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NIRI Data Primer
This page describes NIRI data and its reduction:
Raw data and nprepare
Raw NIRI images are written as multi-extension FITS (MEF) files with a single unnamed extension  containing the image data. Most of the information is contained in the primary header unit (PHU, extension ). Additional important information is added to the PHU by the IRAF task NPREPARE, which is part of the current release of the Gemini IRAF package.
Raw files stored by the Data Handling System (DHS) are written with file names of the form N20080101S0001.fits. The date is the UT date at the beginning of the night. Because the DHS is writing data from multiple instruments, including the wavefront sensors, the NIRI file number sequence is frequently interrupted. Missing file numbers do not necessarily indicate missing NIRI data.
NIRI writes images taken as coadds as a summed, not averaged, image. This means that if one takes 10 coadds of 1 sec each, the final image will have a flux level in ADU equivalent to 10 sec. The task NPREPARE leaves the pixel values as written by NIRI but modifies the header keyword EXPTIME to be the total exposure (the original exposure time multiplied by the number of coadds). NPREPARE adds a keyword COADDEXP that contains the original exposure time for each individual frame. While this behavior may be confusing to some, it is consistent with one ADU in the output image representing a fixed number of detected electrons.
The NIRI array controller averages the data based on the number of digital averages or multiple non-destructive read pairs, so no modification is necessary for different LNRS or NDAVGS values. The flux value will correspond to the exposure time, and the noise will vary as a function of the number of reads.
NPREPARE can help you better understand the raw data by adding a few header keywords. These include GAIN, RDNOISE, SATURATI, NONLINEA, and BIAS which give estimates of the gain (e-/ADU), read noise (e-), saturation level (ADU), the level at which the data start to be non-linear (ADU), and the array bias voltage. These important header keywords are used by other scripts in the NIRI package. NPREPARE refers to a data file named nprepare.dat that contains vital information for adding these header keywords. The user must make sure that the version of NPREPARE and nprepare.dat is appropriate for the data being reduced. nprepare.dat is included with the current release of the NIRI package. nprepare.dat will be modified from time to time to reflect updates in the array parameters or instrument configuration.
Note that the slit centerings are slightly different than before, and we have distributed a modified version of nsappwave.dat to account for a small central wavelength shift.
NPREPARE can also add variance and data quality planes, as described in the help pages for NPREPARE.
Raw NIRI images are dominated by the landscape of the pixel sensitivity variations. You will notice a number of common features:
- small-scale curved "stripes" running vertically. These result from the manufacture of the array and flatten very nicely.
- a circular pattern of ripples resembling a thumbprint in the upper left quadrant. This will also flatten out.
- three small regions of bad pixels, about 10 pixels across, two of which have a partially bad column below them. These are left over from the procedure that excised "photon-emitting defects" from the array, and are totally dead. Dither patterns should be large enough to guarantee that these pixels can be corrected.
- a few hundred hot pixels, mostly in the upper left corner and in a clump near the bottom center
- a prominent crack in the array substrate, seen as a line of bad pixels in the lower right-hand corner
- an overall large-scale bright region in the center of the array with darker regions top and bottom
- offsets in overall sensitivity at the quadrant boundaries
In addition, the array has a frame that can be seen along the top and right edges of the frame, with rounded corners.