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| _STOP_PROCESSING_IF_SIMULATED_ |
| Description: |
This primitive examines the SIMULATE header of the current Frame, and if it's true, processing is halted. The ORAC__TERM constant is returned, which causes the pipeline to stop processing the current Frame and go on to the next one. |
| Notes: |
This primitive is only called in _ADV scripts and not in standard recipes |
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| _REDUCE_SCIENCE_STEER_ |
| Description: |
Set up steering parameters for REDUCE_SCIENCE recipes. |
| Arguments: |
COPY_FRAME = LOGICAL (Given)
Whether or not to copy Frame products to Group products when
there's only one member in the group. [1] |
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| _INSTRUMENT_HELLO_ |
| Description: |
Instrument specific initialisation.Any instrument specific initialisation for the spectroscopy pipeline is done in the instrument specific _INSTRUMENT_HELLO_ primitive. This is called close to the start of _SPECTROSCOPY_HELLO_ near the start of processing for each frame. If a given instrument does not require any specific initialisation, it should not have an _INSTRUMENT_HELLO_ primitive, and this generic, null, one will be called instead. |
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| _QA_WITH_MASKING_ |
| Description: |
Run quality assurance tests and mask out spectra that fail a consistency check between Tsys and observed RMS. This primitive performs quality assurance tests on raw timeseries data, then uses information gleaned from those tests to mask out bad data. |
| Arguments: |
MASK = STRING (Given)
When QA tests are performed, the various JCMT Legacy Surveys have
different thresholds for what counts as bad data. If this string is
set, then that given survey's thresholds will be used when masking
out data. If it is not set, then the value of the SURVEY header for
the current Frame object will be used. If that is not defined, then
the default Telescope thresholds (which are much less stringent
than survey thresholds) will be used. Case-insensitive. ['tele-
scope']
SURVEY_OVERRIDE = STRING (Given)
If defined, override the survey listed in the SURVEY header. The
given survey will be used for QA thresholds. [''] |
| Output: |
_ts : time series data sorted in time order (See _SORT_TIMESERIES_)
_tsmask : masked time series data |
| Tasks: |
None, but see _SORT_TIMESERIES, _QA_SENSITIVITY_VARIATION_, and
_QA_RMS_TSYS_CONSISTENCY_ |
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| _REMOVE_FREQUENCY_ENDS_ |
| Description: |
Remove the ends of a cube's frequency axis. This primitive removes the ends of a cube's frequency axis by copying out a central portion of the cube to a new file. This primitive differs from _MASK_FREQUENCY_ENDS_ in that this primitive does not create a cube with masked-out bad pixels on either ends of the frequency axis, whereas _MASK_FREQUENCY_ENDS_ does. |
| Arguments: |
AXIS = INTEGER (Given)
The axis to trim. For time-series data this should be set to 1. For
spatial cubes this should be set to 3. [3]
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 fre-
quency channels, and the percentage to trim is 10%, then 102 chan-
nels will be trimmed from the lower end. [undef]
PERCENT = 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. [10.0]
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 fre-
quency channels, and the percentage to trim is 10%, then 102 chan-
nels will be trimmed from the upper end. [undef] |
| Notes: |
This primitive will only remove the ends if the Frame's user header
SPECTRAL_TRIMMED does not exist or it exists and is false.
If either of the LOWER or UPPER parameters are given, these will be
used. Otherwise, if both of them are left undefined, then the PER-
CENT parameter will be used. |
| Output: |
_em : Cube with masked frequency ends |
| Tasks: |
KAPPA: NDFCOPY, NDFTRACE |
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| _MERGE_HYBRID_MODE_ |
| Description: |
Merge hybrid mode observations in the frequency domain.
This primitive operates on hybrid mode observations. It first deter-
mines a DC-level offset between corresponding subscan observations,
using the overlap region to determine statistics. If no overlap region
exists, then the entire spectrum is used. The DC offset is added to or
removed from the subscan spectra, and the corresponding subscans are
mosaicked together to form time-series cubes with a greater frequency
extent. |
| Notes: |
This primitive is suitable for ACSIS data taken in hybrid mode.
This primitive only operates if the ISHYBRID user header is set for
the current Frame object.
This primitive currently only operates on observations with one
subscan. |
| Output: |
_dc : the DC corrected time-series cubes
_merge : the merged time-series cube |
| Tasks: |
KAPPA: COLLAPSE, MANIC, MATHS, NDFTRACE, WCSMOSAIC |
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| _THRESHOLD_DATA_ |
| Description: |
Threshold data lower and/or higher than given values.
This recipe thresholds data values that are lower and/or higher than
given values. It is essentially a wrapper around the KAPPA THRESH
application. |
| Arguments: |
HIGH = REAL (Given)
The upper threshold value within the input array. [0]
LOW = REAL (Given)
The lower threshold value within the input array. [0]
NEWHIGH = REAL (Given)
The value to which all input values greater than the upper thresh-
old (HIGH parameter) are set. This can be set to "bad", in which
case the bad value is substituted. [0]
NEWLOW = REAL (Given)
The value to which all input values smaller than the lower thresh-
old (LOW parameter) are set. This can be set to "bad", in which
case the bad value is substituted. [0] |
| Output: |
_thr : the thresholded data |
| Tasks: |
KAPPA: THRESH |
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|
| _SUBTRACT_TIMESERIES_SIGNAL_ |
| Description: |
This primitive subtracts a gross timeseries signal from raw heterodyne
data. It first creates a median instrument spectrum by collapsing along
the receptor axis, then collapses along the central 2/3rds of the chan-
nel axis. This creates a time-series spectrum, which is then grown to
the size of the input cube. The time-series cube is subtracted from the
input cube. The median value of the time-series spectrum is added back
to the subtracted cube. |
| Notes: |
The receptor axis is assumed to be the 2nd axis of the input cube.
This primitive operates on every file in the current Frame. |
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| _SET_TAG_ |
| Description: |
Tag the current Frame for subsequent retrieval.
This primitive can be used to tag the current Frame for subsequent
retrieval. In conjunction with the _RETRIEVE_TAG_ primitive, this prim-
itive can be used to "jump back" to a previous step in processing. |
| Arguments: |
TAG = STRING (Given)
The string to tag the current Frame with. This argument is manda-
tory, and an error will be thrown if it is not defined. |
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| _CREATE_CUBE_FRAME_ |
| Description: |
Create a cube from a time-series ACSIS observation and stuff it in the Frm object. This primitive takes a time-series ACSIS cube and, using SMURF/MAKE-
CUBE, transforms it into a spatial/spectral cube. |
| Arguments: |
BYTES_PER_PIXEL = INTEGER (Given)
The number of bytes per pixel. [4]
DETECTORS = STRING (Given)
A comma-separated list of detectors to use when creating the cube.
If blank or undefined, all detectors will be used. ['']
MAXSIZE = INTEGER (Given)
The maximum size, in bytes, of the output cube. This value does not
include extra information such as variance or weight arrays, FITS
headers, or any other NDF extensions. [512000000]
PARAMS = STRING (Given)
An optional array which consists of additional parameters required
by the Sinc, SincSinc, SincCos, SincGauss, Somb, SombCos, and Gauss
spreading methods (see parameter SPREAD). See documentation for the
PARAMS parameter for MAKECUBE. ['']
SPREAD = STRING (Given)
The interpolation method to use when regridding the cube. This can
be any of those allowed by MAKECUBE, listed in the SPREAD parameter. ['nearest']
SUFFIX = STRING (Given)
Override the default "_cube" suffix with a new value. This is use-
ful when processing an iterative result where we do not want to
improve the initial product (the whole point being to retain it).
PRODUCT = STRING (Given)
Override the default "cube" product designation.
|
| Output: |
A cube whose filename is of the form aYYYYMMDD_NNNNN_SS_cube.sdf,
where YYYYMMDD is the UT date, NNNN is the zero-padded observation
number, and SS is the zero-padded susbystem number. |
| Tasks: |
SMURF: MAKECUBE |
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|
| _REMOVE_BASELINE_ |
| Description: |
This primitive removes the baseline from each spectrum in a cube, using
spectral windows that are assumed to be free of spectral lines. |
| Arguments: |
EDGES = REAL (Given)
Percentage of the full range to fit on either edge of the spectrum.
[0]
GROUP = LOGICAL (Given)
Whether or not to operate on the current Group object. [0]
ORDER = INTEGER (Given)
The order of the fit to use for the baseline. Zero (the default) is
a constant, one is linear, etc. [0]
METHOD = STRING (Given)
The method used to define the baseline regions in automatic mode.
The allowed values are 'region', 'single', and 'global'. This is
not used if the EDGES argument is defined. ['region']
TAG = LOGICAL (Given)
Whether or not to tag the resulting cubes as 'reduced'. [0] |
| Tasks: |
KAPPA: MFITTREND, NDFTRACE |
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| _CREATE_MOMENTS_MAPS_ |
| Description: |
Create moments maps by collapsing along spectral axis.
This primitive is used to create moments maps. The input cube is simply
collapsed along the spectral axis, using the requested estimator. |
| Arguments: |
GROUP = INTEGER (Given)
How to process group files. 0 means use the current Frame object. 1
means use the current Group object. 2 means use each Frame member
of the current Group object. [0]
MOMENTS = STRING (Given)
The moment maps to create. These are any of the values allowed for
the ESTIMATOR parameter to the COLLAPSE method, but in reality this
should probably be 'integ', 'iwc', and/or 'itd'. Any number of
moments can be given in a comma-separated string. ['integ']
TAG = STRING (Given)
Which moment map to tag as a representative image. ['integ'] |
| Output: |
The moments map(s) with suffix equal to the given moment(s) by the
MOMENTS parameter. |
| Tasks: |
_COMPONENT_EXISTS_ , _CREATE_MOMENTS_MAPS_THROUGH_SMOOTHING_ |
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| _CREATE_NOISE_MAP_ |
| Description: |
Create a map of the noise for a given cube.
This primitive is used to create a noise map. It first masks out emis-
sion regions using a previously-defined mask (see _CREATE_BASE-
LINE_MASK_), and then collapses the resulting cube along the frequency
axis using the RMS estimator. |
| Arguments: |
GROUP = INTEGER (Given)
How to process group files. 0 means use the current Frame object. 1
means use the current Group object. 2 means use each Frame member
of the current Group object. [0]
QA = LOGICAL (Given)
Whether or not to perform quality assurance calculations on the
resulting noise map. [0] |
| Output: |
_noise : the noise map |
| Tasks: |
KAPPA: ADD, COLLAPSE, PASTE |
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| _RETRIEVE_TAG_ |
| Description: |
Retrieve a tagged Frame.
This primitive can be used to retrieve a Frame that has been previously
tagged with the _SET_TAG_ primitive or the tagset() Frame method. |
| Arguments: |
TAG = STRING (Given)
The tag to retrieve. This argument is mandatory, and an error will
be thrown if it is not defined. If the tag has not been previously
used, then the current frame will not be changed.
THROW = LOGICAL (Given)
Whether or not to throw an error if the requested tag does not
exist. [1] |
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| _CREATE_CUBE_GROUP_ |
| Description: |
Create a cube from a group of time-series ACSIS observations.
This primitive takes time-series ACSIS cubes from each observation in
the current group and runs MAKECUBE on them to create a spatial/spectral cube. |
| Arguments: |
BYTES_PER_PIXEL = INTEGER (Given)
The number of bytes per pixel. [4]
MAXSIZE = INTEGER (Given)
The maximum size, in bytes, of the output cube. This value does not
include extra information such as variance or weight arrays, FITS
headers, or any other NDF extensions. [512000000]
PARAMS = STRING (Given)
An optional array which consists of additional parameters required
by the Sinc, SincSinc, SincCos, SincGauss, Somb, SombCos, and Gauss
spreading methods (see parameter SPREAD). See documentation for the
PARAMS parameter for MAKECUBE. ['']
SPREAD = STRING (Given)
The interpolation method to use when regridding the cube. This can
be any of those allowed by MAKECUBE, listed in the SPREAD parame-
ter. ['nearest']
TILEBORDER = INTEGER (Given)
The size of the border to be added to tiles. This is used when
smoothing the cube in spatial extent in later processing, so as to
not add edge effects. [0] |
| Output: |
A cube (or set of cubes) whose filename is of the form gaYYYYM-
MDD_NN_SS_cubeMMM.sdf, where YYYYMMDD is the UT date, NN is the
observation number, SS is the zero-padded subsystem number, and MMM
is the zero-padded tile number. Tiles are numbered starting from 1
and increasing monotonically, counting from the bottom left corner
in spatial extent and proceeding in a raster fashion from left to
right. |
| Tasks: |
KAPPA: NDFTRACE. SMURF: MAKECUBE |
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| _REMOVE_BASELINE_ |
| Description: |
This primitive removes the baseline from each spectrum in a cube, using
spectral windows that are assumed to be free of spectral lines. |
| Arguments: |
EDGES = REAL (Given)
Percentage of the full range to fit on either edge of the spectrum.
[0]
GROUP = LOGICAL (Given)
Whether or not to operate on the current Group object. [0]
ORDER = INTEGER (Given)
The order of the fit to use for the baseline. Zero (the default) is
a constant, one is linear, etc. [0]
METHOD = STRING (Given)
The method used to define the baseline regions in automatic mode.
The allowed values are 'region', 'single', and 'global'. This is
not used if the EDGES argument is defined. ['region']
TAG = LOGICAL (Given)
Whether or not to tag the resulting cubes as 'reduced'. |
| Tasks: |
KAPPA: MFITTREND, NDFTRACE |
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|
| _CREATE_MOMENTS_MAPS_ |
| Description: |
Create moments maps by collapsing along spectral axis.
This primitive is used to create moments maps. The input cube is simply
collapsed along the spectral axis, using the requested estimator. |
| Arguments: |
GROUP = INTEGER (Given)
How to process group files. 0 means use the current Frame object. 1
means use the current Group object. 2 means use each Frame member
of the current Group object. [0]
MOMENTS = STRING (Given)
The moment maps to create. These are any of the values allowed for
the ESTIMATOR parameter to the COLLAPSE method, but in reality this
should probably be 'integ', 'iwc', and/or 'itd'. Any number of
moments can be given in a comma-separated string. ['integ']
TAG = STRING (Given)
Which moment map to tag as a representative image. ['integ'] |
| Output: |
The moments map(s) with suffix equal to the given moment(s) by the
MOMENTS parameter. |
| Tasks: |
None, but see _COMPONENT_EXISTS_ |
| See also: |
_CREATE_MOMENTS_MAPS_THROUGH_SMOOTHING_ |
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|
| _CREATE_NOISE_MAP_ |
| Description: |
Create a map of the noise for a given cube.
This primitive is used to create a noise map. It first masks out emis-
sion regions using a previously-defined mask (see _CREATE_BASE-
LINE_MASK_), and then collapses the resulting cube along the frequency
axis using the RMS estimator. |
| Arguments: |
GROUP = INTEGER (Given)
How to process group files. 0 means use the current Frame object. 1
means use the current Group object. 2 means use each Frame member
of the current Group object. [0]
QA = LOGICAL (Given)
Whether or not to perform quality assurance calculations on the
resulting noise map. [0] |
| Output: |
_noise : the noise map |
| Tasks: |
KAPPA: ADD, COLLAPSE, PASTE |
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| _ITERATIVE_GROUP_PRODUCTION_ |
| Description: |
This primitive creates a group co-added cube from all members of the current group. It then baselines the cube and creates moments maps.
In the process of baselining the group cube, this primitive also creates a baseline mask file, masking out emission. It then runs this mask through UNMAKECUBE to create time-series masks. These masks are applied to the original time-series data, which are then baselined. The baselined time-series data are then run through MAKECUBE to create individual baselined cubes for each observation. Moments maps are then made from these cubes. |
| Arguments: |
FREQUENCY_SMOOTH = INTEGER (Given)
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]
MOMENTS = STRING (Given)
The moment maps to create. These are any of the values allowed for the ESTIMATOR parameter to the COLLAPSE method, but in reality this should probably be 'integ', 'iwc', and/or 'itd'. Any number of moments can be given in a comma-separated string. ['integ']
ORDER = INTEGER (Given)
The polynomial order that will be used when estimating baselines. [5]
PARAMS = STRING (Given)
The parameters to pass to MAKECUBE when using the Sinc, SincSinc, SincCos, SincGauss, Somb, SombCos, and Gauss spreading methods (see SPREAD parameter). ['']
SPATIAL_SMOOTH = INTEGER (Given)
The number of pixels to smooth in both spatial axes when smoothing to determine baselines. [3]
SPREAD = STRING (Given)
The method to use when spreading each input pixel value out between a group of neighbouring output pixels when using MAKECUBE to generate a cube. ['nearest']
|
| Tasks: |
_CREATE_CUBE_GROUP_, _REMOVE_BASELINE_THROUGH_SMOOTHING_, _CREATE_MOMENTS_MAPS_THROUGH_SMOOTHING_, _RECREATE_MASKED_TIMESERIES_, _REMOVE_BASELINE_MASKED_TIMESERIES_, _CREATE_CUBE_FRAME_FROM_GROUP_ |
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