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asap.asapfitter.fitter Class Reference

List of all members.

Public Member Functions

def __init__
def set_data
def set_scan
def set_function
def fit
def store_fit
def set_parameters
def set_gauss_parameters
def set_lorentz_parameters
def set_sinusoid_parameters
def add_constraint
def get_area
def get_errors
def get_parameters
def get_estimate
def get_residual
def get_chi2
def get_fit
def commit
def plot
def auto_fit

Public Attributes

 fitter
 x
 y
 mask
 fitfunc
 fitfuncs
 fitted
 data
 components
 uselinear
 blpars

Private Member Functions

def _format_pars

Private Attributes

 _fittedrow
 _p
 _selection
 _constraints

Detailed Description

The fitting class for ASAP.

Definition at line 7 of file asapfitter.py.

Constructor & Destructor Documentation

def asap.asapfitter.fitter.__init__ (   self) 
Create a fitter object. No state is set.

Definition at line 11 of file asapfitter.py.

Member Function Documentation

def asap.asapfitter.fitter._format_pars (   self,
  pars,
  fixed,
  errors,
  area 
) [private]

Definition at line 472 of file asapfitter.py.

References asap.asapfitter.fitter.data, and asap.asapfitter.fitter.fitfunc.

Referenced by asap.asapfitter.fitter.get_estimate(), and asap.asapfitter.fitter.get_parameters().

def asap.asapfitter.fitter.add_constraint (   self,
  xpar,
  y 
) 
Add parameter constraints to the fit. This is done by setting up
linear equations for the related parameters.

For example a two component gaussian fit where the amplitudes are
constraint by amp1 = 2*amp2 and paramaters for the two components
in the order [amp1,peakv1,sigma1,amp2,peakv2,sigma2]
needs a constraint

    add_constraint([1, 0, 0, -2, 0, 0], 0)

as the linear equation is
    
    1*amp1 + 0*peakv1 + 0*sigma1 -2*amp2 + 0*peakv2 + 0*sigma2 = 0

and similarly for a velocity difference of v2-v1=17

    add_constraint([0.,-1.,0.,0.,1.,0.], 17.)

Definition at line 357 of file asapfitter.py.

def asap.asapfitter.fitter.auto_fit (   self,
  insitu = None,
  plot = False 
) 
Return a scan where the function is applied to all rows for
all Beams/IFs/Pols.

Definition at line 682 of file asapfitter.py.

References asap.asapfitter.fitter.data.

def asap.asapfitter.fitter.commit (   self) 
Return a new scan where the fits have been commited (subtracted)

Definition at line 557 of file asapfitter.py.

References asap.asapfitter.fitter.data, asap.asapfitter.fitter.fitted, and asap.asapfitter.fitter.plot().

def asap.asapfitter.fitter.fit (   self,
  row = 0,
  estimate = False 
) 
Execute the actual fitting process. All the state has to be set.
Parameters:
    row:        specify the row in the scantable
    estimate:   auto-compute an initial parameter set (default False)
        This can be used to compute estimates even if fit was
        called before.
Example:
    s = scantable('myscan.asap')
    s.set_cursor(thepol=1)        # select second pol
    f = fitter()
    f.set_scan(s)
    f.set_function(poly=0)
    f.fit(row=0)                  # fit first row

Definition at line 137 of file asapfitter.py.

References asap.asapfitter.fitter._constraints, asap.asapfitter.fitter._fittedrow, asap.asapfitter.fitter.data, asap.asapfitter.fitter.fitfunc, asap.asapfitter.fitter.fitted, tests.test_imcontsub.list, asap.asapfitter.fitter.mask, asap.utils.mask_and(), asap.asapfitter.fitter.uselinear, asap.asapfitter.fitter.x, and asap.asapfitter.fitter.y.

def asap.asapfitter.fitter.get_area (   self,
  component = None 
) 
Return the area under the fitted gaussian/lorentzian component.
Parameters:
      component:   the gaussian/lorentzian component selection,
           default (None) is the sum of all components
Note:
      This will only work for gaussian/lorentzian fits.

Definition at line 380 of file asapfitter.py.

References asap.asapfitter.fitter.components, asap.asapfitter.fitter.fitfunc, asap.asapfitter.fitter.fitted, tests.test_imcontsub.list, and irc_cs_task_regression.sum.

Referenced by asap.asapfitter.fitter.get_parameters().

def asap.asapfitter.fitter.get_chi2 (   self) 
Return chi^2.

Definition at line 535 of file asapfitter.py.

References asap.asapfitter.fitter.fitted.

def asap.asapfitter.fitter.get_errors (   self,
  component = None 
) 
Return the errors in the parameters.
Parameters:
    component:    get the errors for the specified component
          only, default is all components

Definition at line 410 of file asapfitter.py.

References asap.asapfitter.fitter.fitfunc, asap.asapfitter.fitter.fitted, and tests.test_imcontsub.list.

def asap.asapfitter.fitter.get_estimate (   self) 
Return the parameter estimates (for non-linear functions).

Definition at line 515 of file asapfitter.py.

References asap.asapfit.asapfit._format_pars(), and asap.asapfitter.fitter._format_pars().

def asap.asapfitter.fitter.get_fit (   self) 
Return the fitted ordinate values.

Definition at line 547 of file asapfitter.py.

References asap.asapfitter.fitter.fitted.

def asap.asapfitter.fitter.get_parameters (   self,
  component = None,
  errors = False 
) 
Return the fit paramters.
Parameters:
     component:    get the parameters for the specified component
           only, default is all components

Definition at line 432 of file asapfitter.py.

References asap.asapfit.asapfit._format_pars(), asap.asapfitter.fitter._format_pars(), asap.asapfitter.fitter.components, asap.asapfitter.fitter.fitfunc, asap.asapfitter.fitter.fitted, asap.asapfitter.fitter.get_area(), and tests.test_imcontsub.list.

Referenced by asap.asapfitter.fitter.plot().

def asap.asapfitter.fitter.get_residual (   self) 
Return the residual of the fit.

Definition at line 525 of file asapfitter.py.

References asap.asapfitter.fitter.fitted.

Referenced by asap.asapfitter.fitter.plot().

def asap.asapfitter.fitter.plot (   self,
  residual = False,
  components = None,
  plotparms = False,
  filename = None 
) 
Plot the last fit.
Parameters:
    residual:    an optional parameter indicating if the residual
         should be plotted (default 'False')
    components:  a list of components to plot, e.g [0,1],
         -1 plots the total fit. Default is to only
         plot the total fit.
    plotparms:   Inidicates if the parameter values should be present
         on the plot

Definition at line 574 of file asapfitter.py.

References asap.asapfitter.fitter._fittedrow, asap.asapfitter.fitter._p, listvis_regression.array, asap.asapfitter.fitter.components, asap.asapfitter.fitter.data, asap.asapfitter.fitter.fitfuncs, asap.asapfitter.fitter.fitted, asap.asapfitter.fitter.get_parameters(), asap.asapfitter.fitter.get_residual(), asap.asapfitter.fitter.mask, irc_cs_task_regression.max, asap.asapplotter.new_asaplot(), asap.asapfitter.fitter.x, and asap.asapfitter.fitter.y.

Referenced by asap.asapfitter.fitter.commit(), task_sdgrid.sdgrid_worker.finalize(), asap.asaplotbase.asaplotbase.hist(), asap.asapplotter.asapplotter.set_abcissa(), asap.asapplotter.asapplotter.set_colors(), asap.asapplotter.asapplotter.set_data(), asap.asapplotter.asapplotter.set_font(), asap.asapplotter.asapplotter.set_histogram(), asap.asapplotter.asapplotter.set_layout(), asap.asapplotter.asapplotter.set_legend(), asap.asapplotter.asapplotter.set_linestyles(), asap.asapplotter.asapplotter.set_margin(), asap.asapplotter.asapplotter.set_mask(), asap.asapplotter.asapplotter.set_mode(), asap.asapplotter.asapplotter.set_ordinate(), asap.asapplotter.asapplotter.set_range(), asap.asapplotter.asapplotter.set_selection(), and asap.asapplotter.asapplotter.set_title().

def asap.asapfitter.fitter.set_data (   self,
  xdat,
  ydat,
  mask = None 
) 
Set the absissa and ordinate for the fit. Also set the mask
indicating valid points.
This can be used for data vectors retrieved from a scantable.
For scantable fitting use 'fitter.set_scan(scan, mask)'.
Parameters:
    xdat:    the abcissa values
    ydat:    the ordinate values
    mask:    an optional mask

Definition at line 30 of file asapfitter.py.

References asap.utils._n_bools(), asap.asapfitter.fitter.fitted, asap.asapfitter.fitter.mask, asap.asapfitter.fitter.x, and asap.asapfitter.fitter.y.

Referenced by asap.asapplotter.asapplotter.plot(), and asap.asapplotter.asapplotter.plotgrid().

def asap.asapfitter.fitter.set_function (   self,
  kwargs 
) 
Set the function to be fit.
Parameters:
    poly:     use a polynomial of the order given with nonlinear 
      least squares fit
    lpoly:    use polynomial of the order given with linear least 
      squares fit
    gauss:    fit the number of gaussian specified
    lorentz:  fit the number of lorentzian specified
    sinusoid: fit the number of sinusoid specified
Example:
    fitter.set_function(poly=3)  # will fit a 3rd order polynomial 
                         # via nonlinear method
    fitter.set_function(lpoly=3)  # will fit a 3rd order polynomial 
                          # via linear method
    fitter.set_function(gauss=2) # will fit two gaussians
    fitter.set_function(lorentz=2) # will fit two lorentzians
    fitter.set_function(sinusoid=3) # will fit three sinusoids

Definition at line 72 of file asapfitter.py.

References asap.asapfitter.fitter._constraints, asap.asapfitter.fitter.components, asap.asapfitter.fitter.fitfunc, asap.asapfitter.fitter.fitfuncs, asap.asapfitter.fitter.fitted, and asap.asapfitter.fitter.uselinear.

def asap.asapfitter.fitter.set_gauss_parameters (   self,
  peak,
  centre,
  fwhm,
  peakfixed = 0,
  centrefixed = 0,
  fwhmfixed = 0,
  component = 0 
) 
Set the Parameters of a 'Gaussian' component, set with set_function.
Parameters:
    peak, centre, fwhm:  The gaussian parameters
    peakfixed,
    centrefixed,
    fwhmfixed:           Optional parameters to indicate if
                 the paramters should be held fixed during
                 the fitting process. The default is to keep
                 all parameters flexible.
    component:           The number of the component (Default is the
                 component 0)

Definition at line 273 of file asapfitter.py.

References asap.asapfitter.fitter.components, asap.asapfitter.fitter.fitfunc, asap.asapfitter.fitter.set_lorentz_parameters(), and asap.asapfitter.fitter.set_parameters().

Referenced by asap.asapfitter.fitter.set_parameters().

def asap.asapfitter.fitter.set_lorentz_parameters (   self,
  peak,
  centre,
  fwhm,
  peakfixed = 0,
  centrefixed = 0,
  fwhmfixed = 0,
  component = 0 
) 
Set the Parameters of a 'Lorentzian' component, set with set_function.
Parameters:
    peak, centre, fwhm:  The lorentzian parameters
    peakfixed,
    centrefixed,
    fwhmfixed:           Optional parameters to indicate if
                 the paramters should be held fixed during
                 the fitting process. The default is to keep
                 all parameters flexible.
    component:           The number of the component (Default is the
                 component 0)

Definition at line 302 of file asapfitter.py.

References asap.asapfitter.fitter.components, asap.asapfitter.fitter.fitfunc, asap.asapfitter.fitter.set_parameters(), and asap.asapfitter.fitter.set_sinusoid_parameters().

Referenced by asap.asapfitter.fitter.set_gauss_parameters().

def asap.asapfitter.fitter.set_parameters (   self,
  args,
  kwargs 
) 
Set the parameters to be fitted.
Parameters:
      params:    a vector of parameters
      fixed:     a vector of which parameters are to be held fixed
         (default is none)
      component: in case of multiple gaussians/lorentzians/sinusoidals,
         the index of the target component

Definition at line 228 of file asapfitter.py.

References asap.utils._n_bools(), asap.asapfitter.fitter.components, asap.asapfitter.fitter.fitfunc, asap.asapfitter.fitter.fitted, tests.test_imcontsub.list, asap.asapfitter.fitter.set_gauss_parameters(), and irc_cs_task_regression.sum.

Referenced by asap.asapfitter.fitter.set_gauss_parameters(), asap.asapfitter.fitter.set_lorentz_parameters(), and asap.asapfitter.fitter.set_sinusoid_parameters().

def asap.asapfitter.fitter.set_scan (   self,
  thescan = None,
  mask = None 
) 
Set the 'data' (a scantable) of the fitter.
Parameters:
    thescan:     a scantable
    mask:        a msk retrieved from the scantable

Definition at line 52 of file asapfitter.py.

References asap.utils._n_bools(), asap.asapfitter.fitter.data, asap.asapfitter.fitter.fitted, and asap.asapfitter.fitter.mask.

def asap.asapfitter.fitter.set_sinusoid_parameters (   self,
  ampl,
  period,
  x0,
  amplfixed = 0,
  periodfixed = 0,
  x0fixed = 0,
  component = 0 
) 
Set the Parameters of a 'Sinusoidal' component, set with set_function.
Parameters:
    ampl, period, x0:  The sinusoidal parameters
    amplfixed,
    periodfixed,
    x0fixed:             Optional parameters to indicate if
                 the paramters should be held fixed during
                 the fitting process. The default is to keep
                 all parameters flexible.
    component:           The number of the component (Default is the
                 component 0)

Definition at line 331 of file asapfitter.py.

References asap.asapfitter.fitter.components, asap.asapfitter.fitter.fitfunc, and asap.asapfitter.fitter.set_parameters().

Referenced by asap.asapfitter.fitter.set_lorentz_parameters().

def asap.asapfitter.fitter.store_fit (   self,
  filename = None 
) 
Save the fit parameters.
Parameters:
    filename:    if specified save as an ASCII file, if None (default)
         store it in the scnatable

Definition at line 201 of file asapfitter.py.

References asap.asapfitter.fitter._fittedrow, asap.asapfitter.fitter.components, asap.asapfitter.fitter.data, asap.asapfitter.fitter.fitfuncs, asap.asapfitter.fitter.fitted, and tests.test_imcontsub.list.

Member Data Documentation

asap.asapfitter.fitter.fitter

Definition at line 15 of file asapfitter.py.

Referenced by task_sdfit.sdfit_worker.__initial_guess().

asap.asapfitter.fitter._constraints [private]

Definition at line 28 of file asapfitter.py.

Referenced by asap.asapfitter.fitter.fit(), and asap.asapfitter.fitter.set_function().

asap.asapfitter.fitter._fittedrow [private]

Definition at line 24 of file asapfitter.py.

Referenced by asap.asapfitter.fitter.fit(), asap.asapfitter.fitter.plot(), and asap.asapfitter.fitter.store_fit().

asap.asapfitter.fitter._p [private]

Definition at line 25 of file asapfitter.py.

Referenced by asap.asapfitter.fitter.plot().

asap.asapfitter.fitter._selection [private]

Definition at line 26 of file asapfitter.py.

Referenced by asap.asapplotter.asapplotter._plot(), and asap.asapplotter.asapplotter.set_selection().

asap.asapfitter.fitter.blpars

Definition at line 700 of file asapfitter.py.

asap.asapfitter.fitter.components

Definition at line 23 of file asapfitter.py.

Referenced by asap.asapfitter.fitter.get_area(), asap.asapfitter.fitter.get_parameters(), asap.asapfitter.fitter.plot(), asap.asapfitter.fitter.set_function(), asap.asapfitter.fitter.set_gauss_parameters(), asap.asapfitter.fitter.set_lorentz_parameters(), asap.asapfitter.fitter.set_parameters(), asap.asapfitter.fitter.set_sinusoid_parameters(), and asap.asapfitter.fitter.store_fit().

asap.asapfitter.fitter.data

Definition at line 22 of file asapfitter.py.

Referenced by asap.asapfitter.fitter._format_pars(), tests.test_sdgrid.sdgrid_flagging._testresult(), asap.asapfitter.fitter.auto_fit(), asap.asapfitter.fitter.commit(), asap.asapfitter.fitter.fit(), tests.test_sdgrid.sdgrid_unittest_base.getdata(), asap.asapfitter.fitter.plot(), asap.asapfitter.fitter.set_scan(), asap.asapfitter.fitter.store_fit(), tests.test_sdgrid.sdgrid_single_integ.test100(), tests.test_sdgrid.sdgrid_single_integ.test101(), tests.test_sdgrid.sdgrid_single_integ.test102(), tests.test_sdgrid.sdgrid_single_integ.test103(), tests.test_sdgrid.sdgrid_clipping.test200(), tests.test_sdgrid.sdgrid_weighting.test400(), tests.test_sdgrid.sdgrid_weighting.test401(), tests.test_sdgrid.sdgrid_weighting.test402(), tests.test_sdgrid.sdgrid_weighting.test403(), tests.test_sdgrid.sdgrid_map.test500(), tests.test_sdgrid.sdgrid_map.test501(), tests.test_sdgrid.sdgrid_map.test502(), and tests.test_sdgrid.sdgrid_map.test503().

asap.asapfitter.fitter.fitfunc

Definition at line 19 of file asapfitter.py.

Referenced by task_sdfit.sdfit_worker.__initial_guess(), task_sdfit.sdfit_worker.__store_fit(), asap.asapfitter.fitter._format_pars(), asap.asapfitter.fitter.fit(), asap.asapfitter.fitter.get_area(), asap.asapfitter.fitter.get_errors(), asap.asapfitter.fitter.get_parameters(), asap.asapfitter.fitter.set_function(), asap.asapfitter.fitter.set_gauss_parameters(), asap.asapfitter.fitter.set_lorentz_parameters(), asap.asapfitter.fitter.set_parameters(), and asap.asapfitter.fitter.set_sinusoid_parameters().

asap.asapfitter.fitter.fitfuncs

Definition at line 20 of file asapfitter.py.

Referenced by asap.asapfitter.fitter.plot(), asap.asapfitter.fitter.set_function(), and asap.asapfitter.fitter.store_fit().

asap.asapfitter.fitter.fitted

Definition at line 21 of file asapfitter.py.

Referenced by asap.asapfitter.fitter.commit(), asap.asapfitter.fitter.fit(), asap.asapfitter.fitter.get_area(), asap.asapfitter.fitter.get_chi2(), asap.asapfitter.fitter.get_errors(), asap.asapfitter.fitter.get_fit(), asap.asapfitter.fitter.get_parameters(), asap.asapfitter.fitter.get_residual(), asap.asapfitter.fitter.plot(), asap.asapfitter.fitter.set_data(), asap.asapfitter.fitter.set_function(), asap.asapfitter.fitter.set_parameters(), asap.asapfitter.fitter.set_scan(), and asap.asapfitter.fitter.store_fit().

asap.asapfitter.fitter.mask

Definition at line 18 of file asapfitter.py.

Referenced by asap.interactivemask.interactivemask._plot_mask(), asap.interactivemask.interactivemask._update_mask(), asap.asapfitter.fitter.fit(), asap.interactivemask.interactivemask.get_mask(), asap.asapfitter.fitter.plot(), asap.interactivemask.interactivemask.set_basemask(), asap.asapfitter.fitter.set_data(), asap.asapfitter.fitter.set_scan(), and tests.test_clean.clean_multims_test.test_multims5().

asap.asapfitter.fitter.uselinear

Definition at line 27 of file asapfitter.py.

Referenced by asap.asapfitter.fitter.fit(), and asap.asapfitter.fitter.set_function().

asap.asapfitter.fitter.x

Definition at line 16 of file asapfitter.py.

Referenced by asap.asapfitter.fitter.fit(), asap.asapfitter.fitter.plot(), and asap.asapfitter.fitter.set_data().

asap.asapfitter.fitter.y

Definition at line 17 of file asapfitter.py.

Referenced by asap.asapfitter.fitter.fit(), asap.asapfitter.fitter.plot(), and asap.asapfitter.fitter.set_data().

The documentation for this class was generated from the following file:
Generated on Thu Nov 15 2012 15:57:15 for casa by   doxygen 1.8.0