ' / Time system used
DATE-OBS= '2004-10-10' / UT Date of observation (YYYY-MM-DD)
TIME-OBS= '10:40:02.3' / Time of observation
GMOSTHT = 'GOOD ' / Shutter health
NSUBEXP = 1 / Number of sub exposures
UTSTART = '10:40:02.3' / UT at observation start
UTEND = '10:40:32.3' / UT at observation end
EXPTIME = 30.0001728534698 / Exposure time in seconds
ELAPSED = 30.0001728534698 / Elapsed observation time in seconds
DARKTIME= 66.9165539741516 / Dark current integration in seconds
MASKID = 10005353 / Mask/IFU barcode
MASKNAME= '0.75arcsec' / Mask name
MASKTYP = 1 / Mask/IFU type (0=none/-1=IFU/1=mask)
MASKLOC = 0 / Mask/IFU location (-1=unknown/0=FP/1=cassette)
FILTER1 = 'open1-6 ' / Filter 1 name
FILTID1 = 20000018 / Filter 1 barcode
FILTER2 = 'open2-8 ' / Filter 2 name
FILTID2 = 20000008 / Filter 2 barcode
GRATING = 'R400+_G5305' / Grating name
GRATID = 30000006 / Grating barcode
GRWLEN = 680. / Grating central wavelength (nm)
GRORDER = 1 / Grating order
GRTILT = 56.3696 / Grating tilt angle (degrees)
GRSTEP = 6033.8454 / Requested grating motor step position
DTAX = 84.4 / Detector translation X position (microns)
DTAY = 90.4 / Detector translation Y position (microns)
DTAZ = 2374. / Detector translation Z position (microns)
DTAZST = 2374. / Focus at observation start (microns)
DTAZEN = 2374. / Focus at observation end (microns)
DTAZME = 0. / Mean focus during observation (microns)
DTMODE = 'FOLLOW-XY' / Detector translation stage mode
ADCMODE = ' ' / ADC mode
GMOSDC = 'GMOS DC ' / GMOS detector controller s/w
DETTYPE = 'SDSU II CCD' / Detector array type
DETID = 'EEV9273-16-03EEV9273-20-04EEV9273-20-03' / Chip IDs
EXPOSURE= 30. / Requested exposure time in seconds
ADCUSED = 1 / ADC used? (0=yes/1=no)
DETNROI = 1 / No. regions of interest
ADCENPST= 0. / Start entrance prism angle of ADC
ADCENPEN= 0. / End entrance prism angle of ADC
ADCENPME= 0. / Mean entrance prism angle of ADC
ADCEXPST= 0. / Start exit prism angle of ADC
ADCEXPEN= 0. / End exit prism angle of ADC
ADCEXPME= 0. / Mean exit prism angle of ADC
ADCWLEN1= 0. / Lower wavelength for ADC calculation
ADCWLEN2= 0. / Upper wavelength for ADC calculation
DETRO1X = 1 / ROI 1 X start
DETRO1XS= 3072 / ROI 1 X size
DETRO1Y = 1 / ROI 1 Y start
DETRO1YS= 2304 / ROI 1 Y size
AIRMASS = 1.093 / Mean airmass for the observation
AMSTART = 1.093 / Airmass at start of exposure
AMEND = 1.094 / Airmass at end of exposure
RELEASE = '2006-04-10 ' / End of proprietary period YYYY-MM-DD
NSCIEXT = 1 /1 /3 / Number of science extensions
PIXSCALE= 0.1454 / Pixel scale in Y in arcsec/pixel
NEXTEND = 2 /1 /2 /1 /4 / Number of extensions
OBSMODE = 'LONGSLIT ' / Observing mode (IMAGE|IFU|MOS|LONGSLIT)
GPREPARE= 'Tue Mar 7 18:45:10 UTC 2006' / Time stamp for GPREPARE
GEM-TLM = 'Wed Mar 8 17:21:23 UTC 2006' / Last modification with GEMINI
TRIMMED = 'yes ' / Overscan section trimmed
BIASIM = 'N20041006S0055_bias' / Bias image used by GIREDUCE
FLATIM = 'N20041010S0031_flat' / Flat field used by GIREDUCE
GIREDUCE= 'Tue Mar 7 18:45:14 UTC 2006' / Time stamp for GIREDUCE
GSCRREJ = 'Tue Mar 7 18:46:17 UTC 2006' / Time stamp for GSCRREJ
GSCRRES = 4.5 / GSCRREJ equivalent instrumental FWHM
GSCRTHRE= 10. / GSCRREJ sigma rejection threshold
CD1_2 = -1.04631447062649E-05 / WCS matrix element 1 2
CD2_1 = 1.04314816840428E-05 / WCS matrix element 2 1
GMOSAIC = 'Tue Mar 7 18:46:20 UTC 2006' / Time stamp for GMOSAIC
GMSINTER= 'linear ' / Interpolant used by GMOSAIC
GSAPPWAV= 'Tue Mar 7 18:46:21 UTC 2006' / Time stamp for GSAPPWAVE
GSREDUCE= 'Tue Mar 7 18:46:21 UTC 2006' / Time stamp for GSREDUCE
WMEF = 'Wed Mar 8 17:21:23 UTC 2006'
GSTRANSF= 'Wed Mar 8 17:21:23 UTC 2006' / Time stamp for GSTRANSFORM
CTYPE1 = 'LINEAR ' / R.A. in tangent plane projection
CTYPE2 = 'LINEAR ' / DEC. in tangent plane projection
CRPIX1 = 1. / Ref pix of axis 1
CRPIX2 = 1. / Ref pix of axis 2
CRVAL1 = 4696.5439453125 / RA at Ref pix in decimal degrees
CRVAL2 = 1. / DEC at Ref pix in decimal degrees
CD1_1 = 1.36486196517944 / WCS matrix element 1 1
CD2_2 = 1. / WCS matrix element 2 2
CCDSUM = '2 2 ' / CCD sum
GAIN = 1. / Amplifier gain
RDNOISE = 3.3 / Readout noise
WAT0_001= 'system=world'
WAT2_001= 'wtype=linear'
DISPAXIS= 1 /1 / Dispersion axis
DCLOG1 = 'Transform'
DC-FLAG = 0
WCSDIM = 2
CDELT1 = 1.36486196517944
CDELT2 = 1.
LTM1_1 = 1.
LTM2_2 = 1.
WAT1_001= 'wtype=linear label=Wavelength units=angstroms'
WAVTRAN = 'gsN20041010S0144_001' / Name of wavelength transformation

Francisco Valdes wrote on Oct 03, 2006

Hi Paula,

The problem is due to the presence of the diagonal elements of the CD matrix. Initially the GMOS data had an RA/DEC system. After processing it is creating a longslit system (wavelength and spatial) where the axes are expected to be independent. I'm not sure if the fact the CD1_2 and CD2_1 keywords are not removed is a problem in the gemini package or the NOAO/IRAF task which it calls. The solution is to use HEDIT to remove CD1_2 and CD2_1.

Yours,
Frank Valdes

Last post on Oct 03, 2006