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. [undef]
BASELINE_EMISSION_CLIP
This is a
comma-separated list of standard deviations factors for progressive clipping of outlying binned
(see BASELINE_NUMBIN) residuals to an initial linear fit to the baseline. This is used to
determine the fitting ranges automatically. Its purpose is to exclude features that are not part of
the trends. Pixels are rejected at the ith clipping cycle if they lie beyond plus or minus
BASELINE_EMISSION_CLIP(i) times the dispersion about the median of the remaining good pixels.
Thus lower clipping factors will reject more pixels. The normal approach is to start low and
progressively increase the clipping factors, as the dispersion decreases after the exclusion of features.
Between one and five values may be supplied. The minimum value is 1.0. If undefined, the
default for MFITTREND’ s CLIP parameter is used, which is fine in most cases. Where the
emission is intense and extends over a substantial fraction of the spectrum, harsher clipping
is needed to avoid biasing the fits. [undef]
BASELINE_LINEARITY
If set to true (1)
receptors with mostly or all non-linear baselines are excluded from the reduced products. [1]
BASELINE_LINEARITY_CLIP
This is used to reject receptors that have non-linear baselines. It is the
maximum number of standard deviations above the median rms deviations for which a detector’ s
non-linearity is regarded as acceptable. The minimum allowed is 2. A comma-separated list will
perform iterative sigma clipping of outliers, but standard deviations in the list should
not decrease. [" 2.0,2.3,3.0" ]
BASELINE_LINEARITY_LINEWIDTH
This is used to
reject receptors that have transient or mostly non-linear baselines. It specifies the location
of spectral-line emission or the regions to analyse for bad baselines. Allowed values are:
-
" auto" , which requests that the emission be found automatically;
-
" base" meaning test the portions of the spectrum defined by the BASELINE_REGIONS recipe
parameter; or
-
it is the extent(s) of the source spectral line(s) measured in km/s, supplied in a comma-separated list.
For this last option, each range may be given as bounds separated by a colon; or as a single
value being the width about zero. For instance " -20:50" would excise the region -20 to
50 km/s, and " 30" would
exclude the -15 to 15
km/s range. [" auto" ]
BASELINE_LINEARITY_MINRMS
This is used to retain receptors that have
noisy or slightly non-linear baselines, or transient bad baselines (cf. LOWFREQ_INTERFERENCE).
The parameter is the minimum rms deviation from linearity, measured in antenna temperature, for a
receptor to be flagged as bad. The non-linearity identification intercompares the receptors and can
reject an outlier that in practice is not a bad receptor; it is just worse than the other receptors in an
observation. This parameter sets an absolute lower limit to prevent such receptors from being
excluded. Values between 0.05 and 0.2 are normal. Most good receptors will be in 0.02 to 0.05 range.
[0.1]
BASELINE_LINEARITY_SCALELENGTH
This is used to reject receptors that have
non-linear baselines. It is the smoothing scale length in whole pixels. Features narrower than
this are filtered out during the background-level determination. It should be should be
odd (if an even value is supplied, the next higher odd value will be used) and sufficiently
large to remove the noise while not removing the low-frequency patterns in the spectra.
The minimum allowed is 51. It is also used to detect transient non-linear baselines (cf.
LOWFREQ_INTERFERENCE). [101]
BASELINE_METHOD
This specifies how to define the
baseline region. Currently only " auto" is recognised. This requests the automated mode where the
emission is detected and masked before baseline fitting. If undefined or not " auto" , then
BASELINE_EDGES or BASELINE_REGIONS (q.v.) will be used.
BASELINE_NUMBIN
The number
of smoothing bins to used for the baseline determination and hence the emission masking.
The default lets MFITTREND choose (currently 32 bins), and is normally sufficient for
narrow lines. For line forests, more resolution is needed so as not to include emission in the
majority of bins, and so a value that will provide a few bins across the a line’ s width is better,
typically 128, which is the default if the LINEFOREST_BASELINE recipe parameter is
true. []
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 BASELINE_EDGES be
defined and non-negative. These can also be used to define where to test baseline linearity if
BASELINE_LINEARITY_LINEWIDTH is set to " base" . [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. [5]
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. [10]
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]
LOWFREQ_INTERFERENCE
If set to true (1) the spectra for each
receptor are analysed to detect low-frequency interference ripples or bad baselines, and those
spectra deemed too deviant from linearity are excluded from the reduced products. [1]
LOWFREQ_INTERFERENCE_EDGE_CLIP
This is used to reject spectra with low-frequency
interference. It is the standard deviation to clip the profile of summed-deviations from
linearity 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" ]
LOW_FREQ_INTERFERENCE_THRESH_CLIP
This is used to reject spectra with low-frequency
interference. This is the number of standard deviations at which to threshold the non-linearity
profile above its median level. [3.0]
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. [5]
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]
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]
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
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
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
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]
REDUCE_SCIENCE_GRADIENT.