NAME

nicreduce -- reduce a set of multiaccum images

USAGE

nicreduce inputimages finalimage

PARAMETERS

inputimages = ""

Raw input images

finalimage = ""

Output combined image

(darkfile = "niccal$skydark.fits")

Dark frame (.fits). This can be a dark file taken directly from the archive or one created by nicskydark.

(flatfile = "niccal$flath.fits")

A flat-field file, typically taken directly from the archive, though some choose to make their own.

(maskplfile = "niccal$badmask_2_mag.pl")

Magnified bad-pixel mask frame (*.pl) used when combining images.

(mask2file = "niccal$badmask_2.fits")

Unmagnified badpixel mask used by nicfixpix (*.fits)

(tempname = "temp")

All the intermediate results will have this filename prefix

(dotidy = no)

Delete intermediate image files?

(dodark = yes)

Subtract dark frame? This step is mandatory.

(doff= yes)

Find pixel photon-rates using fullfitbam? This step is mandatory.

(dobfix = yes)

Correct bias error estimate (pedestal effect)? Mandatory if dofast=no.

(donbias = yes)

Correct bias levels in individual multiaccum readouts using nicbias (pedestal effect). Mandatory if dofast=no.

(doff= yes)

Find pixel photon-rates using fullfitbam again? (pedestal effect). This iteration uses the results of nicbias. Mandatory if dofast=no.

(doflat = yes)

Do flat-field correction? Mandatory.

(domedian = yes)

Do median filtering to remove striping? This optional step median subtracts the median of each row from that row, and then likewise for columns. This improves the flatness of the background. Not recommended if you have large objects in your frames. Optional.

(domagnif = yes)

Magnify images times 2? Mandatory.

(setmask = yes)

Add spots to mask file? This step lets you interactively mask out bad pixels. Must be done once.

(domask = yes)

Construct final mask? This step takes the list of mask spots and makes the actual maskfiles. Mandatory.

(setshift = yes)

Set image shifts with imexam? Here you mark one object on each of the frames. Must be done once.

(doshift = yes)

Make shifted data? This step shifts the images by integer pixel amounts. Mandatory.

(setxreg = yes)

Set cross-correlation region and weight noise box? The final registration of the images is done by cross-correlating a portion of the image. Here you set that rectangular region, typically surrounding bright objects in the image. Additionally you can specify a blank part of the image to get a measurement of the noise. If you specify a noise region, the images will be weighted based on the noise. This is recommended if you are interested in detecting faint objects, but not if you want the best bright point source images. Must be done once.

(doxreg = yes)

Perform the cross correlation. Mandatory.

(docomb = yes)

Perform the final combination of the images. Mandatory.

(interp = "spline3")

Interpolation type used when magnifying images.

(ff1sigma = 3.)

Cosmic ray rejection threshold in sigma for fullfitbam1.

(ff2sigma = 5.)

Cosmic ray rejection threshold in sigma for fullfitbam2.

(readnoise = 10.)

Readnoise for fullfitbam. This is used for setting the cosmic ray rejection thresholds.

(z= 0., z2 = 2.)

Brightness limits used when displaying images.

(spotsize = 4.)

Default spot radius in pixels when flagging bad pixels.

(dofast = no)

Skips the pedestal correction steps, i.e. biasfix, nicbias, and the 2nd fullfitbam. If your data was taken before 21 August 1997, and you have large areas of blank sky in your frames, you will want dofast=no. A flight software change on 21 August 97 reduced the amplitude of the pedestal effect, so the pedestal correction might not be necessary. If you have large extended objects in your frames, the pedestal correction algorithm will fail, so you should choose dofast=yes.

DESCRIPTION

Nicreduce is the primary task of the nicred package. It performs all of the steps necessary to take a set of raw, dithered multiaccum images and turn them into a final combined image. Some nicred users may choose to use nicreduce for reducing the individual images of a dithered sequence and use their own software for combining the images.

Many of the parameters control whether a given step of the pipeline is executed. Except where noted, all the steps must be executed to reach the final combined image. If you want to repeat part of the reduction process with a different calibration file (say you decide to change to a different flat file), you can specify "no" for all the steps preceding the flat correction. Certain steps (e.g. setting the bad pixel mask) do not need to be repeated on subsequent reductions. These parameters have names of the form "setXXXXX".

The parameters are listed in the same order in which the processing steps are performed, so a look at the parameter list gives a good idea of what happens. Following is a summary of the processing steps, the sub-tasks that perform them, and the names of the files produced by each step.

Summary of the nicreduce pipeline:

Step                                    Primary task    Resulting file
-------------                           ------------    --------------
Subtract dark                           darksub         _sub

Non-linearity correction
  +fitting slopes+CR rejection          fullfitbam      _sub_s

Correct pedestal effect                 biasfix         _sub_scorr
  in _sub_s file

Use _sub_scorr to correct pedestal      nicbias         _bias
effect in each multiaccum 
readout in _sub file.

Redo fullfitbam with pedestal           fullfitbam      _bias_s
  effect corrected to improve
  CR rejection.

Do flatfield correction                 nicflatten      _flt

Interpolate over known bad pixels       nicfixpix       _fix
  to avoid ringing in magnification

Magnify image                           magnify         _mag

Shift each images by integer pixel amt  imcombine       _shift
  to a common coordinate system.
  This also fills in known bad pixels
  with corresponding pixels from 
  other images.

Do fractional pixel shifting            xregister       _xreg

Combine images into final image         imcombine       final.fits

EXAMPLES

TIME REQUIREMENTS

BUGS

SEE ALSO

darksub, fullfitbam, biasfix, nicbias