This recipe reduces a broadline ACSIS science observation.
The following parameters can be set via the -recpars option:
ALIGN_SIDE_BAND
Whether to
enable or disable the alignment of data taken through different side bands when combining them to
create spectral cubes. To combine such data, this parameter should be set true (1) to switch on the
AlignSideBand WCS attribute. However, this is incompatible with some early ACSIS data, where
various changes to some WCS attributes subvert the combination. Should reductions fail with " No
usable spectral channels found" , reduce the two side bands independently. The default is not
not to align sidebands, but ‘raw’ data may have had AlignSideBand enabled from earlier
processing (where the default was to align). Likewise data taken on different epochs with the
same sideband should not have AlignSideBand switched on. [0]
BASELINE_EDGES
Percentage of the full range to fit on either edge of the spectra for baselining purposes. If
set to a non-positive value and BASELINE_REGIONS is undefined, then the baseline is
derived after smoothing and automatic emission detection. If assigned a negative value,
BASELINE_REGIONS, if it is defined, will be used instead to specify where to determine the
baseline. [10]
BASELINE_ORDER
The polynomial order to use when baselining cubes. [1]
BASELINE_REGIONS
A comma-separated list of velocity ranges each in the format
v1:v2, from where the baseline should be estimated. It is countermanded should EDGES be
defined and non-negative. [undef]
CHUNKSIZE
The maximum sum of file sizes in
megabytes of files to process simultaneously in MAKECUBE to avoid a timeout. The choice is
affected by processor speed and memory. The minimum allowed value is 100. [5120]
CREATE_MOMENTS_USING_SNR
If set to true (1), moments maps will be created using a
signal-to-noise map to find emission regions. This could be useful when observations were taken
under differing sky conditions and thus have different noise levels. [0]
CUBE_MAXSIZE
The maximum size, in megabytes, of the output cubes. This value does not include extra
information such as variance or weight arrays, FITS headers, or any other NDF extensions.
[512]
CUBE_WCS
The coordinate system to regrid the cubes to. If undefined, the system
is determined from the data. [undef]
DESPIKE
If set to 1 (true) despiking of spectra
is enabled. [0]
DESPIKE_BOX
The size, in pixels, of the box used to both find the "
background" and for cleaning spikes. This box should be slightly wider than the widest
expected spike. Making this parameter too large will result in signal being identified as a
spike and thus masked out. [9]
DESPIKE_CLIP
The clip standard deviations to use
when finding spikes in the background-subtracted RMS spectrum. Multiple values result in
multiple clip levels. A single clip level should be given verbatim, (e.g. 3). If supplying more
than one level, enclose comma-separated levels within square brackets (e.g. [3,3,5]). [’
[3,5]’ ]
DESPIKE_PER_DETECTOR
Whether or not to treat each detector independently
during despiking. If a spike is not seen in all detectors, consider setting this value to 1
(for true). [0]
FINAL_LOWER_VELOCITY
Set a lower velocity over which the final
products, such as the reduced and binned spectral cubes, and noise and rms images, are to be
created. Unlike RESTRICT_LOWER_VELOCITY, it permits the full baselines to be used
during processing, yet greatly reduces the storage requirements of the final products by
retaining only where the astronomical signals reside. It is typically used in conjunction with
FINAL_UPPER_VELOCITY. If undefined, there is no lower limit. If FINAL_UPPER_VELOCITY is
also undefined, the full velocity range, less trimming of the noisy ends, is used. [undef]
FINAL_UPPER_VELOCITY
Set an upper velocity over which the final products, such as the
reduced and binned spectral cubes, and noise and rms images, are to be created. Unlike
RESTRICT_UPPER_VELOCITY, it permits the full baselines to be used during processing, yet
greatly reduces the storage requirements of the final products by retaining only where the
astronomical signals reside. It is typically used in conjunction with FINAL_LOWER_VELOCITY. If
undefined, there is no upper limit. If FINAL_LOWER_VELOCITY is also undefined, the full
velocity range, less trimming of the noisy ends, is used. [undef]
FLATFIELD
Whether
or not to perform flat-fielding. [0]
FLAT_LOWER_VELOCITY
The requested lower
velocity for the flat-field estimations using the sum or ratio methods. It should be less than
FLAT_LOWER_VELOCITY. [undef]
FLAT_METHOD
When flat-fielding is required (cf.
FLATFIELD parameter) this selects the method used to derive the relative gains between receptors.
The allowed selection comprises ’ ratio’ , which finds the histogram peaks of the ratio of voxel
values; ’ sum’ , which finds the integrated flux; and ’ index’ , which searches and applies a
calibration index of nightly flat-field ratios. The ratio method ought to work well using
all the data, but for some data, especially early observations, it has broken down as the
histogram mode is biased towards zero by noise and possible non-linearity effects. The sum
method currently assumes that every receptor is sampling the same signal, which is only
approximately true. [’ sum’ ]
FLAT_UPPER_VELOCITY
The requested upper velocity for
the flat-field estimations using the the sum or ratio methods. It should be greater than
FLAT_LOWER_VELOCITY. [undef]
FRACTION_BAD
The maximum fraction of bad values
permitted in a receptor (or receptor’ s subband for a hybrid observation) permitted before the a
receptor is deemed to be bad. It must lie between 0.1 and 1.0 otherwise the default fraction
is substituted. [0.9]
FREQUENCY_SMOOTH
The number of channels to smooth in
the frequency axis when smoothing to determine baselines. This number should be small
(10) for narrow-line
observations and large (25)
for broad-line observations. [25]
HIGHFREQ_INTERFERENCE
If set to true (1) the spectra for each
receptor are analysed to detect high-frequency interference noise, and those spectra deemed too noisy
are excluded from the reduced products. [1]
HIGHFREQ_INTERFERENCE_EDGE_CLIP
This is
used to reject spectra with high-frequency noise. It is the standard deviation to clip the
summed-edginess profile iteratively in order to measure the mean and standard deviation of the
profile unaffected by bad spectra. A comma-separated list will perform iterative sigma clipping
of outliers, but standard deviations in the list should not decrease. [" 2.0,2.0,2.5,3.0" ]
HIGHFREQ_INTERFERENCE_THRESH_CLIP
This is used to reject spectra with high-frequency
noise. This is the number of standard deviations at which to threshold the noise profile above its
median level. [4.0]
HIGHFREQ_RINGING
Whether or not to test for high-frequency ringing in
the spectra. This is where a band of spectra in the time series have the same oscillation
frequency and origin with smoothly varying amplitude over time. The amplitude is an order of
magnitude or more lower than the regular high-frequency interference, but because it
extends over tens to over 200 spectra, its affect can be as potent. Even if set to 1 (true), at least
HIGHFREQ_RINGING_MIN_SPECTRA spectra are required to give a sufficient baseline
against which to detect spectra with ringing. The HIGHFREQ_INTERFERENCE parameter
must be true to apply this filter. [0]
HIGHFREQ_RINGING_MIN_SPECTRA
Minimum
number of good spectra for ringing filtering to be attempted. See HIGHFREQ_RINGING. The
filter needs to be able to discriminate between the normal unaffected spectra from those
with ringing. The value should be at least a few times larger than the number of affected
spectra. Hence there is a minimum allowed value of 100. The default is an empirical guess;
for the worst cases it will be too small. If there are insufficient spectra the filtering may
still work to some degree. [400]
LV_AXIS
The axis to collapse in the cube to form the
LV image. Can be the axis’ s index or its generic " skylat" or " skylon" . [" skylat" ]
LV_ESTIMATOR
The statistic to use to collapse the spatial axis to form the LV image. See the
KAPPA:COLLAPSE:ESTIMATOR documentation for a list of allowed statistics. [" mean" ]
LV_IMAGE
A longitude-velocity map is made from the reduced group cube, if this parameter is
set to true (1). The longitude here carries its generic meaning, so it could equally well be
right ascension or galactic longitude; the actual axis derives from the chosen co-ordinate
system (see CUBE_WCS). [undef]
MOMENTS
A comma-separated list of moments
maps to create. [" integ,iwc" ]
MOMENTS_LOWER_VELOCITY
Set a lower velocity
over which the moments maps are to be created. It is typically used in conjunction with
MOMENTS_UPPER_VELOCITY. If undefined, the full velocity range, less trimming of the
noisy ends, is used. [undef]
MOMENTS_UPPER_VELOCITY
Set an upper velocity
over which the moments maps are to be created. It is typically used in conjunction with
MOMENTS_LOWER_VELOCITY. If undefined, the full velocity range, less trimming of
the noisy ends, is used. [undef]
PIXEL_SCALE
Pixel scale, in arcseconds, of cubes. If
undefined it is determined from the data. [undef]
REBIN
A comma-separated list of velocity
resolutions to rebin the final cube to. If undefined, the observed resolution is used. [undef]
RESTRICT_LOWER_VELOCITY
Trim all data to this lower velocity. It is typically used in
conjunction with RESTRICT_UPPER_VELOCITY. If undefined, the full velocity range, less trimming
of the noisy ends, is used. [undef]
RESTRICT_UPPER_VELOCITY
Trim all data to this upper
velocity. It is typically used in conjunction with RESTRICT_LOWER_VELOCITY. If undefined, the full
velocity range, less trimming of the noisy ends, is used. [undef]
SPATIAL_SMOOTH
The
number of pixels to smooth in both spatial axes when smoothing to determine baselines. [3]
SPREAD_FWHM_OR_ZERO
Depending on the spreading method, this parameter controls the
number of arcseconds at which the envelope of the spreading function goes to zero, or the
full-width at half-maximum for the Gaussian envelope. See the PARAMS parameter in
SMURF/MAKECUBE for more information. [undef]
SPREAD_METHOD
The method to
use when spreading each input pixel value out between a group of neighbouring output
pixels when regridding cubes. See the SPREAD parameter in SMURF/MAKECUBE for
available spreading methods. [" nearest" ]
SPREAD_WIDTH
The number of arcseconds
on either side of the output position which are to receive contributions from the input
pixel. See the PARAMS parameter in SMURF/MAKECUBE for more information. [0]
TILE
Whether or not to make tiled spectral cubes. A true value (1) performs tiling so as to
restrict the data-processing resource requirements. Such tiled cubes abut each other in
pixel co-ordinates and may be pasted together to form the complete spectral cube. [1]
TRIM_MINIMUM_OVERLAP
The minimum number of desired channels that should
overlap after trimming hybrid-mode observations. If the number of overlapping channels
is fewer than this, then the fixed number of channels will be trimmed according to the
TRIM_PERCENTAGE, TRIM_PERCENTAGE_LOWER, and TRIM_PERCENTAGE_UPPER
parameters. [10]
TRIM_PERCENTAGE_LOWER = REAL (Given)
The percentage of the
total frequency range to trim from the lower end of the frequency range. For example, if a
cube has 1024 frequency channels, and the percentage to trim is 10%, then 102 channels
will be trimmed from the lower end. If it and TRIM_PERCENTAGE are undefined, the
lower-end trimming defaults to 2.75% for ACSIS and 7.5% for DAS observations. [undef]
TRIM_PERCENTAGE = REAL (Given)
The percentage of the total frequency range to trim
from either end. For example, if a cube has 1024 frequency channels, and the percentage
to trim is 10%, then 102 channels will be trimmed from either end. This parameter only
takes effect if both TRIM_PERCENTAGE_LOWER and TRIM_PERCENTAGE_UPPER are
undefined. If it too is undefined, the upper-frequency trimming defaults to 2.75% for ACSIS and
7.5% for DAS observations. [undef]
TRIM_PERCENTAGE_UPPER = REAL (Given)
The
percentage of the total frequency range to trim from the higher end of the frequency range.
For example, if a cube has 1024 frequency channels, and the percentage to trim is 10%,
then 102 channels will be trimmed from the upper end. If it and TRIM_PERCENTAGE
are undefined, it defaults to 2.75% for ACSIS and 7.5% for DAS observations. [undef]
VELOCITY_BIN_FACTOR
This is an integer factor by which the spectral axis may be
compressed by averaging adjacent channels. The rationale is to make the reduced spectral
cubes files substantially smaller; processing much faster; and to reduce the noise so that,
for example, emission features are more easily identified and masked while determining
the baselines. It is intended for ACSIS modes, such as BW250, possessing high spectral
resolution not warranted by the signal-to-noise. Note that this compression is applied
after any filtering of high-frequency artefacts performed on adjacent channels. A typical
factor is 4. There is no compression if this parameter is undefined. [undef]