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casa
$Rev:20696$
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casa
$Rev:20696$
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Functions | |
| def | sdreduce |
| def sdreduce.sdreduce | ( | infile = '', |
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antenna = 0, |
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fluxunit = '', |
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telescopeparm = '', |
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specunit = '', |
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restfreq = '', |
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frame = '', |
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doppler = '', |
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calmode = 'none', |
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fraction = '10%', |
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noff = -1, |
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width = 0.5, |
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elongated = False, |
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markonly = False, |
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plotpointings = False, |
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scanlist = [], |
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field = '', |
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iflist = [], |
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pollist = [], |
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channelrange = [], |
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average = False, |
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scanaverage = False, |
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timeaverage = False, |
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tweight = 'none', |
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averageall = False, |
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polaverage = False, |
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pweight = 'none', |
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tau = 0.0, |
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kernel = 'none', |
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kwidth = 5, |
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chanwidth = '5', |
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masklist = [], |
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maskmode = 'auto', |
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thresh = 5.0, |
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avg_limit = 4, |
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edge = [0], |
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blfunc = 'none', |
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order = 5, |
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npiece = 2, |
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applyfft = True, |
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fftmethod = 'fft', |
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fftthresh = 3.0, |
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addwn = [], |
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rejwn = [], |
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clipthresh = 3.0, |
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clipniter = 0, |
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verifycal = False, |
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verifysm = False, |
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verifybl = False, |
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verbosebl = True, |
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bloutput = True, |
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blformat = '', |
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showprogress = True, |
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minnrow = 1000, |
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outfile = '', |
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outform = 'ASAP', |
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overwrite = False, |
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plotlevel = 0 |
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| ) |
ASAP SD task: do sdcal, sdsmooth, and sdbaseline in one task
Keyword arguments:
infile -- name of input SD dataset
antenna -- antenna name or id (only effective for MS input).
fluxunit -- units for line flux
options: 'K','Jy',''
default: '' (keep current fluxunit)
WARNING: For GBT data, see description below.
>>> fluxunit expandable parameter
telescopeparm -- the telescope characteristics
options: (str) name or (list) list of gain info
default: '' (none set)
example: if telescopeparm='', 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.
telescopeparm=[104.9,0.43] diameter(m), ap.eff.
telescopeparm=[0.743] gain in Jy/K
telescopeparm='FIX' to change default fluxunit
see description below
specunit -- units for spectral axis
options: (str) 'channel','km/s','GHz','MHz','kHz','Hz',''
default: '' (=current)
example: this will be the units for masklist
>>> specunit expandable parameters
restfreq -- 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 nIF. dictionary
input should be a pair of molecule name and frequency with
keys of 'name' and 'value', respectively. values in the
dictionary input follows the same manner 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 frame for spectral axis
options: (str) 'LSRK','REST','TOPO','LSRD','BARY',
'GEO','GALACTO','LGROUP','CMB'
default: currently set frame in scantable
WARNING: frame='REST' not yet implemented
doppler -- doppler mode
options: (str) 'RADIO','OPTICAL','Z','BETA','GAMMA'
default: currently set doppler in scantable
calmode -- calibration mode
options: 'ps','nod','fs','fsotf','quotient','none'
default: 'none'
example: choose mode 'none' if you have
already calibrated and want to
try baselines or averaging
>>> calmode expandable parameter
fraction -- Edge marking parameter for 'otf' and 'otfraster'.
specify a number of OFF scans as a fraction of
total number of data points.
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.
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.
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.
default: False
scanlist -- list of scan numbers to process
default: [] (use all scans)
example: [21,22,23,24]
this selection is in addition to field, iflist, and pollist
field -- selection string for selecting scans by name
default: '' (no name selection)
example: 'FLS3a*'
this selection is in addition to scanlist, iflist, and pollist
iflist -- list of IF id numbers to select
default: [] (use all IFs)
example: [15]
this selection is in addition to scanlist, field, and pollist
pollist -- list of polarization id numbers to select
default: [] (use all polarizations)
example: [1]
this selection is in addition to scanlist, field, and iflist
channelrange -- channel range selection
default: [] (use all channel)
example: [0,5000]
Note that specified values are recognized as 'channel'
regardless of the value of specunit
average -- averaging on spectral data
options: (bool) True,False
default: False
>>>average expandable parameter
scanaverage -- average integrations within scans
options: (bool) True,False
default: False
example: if True, this happens in read-in
For GBT, set False!
timeaverage -- average times for multiple scan cycles
options: (bool) True,False
default: False
example: if True, this happens after calibration
tweight -- weighting for time average
options: 'none'
'var' (1/var(spec) weighted)
'tsys' (1/Tsys**2 weighted)
'tint' (integration time weighted)
'tintsys' (Tint/Tsys**2)
'median' ( median averaging)
default: 'none'
averageall -- average multi-resolution spectra
spectra are averaged by referring
their frequency coverage
default: False
polaverage -- average polarizations
options: (bool) True,False
default: False
pweight -- weighting for polarization average
options: 'none'
'var' (1/var(spec) weighted)
'tsys' (1/Tsys**2 weighted)
tau -- atmospheric optical depth
default: 0.0 (no correction)
kernel -- type of spectral smoothing
options: 'none','hanning','gaussian','boxcar','regrid'
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'
masklist -- list or string of mask regions to INCLUDE in BASELINE fit
a string masklist allows per IF selection of channels.
default: [] (entire spectrum)
example: [[1000,3000],[5000,7000]]
'0:1000~3000;5000~7000, 1:200~350;450~600'
when maskmode is 'auto' or 'interact', this mask
will be applied first before fitting as base mask
maskmode -- mode of setting additional channel masks for baselining
options: (str) 'auto','list','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
default: 5
example: a single channel S/N ratio above which the channel is
considered to be a detection
avg_limit -- channel averaging for broad lines
default: 4
example: a number of consecutive channels not greater than
this parameter can be averaged to search for broad lines
edge -- channels to drop at beginning and end of spectrum
default: 0
example: [1000] drops 1000 channels at beginning AND end
[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: (str) 'none','poly','chebyshev','cspline','sinusoid'
default: 'none' (no baselining)
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 polynomial
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,
e.g., '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).
default: []
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
default: 0 (no iteration, i.e., no clipping)
verifycal -- verify the results of calibration
options: (bool) True,False
default: False
WARNING: Currently verifying parameters just asks whether you
accept the displayed calibraion/fit and if not,
continues without doing any calibraion/baseline fit.
verifysm -- verify the results of smoothing
options: (bool) True,False
default: False
Note: verification is not yet available for kernel='regrid'
verifybl -- verify the results of baseline fitting
options: (bool) True,False
default: False
NOTE: Currently available only when blfunc='poly'
verbosebl -- output fitting results to logger
default: True
example: If False, the fitting results including coefficients,
residual rms, etc., are not output to the CASA logger,
while the processing speed gets faster
bloutput -- output fitting results to a text file
default: True
example: 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
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
default: True
minnrow -- minimum number of input spectra to show progress status
default: 1000
outfile -- Name of output file
default: '' (<infile>_cal)
outform -- format of output file
options: 'ASCII','SDFITS','MS','ASAP'
default: 'ASAP'
example: the ASAP format is easiest for further sd
processing; use MS 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
WARNING: if outform='ASCII', this parameter is ignored
plotlevel -- control for plotting of results
options: (int) 0=none, 1=some, 2=more, <0=hardcopy
default: 0 (no plotting)
example: plotlevel<0 as abs(plotlevel), e.g.
-1 => hardcopy of final plot (will be named
<outfile>_calspec.eps)
WARNING: be careful plotting in fsotf mode!
DESCRIPTION:
Task sdreduce performs data selection, calibration, and/or spectral
baseline fitting for single-dish spectra. This task internally calls the
tasks, sdcal, sdsmooth, and sdbaseline and it can be used to run all the
three steps in one task execution.
By setting calmode='none', one can run sdreduce on already calibrated data,
for further selection, averaging and atmospheric optical depth correction.
To save the output spectra in a certain range of channels, you set the
range in channelrange.
If you give multiple IFs in iflist, then your scantable will have
multiple IFs by default. Averaging of multi-resolution (multi-IFs)
spectra can be achieved by setting a sub-parameter of average,
averageall, to True. It handles multi-IFs by selecting overlaps in
frequency coverages and assigning new IFs in the output spectra.
ASAP recognizes the data of the "AT" telescopes, but currently
does not know about the GBT or any other telescope. This task
does know about GBT. Telescope name is obtained from the data.
If you wish to change the fluxunit (see below), by leaving
the sub-parameter telescopeparm unset (telescopeparm=''),
it will use internal telescope parameters for
flux conversion for the data from AT telescopes and it will use an
approximate aperture efficiency conversion for the GBT data.
If you give telescopeparm a list, then if the list has a single float it
is assumed to be the gain in Jy/K, if two or more elements they are assumed
to be telescope diameter (m) and aperture efficiency
respectively.
Note that sdreduce assumes that the fluxunit is set correctly in
the data already. If not, then set telescopeparm='FIX' and it
will set the default units to fluxunit without conversion.
NOTE: If the data in infile is an ms from GBT and the default flux
unit is missing and this task automatically fixes the default fluxunit
to 'K' before the conversion.
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. Definition at line 13 of file sdreduce.py.
References task_sdreduce.sdreduce(), and vla_uvfits_line_sf.verify.
1.8.0