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!!! What does eis_prep do?

The EIS data presented here were all calibrated from the
level-0 FITS files using the EIS PREP routine available in
the Solarsoft1 IDL distribution. 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. In this work all such pixels
were marked as 'missing' data and not included in the
data analysis. 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. The steps performed by the current version of
EIS PREP at the time of this analysis are described below
in detail.

!! 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 satura-
tion 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.

!! Step 3: flagging hot pixels

Anomalously bright pixels are found on the EIS CCD
images that arise from 'hot pixels', 'warm pixels' and cosmic
rays. Both hot pixels and warm pixels are single pixels
that have anomalously high DN values. A hot pixel is de-
fined 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. Maps of the locations
of hot 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 hot pixel map that is closest in
time to the science observation is used by EIS PREP to
mark the hot pixels as missing data.

!! Step 4: flagging dust pixels

Before removing warm pixels and cosmic rays, 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 5: flagging warm pixels and cosmic rays

At the time of performing the present analysis,
EIS PREP did not specifically remove warm pixels, but
many of these were removed naturally by the cosmic ray
removal routine, EIS DESPIKE. This latter is 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 ≈5 minute
passes through the South Atlantic Anomaly, and the most
useful function of EIS DESPIKE is actually to flag warm
pixels. Since warm pixels are only single pixel events, then
the nearest-neighbour option is 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
many weak warm pixels found within spectral lines are not
removed, artificially enhancing the emission line intensities
at these locations. For the 2007 May data-sets analysed in
the present work only around 2 % of the CCD pixels are
warm pixels and so this is not a significant problem.

!! 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 of the dark current of 2.5 DN.