This section provides a more detailed description of the calibration processing steps and algorithms applied by calcos, including the switches, reference file inputs, science file inputs, and the output products. Setting the calibration switch to PERFORM enables the execution of the corresponding pipeline calibration task.
Future modifications and updates to calcos will be announced in STScI Analysis Newsletters (STANs) and documented at the Web site:
The calibration steps for FUV time-tag data in the pipeline processing flow are described next. When present, each sub-section header begins with the switch that activates the module.
When the pipeline is initiated, it first opens an association file to determine which files should be processed together. For time-tag data, it also creates a
_corrtag file before anything else is done. The initial contents of this file are simply a copy of the
_rawtag file, except that new columns have been added to the
_corrtag file. It is then updated throughout the running of the pipeline.
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Header keywords updated: TBRST_A, TBRST_B (time affected by bursts in segments A and B), NBRST_A, NBRST_B (number of events flagged as bursts in segments A and B), EXPTIME,EXPTIMEA, EXPTIMEB.
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Updates _corrtag file for time-tag data.
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Screening for bursts is then done in two steps. The first step identifies large count rate bursts by calculating the median of the counts in the background regions, defined in the XTRACTAB table, over certain time intervals (DELTA_T or DELTA_T_HIGH for high overall count rate data). Events with count rates larger than MEDIAN_N times the median are flagged as large bursts.
All events that have been identified as bursts are flagged in the data quality column (DQ in the corrtag table) with data quality bit = 64. In addition calcos updates the following header keywords to take into account time and events lost to burst screening:
TBRST_A and
TBRST_B (time lost to bursts in segments A and B);
NBRST_A,
NBRST_B (number of events lost to bursts in segments A and B),
EXPTIME,
EXPTIMEA and
EXPTIMEB. Keywords
EXPTIMEA and
EXPTIMEB are the sums of the values in the input
_x1d files.
For
_x1dsum files the value of the
EXPTIME keyword is that corresponding to the larger value of
EXPTIMEA and
EXPTIMEB. The
EXPTIME for each segment is contained in a table column in the first extension of the
x1dsum file.
When running calcos a user can specify that the information about bursts be saved into a file. This output file contains four columns, each with one row per time interval (DELTA_T or DELTA_T_HIGH). Column 1 contains the time (seconds) at the middle of the time interval, column 2 contains the background counts for that time interval, column 3 contains a 1 for time intervals with large bursts and is 0 elsewhere, and column 4 contains a 1 for time intervals with small bursts and is 0 elsewhere.
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Header keywords updated: EXPTIME, Exptimea and exptimeb (for FUV data) , NBADT, or Nbadt_A and nbaDt_B (number of events flagged for NUV or FUVA and B, respectively) and TBadt or Tbadt_a and tbadt_b (time lost to bad events in NUV or FUVA and FUVB, respectively).
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Updates corrtag file for TIME-TAG data.
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The BADTTAB table lists zero or more intervals of time which will be excluded from the final spectrum for various reasons. This file is currently empty, but it could be populated by the COS team if events occur on orbit which they feel render data collected during specific time intervals not scientifically useful. It is also available for the convenience of the user. For example, the user may wish to eliminate observations obtained in the daytime portion of the orbit to minimize airglow contamination, or they may want to isolate a certain portion of an exposure. In these cases, modifying
BADTTAB may be the most convenient means to accomplish this. Events in the
rawtag file having times within any bad time interval in
BADTTAB are flagged in the DQ column of the
corrtag table with data quality = 2048. The exposure time is updated to reflect the sum of the good time intervals. This step applies only to
TIME-TAG data.
This module works differently for FUV TIME-TAG and
ACCUM data. It is not used for NUV data.
For FUV TIME-TAG data, each photon event includes a 5 bit (0 - 31) Pulse Height Amplitude (PHA). The value of the pulse height is a measure of the charge produced by the microchannel plate stack, and can be used to identify events which are likely due to cosmic rays or detector background. The
PHATAB reference file lists lower and upper pulse height thresholds expected for valid photon events for each detector segment. The PHACORR module compares each event’s pulse height to these thresholds, and if the pulse height is below the Lower Level Threshold (LLT) or above the Upper Level Threshold (ULT), the event is flagged in the DQ column of the corrtag table with a data quality bit of 512. The upper and lower thresholds are also written to the
PHALOWRA (
PHALOWRB) and
PHAUPPRA (
PHALOWRB) keywords in the output data files for segment A (B), while the number of events flagged is written to the
NPHA_A and
NPHA_B keywords.
With continuing exposure to photons, pulses from the MCPs have smaller amplitudes, a phenomenon known as “gain sag”. As this occurs, the thresholds in the PHATAB will be updated to maximize the number of real events counted. Which
PHATAB is used for data collected at a particular time will be handled by the USEAFTER date keyword in the calibration file header.
The PHAFILE reference file is an alternative to the
PHATAB, and allows pulse-height limits to be specified on a per-pixel basis rather than a per-segment basis. The PHAFILE has a primary header and four data extensions, consisting of the FUVA PHA lower limits, FUVA PHA upper limits, FUVB PHA lower limits, and FUVB PHA upper limits respectively. The use of a
PHAFILE instead of a
PHATAB (if both are specified and
PHACORR = ‘PERFORM’, the
PHAFILE will take precedence) allows a number of adjustments, including (for example) the use of a lower PHA threshold in gain-sagged regions, thus allowing more background events to be filtered out while still continuing to detect photon events in gain-sagged regions. As of August 2012, no
PHAFILE has been produced by the COS team, but in the future one or more such files may be produced for use with FUV TIME-TAG data. Note that the use of a
PHAFILE requires
calcos 2.14 or later.
For FUV ACCUM data, pulse height information is not available for individual events. However, a 7 bit (0 - 127) Pulse Height Distribution (PHD) array, containing a histogram of the number of occurrences of each pulse height value over the entire detector segment, is created onboard for each exposure. PHACORR compares the data in this
pha file to the values in the
PHATAB file. Warnings are issued if the peak of the distribution (modal gain) does not fall between the scaled values of LLT and ULT; or if the average of the distribution (mean gain) does not fall between the MIN_PEAK and MAX_PEAK values in
PHATAB. The
PHALOWRA and
PHAUPPRA, or
PHALOWRB and
PHAUPPRB keywords are also populated in the output files with the LLT and ULT values from the
PHATAB.
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Updates corrtag file for TIME-TAG data.
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The WALKTAB table contains parameters for the polynomial used to correct Y-walk caused by gain sag. Y-walk causes events on the XDL detector to appear to have originated lower on the detector than their actual location. Currently, the Y-walk correction involves an equation of the form:
dx = x1 * (PHA - x
0) + x
2 * (PHA - x
0)
2
dy = y1 * (PHA - y
0) + y
2 * (PHA - y
0)
2
where xn and y
n are coefficients which are, in turn, calculated from the event X and Y location, and a variable-length series of other coefficients stored in the reference file. For example, for the case with three X coefficients and three Y coefficients, the x
n coefficients are calculated as follows:
x0 = a
000 + a
100*x + a
010*y + a
200*x
2 + a
110*x*y + a
020*y
2
x1 = a
001 + a
101*x + a
011*y + a
201*x
2 + a
111*x*y + a
021*y
2
x2 = a
002 + a
102*x + a
012*y + a
202*x
2 + a
112*x*y + a
022*y
2
where amno is the item at location m,n,o in the coefficient matrix.
The WALKTAB table contains the following items for each FUV segment:
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X0: subtracted from x before evaluating coefficient polynomials. Set to 8192.
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Y0: as X 0, but for y. Set to 512.
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Updates corrtag file for TIME-TAG data and a virtual corrtag file for ACCUM data.
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For FUV TIME-TAG data RANDCORR adds random numbers to the raw coordinates of each event, i.e.:
Where Δx and Δy are uniformly distributed, pseudo-random numbers in the interval -0.5 < Δx, Δy
≤ +0.5.
For FUV ACCUM data, a pseudo
TIME-TAG list of x and y values is created with an entry for each recorded count. Next, a unique Δx and Δy are added to each entry.
If the RANDSEED keyword in the raw data file is set to its default value of -1, the system clock is used to create a seed for the random number generator. This seed value is then written to the
RANDSEED keyword in the output files. Alternatively, an integer seed (other than -1) in the range -2147483648 to +2147483647 can be specified by modifying the
RANDSEED keyword in the raw data file. Doing so will ensure that identical results will be obtained on multiple runs.
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Updates corrtag file for TIME-TAG data and flt file for ACCUM.
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To measure the magnitude of this effect, electronic pulses (Figure 1.6) are recorded at two reference points in the image (“electronic stims”) at specified time intervals throughout each observation. TEMPCORR first determines the locations and separations of the recorded stim positions and then compares them to their expected locations in a standard reference frame (as defined in columns SX1, SY1, SX2, and SY2 of the
BRFTAB file). The differences between the observed and reference stim positions are used to construct a linear transformation between the observed and reference frame locations for each event (or pseudo-event in the case of
ACCUM data). TEMPCORR then applies this transformation to the observed events, placing them in the standard reference frame.
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Updates corrtag file for time-tag data and flt file for accum.
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GEOFILE was created by using a ray-trace analysis of the COS FUV optical system. A set of wavelength calibration exposures was taken while stepping the aperture mechanism in the cross-dispersion direction to create an image of dispersed line profiles. The ray trace and measured line positions were compared to determine the shift between the measured (uncorrected) and predicted (corrected) line positions (see
Figure 3.6).
This module corrects for the effect that the orbital motion of HST has on the arrival location of a photon in the dispersion direction.
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Updates corrtag file for TIME-TAG data
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During a given exposure the photons arriving on the FUV and NUV detectors are Doppler shifted due to the orbital motion of HST. The orbital velocity of
HST is 7.5 km/s, so spectral lines in objects located close to the orbital plane of
HST can be broadened up to 15 km/s, which can be more than a resolution element.
DOPPCORR is the calcos routine which corrects for the orbital motion of
HST. It operates differently on TIME-TAG and ACCUM files:
For ACCUM files Doppler correction is applied onboard and is not performed by calcos. This means, however, that the pixel coordinates of a spectral feature can differ from where the photon actually hit the detector - a factor which affects the data quality initialization and flat-field correction. Therefore for ACCUM images DOPPCORR shifts the positions of pixels in the bad pixel table to determine the maximum bounds that could be affected. It is also used to convolve the flat-field image by an amount corresponding to the Doppler shift which was computed on orbit. The information for these calculations are contained in the following header keywords:
DOPPCORR assumes that the Doppler shifts vary sinusoidally with time according to the orbital movement of HST. The following keywords are used to perform the correction and are obtained from the first extension (EVENTS) in the _rawtag:
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EXPSTART - start time of the exposure (MJD)
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DOPPZERO - the time (MJD) when the Doppler shift was zero and increasing (i.e., when HST was closest to the target)
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DOPPMAG - The number of pixels corresponding to the Doppler shift (used only for shifting the data quality flag arrays and flat fields)
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ORBITPER - the orbital period of HST in seconds
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The data columns used in the correction are TIME (elapsed seconds since EXPSTART) and RAWX (position of photon along dispersion direction). The Doppler correction to be applied is then
SHIFT = -(DOPPMAGV/(c*d))*λ(XCORR)*sin(2*pi*t/ORBITPER)
where c is the speed of light (km/s), d is the dispersion of the grating used in the observation (Å?/pixel),
λ(XCORR) is the wavelength at the XCORR position being corrected (obtained from the dispersion solution for that grating and aperture in the
DISPTAB reference file) and t is defined as
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Updates corrtag file for TIME-TAG data and flt for ACCUM.
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The efficiency of the detector’s photon counting is calculated as the ratio of the true count rate and the observed count rate. This value is referred to as the deadtime. The deadtime for each detector is modeled and the reference file DEADTAB contains a lookup table of the correction for various count rates.
Figure 3.7 shows how the measured count rates deviate from the actual count rates as a function of the actual count rate for the NUV detector, and segment B of the FUV detector (the FUV segment A curve is nearly identical).
For TIME-TAG data the deadtime correction is computed every 10 seconds. The observed count rate is the number of events within that time interval, and the deadtime factor is determined by interpolation within the values in
DEADTAB. The values in the EPSILON column in the _corrtag file for events within that time interval will then be divided by the deadtime factor. For
ACCUM data the observed average count rate is taken from a header keyword for the digital event counter. The deadtime factor is then found by interpolation within the
DEADTAB, the same as for
TIME-TAG data, and the science and error arrays will be divided by the deadtime factor.
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Updates corrtag file for TIME-TAG data and flt for ACCUM.
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The FLATCORR step corrects for high frequency, pixel-to-pixel sensitivity differences across the detector. It uses a flat-field image located in the file specified by the FLATFILE header keyword.
Figure 3.8 shows an NUV flat. For spectroscopic data, any wavelength dependence of the detector response or remaining low frequency spatial variations are removed by the flux calibration step (FLUXCORR,
Section 3.4.17). Flat fielding is performed in geometrically corrected space, and because the pixel-to-pixel variations should be largely wavelength independent, only one reference image is used per detector or detector segment (NUV, FUVA, and FUVB). The flat-field correction is applied differently for
TIME-TAG and
ACCUM mode data for both spectroscopic and imaging modes.
For spectroscopic TIME-TAG exposures, each photon in the events list is individually corrected. In the
_corrtag file, the photon weight in the EPSILON column is divided by the flat-field value at the event’s detector location rounded to the nearest pixel (XCORR, YCORR for FUV; RAWX, RAWY for NUV).
For spectroscopic ACCUM mode data, photons are summed into an image onboard by the COS electronics. To compensate for the motion of
HST during the observation, spectroscopic exposures are normally taken with Doppler compensation performed during the accumulation (science header keyword
DOPPONT=TRUE). During Doppler compensation, photon locations are shifted as the data are received, and the underlying flat field at each imaged pixel is an average of the original pixel position sensitivities. FLATCORR replicates this averaging for the flat-field correction using the same control parameters as those onboard (
DOPPMAGT,
DOPZEROT,
ORBTPERT) if
DOPPCORR=PERFORM (
Section 3.4.9). The convolved flat-field image is divided into the
rawaccum data, which is then divided by the exposure time to create the
flt image file.
NUV images using the mirrors are not Doppler corrected. In this case, DOPPCORR=OMIT, and the input data are divided by the flat field without convolution.
For both the flt and
counts files, error arrays are created based on counting statistics (
Section 2.7), but they are not used in further processing.
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Updates corrtag file for TIME-TAG data.
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Creates lampflash file for TAGFLASH data.
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The wavecal step of calcos determines the shift of the 2-D image on the detector along each axis resulting from thermal motions and drifts within an OSM encoder position. This step applies only to spectroscopic data,
TIME-TAG and
ACCUM, for both the FUV and NUV detectors. The shifts are determined from one or more contemporaneous wavelength calibration observations of a spectral line lamp (wavecal) which must be obtained without moving the OSM between the science and wavecal exposures.
There are two types of wavecals. For ACCUM data the spectrum of the calibration lamp is contained in an exposure that is separate from that of the science (AUTO or GO wavecals). For
TIME-TAG data the wavecals can also be separate exposures, but the default when observing with the PSA aperture is
tagflash mode. In the
tagflash mode the line lamp is turned on and off (flashed) one or more times during a single science exposure, producing a wavecal spectrum that is offset in the cross-dispersion direction from the science spectrum (See
Figure 1.7, and
Figure 1.9). The algorithm used to determine the shifts is the same in either case, but the way that the shift is determined at the time of the observation differs. Thus, we begin by describing how the offsets are found.
For each wavecal, the location of the spectrum in the cross-dispersion direction is determined by collapsing the spectrum along the dispersion direction using the extraction slope defined in the XTRACTAB table (SLOPE). The location of the brightest pixel, after boxcar smoothing, is taken as the spectrum location and that location is compared to the nominal position defined in the
XTRACTAB table. The offsets from nominal positions for segments A and B (FUV) or stripes A, B, and C (NUV) are recorded in the
lampflash file (which is created at this stage) in the
SHIFT_XDISP field. The two FUV segments are processed independently. Cross-dispersion shifts are determined for each NUV stripe and then the average is computed and applied to all three stripes. The sign of the
SHIFT_XDISP entry is positive if the spectrum was found at a larger pixel number than the nominal location.
To determine the offsets in the dispersion direction, the wavecal spectrum is collapsed along the cross-dispersion direction and compared to the template wavecal (LAMPTAB) taken with the same grating and central wavelength. For the NUV wavecal spectra for each stripe are determined independently. The positions are determined from a least squares fit to a shifted and scaled version of the template spectrum. The maximum range for shifting the wavecal and template wavecal spectra is defined by the value of
XC_RANGE in the
WCPTAB table.
Calcos takes into account the
FPPOS of the wavecal spectrum by shifting it by
FP_PIXEL_SHIFT (from the column in the
lamptab) before fitting it to the template wavecal. The final shift is stored as
SHIFT_DISP in the lampflash file and the minimum value of chi squared is stored in the
CHI_SQUARE array.
The way the offsets are applied to the spectral data depends on whether the data were obtained with AUTO or GO wavecals or with TAGFLASH wavecals. For AUTO or GO wavecals, the wavecals are obtained at different times than the spectral data and temporal interpolation is done to determine the appropriate shifts. For
TAGFLASH data, the wavecals are interspersed with the spectral data, allowing more precise and, consequently, more intricate corrections to be made. In either case, the result is the
X[Y]FULL entries in the
corrtag file. Because, as we shall see, the corrections can be time dependent, the differences between
X[Y]CORR and
X[Y]FULL can also be time dependent. This step of the calibration amounts to a time dependent translation of the detector coordinate system to a coordinate system relative to the wavecal spectrum, which is more appropriate for wavelength calibration.
For ACCUM science exposures which are bracketed by AUTO or GO wavecal observations, the shifts determined from the bracketing wavecal exposures are interpolated (linearly) to the middle time of the science observation, and the interpolated values are assigned to the
SHIFT1[
A-
C] and
SHIFT2[
A-
C] keywords in the science data header. If there is just one wavecal observation in a dataset, or if there are more than one but they don’t bracket the science observation, the
SHIFT1[
A-
C] and
SHIFT2[
A-
C] keywords are just copied from the nearest wavecal to the science data header.
For non-TAGFLASH TIME-TAG science exposures bracketed by AUTO or GO wavecal observations, the shifts determined from the wavecals are interpolated (linearly) so that each event in the
corrtag file is shifted according to its arrival time. The
SHIFT1[
A-
C] and
SHIFT2[
A-
C] keywords recorded in the science data header are in this case the averages of the values applied. As in the
ACCUM case, if there is only one wavecal observation in a dataset, or if there are more than one but they do not bracket the science observation, the
SHIFT1[
A-
C] and
SHIFT2[
A-
C] keywords are just copied from the nearest wavecal to the science data header.
A tagflash wavecal is a lamp exposure that is taken concurrently with a
TIME-TAG science exposure, and the photon events for both the wavecal lamp and the science target are mixed together in the same events table. In many respects,
TAGFLASH wavecals are handled differently from conventional wavecals.
The nominal start and stop times for each lamp flash are read from keywords in the corrtag table. The actual start and stop times can differ from the nominal times, so
calcos determines the actual times (restricted to being within the nominal start-to-stop intervals) by examining the number of photon events within each 0.2-second interval in the wavecal region defined in the
XTRACTAB table. A histogram of the count rate is constructed. The histogram is expected to have one peak near zero, corresponding to dark counts, and another at high count rate, due to the lamp illumination. The average count rate when the lamp is on is taken to be the count rate for the second peak of the histogram. The lamp turn-on and turn-off times are taken to be the times when the count rate rises above or sinks below half the lamp-on count rate.
Calcos uses the time of the median photon event within a lamp turn-on and turn-off interval as the time of the flash. The keywords
LMP_ONi and
LMP_OFFi (i is the flash number) are updated with the actual turn-on and turn-off times, in seconds, since the beginning of the science exposure. The keywords
LMPDURi and
LMPMEDi are updated with the actual duration and median time of the flash.
As before, the cross dispersion location of each wavecal spectrum is determined by collapsing it along the dispersion direction and comparing it with the template in the XTRACTAB table to produce the
SHIFT_XDISP entries in the
lampflash file. The wavecal spectrum is then collapsed along the cross-dispersion direction to produce a 1-D spectrum that is fit to the template spectrum to obtain the
SHIFT_DISP entries. Typically there will be more than one wavecal flash during a science exposure; so the shifts will be piece-wise linearly interpolated between flashes. The
SHIFT1[
A-
C] and
SHIFT2[
A-
C] values that are recorded in the science data header are the average of the shift values found from the different flashes.
Additional Functions: WAVECORR also corrects the _flt and _counts files which result from both
ACCUM and
TIME-TAG science data for the offsets in the dispersion and cross-dispersion directions. However, since these images are in pixel space they can only be corrected by an integer number of pixels. The
_flt and
_counts images are corrected by the nearest integer to
SHIFT1[
A-
C] and
SHIFT2[
A-
C].
DPIXEL1[A-C] is the average of the difference between
XFULL and the nearest integer to
XFULL, where
XFULL is the column by that name in the
_corrtag table. This is the average binning error in the dispersion direction when the
_flt and
_counts images are created from the
_corrtag table.
DPIXEL1[A-C] is zero for ACCUM data. This shift is used when computing wavelengths during the X1DCORR step.
The DQICORR step maps data quality flags for suspect detector pixels listed in the BPIXTAB table to the science data. The COS data quality flags are discussed in
Section 2.7.2 and are listed in
Table 2.19.
Figure 3.9 shows examples of the types of regions isolated by the DQ flags and the effect that they can have on an extracted spectrum. DQICORR proceeds differently for
TIME-TAG and
ACCUM mode exposures, but the flags in the
flt and
counts images are created similarly in preparation for spectral extraction. Consequently, we describe each mode separately.
TIME-TAG: DQICORR compares the XCORR, YCORR pixel location of each event in the
corrtag file to the rectangular regions flagged in the
BPIXTAB table. The value in the DQ column for that event is then updated with the flags of all the regions (if any) that contain that pixel location.When the
flt and
counts images are generated from the
corrtag file, photons which arrived during bad times or bursts are omitted from the image and ERR array. For FUV data, events whose PHAs were flagged as out of bounds are omitted as well. However, data with spatial DQ flags are retained at this stage. Several of these blemishes are illustrated in
Figure 3.9
The third FITS extension of the flt and
counts files is an array of data quality values generated directly from the
BPIXTAB table. If
DOPPCORR=PERFORM, the
BPIXTAB locations are Doppler-smeared and the flags from all neighboring pixels that contribute to the
flt and
counts image pixels are combined.
ACCUM: For
ACCUM exposures, the
rawaccum image file will already have a third FITS extension of data quality values if any pixel had been flagged when constructing the raw image. The extension will be a null image if all initial data quality flags are zero. This is usually the case for NUV data, but not FUV. For FUV
ACCUM exposures, photons are collected for only part of the detector segment and an initial data quality array is created to mark the pixels outside those subimage boundaries (flag=128, outside active area). When
calcos creates the
flt and
counts images, it first converts the
rawaccum image to a pseudo-time-tag table. In this table, the DQ column is updated with the DQ flags from
BPIXTAB just as for the
TIME-TAG data. In addition, the third extension of the
flt and
counts files contains a Doppler-smeared version of the
BPIXTAB table, but it also includes the initial flag assignments in the
rawaccum DQ extension.
STATFLAG enables the reporting of statistics for COS observations. STATFLAG is enabled by default for all science observations and operates on x1d,
counts, and
flt data products. STATFLAG is intended to provide a very basic statistical characterization of the events and locations on the detectors that are known to be good. The SDQFLAGS header keyword (Serious Data Quality FLAGS), indicates which DQ values (see
Table 2.19 for definitions) should be excluded from the statistical calculations. Numerically, the default value of SDQFLAGS for NUV is 184. For FUV, SDQFLAG varies with grating. For FUV/G130M and G160M the default value is 8376, and 8380 for FUV/G140L.
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NGOODPIX: The number of good pixels or collapsed spectral columns. For the counts and flt images, this is the number of pixels in the spectral extraction or imaging region. For the x1d file, each ’Y’ column in the spectral extraction region of the flt file is combined to produce the one-dimensional spectrum. The DQ of each column is the logical OR of the DQ flags of the individual pixels. Only collapsed spectral columns that pass the DQ conditions indicated by SDQFLAGS are considered good for purposes of calculating statistics.
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A 1-D spectrum and its error array are extracted from the flt and
counts images by summing the counts in the cross-dispersion direction within a band centered on the spectrum. The data are not resampled in the dispersion direction. Wavelengths are assigned by evaluating a polynomial function (dispersion relation) of the pixel coordinates. Background is subtracted (see BACKCORR) to get the net count rate, and the absolute flux is computed from the net count rate (see FLUXCORR).
This section provides the details of the spectral extraction process and the construction of the arrays which populate the x1d files.
Table 3.1 lists these arrays along with others that are used to calculate them. The following discusses how each array is calculated in detail. The summed
_x1dsum[n] files are described in
Section 3.4.19.
Table 3.1 defines the variables used in the 1-D spectral extraction. Variables beginning with a capital letter are saved in the output
x1d file. An ‘“[i]” represents array element i in the dispersion direction.
SEGMENT: A string array listing the segments/stripes, contained in the file.
NELEM: An array listing the number of elements in the extracted arrays.
EXPTIME: An array of the exposure times used for each segment (these can differ for FUV data).
GROSS: The GROSS count rate spectrum is obtained from the
counts file. The extraction is performed over a parallelogram, whose shorter edges are parallel to the image boundaries and longer (slightly sloping) edges are parallel to the spectrum (see,
Figure 3.10). The columns within the parallelogram are summed in the cross-dispersion direction to obtain each element of the GROSS spectrum. Note that in some cases the spectral lines are obviously tilted, i.e., not aligned with the columns, but the sum ignores any such tilt. The location of the parallelogram in the cross-dispersion direction is taken from column
B_SPEC in the
XTRACTAB.
GCOUNTS: This is simply the number of gross counts, or
GROSS times
EXPTIME.
BACKGROUND: Two background regions are sampled on the
counts array to obtain a mean background count rate spectrum. For the FUV data, these are above and below the spectrum, and for the NUV data they are above stripe C and below stripe A (see,
Figure 3.10 and
Figure 3.11). The background regions are extracted in the same way as the spectrum. The values in the two background regions are added, boxcar smoothed in the dispersion direction, and scaled by the sizes of their extraction regions before being subtracted from the science spectrum. Details of the background extractions are given in
Section 3.4.16.
NET: The NET spectrum is the difference between the GROSS spectrum and a properly scaled BACKROUND spectrum multiplied by an array which accounts for flat-field and dead-time effects. This array is eps[i] = e[i]/GROSS[i], where e[i] is an element in an array extracted from the
_flt file in exactly the same way as the GROSS spectrum is extracted from the
counts file. Consequently, this factor corrects the NET spectrum for flat-field and dead-time effects.
DQ: The DQ array in the
x1d file is the bitwise OR of the members of the DQ array, contained in the third FITS extension of the
counts file, for all of the points in the
counts image that contribute to an element of the GROSS spectrum. Consequently, if anything is flagged within the extraction region, it is reflected in the
x1d DQ array.
DQ_WGT: The DQ_WGT array has one point for each extracted point in the spectrum. It is 0 or 1 depending on whether the DQ for a given point is allowed according to the header keyword, SDQFLAGS. The SDQFLAG value depends on the configuration of the instrument. For FUV/G130M and G160M the SDQFLAG default value is 8376. For FUV/G140L the value is 8380, and for all NUV modes, 184. These SDQFLAG values set the DQ_WGTS to 0 for events that are near the edge of the detector, dead spots, hot spots or outside of the subarray (see,
Table 2.19). Otherwise, DQ_WGTS = 1. The DQ_WGTS array is used to construct the
x1dsum file discussed in
Section 3.4.19.
ERROR: The ERROR array is calculated from a combination of variables needed to track the detected counts and the different scale factors which multiply them. The raw ERROR array involves elements from both the
_flt and the
_counts files. It is calculated as follows:
term2[i] = eps[i]2 exptime*(GROSS[i] + BACKGROUND[i]
∗(bkg_norm/bkg_smooth))
The ERROR array contained in the _x1d file differs from this one only in the sense that it has the absolute flux calibration applied (see
Section 3.4.17).
WAVELENGTH: As part of the spectral extraction,
calcos assigns wavelengths to pixels in the extracted spectra using dispersion coefficients from the reference table
DISPTAB. For each grating, central wavelength, and aperture, the
DISPTAB table contains the dispersion solution with respect to the template spectral lamp table that was used in the WAVECORR step. The dispersion solution has the following form:
WAVELENGTH[i] = A0 + A
1 x[i] + A
2 x[i]
2 + A
3 x[i]
3
where WAVELENGTH[i] is the wavelength in Angstroms, x[i] is the pixel coordinate in the dispersion direction, and Ai are the dispersion coefficients. Offsets due to an OSM shift determined from WAVECORR (
Section 3.4.12) are corrected for by applying a linear offset after all other corrections have been made. For all modes, small residual offsets occur because of thermal drifts and drifts in the positioning of the OSM. The precision of the OSM positioning and the impact of small offsets in the spectra are discussed further in
Chapter 4:COS Error Sources
FLUX: The FLUX array in the
x1d file is the NET spectrum corrected by the appropriate, time dependent sensitivity curve. The details of this process are discussed in
Section 3.4.17.
The SP_ KEYWORDS: This set of keywords provides useful information on the location of the spectrum in the cross dispersion direction and the location where the spectrum is extracted. The actual location of the spectrum is found from the
_flt file through a two step process. First, the image of the active area is collapsed along the extraction window to produce a mean cross-dispersion profile. Second, a quadratic is fit to full-width-half-maximum pixels (but minimum of 5) point region centered on the maximum of the profile. The difference between this value and the expected location,
SP_NOM_A[B], is given as
SP_OFF_A[B].
The actual location where the spectrum is extracted is given by SP_LOC_A[B]. For normal pipeline extractions,
SP_LOC_A[B] = SP_NOM_A[B], and
SP_OFF_A[B] is listed for informational purposes only. However, it is possible to override these values and extract a spectrum at the
SP_OFF location or any other by using the stand alone version of
x1dcorr discussed in
Section 5.1.1
where m is the slope of the background (keyword SLOPE), and b is the Y-intercept of the background region (B_BKG1 or B_BKG2). At the i-th pixel along the dispersion direction (X) the background is computed by first summing all of the counts in pixels in the cross-dispersion within +/- (BHEIGHT/2) of the central Y pixel of the background box. All DQ spatially related DQ flags are ignored (note that counts which occur during bad time intervals or which have out of bounds PHAs, never make it to the counts file). Once this is done for all X pixels, the result is averaged over +/- BWIDTH/2 pixels along the dispersion direction. This gives a local average background (with known anomalous pixels such as dead spots or strong hot spots excluded). The background regions below and above the object spectrum are both computed in this way, and then they are summed and divided by 2 to yield an average background rate. This average is then scaled to the number of pixels in the object extraction box by multiplying it by the factor “HEIGHT / BHEIGHT”. The result is the background count rate BK[i] in
Table 3.1, which is written to the BACKGROUND column in the
x1d file. The background-subtracted count rate (corrected for flat field and dead time) is written to the NET column in the
x1d table.
If FLUXCORR=PERFORM, FLUXCORR divides the NET and ERROR columns by the appropriate sensitivity curve read from the
fluxTAB reference table, which converts them to flux units (erg cm
-2 s
-1 Å
-1). The NET divided by the sensitivity is written to the FLUX column of the
x1d file, while the ERROR column is modified in-place.
If TDSCORR=PERFORM, then the module TDSCORR will correct for temporal changes in the instrumental sensitivity relative to the reference time given by
REF_TIME keyword in the FITS header of
TDSTAB.
TDSTAB provides the slopes and intercepts needed to construct a
relative sensitivity curve. The curve for the epoch of the observation is determined by piecewise linear interpolation in time using the slopes and intercepts closest to the time of the observation. The sensitivity may be discontinuous at an endpoint of a time interval. Different piecewise linear functions may be specified for each of the wavelengths listed in the table. This process results in a relative sensitivity at the epoch of the observation, at the wavelengths given in the reference table. Interpolation between these wavelengths to the observed wavelength array is also accomplished by piecewise linear interpolation.
In addition to the Doppler smearing from HST orbital motion, the photons acquired during an observation are also Doppler shifted due to the orbital motion of the Earth around the Sun (V ~ 29.8 km/s). The sign and magnitude of the Doppler shift depend on the time of the observation as well as the coordinates of the target (i.e., the position of the target relative to the orbital plane of the Earth).
The HELCORR module in calcos transforms wavelengths of a spectrum to the heliocentric reference frame. It is applied to the extracted 1D spectrum during the operation of X1DCORR, by utilizing the keyword
V_HELIO, which is the contribution of the Earth’s velocity around the Sun to the radial velocity of the target (increasing distance is positive), in km/s. It is computed by
calcos and written to the science data header of the output
corrtag file before spectral extraction is performed.
λHelio =
λObs [1 - (V
Helio/c)]
where λHelio is the corrected wavelength (Å), c is the speed of light in km/s and
λObs is the wavelength before the Heliocentric correction.
SPECTROSCOPY: Once the processing is complete, an
x1d file is written for each spectroscopic exposure. This file includes spectra from both segments A and B for the FUV detector, and from all three stripes for the NUV detector (see,
Section 2.4.3). In addition, one or more
x1dsum files are created. This is done even if only one spectrum was obtained.
The x1dsum files differ from the
x1d files in one important respect. When an
x1dsum file is created the DQ_WGT array (
Section 3.4.19) is used to determine whether a point is good or bad. When only a single file contributes to the
x1dsum file, if DQ_WGT = 0 for a pixel, then the counts, net and flux arrays for that point are set to zero. If the
x1dsum or
x1dsum<n> (for FPPOS observations) includes several
x1d files, then, for each point in the spectrum, only those files with a DQ_WGT = 1 at that point are included (weighted by the individual exposure times), and the DQ_WGT array in the
x1dsum file is updated to reflect the number of individual spectra which contributed to the point. If the updated value of DQ_WGT for a particular point is 0, then the value of the spectrum at that point is set to 0 in the
x1dsum file.
NUV IMAGING: The end product for NUV imaging is an
fltsum file. Like the
x1dsum files, an
fltsum file is created even if only one exposure is processed. However, since no shifting is performed for imaging observations (see,
Figure 3.5), the
fltsum file is a simple exposure time weighted mean of the individual
flt files (and it is identical to the
flt file if only one exposure contributed to it). The DQ flags image of the
fltsum file and, for that matter, all of the individual
flt images, are identical. This is because the only data which make it into an
flt or
counts image are free of temporal or event flags (see,
Section 2.7). Consequently, in the absence of shifting, all of their spatial flags should be identical.
3.4.12 WAVECORR: Wavecal Correction
