|
|||
NRAO Home > CASA > CASA Task Reference Manual |
|
0.1.113 sdreduceold
Requires:
Synopsis
ASAP SD task [DEPRECATED]: do sdcal, sdaverage, and sdbaseline in one
task
Description
### DEPRECATION WARNING
#################################################
This task will be removed in CASA 5.1. The functionality of this task with
MeasurementSet format is replicated with sdcal, sdbaseline, sdsmooth, and
mstransform.
#########################################################################
Task sdreduceold performs data selection, calibration, spectral averaging and/or baseline fitting for single-dish spectra. This task internally calls the tasks, sdcal, sdaverage, and sdbaseline and it can be used to run all the three steps in one task execution. This task has better performance than invoking the three tasks separately because it runs all three steps without writing intermediate data to disk.
It is possible to skip arbitrary operations by setting calmode = ’none’ (for calibration), average=False (for time and polarization averaging), kernel = ’none’ (for smoothing), and/or blfunc=’none’ (for baseline fitting).
Please take a look at descriptions of tasks, sdcal, sdaverage, and sdbalseline,
for more information.
Arguments
Inputs |
| ||
infile |
| name of input SD dataset
| |
| allowed: | string |
|
| Default: |
|
|
antenna |
| select an antenna name or ID, e.g. ’PM03’ (only effective
for MS input)
| |
| allowed: | any |
|
| Default: | variant 0 |
|
fluxunit |
| units of the flux (”=current)
| |
| allowed: | string |
|
| Default: |
|
|
telescopeparam |
| parameters of telescope for flux conversion (see
description in help of sdcal)
| |
| allowed: | string |
|
| Default: |
|
|
field |
| select data by field IDs and names, e.g. ’3C2*’ (”=all)
| |
| allowed: | string |
|
| Default: |
|
|
spw |
| select data by IF IDs (spectral windows), e.g. ’3,5,7’
(”=all)
| |
| allowed: | string |
|
| Default: |
|
|
restfreq |
| the rest frequency, e.g. ’1.41GHz’ (default unit: Hz) (see
examples in help)
| |
| allowed: | any |
|
| Default: | variant
|
|
frame |
| frequency reference frame (”=current)
| |
| allowed: | string |
|
| Default: |
|
|
doppler |
| doppler convention (”=current). Effective only when
spw selection is in velocity unit.
| |
| allowed: | string |
|
| Default: |
|
|
timerange |
| select data by time range, e.g. ’09:14:0~09:54:0’ (”=all)
(see examples in help of sdcal)
| |
| allowed: | string |
|
| Default: |
|
|
scan |
| select data by scan numbers, e.g. ’21~23’ (”=all)
| |
| allowed: | string |
|
| Default: |
|
|
pol |
| select data by polarization IDs, e.g. ’0,1’ (”=all)
| |
| allowed: | string |
|
| Default: |
|
|
calmode |
| SD calibration mode (’none’ = skip calibration)
| |
| allowed: | string |
|
| Default: | none | |
fraction |
| fraction of the OFF data to mark as OFF spectra, e.g.,
’10%’
| |
| allowed: | any |
|
| Default: | variant 10% |
|
noff |
| number of the OFF data to mark (-1 = use fraction
instead of number)
| |
| allowed: | int | |
| Default: | -1 |
|
width |
| width of the pixel for edge detection
| |
| allowed: | double | |
| Default: | 0.5 |
|
elongated |
| the observed area is elongated in one direction
| |
| allowed: | bool | |
| Default: | False |
|
markonly |
| do calibration (False) or just mark OFF (True)
| |
| allowed: | bool | |
| Default: | False |
|
plotpointings |
| plot pointing direction for ON and OFF
| |
| allowed: | bool | |
| Default: | False |
|
tau |
| the zenith atmospheric optical depth for correction (0.
= no correction)
| |
| allowed: | double | |
| Default: | 0.0 |
|
average |
| data averaging [True, False]
| |
| allowed: | bool | |
| Default: | False |
|
timeaverage |
| average spectra over time [True, False] (see examples in
help of sdaverage)
| |
| allowed: | bool | |
| Default: | False |
|
tweight |
| weighting for time averaging
| |
| allowed: | string |
|
| Default: | tintsys |
|
scanaverage |
| average spectra within a scan number [True, False] (see
examples in help of sdaverage)
| |
| allowed: | bool | |
| Default: | False |
|
averageall |
| set True only when averaging spectra with different
spectral resolutions
| |
| allowed: | bool | |
| Default: | False |
|
polaverage |
| average spectra over polarizations [True, False]
| |
| allowed: | bool | |
| Default: | False |
|
pweight |
| weighting for polarization averaging
| |
| allowed: | string |
|
| Default: | tsys |
|
kernel |
| type of spectral smoothing kernel (’none’=no
smoothing)
| |
| allowed: | string |
|
| Default: | none |
|
kwidth |
| width of smoothing kernel in channels
| |
| allowed: | int |
|
| Default: | 5 |
|
chanwidth |
| width of regridded channels
| |
| allowed: | string |
|
| Default: | 5 |
|
maskmode |
| mode of setting additional channel masks
| |
| allowed: | string |
|
| Default: | auto |
|
thresh |
| S/N threshold for linefinder
| |
| allowed: | double |
|
| Default: | 5.0 |
|
avg_limit |
| channel averaging for broad lines
| |
| allowed: | int |
|
| Default: | 4 |
|
edge |
| channels to drop at beginning and end of spectrum
| |
| allowed: | intArray |
|
| Default: | 0 |
|
blfunc |
| baseline model function (’none’ = skip baseline fit)
| |
| allowed: | string |
|
| Default: | none |
|
order |
| order of baseline model function
| |
| allowed: | int |
|
| Default: | 5 |
|
npiece |
| number of element polynomials for cubic spline curve
| |
| allowed: | int |
|
| Default: | 2 |
|
applyfft |
| automatically set wave numbers of sinusoids [True,
False]
| |
| allowed: | bool |
|
| Default: | True |
|
fftmethod |
| method for automatically set wave numbers of sinusoids
| |
| allowed: | string |
|
| Default: | fft |
|
fftthresh |
| threshold to select wave numbers of sinusoids
| |
| allowed: | any |
|
| Default: | 3.0 |
|
addwn |
| additional wave numbers to use
| |
| allowed: | any |
|
| Default: | 0 |
|
rejwn |
| wave numbers NOT to use
| |
| allowed: | any |
|
| Default: |
|
|
clipthresh |
| clipping threshold for iterative fitting
| |
| allowed: | double |
|
| Default: | 3.0 |
|
clipniter |
| maximum iteration number for iterative fitting
| |
| allowed: | int |
|
| Default: | 0 |
|
verifycal |
| interactively verify the results of calibration [True, False]
(see description in sdcal)
| |
| allowed: | bool |
|
| Default: | False |
|
verifysm |
| interactively verify the results of smoothing for each
spectrum. [not available for kernel=”regrid”]
| |
| allowed: | bool |
|
| Default: | False |
|
verifybl |
| interactively verify the results of baseline fitting for each
spectrum (only for blfunc=”poly”. see description in
help)
| |
| allowed: | bool |
|
| Default: | False |
|
verbosebl |
| output baseline fitting results to logger [True, False]
| |
| allowed: | bool |
|
| Default: | True |
|
bloutput |
| output baseline fitting results to a text file [True, False]
| |
| allowed: | bool |
|
| Default: | True |
|
blformat |
| format of the text file specified with bloutput
| |
| allowed: | string |
|
| Default: |
|
|
showprogress |
| show progress status for large data [True, False]
| |
| allowed: | bool |
|
| Default: | True |
|
minnrow |
| minimum number of input spectra to show progress
status in baseline fitting
| |
| allowed: | int |
|
| Default: | 1000 |
|
outfile |
| name of output file (See a WARNING in help)
| |
| allowed: | string |
|
| Default: |
|
|
outform |
| output file format (See a WARNING in help)
| |
| allowed: | string |
|
| Default: | ASAP |
|
overwrite |
| overwrite the output file if already exists [True, False]
| |
| allowed: | bool |
|
| Default: | False |
|
plotlevel |
| plot and summarize results (0=none). See description in
each task
| |
| allowed: | int |
|
| Default: | 0 |
|
void
Example
Keyword arguments:
infile -- name of input SD dataset
antenna -- select an antenna name or ID
default: 0
example: ’PM03’
NOTE this parameter is effective only for MS input
fluxunit -- units for line flux
options: ’K’,’Jy’,’’
default: ’’ (keep current fluxunit in data)
WARNING: For GBT data, see description below.
>>> fluxunit expandable parameter
telescopeparam -- parameters of telescope for flux conversion
options: (str) name or (list) list of gain info
default: ’’ (none set)
example: if telescopeparam=’’, it tries to get the telescope
name from the data.
Full antenna parameters (diameter,ap.eff.) known
to ASAP are
’ATPKSMB’, ’ATPKSHOH’, ’ATMOPRA’, ’DSS-43’,
’CEDUNA’,’HOBART’. For GBT, it fixes default fluxunit
to ’K’ first then convert to a new fluxunit.
telescopeparam=[104.9,0.43] diameter(m), ap.eff.
telescopeparam=[0.743] gain in Jy/K
telescopeparam=’FIX’ to change default fluxunit
see description below
field -- select data by field IDs and names
default: ’’ (use all fields)
example: field=’3C2*’ (all names starting with 3C2)
field=’0,4,5~7’ (field IDs 0,4,5,6,7)
field=’0,3C273’ (field ID 0 or field named 3C273)
this selection is in addition to the other selections to data
spw -- select data by IF IDs (spectral windows)/channels
NOTE channel range selections are interpreted as mask regions to
INCLUDE in BASELINE fit, and ignored in the other operations.
when maskmode is ’auto’ or ’interact’, the channel mask
will be applied first before fitting as base mask
default: ’’ (use all IFs and channels)
example: spw=’3,5,7’ (IF IDs 3,5,7; all channels)
spw=’<2’ (IF IDs less than 2, i.e., 0,1; all channels)
spw=’30~45GHz’ (IF IDs with the center frequencies in range 30-45GHz; all channels)
spw=’0:5~61’ (IF ID 0; channels 5 to 61)
spw=’3:10~20;50~60’ (select multiple channel ranges within IF ID 3)
spw=’3:10~20,4:0~30’ (select different channel ranges for IF IDs 3 and 4)
spw=’1~4;6:15~48’ (for channels 15 through 48 for IF IDs 1,2,3,4 and 6)
this selection is in addition to the other selections to data
>>> spw expandable parameters
restfreq -- the rest frequency
available type includes float, int, string, list of float,
list of int, list of string, and list of dictionary. the
default unit of restfreq in case of float, int, or string
without unit is Hz. string input can be a value only
(treated as Hz) or a value followed by unit for which ’GHz’,
’MHz’,’kHz’,and ’Hz’ are available.
a list can be used to set different rest frequencies for
each IF. the length of list input must be number of IFs.
dictionary input should be a pair of line name and
frequency with keys of ’name’ and ’value’, respectively.
values in the dictionary input follows the same manner as
as for single float or string input.
example: 345.796
’1420MHz’
[345.8, 347.0, 356.7]
[’345.8MHz’, ’347.0MHz’, ’356.7MHz’]
[{’name’:’CO’,’value’:345}]
frame -- frequency reference frame
options: ’LSRK’, ’TOPO’, ’LSRD’, ’BARY’, ’GALACTO’, ’LGROUP’, ’CMB’
default: ’’ (keep current frame in data)
doppler -- doppler convention (effective only when spw is in
velocity unit)
options: ’RADIO’, ’OPTICAL’, ’Z’, ’BETA’, or ’GAMMA’
default: ’’ (keep current doppler setting in data)
timerange -- select data by time range
default: ’’ (use all)
example: timerange = ’YYYY/MM/DD/hh:mm:ss~YYYY/MM/DD/hh:mm:ss’
Note: YYYY/MM/DD can be dropped as needed:
timerange=’09:14:00~09:54:00’ # this time range
timerange=’09:44:00’ # data within one integration of time
timerange=’>10:24:00’ # data after this time
timerange=’09:44:00+00:13:00’ #data 13 minutes after time
this selection is in addition to the other selections to data
scan -- select data by scan numbers
default: ’’ (use all scans)
example: scan=’21~23’ (scan IDs 21,22,23)
this selection is in addition to the other selections to data
pol -- select data by polarization IDs
default: ’’ (use all polarizations)
example: pol=’0,1’ (polarization IDs 0,1)
this selection is in addition to the other selections to data
calmode -- calibration mode
options: ’ps’,’nod’,’otf’,’otfraster’,
’fs’,’quotient’,’none’
default: ’none’
example: choose mode ’none’ if you have already calibrated
and want to correct for atmospheric opacity defined
by tau, subtract baseline or average/smooth spectra.
>>> calmode expandable parameter
fraction -- edge marker parameter of ’otf’ and ’otfraster’.
Specify a number of OFF integrations (at each
side of the raster rows in ’otfraster’ mode)
as a fraction of total number of integrations.
In ’otfraster’ mode, number of integrations
to be marked as OFF, n_off, is determined by
the following formula,
n_off = floor(fraction * n),
where n is number of integrations per raster
row. Note that n_off from both sides will be
marked as OFF so that twice of specified
fraction will be marked at most. For example,
if you specify fraction=’10%’, resultant
fraction of OFF integrations will be 20% at
most.
In ’otf’ mode, n_off is given by,
n_off = floor(fraction * n),
where n is number of total integrations.
n_off is used as criterion of iterative marking
process. Therefore, resulting total number of
OFFs will be larger than n_off. In practice,
fraction is a geometrical fraction of edge
region. Thus, if integrations are concentrated
on edge region (e.g. some of Lissajous
patterns), then resulting n_off may be
unexpectedly large.
default: ’10%’
options: ’20%’ in string style or float value less
than 1.0 (e.g. 0.15).
’auto’ is available only for ’otfraster’.
noff -- edge marking parameter for ’otfraster’.
It is used to specify a number of OFF scans near
edge directly. Value of noff comes before setting
by fraction. Note that n_off from both sides will
be marked as OFF so that twice of specified noff
will be marked at most.
default: -1 (use fraction)
options: any positive integer
width -- edge marking parameter for ’otf’.
Pixel width with respect to a median spatial
separation between neighboring two data in time.
Default will be fine in most cases.
default: 0.5
options: float value
elongated -- edge marking parameter for ’otf’.
Set True only if observed area is elongeted
in one direction.
options: (bool) True, False
default: False
markonly -- set True if you want to save data just after
edge marking (i.e. uncalibrated data) to see
how OFF scans are defined.
options: (bool) True, False
default: False
plotpointings -- load plotter and plot pointing directions of
ON and OFF scans.
options: (bool) True, False
default: False
tau -- the zenith atmospheric optical depth for correction
default: 0.0 (no correction)
average -- averaging on spectral data
options: (bool) True,False
default: False
>>>average expandable parameter
timeaverage -- average spectra over time
options: (bool) True, False
default: False
example: if True, this happens after calibration
tweight -- weighting for time averaging (effective only when
timeaverage=True)
options: ’var’ (1/var(spec) weighted)
’tsys’ (1/Tsys**2 weighted)
’tint’ (integration time weighted)
’tintsys’ (Tint/Tsys**2)
’median’ ( median averaging)
default: ’tintsys’
scanaverage -- average spectra within a scan number (effective
only when timeaverage=True)
when True, spectra are NOT averaged over
different scan numbers.
options: (bool) True, False
default: False
averageall -- average multi-resolution spectra (effective only
when timeaverage=True)
spectra are averaged by referring their frequency
coverage
default: False
polaverage -- average spectra over polarizations
options: (bool) True, False
default: False
pweight -- weighting for polarization averaging (effective only
when polaverage=True)
options: ’var’ (1/var(spec) weighted)
’tsys’ (1/Tsys**2 weighted)
default: ’tsys’
kernel -- type of spectral smoothing kernel
options: ’none’, ’hanning’,’gaussian’,’boxcar’,’regrid’, ’’(=’none’)
default: ’none’ (no smoothing)
>>>kernel expandable parameter
kwidth -- width of spectral smoothing kernel
options: (int) in channels
default: 5
example: 5 or 10 seem to be popular for boxcar
ignored for hanning (fixed at 5 chans)
(0 will turn off gaussian or boxcar)
chanwidth -- channel width of regridded spectra
default: ’5’ (in channels)
example: ’500MHz’, ’0.2km/s’
maskmode -- mode of setting additional channel masks
options: ’auto’, ’list’, or ’interact’
default: ’auto’
example: maskmode=’auto’ runs linefinder to detect line regions
to be excluded from fitting. this mode requires three
expandable parameters: thresh, avg_limit, and edge.
USE WITH CARE! May need to tweak the expandable parameters.
maskmode=’list’ uses the given masklist only: no additional
masks applied.
maskmode=’interact’ allows users to manually modify the
mask regions by dragging mouse on the spectrum plotter GUI.
use LEFT or RIGHT button to add or delete regions,
respectively.
>>> maskmode expandable parameters
thresh -- S/N threshold for linefinder. a single channel S/N ratio
above which the channel is considered to be a detection.
default: 5
avg_limit -- channel averaging for broad lines. a number of
consecutive channels not greater than this parameter
can be averaged to search for broad lines.
default: 4
edge -- channels to drop at beginning and end of spectrum
default: 0
example: edge=[1000] drops 1000 channels at beginning AND end.
edge=[1000,500] drops 1000 from beginning and 500
from end.
Note: For bad baselines threshold should be increased,
and avg_limit decreased (or even switched off completely by
setting this parameter to 1) to avoid detecting baseline
undulations instead of real lines.
blfunc -- baseline model function
options: ’poly’, ’chebyshev’, ’cspline’, or ’sinusoid’
default: ’none’ (no baseline fit)
example: blfunc=’poly’ uses a single polynomial line of
any order which should be given as an expandable
parameter ’order’ to fit baseline.
blfunc=’chebyshev’ uses Chebyshev polynomials.
blfunc=’cspline’ uses a cubic spline function, a piecewise
cubic polynomial having C2-continuity (i.e., the second
derivative is continuous at the joining points).
blfunc=’sinusoid’ uses a combination of sinusoidal curves.
>>> blfunc expandable parameters
order -- order of baseline model function
options: (int) (<0 turns off baseline fitting)
default: 5
example: typically in range 2-9 (higher values
seem to be needed for GBT)
npiece -- number of the element polynomials of cubic spline curve
options: (int) (<0 turns off baseline fitting)
default: 2
applyfft -- automatically set wave numbers of sinusoidal functions
for fitting by applying some method like FFT.
options: (bool) True, False
default: True
fftmethod -- method to be used when applyfft=True. Now only
’fft’ is available and it is the default.
fftthresh -- threshold to select wave numbers to be used for
sinusoidal fitting. both (float) and (str) accepted.
given a float value, the unit is set to sigma.
for string values, allowed formats include:
’xsigma’ or ’x’ (= x-sigma level. e.g., ’3sigma’), or
’topx’ (= the x strongest ones, e.g. ’top5’).
default is 3.0 (unit: sigma).
addwn -- additional wave number(s) of sinusoids to be used
for fitting.
(list) and (int) are accepted to specify every
wave numbers. also (str) can be used in case
you need to specify wave numbers in a certain range.
default: [0] (i.e., constant is subtracted at least)
example: 0
[0,1,2]
’a-b’ (= a, a+1, a+2, ..., b-1, b),
’<a’ (= 0,1,...,a-2,a-1),
’>=a’ (= a, a+1, ... up to the maximum wave
number corresponding to the Nyquist
frequency for the case of FFT).
rejwn -- wave number(s) of sinusoid NOT to be used for fitting.
can be set just as addwn but has higher priority:
wave numbers which are specified both in addwn
and rejwn will NOT be used.
default: []
clipthresh -- clipping threshold for iterative fitting
default: 3
clipniter -- maximum iteration number for iterative fitting
default: 0 (no iteration, i.e., no clipping)
verifycal -- interactively verify the results of calibration
See description of verify parameter in the task, sdcal,
for details.
options: (bool) True,False
default: False
verifysm -- interactively verify the results of smoothing for each
spectrum.
See description of verify parameter in the task, sdaverage,
for details.
options: (bool) True,False
default: False
Note: verification is not yet available for kernel=’regrid’
verifybl -- interactively verify the results of baseline fitting for
each spectrum.
See description of verify parameter in the task, sdbaseline,
for details.
options: (bool) True,False
default: False
NOTE: Currently available only when blfunc=’poly’
verbosebl -- output fitting results to logger. If False, the fitting results
including coefficients, residual rms, etc., are not output to
the CASA logger, while the processing speed gets faster.
options: (bool) True, False
default: True
bloutput -- output fitting results to a text file. if False, the fitting
results including coefficients, residual rms, etc., are not
output to a text file (<outfile>_blparam.txt), while
the processing speed gets faster.
options: (bool) True, False
default: True
blformat -- format of the logger output and text file specified with bloutput
options: ’’, ’csv’
default: ’’ (same as in the past, easy to read but huge)
showprogress -- show progress status for large data
options: (bool) True, False
default: True
>>> showprogress expandable parameter
minnrow -- minimum number of input spectra to show progress status
default: 1000
outfile -- name of output file
default: ’’ (<infile>_cal)
outform -- output file format
options: ’ASAP’,’MS2’, ’ASCII’,’SDFITS’
default: ’ASAP’
NOTE the ASAP format is easiest for further sd
processing; use MS2 for CASA imaging.
If ASCII, then will append some stuff to
the outfile name
overwrite -- overwrite the output file if already exists
options: (bool) True,False
default: False
NOTE this parameter is ignored when outform=’ASCII’
plotlevel -- control for plotting and summary of results
options: (int) 0, 1, 2, and their negative counterparts
default: 0 (no plotting)
example: plotlevel=1; show plot of spectra (see description of
the parameter in sdcal, sdaverage, and sdbaseline)
plotlevel=2; additionally list data before and after operation.
plotlevel<0 as abs(plotlevel), e.g.
-1 => hardcopy of final plot at each step, i.e.,
<outfile>_calspec.eps, <outfile>_smspec.eps, and/or
<outfile>_bsspec.eps
-------
WARNING
-------
For the GBT raw SDFITS format data as input:
SDtasks are able to handle GBT raw SDFITS format data since the
data filler is available. However, the functionality is not well
tested yet, so that there may be unknown bugs.
More information about CASA may be found at the
CASA web page
Copyright © 2016 Associated Universities Inc., Washington, D.C.
This code is available under the terms of the GNU General Public Lincense
Home |
Contact Us |
Directories |
Site Map |
Help |
Privacy Policy |
Search