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Hubble Space Telescope
STAN - Sept 2009

| STScI Analysis Newsletter (STAN)
| Cosmic Origins Spectrograph (COS)
| September 2009


1. Retrieving COS SMOV and ERO Data

2. CALCOS and the STScI Archive Pipeline

3. CALCOS Reference Files

4. Caveats when Analyzing COS Data


1. Retrieving COS SMOV and ERO Data

All COS Early-Release Observations (ERO) and Servicing Mission
Observatory Verification (SMOV) calibration data are now available
to the community. GO and GTO observations are expected to begin
in mid September. COS is a new instrument, and its calibration files
and software remain in a state of flux. To most easily retrieve
and analyze COS data, we recommend the following:

ERO Data

All ERO data have been calibrated by the COS Instrument
Development Team (IDT) and are available from this web site:

Be sure to check the README file, which gives information about how
the data were calibrated.


All COS calibration data obtained during SMOV are available from
the MAST archive. (Of course, GO and GTO data may be retrieved
only by their respective PIs.) Beware that the version of CALCOS
currently installed in the STScI Archive Pipeline uses pre-flight
software and calibration reference files (see below). If you would
like to reduce COS data on your own, we suggest that you retrieve
the README file from the above web site and run CALCOS using the
IDT recommendations, including revised reference files.

2. CALCOS and the STScI Archive Pipeline

The STScI Archive Pipeline currently employs pre-flight versions
of both CALCOS (2.8c) and its associated calibration reference
files. The resulting calibrated spectra are not suitable for
scientific analysis. In particular, the extraction boxes used to
construct _x1d spectral files may not include all of the flux for
a particular target.

During the period of calibration and testing since SM4, the COS
team has developed new software and reference files that greatly
improve the quality of the extracted spectra.  Version 2.11b of
CALCOS, together with revised reference files, will be installed
in the Archive Pipeline on or about 14 September 2009.  Once the
new software is in place, it will be used for all COS data requests.
We recommended that you request (or re-request) your data from MAST
after the new software is installed. Users who would like to use a
test version of CALCOS 2.11b before installation in the Archive
pipeline are encouraged to contact the help desk.

Check the COS web site or the COS Pipeline Release Notes 
website (
for an announcement on the release of the new software in the pipeline.

Over the next few months, the COS team will continue to improve the
calibration software and reference files. Users who wish to be
notified when new reference files become available can join the
mailing list (Register by sending an
e-mail to with "subscribe cos_reffiles_upd" in
the body of the message.) Major releases of CALCOS will be advertised
via COS STANs and the COS Pipeline Release Notes webpages

Version 2.11b of CALCOS will be included in the next release of
STSDAS, currently scheduled for early November.

3. CALCOS Reference Files

The following new reference files will be delivered with CALCOS
2.11b in mid-September or immediately afterwards:

- NUV and FUV 1dx files, which define new extraction regions for
each spectral stripe.

- NUV and FUV wavelength dispersion and lamp template files.

- NUV and FUV sensitivity files. The sensitivities are updated with
on-orbit estimates for the PSA only. The G230L 3360A NUVB 2nd-order
contamination region will be set so that the resultant fluxes are
zero. Users who wish to examine that part of the spectrum must
work with net counts. The FUV sensitivity assumes no screening of
pulse heights (i.e., the valid range is 0-31, as in the current PHA

- NUV flat field with an updated correction of unity in the wavecal

4. Caveats when Analyzing COS Data
FUV Pulse-Height Thresholds

FUV data taken in TIME-TAG mode include a pulse-height value for
each photon event. Eventually, pulse-height thresholds will be
applied to improve the quality of the data. At present, however,
all pulse heights (0-31) are included in the data extraction. This
may result in a higher (but still very low) detector background.
It may also result in the appearance of several low-gain detector
features on segment B.

See Section 3.4.4 of the COS Data Handbook for more information on
how to use pulse-height filtering in CALCOS, but be aware that
adjusting pulse-height thresholds may cause other complications.
Since all of the current calcos reference files have been generated
using the full range of pulse heights, they may not be appropriate
if you choose to apply a different set of thresholds. In particular,
the sensitivity, background, and flat field are all dependent on
the pulse-height thresholds chosen.

Change in FUV Detector Gain

Early FUV spectra showed a distinctive pair of emission and absorption
features, dubbed the "divot and clod." The divot is a deficit of
counts located ~ 4000-5000 pixels from the blue edge of the spectrum
and the clod is a corresponding excess of counts located ~ 1000
pixels blueward of the divot. It turns out that the X coordinates
of high-gain photon events falling on a particular region of the
detector were being systematically mis-calculated, resulting in the
counts' being shifted from one region of the detector to another.
Lowering the detector gain eliminated these features.

The gain was lowered on 12 August 2009. FUV spectra obtained
before that date may show spurious features.

FUV Flat Field

Beware of fixed-pattern noise on the FUV detector. COS FUV spectra
will not be properly flat fielded for some time (no on-orbit flat
exists yet), so observers should be cautious not to over-interpret
features in the data. Data obtained at multiple FP-POS offsets are
less susceptible, but even for those spectra the fixed-pattern noise
will be present, albeit at a reduced level. A similar warning
applies to areas with QE grid shadows, but in those areas the
data-quality flag will indicate the presence of a shadow.

Change in Instrument Focus

As part of the initial COS alignment and focus procedure, the NUV
channel focus position was changed a number of times during SMOV.
These changes were followed by an OTA secondary mirror adjustment
on 20 July 2009. All NUV-channel data taken since that date can be
considered in focus.

Two FUV focus adjustments have been made since launch. The first,
made on 26 July 2009, moved the M gratings slightly further from
best focus than their initial launch positions. The second adjustment,
on 28 August 2009, brought all the FUV gratings to their current
best-focus positions.

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