The document provides instructions for combining bias frames, creating a master flat field, removing the flat field from science images, detecting and removing cosmic rays, identifying emission lines in a HeAr lamp calibration frame, and adding header information to processed science and standard star images.

1. PACKAGE = images.immatch
TASK = imcombine
input = bi*.fit List of images to combine
output = zero.fit List of output images
(rejmask= ) List of rejection masks (optional)
(plfile = ) List of pixel list files (optional)
(sigma = ) List of sigma images (optional)
(logfile= STDOUT) Log file
(combine= median) Type of combine operation
(reject = none) Type of rejection
(project= no) Project highest dimension of input
images?
(outtype= real) Output image pixel datatype
(outlimi= ) Output limits (x1 x2 y1 y2 ...)
(offsets= none) Input image offsets
(masktyp= none) Mask type
(maskval= 0.) Mask value
(blank = 0.) Value if there are no pixels
(scale = median) Image scaling
(zero = none) Image zero point offset
(weight = none) Image weights
(statsec= ) Image section for computing statistics
(expname= ) Image header exposure time keyword
Combine Bias
(lthresh= INDEF) Lower threshold
(hthresh= INDEF) Upper threshold
(nlow = 1) minmax: Number of low pixels to reject
(nhigh = 1) minmax: Number of high pixels to reject
(nkeep = 1) Minimum to keep (pos) or maximum to
reject (neg)
(mclip = yes) Use median in sigma clipping
algorithms?
(lsigma = 3.) Lower sigma clipping factor
(hsigma = 3.) Upper sigma clipping factor
(rdnoise= 0.) ccdclip: CCD readout noise (electrons)
(gain = 1.) ccdclip: CCD gain (electrons/DN)
(snoise = 0.) ccdclip: Sensitivity noise (fraction)
(sigscal= 0.1) Tolerance for sigma clipping scaling
corrections
(pclip = -0.5) pclip: Percentile clipping parameter
(grow = 0.) Radius (pixels) for neighbor rejection
(mode = ql)

2. Combined bias (zero.fits)

3. files *.fits > lista
Remove bi*.fits from lista
PACKAGE = images.imutil
TASK = imarith
operand1= @lista Operand image or numerical constant
op = - Operator
operand2= zero.fits Operand image or numerical constant
result = @lista Resultant image
(title = ) Title for resultant image
(divzero= 0.) Replacement value for division by zero
(hparams= ) List of header parameters
(pixtype= ) Pixel type for resultant image
(calctyp= ) Calculation data type
(verbose= yes) Print operations?
(noact = no) Print operations without performing them?
(mode = ql)
Images should have (close to) zero counts
Bias remotion

4. PACKAGE = immatch
TASK = imcombine
input = ff*.fits List of images to combine
output = flat.fits List of output images
(rejmask= ) List of rejection masks (optional)
(plfile = ) List of pixel list files (optional)
(sigma = ) List of sigma images (optional)
(logfile= STDOUT) Log file
(combine= median) Type of combine operation
(reject = none) Type of rejection
(project= no) Project highest dimension of input
images?
(outtype= real) Output image pixel datatype
(offsets= none) Input image offsets
(masktyp= none) Mask type
(maskval= 0.) Mask value
(blank = 0.) Value if there are no pixels
(scale = median) Image scaling
(zero = none) Image zero point offset
(weight = none) Image weights
(statsec= ) Image section for computing statistics
(expname= ) Image header exposure time keyword
Combine Flats
(lthresh= INDEF) Lower threshold
(hthresh= INDEF) Upper threshold
(nlow = 1) minmax: Number of low pixels to reject
(nhigh = 1) minmax: Number of high pixels to reject
(nkeep = 1) Minimum to keep (pos) or maximum to
reject (neg)
(mclip = yes) Use median in sigma clipping
algorithms?
(lsigma = 3.) Lower sigma clipping factor
(hsigma = 3.) Upper sigma clipping factor
(rdnoise= 0.) ccdclip: CCD readout noise (electrons)
(gain = 1.) ccdclip: CCD gain (electrons/DN)
(snoise = 0.) ccdclip: Sensitivity noise (fraction)
(sigscal= 0.1) Tolerance for sigma clipping scaling
corrections
(pclip = -0.5) pclip: Percentile clipping parameter
(grow = 0.) Radius (pixels) for neighbor rejection
(mode = ql)

5. Combined Flat (flat.fits)

6. Make a good fit in response function changing the order of fitting function
PACKAGE = noao.twodspec.longslit
TASK = response
calibrat= flat.fits Longslit calibration images
normaliz= flat.fits Normalization spectrum images
response= flatfin.fits Response function images
(interac= yes) Fit normalization spectrum interactively?
(thresho= INDEF) Response threshold
(sample = *) Sample of points to use in fit
(naverag= 1) Number of points in sample averaging
(functio= spline3) Fitting function
(order = 20) Order of fitting function
(low_rej= 0.) Low rejection in sigma of fit
(high_re= 0.) High rejection in sigma of fit
(niterat= 1) Number of rejection iterations
(grow = 0.) Rejection growing radius
(graphic= stdgraph) Graphics output device
(cursor = ) Graphics cursor input
(mode = ql)
Fit the normalization spectrum for flat.fits interactively (yes): y
Dispersion axis (1=along lines, 2=along columns, 3=along z) (1:3) (1): 1
Response function of Flats
Interactive fitting: try to make a good fit
increasing the order with
o: # where # is the order of the function
f to fit
h x vs. y fiting
l x vs. n (non linear part)
j x vs. r (residuals)
q quit once a good fit is made

7. Final flat field

8. Remove Flat field
Delete ff*.fits from lista
PACKAGE = imutil
TASK = imarith
operand1= @lista Operand image or numerical constant
op = / Operator
operand2= flatfin.fits Operand image or numerical constant
result = @lista Resultant image
(title = ) Title for resultant image
(divzero= 0.) Replacement value for division by zero
(hparams= ) List of header parameters
(pixtype= ) Pixel type for resultant image
(calctyp= ) Calculation data type
(verbose= yes) Print operations?
(noact = no) Print operations without performing them?
(mode = ql)

9. PACKAGE = noao.imred.crutil
TASK = cosmicrays
input = n4151.fits List of images in which to detect cosmic rays
output = n4151nc.fits List of cosmic ray replaced output images (optio
(badpix = ) List of bad pixel files (optional)
(thresho= 20.) Detection threshold above mean
(fluxrat= 10.) Flux ratio threshold (in percent)
(npasses= 5) Number of detection passes
(window = 5) Size of detection window
(interac= no) Examine parameters interactively?
answer = no) Examine parameters interactively?
(train = no) Use training objects?
(objects= ) Cursor list of training objects
(savefil= ) File to save train objects
(verbose= yes) Print log information to the standard output?
(logfile= ) Text log file
(plotfil= ) Log metacode plot file
(graphic= stdgraph) Interactive graphics output device
(cursor = ) Graphics cursor input
(ccdtype= )
(instrum= )
(mode = ql)
Review parameters for a particular image? (no|yes|NO|YES) (yes): N
Repeat for standard star bd75325
Remove cosmic rays

10. Image with cosmic rays

11. Remove remnant cosmic rays
PACKAGE = images.tv
TASK = imedit
input = n4151nc.fits Images to be edited
output = n4151ncc.fits Output images
(cursor = y) Cursor input
(logfile= ) Logfile for record of cursor commands
(display= yes) Display images?
(autodis= yes) Automatic image display?
(autosur= yes) Automatic surface plots?
(apertur= circular) Aperture type
(radius = 2.) Substitution radius
(search = 2.) Search radius
(buffer = 1.) Background buffer width
(width = 2.) Background width
(xorder = 2) Background x order
(yorder = 2) Background y order
(value = 0.) Constant value substitution
(sigma = INDEF) Added noise sigma
(angh = -33.) Horizontal viewing angle (degrees)
(angv = 25.) Vertical viewing angle (degrees)
(command= display $image 1 erase=$erase fill=yes order=0 >&
dev$null) Display co
(graphic= stdgraph) Graphics device
(default= b) Default option for x-y input
(fixpix = no) Fixpix style input?
(mode = ql)
Interactive remotion keystrokes:
b background replacement (aperture)
+ increase radius
- decrease radius
Q quit without save
q quit and save
Repeat for standard star

12. Removing cosmic rays

13. Image without cosmic rays
Sky lines

14. Calibration HeAr lamp

15. PACKAGE = noao.twodspec.longslit
TASK = identify
images = lamp.fits Images containing features to be identified
(section= middle line) Section to apply to two dimensional images
(databas= database) Database in which to record feature data
(coordli= linelists$idhear_br.dat) User coordinate list
(units = ) Coordinate units
(nsum = 10) Number of lines/columns/bands to sum in 2D image
(match = -3.) Coordinate list matching limit
(maxfeat= 50) Maximum number of features for automatic identif
(zwidth = 100.) Zoom graph width in user units
(ftype = emission) Feature type
(fwidth = 4.) Feature width in pixels
(cradius= 5.) Centering radius in pixels
(thresho= 0.) Feature threshold for centering
(minsep = 2.) Minimum pixel separation
(functio= spline3) Coordinate function
(order = 1) Order of coordinate function
(sample = *) Coordinate sample regions
(niterat= 0) Rejection iterations
(low_rej= 3.) Lower rejection sigma
(high_re= 3.) Upper rejection sigma
(grow = 0.) Rejection growing radius
(autowri= no) Automatically write to database
(graphic= stdgraph) Graphics output device
Write feature data to the database (yes)? y
Identify lamp lines
keystrokes:
m mark a line and identify it
f make a fit
q quit

16. Mark and identify some lines

17. Make a good fit

18. PACKAGE = longslit
TASK = reidentify
referenc= lamp Reference image
images = lamp Images to be reidentified
(interac= no) Interactive fitting?
(section= middle line) Section to apply to two dimensional images
(newaps = yes) Reidentify apertures in images not in
reference?
(overrid= no) Override previous solutions?
(refit = yes) Refit coordinate function?
(trace = yes) Trace reference image?
(step = 5) Step in lines/columns/bands for tracing an
image
(nsum = 10) Number of lines/columns/bands to sum
(shift = 0.) Shift to add to reference features (INDEF to sea
(search = 0.) Search radius
(nlost = 0) Maximum number of features which may be lost
(cradius= 5.) Centering radius
(thresho= 0.) Feature threshold for centering
(addfeat= no) Add features from a line list?
(coordli= linelists$idhear_br.dat) User coordinate list
(match = -3.) Coordinate list matching limit
(maxfeat= 50) Maximum number of features for automatic
identif
(minsep = 2.) Minimum pixel separation
Reidentify lamp lines

19. Put header
PACKAGE = images.imutil
TASK = hedit
images = n4151ncc.fits,bd75325ncc.fits images to be edited
fields = REFSPEC1 fields to be edited
value = lamp value expression
(add = yes) add rather than edit fields
(delete = no) delete rather than edit fields
(verify = yes) verify each edit operation
(show = yes) print record of each edit operation
(update = yes) enable updating of the image header
(mode = )
add n4151ncc.fits,REFSPEC1 = lamp
update n4151ncc.fits ? (yes): y
add bd75325ncc.fits,REFSPEC1 = lamp
update bd75325ncc.fits ? (yes):
bd75325ncc.fits updated

20. PACKAGE = longslit
TASK = fitcoords
images = lamp Images whose coordinates
are to be fit
(fitname= lamp) Name for coordinate fit in the
database
(interac= yes) Fit coordinates interactively?
(combine= no) Combine input coordinates
for a single fit?
(databas= database) Database
(deletio= deletions.db) Deletion list file (not used if
null)
(functio= chebyshev) Type of fitting function
(xorder = 4) X order of fitting function
(yorder = 1) Y order of fitting function
(logfile= STDOUT,logfile) Log files
(plotfil= plotfile) Plot log file
(graphic= stdgraph) Graphics output device
(cursor = ) Graphics cursor input
(mode = ql)
Fit lamp interactively (yes): y
Fit coordinates

21. Fit coordinates
keystrokes:
xo,yo change x,y orders of fitting
d p delete points
f fit
q quit

22. PACKAGE = longslit
TASK = transform
input = n4151ncc.fits,bd75325ncc.fits Input images
output = n4151t.fits,bd75325t.fits Output images
fitnames= lamplamp Names of coordinate fits in the database
(databas= database) Identify database
(interpt= spline3) Interpolation type
(x1 = INDEF) Output starting x coordinate
(x2 = INDEF) Output ending x coordinate
(dx = INDEF) Output X pixel interval
(nx = INDEF) Number of output x pixels
(xlog = no) Logarithmic x coordinate?
(y1 = INDEF) Output starting y coordinate
(y2 = INDEF) Output ending y coordinate
(dy = INDEF) Output Y pixel interval
(ny = INDEF) Number of output y pixels
(ylog = no) Logarithmic y coordinate?
(flux = yes) Conserve flux per pixel?
(logfile= STDOUT,logfile) List of log files
(mode = ql)
Dispersion axis (1=along lines, 2=along columns, 3=along z) (1:3) (1): 1
Transform pixels to wavelength

23. Object calibrated in wavelength

24. PACKAGE = longslit
TASK = background
input = n4151t.fits Input images to be background subtracted
output = n4151b.fits Output background subtracted images
(axis = 2) Axis along which background is fit and subtracte
(interac= yes) Set fitting parameters interactively?
(sample = *) Sample of points to use in fit
(naverag= 1) Number of points in sample averaging
(functio= chebyshev) Fitting function
(order = 3) Order of fitting function
(low_rej= 0.) Low rejection in sigma of fit
(high_re= 0.) High rejection in sigma of fit
(niterat= 1) Number of rejection iterations
(grow = 0.) Rejection growing radius
(graphic= stdgraph) Graphics output device
(cursor = ) Graphics cursor input
(mode = ql)
Fit Column= 512
Repeat for standard
Remove background
Keystrokes:
s to mark level to substract
q quit

25. s s s
s

26. Image without background should not have sky lines

27. PACKAGE = noao.twodspec.apextract
TASK = apall
input = n4151b.fits List of input images
(output = NGC4151.fits) List of output spectra
(apertur= 1) Apertures
(format = multispec) Extracted spectra format
(referen= ) List of aperture reference images
(profile= ) List of aperture profile images
(interac= yes) Run task interactively?
(find = yes) Find apertures?
(recente= yes) Recenter apertures?
(resize = yes) Resize apertures?
(edit = yes) Edit apertures?
(trace = yes) Trace apertures?
(fittrac= yes) Fit the traced points interactively?
(extract= yes) Extract spectra?
(extras = yes) Extract sky, sigma, etc.?
(review = yes) Review extractions?
(line = INDEF) Dispersion line
(nsum = 10) Number of dispersion lines to sum or
median
# DEFAULT APERTURE PARAMETERS
(lower = -5.) Lower aperture limit relative to center
(upper = 5.) Upper aperture limit relative to center
(apidtab= ) Aperture ID table (optional)
Extract spectrum
# DEFAULT BACKGROUND PARAMETERS
(b_funct= chebyshev) Background function
(b_order= 1) Background function order
(b_sampl= -10:-6,6:10) Background sample regions
(b_naver= -3) Background average or median
(b_niter= 0) Background rejection iterations
(b_low_r= 3.) Background lower rejection sigma
(b_high_= 3.) Background upper rejection sigma
(b_grow = 0.) Background rejection growing radius
# APERTURE CENTERING PARAMETERS
(width = 5.) Profile centering width
(radius = 10.) Profile centering radius
(thresho= 0.) Detection threshold for profile centering
# AUTOMATIC FINDING AND ORDERING PARAMETERS
nfind = 1 Number of apertures to be found
automatically
(minsep = 5.) Minimum separation between spectra
(maxsep = 1000.) Maximum separation between
spectra
(order = increasing) Order of apertures
# RECENTERING PARAMETERS
(aprecen= ) Apertures for recentering calculation
(npeaks = INDEF) Select brightest peaks
(shift = yes) Use average shift instead of recentering?

28. Extract spectrum (cont…)
# RECENTERING PARAMETERS
(aprecen= ) Apertures for recentering calculation
(npeaks = INDEF) Select brightest peaks
(shift = yes) Use average shift instead of recentering?
# RESIZING PARAMETERS
(llimit = INDEF) Lower aperture limit relative to center
(ulimit = INDEF) Upper aperture limit relative to center
(ylevel = 0.1) Fraction of peak or intensity for
automatic widt
(peak = yes) Is ylevel a fraction of the peak?
(bkg = yes) Subtract background in automatic
width?
(r_grow = 0.) Grow limits by this factor
(avglimi= no) Average limits over all apertures?
# TRACING PARAMETERS
(t_nsum = 10) Number of dispersion lines to sum
(t_step = 10) Tracing step
(t_nlost= 3) Number of consecutive times profile is
lost befo
(t_funct= spline3) Trace fitting function
(t_order= 2) Trace fitting function order
(t_sampl= *) Trace sample regions
(t_naver= 1) Trace average or median
(t_niter= 0) Trace rejection iterations
(t_low_r= 3.) Trace lower rejection sigma
(t_high_= 3.) Trace upper rejection sigma
(t_grow = 0.) Trace rejection growing radius
# EXTRACTION PARAMETERS
(backgro= none) Background to subtract
(skybox = 1) Box car smoothing length for sky
(weights= none) Extraction weights (none|variance)
(pfit = fit1d) Profile fitting type (fit1d|fit2d)
(clean = no) Detect and replace bad pixels?
(saturat= INDEF) Saturation level
(readnoi= 0.) Read out noise sigma (photons)
(gain = 1.) Photon gain (photons/data number)
(lsigma = 4.) Lower rejection threshold
(usigma = 4.) Upper rejection threshold
(nsubaps= 1) Number of subapertures per aperture
(mode = ql)
Find apertures for n4151b.fits ? (yes): y
Number of apertures to be found automatically (1): 1
Resize apertures for n4151b.fits ? (yes): y
Edit apertures for n4151b.fits ? (yes): y
Keystrokes:
l lower limit of aperture
u upper limit
q quit
d p delete a point
f fit

29. Resize apertures with keystrokes u & l

30. Spectrum aperture fitting
Delete departing points

31. Extracted spectrum

32. Verify with splot NGC4151.fits
should be calibrated in wavelength
Repeat for Standard star

33. Resize standard apertures with keystrokes u & l

34. Standard spectrum aperture fitting

35. Standard Spectrum extracted

36. Standard Spectrum calibrated in wavelength

37. Extract one-dimensional spectrum
of standard star
PACKAGE = noao.onedspec
TASK = standard
input = BD+75325.fits Input image file root name
output = std Output flux file (used by
SENSFUNC)
(samesta= yes) Same star in all apertures?
(beam_sw= no) Beam switch spectra?
(apertur= ) Aperture selection list
(bandwid= INDEF) Bandpass widths
(bandsep= INDEF) Bandpass separation
(fnuzero= 3.6800000000000E-20) Absolute flux zero point
(extinct= onedstds$kpnoextinct.dat) Extinction file
(caldir = onedstds$local/) Directory containing calibration
(observa= oagh) Observatory for data
(interac= yes) Graphic interaction to define new
bandpasses
(graphic= stdgraph) Graphics output device
(cursor = ) Graphics cursor input
star_nam= bd75d325 Star name in calibration list
airmass = 1.4 Airmass
exptime = 600 Exposure time (seconds)
answer = y (no|yes|NO|YES|NO!|YES!)
(mode = ql)

38. Edit absorption lines
Keystrokes:
d delete features
shift x resolution
r redraw
q quit

39. PACKAGE = onedspec
TASK = sensfunc
standard= std Input standard star data file (from STANDARD)
sensitiv= sens Output root sensitivity function imagename
(apertur= ) Aperture selection list
(ignorea= no) Ignore apertures and make one sensitivity functi
(logfile= logfile) Output log for statistics information
(extinct= onedstds$kpnoextinct.dat) Extinction file
(newexti= extinct.dat) Output revised extinction file
(observa= oagh) Observatory of data
(functio= spline3) Fitting function
(order = 6) Order of fit
(interac= yes) Determine sensitivity function interactively?
(graphs = sri) Graphs per frame
(marks = plus cross box) Data mark types (marks deleted added)
(colors = 2 1 3 4) Colors (lines marks deleted added)
(cursor = sri) Graphics cursor input
(device = stdgraph) Graphics output device
answer = yes (no|yes|NO|YES)
(mode = ql)
No extinction correction applied
Fit aperture 1 interactively? (no|yes|NO|YES): Y
Sensitivity function

40. Keystrokes:
d p delete point
r redraw-fit
o change order of funct.
Sensitivity function fitting

41. Flux calibration of standard
PACKAGE = onedspec
TASK = calibrate
input = BD+75325.fits Input spectra to calibrate
output = BD+75325C.fits Output calibrated spectra
(extinct= yes) Apply extinction correction?
(flux = yes) Apply flux calibration?
(extinct= onedstds$kpnoextinct.dat) Extinction file
(observa= oagh) Observatory of observation
(ignorea= no) Ignore aperture numbers in
flux calibration?
(sensiti= sens) Image root name for
sensitivity spectra
(fnu = no) Create spectra having units of
FNU?
airmass = 1.4 Airmass
exptime = 1800 Exposure time (seconds)
(mode = ql)
BD+75325C.fits:
Extinction correction applied
Flux calibration applied

42. Standard calibrated in flux

43. Flux calibration of object
PACKAGE = onedspec
TASK = calibrate
input = NGC4151.fits Input spectra to calibrate
output = NGC4151C.fits Output calibrated spectra
(extinct= yes) Apply extinction correction?
(flux = yes) Apply flux calibration?
(extinct= onedstds$kpnoextinct.dat) Extinction file
(observa= oagh) Observatory of observation
(ignorea= no) Ignore aperture numbers in
flux calibration?
(sensiti= sens) Image root name for
sensitivity spectra
(fnu = no) Create spectra having units of
FNU?
airmass = 1.1 Airmass
exptime = 1800 Exposure time (seconds)
(mode = ql)
NGC4151C.fits:
Extinction correction applied
Flux calibration applied

44. Object calibrated in flux