The recipes REDUCE_SCIENCE_NARROWLINE, REDUCE_SCIENCE_GRADIENT,
REDUCE_SCIENCE_LINEFOREST, and REDUCE_SCIENCE_BROADLINE support the following parameters,
except where noted. Recipe parameters should be supplied in an external file and called by the
command line option -recpars <params.ini>
. For an example recipe-parameter file see Section 6.2.
The parameters are classified for easier identification.
Parameter | Description |
CLUMP_METHOD | Method for identifying emission clumps: Clumpfind, Fellwalker, or Thresh. |
CUBE_WCS | The co-ordinate system in which to regrid cubes. |
FINAL_LOWER_VELOCITY | Lower velocity limit for all the cube products. |
FINAL_UPPER_VELOCITY | Upper velocity limit for all the cube products. |
ITERATIONS | Number of iterations. Further iterations refine the identification of emission to exclude from baseline subtraction. One iteration is usually sufficient. |
PIXEL_SCALE | The pixel scale, in arcseconds, of cubes. |
REBIN | List of velocity resolutions to rebin the final cube to. |
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. |
SPREAD_METHOD | The method to use when spreading each input pixel between a group of neighbouring output pixels when regridding cubes. |
SPREAD_WIDTH | The number of arcseconds on either side of the output position which receive contributions from the input pixel. |
Parameter | Description |
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. |
RESTRICT_LOWER_VELOCITY | Trims all data to this lower velocity, not just at the end for the products. |
RESTRICT_UPPER_VELOCITY | Trims all data to this upper velocity, not just at the end for the products. |
TRIM_MINIMUM_OVERLAP | The minimum number of desired channels that should overlap after trimming hybrid-mode observations. |
TRIM_PERCENTAGE | The percentage of the total frequency range to trim
from either end. This parameter only takes effect if both
|
TRIM_PERCENTAGE_LOWER | The percentage of the total frequency range to trim from the lower end of the frequency range. |
TRIM_PERCENTAGE_UPPER | The percentage of the total frequency range to trim from the higher end of the frequency range. |
Parameter | Description |
BASELINE_ORDER | The polynomial order to use when baselining cubes. |
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. |
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 positive.
These can also be used to define where to test baseline
linearity if BASELINE_LINEARITY_LINEWIDTH is
set to |
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. |
SPATIAL_SMOOTH | The number of pixels to smooth in both spatial axes when smoothing to determine baselines. |
There are a number of ways to define the baseline regions:
The first two are suitable for broadline emission. The second is desirable in the presence of many lines. The third is the default and most appropriate for a single narrow line.
Parameter | Description |
LV_IMAGE | Permits creation of a longitude-velocity map via primitive _CREATE_LV_IMAGE_ |
LV_AXIS | Specify the axis to collapse in the creation of the longitude-velocity map. |
LV_ESTIMATOR | Specify the collapse statistic in the creation of the longitude-velocity map. |
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 is useful when observations were taken under differing sky conditions and have different noise levels. |
MOMENTS | Comma separated list of the moments maps to create (integ,iwc). |
MOMENTS_LOWER_VELOCITY | The lower velocity range from which the moments maps will be created. |
MOMENTS_UPPER_VELOCITY | The upper velocity range from which the moments maps will be created. |
Parameter | Description |
FLATFIELD | Whether or not to perform flat-fielding. |
FLAT_APPLY | Whether or not to apply the calculated flatfield. If set false the ratios are still calculated and logged. |
FLAT_METHOD | Flatfield option to ratio voxel by voxel. |
FLAT_LOWER | Sets the lower limit by which to restrict the velocity range where there is astronomical signal for FLAT_METHOD. |
FLAT_UPPER | Sets the upper limit by which to restrict the velocity range where there is astronomical signal for FLAT_METHOD. |
MINSNR | Allow selection of higher signal-to-noise voxels for FLAT_METHOD. |
Parameter | Description |
DESPIKE | Whether or not to perform despiking. |
DESPIKE_BOX | The size, in pixels, of the box used to both find the "background" and for cleaning spikes. |
DESPIKE_CLIP | The clip standard deviations to use when finding spikes in the background-subtracted RMS spectrum. |
DESPIKE_PER_DETECTOR | If a spike is not seen in all detectors, consider setting this value to 1. |
Parameter | Description |
CHUNKSIZE | Maximum sized chunk used for the group cube. |
CUBE_MAXSIZE | Controls the maximum size of the reduced cube. |
TILE | A true value (1) performs tiling of the cube to restrict the memory requirements. Such tiled cubes abut each other in pixel co-ordinates and may be pasted together to form the complete spectral cube. |
Parameter | Description |
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. |
HIGHFREQ_INTERFERENCE_EDGE_CLIP | 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. |
HIGHFREQ_INTERFERENCE_THRESH_CLIP | 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. |
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. |
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. |
Parameter | Description |
LOWFREQ_INTERFERENCE | If set to true (1) the spectra for each receptor are analysed to detect low-frequency local interference ripples or bad baselines, and those spectra deemed too deviant from linearity are excluded from the reduced products. |
LOWFREQ_INTERFERENCE_EDGE_CLIP | 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. |
LOWFREQ_INTERFERENCE_MAX_THRESHOLD | Spectra are deemed to be non-linear if their non-linearity exceeds this threshold. |
LOWFREQ_INTERFERENCE_MIN_THRESHOLD | No spectra with non-linearity below this threshold will be rejected. |
LOWFREQ_INTERFERENCE_THRESH_CLIP | 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. |
BASELINE_LINEARITY
and related parameters below.
These parameters are not available in the REDUCE_SCIENCE_BROADLINE recipe. Parameter | Description |
BASELINE_LINEARITY | If set to true, receptors with mostly or all non-linear baselines are excluded from the reduced products. |
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. |
BASELINE_LINEARITY_LINEWIDTH | This is used to reject receptors that have non-linear baselines. It is the extent of the source spectral line measured in km/s, which is excluded from the non-linearity tests. |
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. |
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 and sufficiently large to remove the noise while not removing the low-frequency patterns in the spectra. |