NIFS Data Reduction Richard McDermid Gemini Data Reduction Workshop Tucson, July 2010

NIFS Data Reduction Richard McDermid Gemini Data Reduction Workshop Tucson, July 2010
NIFS Data Reduction
Richard McDermid
Gemini Data Reduction Workshop
Tucson, July 2010
IFU Zoo: How to map 3D on 2D
NIFS
“Spaxel”
IFU Techniques:
Image Slicer
Pros:
– Compact design
– High throughput
– Easy cryogenics
Cons:
– Difficult to
manufacture
MIRI JWST
Rectangular Pixels
•
•
•
•
•
NIFS has different (x,y) spatial sampling
Along the slice is sampled by the detector
Across the slice is sampled by the slicer
Cross-slice sets spectral PSF - should be sampled on ~2 pixels
Gives rectangular spaxels on the sky
Sky x
Cross Slice
Sky Plane
Sky y
Detector
Plane
NIFS
•
•
•
•
Near-infrared Integral Field Spectrograph
Cryogenic slicer design
Z,J,H,K bands, R~5,000
One spatial setting:
– 3”x3” FoV
– 0.1”x0.04” sampling
• Optimized for use with AO
• Science: young stars, exo-planets, solar
system, black holes, jets, stellar
populations, hi-z galaxies….
Typical NIFS Observation
• ‘Before’ telluric star
–
–
–
–
NGS-AO
Acquire star
Sequence of on/off exposures
Same instrument config as science (inc. e.g. field lens for LGS)
• Science observation
– Acquisition
– Observation sequence:
• Arc (grating position is not 100% repeatable)
• Sequence of on/off exposures
• ‘After’ telluric (if science >~1.5hr)
• Daytime calibrations:
– Baseline set:
• Flat-lamps (with darks)
• ‘Ronchi mask’ flats (with dark)
• Darks for the arc
– Darks for science (if sky emission to be used for wavelength
calibration)
Typical NIFS Data
Science Object
Arc Lamp
Flat Lamp
Ronchi Mask
Slice
Wavelength
Arranging your files - suggestion
Daycals/ - All baseline daytime calibrations
YYYYMMDD/ - cals from different dates
Science/ - All science data
Obj1/
- First science object
YYYYMMDD/
Config/
Telluric/
Merged/
Scripts/
- First obs date (if split over >1 nights)
- e.g. ‘K’ (if using multiple configs)
- telluric data for this science obs
- Merged science and subsequent analysis
NIFS Reduction: Example scripts
• Three IRAF scripts on the web:
– Calibrations
– Telluric
– Science
• Form the basis of this tutorial
• Data set:
– Science object (star)
– Telluric correction star
– Daytime calibrations
• Update the path and file numbers at the top
of each script
• Excellent starting point for basic reduction
Lamp Calibrations
• Three basic calibrations:
– Flat (DAYCAL)
• Correct for transmission and illumination
• Locate the spectra on the detector
– Ronchi Mask (DAYCAL)
• Spatial distortion
– Arc (NIGHTCAL)
• Wavelength calibration
•
•
•
•
Each has associated dark frames
May have multiple exposures to co-add
DAYCAL are approx. 1 per observation date
NIGHTCAL are usually once per science
target, but can be common between targets if
grating config not changed
Calibration 1: Flat-Field
• Step 1: Locate the spectra
– Mask Definition File (MDF) provides relative
location of slices on detector
– Use nfprepare to match this to the absolute
position for your data:
Input file
Path to data
Prefix for new output file
X-shift for MDF
nfprepare(calflat,rawpath=raw_data, outpref="s", shiftx=INDEF,
shifty=INDEF, fl_vardq-, fl_corr-, fl_nonl-)
Y-shift for MDF
Do not create a
variance extension
Do not correct for
non-linearity
Do not try to flag
non-linear pixels
– Offset is stored in a new image
– This exposure is then referenced in subsequent
steps that need to know where the spectra are on
the chip
Calibration 1: Flat-Field
• Step 2.1: Update flat images with offset value
• Step 2.2: Generate variance and data quality
extensions
• Nfprepare is called again (once) to do both these
tasks:
Reference image with shift
Input file list
nfprepare("@flatlist”, rawpath=raw_data, shiftim="s"//calflat,
fl_vardq+, fl_int+, fl_corr-, fl_nonl-)
Create variance and
data quality planes
Run interactively
• Apply same process to dark frames
Calibration 1: Flat-Field
• Step 2.3: Combine flats and darks using gemcombine:
Input file list
gemcombine("n//@flatlist",output="gn"//calflat,
fl_dqpr+, fl_vardq+, masktype="none", logfile="nifs.log”)
Propagate DQ
Generate
VAR/DQ planes
No pixel masking
Append outputs
to a log file
• Repeat for darks…
• Now have 2D images with DQ and VAR extensions.
Ready to go to 3D…
Calibration 1: Flat-Field
• Step 3.1: Extract the slices using nsreduce:
‘cut’ out the slices from the 2D image
Apply first order wavelength coordinate system
nsreduce("gn"//calflat, fl_nscut+, fl_nsappw+, fl_vardq+,
fl_sky-, fl_dark-, fl_flat-, logfile="nifs.log”)
• Step 3.2: Create slice-by-slice flat field using nsflat:
nsflat("rgn"//calflat, darks="rgn"//flatdark,
flatfile="rn"//calflat//"_sflat”, darkfile="rn"//flatdark//"_dark",
fl_save_dark+, process="fit”, thr_flo=0.15, thr_fup=1.55,
fl_vardq+,logfile="nifs.log")
Output flat image
LOwer and UPper limits for ‘bad’ pixels
– Divides each spectrum (row) in a slice by a fit to the
average slice spectrum, with coarse renormalizing
– Also creates a bad pixel mask from the darks
Calibration 1: Flat-Field
Calibration 1: Flat-Field
• Step 3.3: Renormalize the slices to
account for slice-to-slice variations using
nsslitfunction:
Final flat-field correction frame
nsslitfunction("rgn"//calflat, "rn"//calflat//"_flat",
flat="rn"//calflat//"_sflat”, dark="rn"//flatdark//"_dark",
combine="median”, order=3, fl_vary-, logfile="nifs.log”)
Method to collapse
in spectral
direction
Order of fit across slices
– Fits a function in spatial direction to set slice
normalization
– Outputs the final flat field, with both spatial
and spectral flat information
Calibration 1: Flat-Field
Bin for
fitting slit
function
Calibration 1: Flat-Field
Fit to illumination along slice
Calibration 2: Wavelength Calibration
• Step 1: Repeat nfprepare, gemcombine and
nsreduce -> extracted slices
• Step 2: Correctly identify the arc lines, and
determine the dispersion function for each slice
– Should run this interactively the first time through to
ensure correct identification of lines and appropriate
fit function
– First solution is starting point for subsequent fits
– Should robustly determine good solution for
subsequent spectra
• Result is a series of files in a ‘database/’ directory
containing the wavelength solutions of each slice
nswavelength("rgn"//arc, coordli=clist, nsum=10,
thresho=my_thresh, trace=yes, fwidth=2.0, match=-6, cradius=8.0,
fl_inter+, nfound=10, nlost=10, logfile="nifs.log”)
Calibration 2: Wavelength Calibration
Calibration 2: Wavelength Calibration
Calibration 3: Spatial Distortion
• Need to correct for distortions along the
slices, and registration between slices
• This is done using the Ronchi mask as a
reference
• Analogous to wavelength calibration, but
in spatial domain
NIFS: Ronchi Mask
Ronchi Mask
NIFS Field
One slice
NIFS: Ronchi Mask
Reconstructed image
Transformation to make lines straight gives geometric correction
Calibration 3: Spatial Distortion
• Step 1: Repeat nfprepare, gemcombine and
nsreduce -> extracted slices
• Step 2: run nfsdist
– Reference peaks are very regular, so easy to fall foul
of aliasing when run automatically
– Recommend running interactively for each daycal set
nfsdist("rgn"//ronchiflat, fwidth=6.0, cradius=8.0, glshift=2.8,
minsep=6.5, thresh=2000.0, nlost=3, fl_int+, logfile="nifs.log”)
• TIP: apply the distortion correction to the Ronchi
frame itself, and check its OK
Calibration 3: Spatial Distortion
TIP:
• If the peaks are shifted, try ‘i’ to initialize, then ‘x’ to fit
• Identify with ‘m’ missed peaks if possible
Calibration 3: Spatial Distortion
BAD….
Bottom slice
is truncated
- Slit is
extrapolated
GOOD!
Lamp Calibrations: Summary
You now have:
1. Shift reference file: "s"+calflat
2. Flat field: "rn"+calflat+"_flat"
3. Flat BPM (for DQ plane generation):
"rn"+calflat+"_flat_bpm.pl”
4. Wavelength referenced Arc: "wrn"+arc
5. Spatially referenced Ronchi Flat: "rn"+ronchiflat
Notes:
–
–
–
1-3 are files that you need
4 & 5 are files with associated files in the ‘database/’ dir
Arcs are likely together with science data
Telluric Star
• Similar to science reduction up to a point:
– Sky subtraction
– Spectra extraction => 3D
– Wavelength calibration
– Flat fielding
• Then extract 1D spectra, co-add separate
observations, and derive the telluric
correction spectrum
Telluric Star
• Preliminaries:
– Copy the calibration files you will need into
telluric directory:
–
–
–
–
–
Shift file
Flat
Bad pixel mask (BPM)
Ronchi mask + database dir+files
Arc file + database dir+files
– Make two files listing filenames with (‘object’)
and without (‘sky’) star in field
Telluric Star
• Step 1.1: Run nfprepare, making use of
the shift file and BPM
• Step 1.2: Combine the blank sky frames:
– Skies are close in time
– Use gemcombine and your list of sky frames
to create a median sky
• Step 1.3: Subtract the combined sky from
each object frame with gemarith
Telluric Star
• Step 2.1: Run nsreduce, this time
including the flat:
nsreduce("sn@telluriclist",outpref="r",
flatim=cal_data//"rn"//calflat//"_flat”, fl_nscut+, fl_nsappw-,
fl_vardq+, fl_sky-, fl_dark-, fl_flat+, logfile=log_file)
• Step 2.2: Replace bad pixels with values
interpolated from fitting neighbours
nffixbad("rsn@telluriclist",outpref="b",logfile=log_file)
– Uses the Data Quality (QD) plane
Telluric Star
• Step 3.1: Derive the 2D spectral and spatial
transformation for each slice using nsfitcoords
– This combines the ‘1D’ dispersion and distortion
solutions derived separately from nswavelength and
nsdist into a 2D surface that is linear in wavelength
and angular scales
– The parameters of the fitted surface are associated
to the object frame via files in the database directory
nffitcoords("brsn@telluriclist", outpref="f", fl_int+,
lamptr="wrgn"//arc, sdisttr="rgn"//ronchiflat, lxorder=3,
lyorder=3, sxorder=3, syorder=3, logfile=log_file)
Nsfitcoords - spectral
Nsfitcoords - spectral
Nsfitcoords - spatial
Nsfitcoords - spatial
Telluric Star
• Step 3.2: Transform the slice images to the
linear physical coordinates using nstransform
– Uses transforms defined by nsfitcoords
– Generates slices that are sampled in constant
steps of wavelength and arcsec
• This is essentially a data-cube (even though
its not a cube…)
– Can run analysis directly from this point
Telluric Star
• Step 4.1: Extract 1D aperture spectra from the data
cube
– Use nfextract to define an aperture (radius and centre)
and sum spectra within it
– Outputs a 1D spectrum
• Step 4.2: Co-add the 1D spectra using gemcombine
Science Data
• Same preliminaries as telluric:
– Copy database and arc+Ronchi files
– Copy shift file, flat and BPM
– Identify sky and object frames
• In addition, we make use of the 1D telluric
• Generally need to combine separate (and
dithered) data-cubes
Science Data
• Initial steps:
– Nfprepare as per telluric
– Subtract sky using gemarith
• Usually have one unique sky per object: ABAB
• Can have ABA – two science share a sky
– Nsreduce (inc. flat field)
– Nffixbad, nsfitcoords, nstransform
• Now have data-cube with linear physical
coordinates
Science Data: Telluric correction
• Telluric spectrum is not only atmosphere,
but also stellar spectrum:
– Need to account for stellar absorption
features
– AND account for black-body continuum
• Needs some ‘by-hand’ steps to prepare
the telluric star spectrum
– Remove strong stellar features with splot
– Remove BB shape with a BB spectrum
Science Data: Telluric correction
BB @ 8000K
Science Data: Telluric correction
BB @ 8000K
Telluric Absorption
• Alternative approach is to fit a stellar template (Vacca et
al. 2003)
• Need good template
• Can use solar-type stars, but needs careful treatment…
Science Data: Telluric correction
• Finally, run nftelluric
– Computes the normalized correction spectrum
– Allows for shifts and amplitude scaling
– Divides the correction spectrum through the data
Science
Telluric
Science Data: Merging
• Now have series of data-cubes:
–
–
–
–
–
No dark current or sky (sky-subtracted)
Spatially and spectrally linearized
Bad pixels interpolated over
No instrumental transmission (flat-fielded)
No atmospheric transmission (telluric-corrected)
• Need to combine the data-cubes
• Will do this in three steps:
– Convert MEF ‘cubes’ to real 3D arrays
– Determine the relative spatial origin and adapt the
WCS headers
– Use gemcube to combine the cubes
Science Data: Merging
• Use nfcube to create the 3D arrays
– Uses interpolation to go from series of 2D slices to
one rectilinear 3D array
– Default pixel scale is 0.05”x0.05” (arrays need
square pixels..)
• These cubes are easily displayed using ds9
– Load as an array, scroll through the slices
• Find a reference pixel coordinate
– Should be easily recognizable in the cube
– Should be common to all cubes
• Adapt the headers to reflect the common spatial
axes origin
• Run gemcube
Science Data: Merging
• This approach involves (at least) one
superfluous interpolation: nifcube + gemcube
both interpolate
• Might be possible to use gemcube directly from
transformed data, but may need wrapper (TBD:
works on single slices, so can be adapted)
• Nifcube step is convenient for determining
reference coordinate
• At least gives a way to combine your data at
this point – stay tuned for updated
documentation
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