What does eis_prep do?#
The eis_prep routine in Solarsoft takes the EIS level-0 FITS files and produces as output a level-1 FITS file. In addition to converting the measured CCD signal into calibrated intensity units, a key part of EIS PREP is to flag bad data points. These can arise through pixel saturation, cosmic ray hits, or simply defective pixels on the CCD. The bad points are referred to as missing pixels. The central outputs of EIS PREP are two level-1 FITS files, one containing calibrated intensities at each pixel, and the other containing error bars on these intensities. Note that the missing pixels are assigned a value of -100 in the error file, not the intensity file. The bad points in the intensity file are replaced with the median of the neighbouring pixels.
The sequential steps performed by eis_prep are as follows.
Step 1: flagging saturated data#
The first step of EIS PREP is to flag any saturated data. The EIS CCDs have a 14 bit dynamic range and so saturation occurs at 16,383 data numbers (DN). All such pixels are flagged as missing as described above.
Step 2: dark current and pedestal subtraction#
In the raw data, the spectra are found to sit on a background of around 500 DN that arises principally from the CCD bias, and secondly from the CCD dark current. It is not possible to estimate the CCD bias level directly for EIS data, so the bias and dark current levels are estimated directly from the science data as follows. For each 3D data window 2 % of the detector pixels are isolated that have the lowest DN values. The median DN value of these 2 % pixels is then set to be the background level and it is subtracted from the DN values of each pixel.
For full CCD spectra, a different approach is used. Sections of the CCD have been identified where there are no (or very weak) emission lines and so it can be assumed that the background here represents a measure of the CCD background. The regions are then averaged to yield the background level which is subtracted from the spectra.
It is to be noted that both of these methods will yield some pixels with negative DN values. For window data it will only be 1 % of pixels because of the method used, but for full CCD spectra it can be up to 50 % of pixels if the raster contains very weak emission (e.g., coronal holes or off-limb spectra). The default mode for eis_prep sets pixels with zero or negative DN values to be missing data. This is because it is not possible to assign a photon noise error to the data points. (Note that negative DN values are expected since, if there are zero solar counts, then the uncertainty in the CCD counts will be 0 +/- read noise.)
By setting the /RETAIN keyword in eis_prep, pixels with zero or negative DN values will not be flagged as missing. The errors for the pixels will be set to the dark current error estimate (see Step 6).
Step 3: cosmic rays removal#
Anomalously bright pixels are found on the EIS CCD images that arise from 'hot pixels', 'warm pixels' and cosmic rays. The cosmic ray removal is performed by EIS DESPIKE, a wrapper routine that calls NEW SPIKE, a routine developed for removing cosmic rays from SOHO/Coronal Diagnostic Spectrometer (CDS) data-sets (Thompson et al., 1998; Pike & Harrison, 2000). For CDS data processing it was typical for not only the identified CCD pixels to be flagged, but also the nearest-neighbour pixels on the CCD. This is because there is often residual signal from the cosmic ray next to the brightest pixels. EIS sees significantly less cosmic rays than CDS apart from during the approximately 5 minute passes through the South Atlantic Anomaly. As the most useful function of EIS DESPIKE was actually to flag warm pixels, and since warm pixels are only single pixel events, then the nearest-neighbour option is usually switched off for EIS. It is to be noted that the NEW SPIKE routine was designed to be cautious when removing cosmic rays from line profiles, thus possibly artificially enhancing the emission line intensities at these locations.
Step 4: flagging hot and warm pixels#
Both hot pixels and warm pixels are single pixels
that have anomalously high DN values. A hot pixel is defined to be one
that yields 25,000 electrons pixel-1 s-1 at
room temperature (a specification from the CCD manufacturer).
Pixels that fall below this threshold but are still
clearly identified as being anomalous when inspecting the
data are referred to as 'warm' pixels. Separate maps of the locations
of hot and warm pixels are generated by the EIS team every 2-4 weeks
following inspection of 100 s dark exposures and they are
stored in Solarsoft. The pixel maps that are closest in
time to the science observation are used by EIS PREP to
mark the hot and warm pixels as missing data.
Please also check the post Top and bottom of hot/warm pixels maps for more details.
Step 5: flagging dusty pixels#
The next step for EIS PREP is to flag the pixels affected by dust on the CCD. Several small pieces of dust accumulated on the CCD before launch and are found to completely block the solar signal on the CCD at their locations. They are fixed in position and cover less than 0.1 % of the CCD, however two of the pieces do affect the strong lines Fe XI 188.23, 188.30 and Fe XII 193.51 such that the lines can not be used over 15-30" spatial ranges in solar-Y.
Step 6: radiometric calibration#
The final step of EIS PREP is to convert DN values into intensities in units erg cm-2 s-1 sr-1 A-1. The errors on the intensities are computed assuming photon statistics together with an error estimate for the dark current. This varies from 2.24 to 2.37 DN for the four CCD quadrants.