Public Member Functions
def	__init__
def	result
def	__call__
def	paramgui
def	defaults
def	check_params
def	description
def	itsdefault
Public Attributes
	parameters
Static Public Attributes
	rkey
	Handle globals or user over-ride of arguments.
	i_am_a_casapy_task
list	retval
	This function sets the default values but also will return the list of parameters or the default value of a given parameter.
string	valornotval
tuple	retval
Private Attributes
	__bases__
	__doc__
	__globals__
Static Private Attributes
string	__name__
dictionary	__async__

Detailed Description

Definition at line 18 of file sdbaseline_cli.py.

Constructor & Destructor Documentation

def sdbaseline_cli.sdbaseline_cli_.__init__ ( self )

Definition at line 26 of file sdbaseline_cli.py.

Member Function Documentation

def sdbaseline_cli.sdbaseline_cli_.__call__	(	self,
		infile = `None`,
		antenna = `None`,
		fluxunit = `None`,
		telescopeparm = `None`,
		specunit = `None`,
		restfreq = `None`,
		frame = `None`,
		doppler = `None`,
		scanlist = `None`,
		field = `None`,
		iflist = `None`,
		pollist = `None`,
		tau = `None`,
		masklist = `None`,
		maskmode = `None`,
		thresh = `None`,
		avg_limit = `None`,
		edge = `None`,
		blfunc = `None`,
		order = `None`,
		npiece = `None`,
		applyfft = `None`,
		fftmethod = `None`,
		fftthresh = `None`,
		addwn = `None`,
		rejwn = `None`,
		clipthresh = `None`,
		clipniter = `None`,
		verify = `None`,
		verbose = `None`,
		bloutput = `None`,
		blformat = `None`,
		showprogress = `None`,
		minnrow = `None`,
		outfile = `None`,
		outform = `None`,
		overwrite = `None`,
		plotlevel = `None`,
		async = `None`
	)

ASAP SD task: fit/subtract a spectral baseline 
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
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
tau -- atmospheric optical depth
default: 0.0 (no correction)
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
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) 'poly','chebyshev','cspline','sinusoid'
default: 'poly'
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: [0] (i.e., constant is subtracted at least)
 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)
verify -- verify the results of baseline fitting
options: (bool) True,False
default: False
NOTE: Currently available only when blfunc='poly'
WARNING: Currently this just asks whether you accept
         the displayed fit and if not, continues
         without doing any baseline fit.
verbose -- 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>_bs)
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>_bspec.eps)
WARNING: be careful plotting in fsotf mode!



DESCRIPTION:

Task sdbaseline performs baseline fitting/removal for single-dish spectra.
The fit parameters, terms and rms of base-line are saved to an ascii 
file, '<outfile>_blparam.txt'. 

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), and telescopeparm='',
for the AT telescopes it will use internal telescope parameters for
flux conversion. For GBT, it will use an approximate aperture
efficiency conversion.  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 sdbaseline 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 46 of file sdbaseline_cli.py.

def sdbaseline_cli.sdbaseline_cli_.check_params	(	self,
		param = `None`,
		value = `None`,
		ipython_globals = `None`
	)

Definition at line 592 of file sdbaseline_cli.py.

def sdbaseline_cli.sdbaseline_cli_.defaults	(	self,
		param = `None`,
		ipython_globals = `None`,
		paramvalue = `None`,
		subparam = `None`
	)

Definition at line 498 of file sdbaseline_cli.py.

def sdbaseline_cli.sdbaseline_cli_.description	(	self,
		key = `'sdbaseline'`,
		subkey = `None`
	)

Definition at line 623 of file sdbaseline_cli.py.

def sdbaseline_cli.sdbaseline_cli_.itsdefault	(	self,
		paramname
	)

Definition at line 674 of file sdbaseline_cli.py.

def sdbaseline_cli.sdbaseline_cli_.paramgui	(	self,
		useGlobals = `True`,
		ipython_globals = `None`
	)

Opens a parameter GUI for this task.  If useGlobals is true, then any relevant global parameter settings are used.

Definition at line 474 of file sdbaseline_cli.py.

def sdbaseline_cli.sdbaseline_cli_.result	(	self,
		key = `None`
	)

Definition at line 33 of file sdbaseline_cli.py.

References accum_cli.accum_cli_.__async__, sdbaseline_cli.sdbaseline_cli_.__async__, rmtables_cli.rmtables_cli_.__async__, predictcomp_cli.predictcomp_cli_.__async__, polcal_cli.polcal_cli_.__async__, plotxy_cli.plotxy_cli_.__async__, plotweather_cli.plotweather_cli_.__async__, plotuv_cli.plotuv_cli_.__async__, plotms_cli.plotms_cli_.__async__, plotcal_cli.plotcal_cli_.__async__, plotants_cli.plotants_cli_.__async__, peel_cli.peel_cli_.__async__, pclean_cli.pclean_cli_.__async__, partition_cli.partition_cli_.__async__, msview_cli.msview_cli_.__async__, msmoments_cli.msmoments_cli_.__async__, mosaic_cli.mosaic_cli_.__async__, makemask_cli.makemask_cli_.__async__, listvis_cli.listvis_cli_.__async__, listsdm_cli.listsdm_cli_.__async__, listpartition_cli.listpartition_cli_.__async__, listobs_cli.listobs_cli_.__async__, listhistory_cli.listhistory_cli_.__async__, listfits_cli.listfits_cli_.__async__, listcal_cli.listcal_cli_.__async__, imview_cli.imview_cli_.__async__, imval_cli.imval_cli_.__async__, imtrans_cli.imtrans_cli_.__async__, imsubimage_cli.imsubimage_cli_.__async__, imstat_cli.imstat_cli_.__async__, imsmooth_cli.imsmooth_cli_.__async__, imregrid_cli.imregrid_cli_.__async__, imreframe_cli.imreframe_cli_.__async__, importvla_cli.importvla_cli_.__async__, importuvfits_cli.importuvfits_cli_.__async__, importgmrt_cli.importgmrt_cli_.__async__, importfitsidi_cli.importfitsidi_cli_.__async__, importfits_cli.importfits_cli_.__async__, importevla_cli.importevla_cli_.__async__, importasdm_cli.importasdm_cli_.__async__, impbcor_cli.impbcor_cli_.__async__, immoments_cli.immoments_cli_.__async__, immath_cli.immath_cli_.__async__, imhead_cli.imhead_cli_.__async__, imfit_cli.imfit_cli_.__async__, imcontsub_cli.imcontsub_cli_.__async__, imcollapse_cli.imcollapse_cli_.__async__, hanningsmooth_cli.hanningsmooth_cli_.__async__, gencal_cli.gencal_cli_.__async__, gaincal_cli.gaincal_cli_.__async__, ft_cli.ft_cli_.__async__, fluxscale_cli.fluxscale_cli_.__async__, flagmanager_cli.flagmanager_cli_.__async__, flagdata_cli.flagdata_cli_.__async__, flagcmd_cli.flagcmd_cli_.__async__, fixvis_cli.fixvis_cli_.__async__, fixplanets_cli.fixplanets_cli_.__async__, find_cli.find_cli_.__async__, feather_cli.feather_cli_.__async__, exportuvfits_cli.exportuvfits_cli_.__async__, exportfits_cli.exportfits_cli_.__async__, exportasdm_cli.exportasdm_cli_.__async__, delmod_cli.delmod_cli_.__async__, deconvolve_cli.deconvolve_cli_.__async__, cvel_cli.cvel_cli_.__async__, csvclean_cli.csvclean_cli_.__async__, conjugatevis_cli.conjugatevis_cli_.__async__, concat_cli.concat_cli_.__async__, clearstat_cli.clearstat_cli_.__async__, clearplot_cli.clearplot_cli_.__async__, clearcal_cli.clearcal_cli_.__async__, clean_cli.clean_cli_.__async__, caltabconvert_cli.caltabconvert_cli_.__async__, calstat_cli.calstat_cli_.__async__, browsetable_cli.browsetable_cli_.__async__, boxit_cli.boxit_cli_.__async__, blcal_cli.blcal_cli_.__async__, bandpass_cli.bandpass_cli_.__async__, autoclean_cli.autoclean_cli_.__async__, asdmsummary_cli.asdmsummary_cli_.__async__, and applycal_cli.applycal_cli_.__async__.

Member Data Documentation

dictionary sdbaseline_cli.sdbaseline_cli_.__async__ [static, private]

Definition at line 20 of file sdbaseline_cli.py.

Referenced by sdbaseline_cli.sdbaseline_cli_.result(), wvrgcal_cli.wvrgcal_cli_.result(), widefield_cli.widefield_cli_.result(), widebandpbcor_cli.widebandpbcor_cli_.result(), visstat_cli.visstat_cli_.result(), vishead_cli.vishead_cli_.result(), virtualconcat_cli.virtualconcat_cli_.result(), viewer_cli.viewer_cli_.result(), uvsub_cli.uvsub_cli_.result(), uvmodelfit_cli.uvmodelfit_cli_.result(), uvcontsub_cli.uvcontsub_cli_.result(), uvcontsub3_cli.uvcontsub3_cli_.result(), uvcontsub2_cli.uvcontsub2_cli_.result(), testconcat_cli.testconcat_cli_.result(), tclean_cli.tclean_cli_.result(), statwt_cli.statwt_cli_.result(), ssoflux_cli.ssoflux_cli_.result(), split_cli.split_cli_.result(), splattotable_cli.splattotable_cli_.result(), specfit_cli.specfit_cli_.result(), smoothcal_cli.smoothcal_cli_.result(), slsearch_cli.slsearch_cli_.result(), simobserve_cli.simobserve_cli_.result(), simanalyze_cli.simanalyze_cli_.result(), simalma_cli.simalma_cli_.result(), setjy_cli.setjy_cli_.result(), sdtpimaging_cli.sdtpimaging_cli_.result(), sdstat_cli.sdstat_cli_.result(), sdsmooth_cli.sdsmooth_cli_.result(), sdscale_cli.sdscale_cli_.result(), sdsave_cli.sdsave_cli_.result(), sdreduce_cli.sdreduce_cli_.result(), sdplot_cli.sdplot_cli_.result(), sdmath_cli.sdmath_cli_.result(), sdlist_cli.sdlist_cli_.result(), sdimprocess_cli.sdimprocess_cli_.result(), sdimaging_cli.sdimaging_cli_.result(), sdgrid_cli.sdgrid_cli_.result(), sdflagmanager_cli.sdflagmanager_cli_.result(), sdflag_cli.sdflag_cli_.result(), sdfit_cli.sdfit_cli_.result(), sdcoadd_cli.sdcoadd_cli_.result(), and sdcal_cli.sdcal_cli_.result().

sdbaseline_cli.sdbaseline_cli_.__bases__ [private]

Definition at line 27 of file sdbaseline_cli.py.

sdbaseline_cli.sdbaseline_cli_.__doc__ [private]

Definition at line 28 of file sdbaseline_cli.py.

sdbaseline_cli.sdbaseline_cli_.__globals__ [private]

Definition at line 291 of file sdbaseline_cli.py.

string sdbaseline_cli.sdbaseline_cli_.__name__ [static, private]

Definition at line 19 of file sdbaseline_cli.py.

sdbaseline_cli.sdbaseline_cli_.i_am_a_casapy_task [static]

Definition at line 22 of file sdbaseline_cli.py.

sdbaseline_cli.sdbaseline_cli_.parameters

Definition at line 30 of file sdbaseline_cli.py.

tuple sdbaseline_cli.sdbaseline_cli_.retval [static]

This function sets the default values but also will return the list of parameters or the default value of a given parameter.

Definition at line 571 of file sdbaseline_cli.py.

tuple sdbaseline_cli.sdbaseline_cli_.retval [static]

Definition at line 584 of file sdbaseline_cli.py.

sdbaseline_cli.sdbaseline_cli_.rkey [static]

Handle globals or user over-ride of arguments.

Definition at line 21 of file sdbaseline_cli.py.

string sdbaseline_cli.sdbaseline_cli_.valornotval [static]

Definition at line 574 of file sdbaseline_cli.py.

The documentation for this class was generated from the following file:

sdbaseline_cli.py

Public Member Functions

Public Attributes

Static Public Attributes

Private Attributes

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation