| [113] | 1 | import _asap
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| [259] | 2 | from asap import rcParams
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| [113] | 3 |
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| 4 | class fitter:
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| 5 | """
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| 6 | The fitting class for ASAP.
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| 7 | """
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| 8 | def _verbose(self, *args):
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| 9 | """
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| 10 | Set stdout output.
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| 11 | """
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| 12 | if type(args[0]) is bool:
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| 13 | self._vb = args[0]
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| 14 | return
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| 15 | elif len(args) == 0:
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| 16 | return self._vb
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| 17 |
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| 18 | def __init__(self):
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| 19 | """
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| 20 | Create a fitter object. No state is set.
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| 21 | """
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| 22 | self.fitter = _asap.fitter()
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| 23 | self.x = None
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| 24 | self.y = None
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| 25 | self.mask = None
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| 26 | self.fitfunc = None
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| [515] | 27 | self.fitfuncs = None
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| [113] | 28 | self.fitted = False
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| 29 | self.data = None
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| [515] | 30 | self.components = 0
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| 31 | self._fittedrow = 0
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| [113] | 32 | self._p = None
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| 33 | self._vb = True
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| [515] | 34 | self._selection = None
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| [113] | 35 |
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| 36 | def set_data(self, xdat, ydat, mask=None):
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| 37 | """
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| [158] | 38 | Set the absissa and ordinate for the fit. Also set the mask
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| [113] | 39 | indicationg valid points.
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| 40 | This can be used for data vectors retrieved from a scantable.
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| 41 | For scantable fitting use 'fitter.set_scan(scan, mask)'.
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| 42 | Parameters:
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| [158] | 43 | xdat: the abcissa values
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| [113] | 44 | ydat: the ordinate values
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| 45 | mask: an optional mask
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| 46 |
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| 47 | """
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| 48 | self.fitted = False
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| 49 | self.x = xdat
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| 50 | self.y = ydat
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| 51 | if mask == None:
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| 52 | from numarray import ones
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| 53 | self.mask = ones(len(xdat))
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| 54 | else:
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| 55 | self.mask = mask
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| 56 | return
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| 57 |
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| 58 | def set_scan(self, thescan=None, mask=None):
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| 59 | """
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| 60 | Set the 'data' (a scantable) of the fitter.
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| 61 | Parameters:
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| 62 | thescan: a scantable
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| 63 | mask: a msk retireved from the scantable
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| 64 | """
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| 65 | if not thescan:
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| 66 | print "Please give a correct scan"
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| 67 | self.fitted = False
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| 68 | self.data = thescan
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| 69 | if mask is None:
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| 70 | from numarray import ones
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| 71 | self.mask = ones(self.data.nchan())
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| 72 | else:
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| 73 | self.mask = mask
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| 74 | return
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| 75 |
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| 76 | def set_function(self, **kwargs):
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| 77 | """
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| 78 | Set the function to be fit.
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| 79 | Parameters:
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| 80 | poly: use a polynomial of the order given
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| 81 | gauss: fit the number of gaussian specified
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| 82 | Example:
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| 83 | fitter.set_function(gauss=2) # will fit two gaussians
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| 84 | fitter.set_function(poly=3) # will fit a 3rd order polynomial
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| 85 | """
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| [515] | 86 | #default poly order 0
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| 87 | n=0
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| [113] | 88 | if kwargs.has_key('poly'):
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| 89 | self.fitfunc = 'poly'
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| 90 | n = kwargs.get('poly')
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| [515] | 91 | self.components = [n]
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| [113] | 92 | elif kwargs.has_key('gauss'):
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| 93 | n = kwargs.get('gauss')
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| 94 | self.fitfunc = 'gauss'
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| [515] | 95 | self.fitfuncs = [ 'gauss' for i in range(n) ]
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| 96 | self.components = [ 3 for i in range(n) ]
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| 97 | else:
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| 98 | print "Invalid function type."
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| 99 | return
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| [113] | 100 | self.fitter.setexpression(self.fitfunc,n)
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| 101 | return
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| 102 |
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| [515] | 103 | def fit(self, row=0):
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| [113] | 104 | """
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| 105 | Execute the actual fitting process. All the state has to be set.
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| 106 | Parameters:
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| [526] | 107 | row: specify the row in the scantable
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| [113] | 108 | Example:
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| [515] | 109 | s = scantable('myscan.asap')
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| 110 | s.set_cursor(thepol=1) # select second pol
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| [113] | 111 | f = fitter()
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| 112 | f.set_scan(s)
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| 113 | f.set_function(poly=0)
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| [515] | 114 | f.fit(row=0) # fit first row
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| [113] | 115 | """
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| 116 | if ((self.x is None or self.y is None) and self.data is None) \
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| 117 | or self.fitfunc is None:
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| 118 | print "Fitter not yet initialised. Please set data & fit function"
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| 119 | return
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| 120 | else:
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| 121 | if self.data is not None:
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| [515] | 122 | self.x = self.data._getabcissa(row)
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| 123 | self.y = self.data._getspectrum(row)
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| [113] | 124 | print "Fitting:"
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| [259] | 125 | vb = self.data._vb
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| 126 | self.data._vb = True
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| [515] | 127 | self.selection = self.data.get_cursor()
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| [259] | 128 | self.data._vb = vb
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| [515] | 129 | self.fitter.setdata(self.x, self.y, self.mask)
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| [113] | 130 | if self.fitfunc == 'gauss':
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| 131 | ps = self.fitter.getparameters()
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| 132 | if len(ps) == 0:
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| 133 | self.fitter.estimate()
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| [626] | 134 | try:
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| 135 | self.fitter.fit()
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| 136 | except RuntimeError, msg:
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| 137 | print msg
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| [515] | 138 | self._fittedrow = row
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| [113] | 139 | self.fitted = True
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| 140 | return
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| 141 |
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| [515] | 142 | def store_fit(self):
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| [526] | 143 | """
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| 144 | Store the fit parameters in the scantable.
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| 145 | """
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| [515] | 146 | if self.fitted and self.data is not None:
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| 147 | pars = list(self.fitter.getparameters())
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| 148 | fixed = list(self.fitter.getfixedparameters())
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| 149 | self.data._addfit(self._fittedrow, pars, fixed,
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| 150 | self.fitfuncs, self.components)
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| 151 |
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| 152 | def set_parameters(self, params, fixed=None, component=None):
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| [526] | 153 | """
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| 154 | Set the parameters to be fitted.
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| 155 | Parameters:
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| 156 | params: a vector of parameters
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| 157 | fixed: a vector of which parameters are to be held fixed
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| 158 | (default is none)
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| 159 | component: in case of multiple gaussians, the index of the
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| 160 | component
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| 161 | """
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| [515] | 162 | if self.fitfunc is None:
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| 163 | print "Please specify a fitting function first."
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| 164 | return
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| 165 | if self.fitfunc == "gauss" and component is not None:
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| 166 | if not self.fitted:
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| 167 | from numarray import zeros
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| 168 | pars = list(zeros(len(self.components)*3))
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| 169 | fxd = list(zeros(len(pars)))
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| 170 | else:
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| 171 | pars = list(self.fitter.getparameters())
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| 172 | fxd = list(self.fitter.getfixedparameters())
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| 173 | i = 3*component
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| 174 | pars[i:i+3] = params
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| 175 | fxd[i:i+3] = fixed
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| 176 | params = pars
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| 177 | fixed = fxd
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| [113] | 178 | self.fitter.setparameters(params)
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| 179 | if fixed is not None:
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| 180 | self.fitter.setfixedparameters(fixed)
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| 181 | return
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| [515] | 182 |
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| 183 | def set_gauss_parameters(self, peak, centre, fhwm,
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| 184 | peakfixed=False, centerfixed=False,
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| 185 | fhwmfixed=False,
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| 186 | component=0):
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| [113] | 187 | """
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| [515] | 188 | Set the Parameters of a 'Gaussian' component, set with set_function.
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| 189 | Parameters:
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| 190 | peak, centre, fhwm: The gaussian parameters
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| 191 | peakfixed,
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| 192 | centerfixed,
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| 193 | fhwmfixed: Optional parameters to indicate if
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| 194 | the paramters should be held fixed during
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| 195 | the fitting process. The default is to keep
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| 196 | all parameters flexible.
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| [526] | 197 | component: The number of the component (Default is the
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| 198 | component 0)
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| [515] | 199 | """
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| 200 | if self.fitfunc != "gauss":
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| 201 | print "Function only operates on Gaussian components."
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| 202 | return
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| 203 | if 0 <= component < len(self.components):
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| 204 | self.set_parameters([peak, centre, fhwm],
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| 205 | [peakfixed, centerfixed, fhwmfixed],
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| 206 | component)
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| 207 | else:
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| 208 | print "Please select a valid component."
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| 209 | return
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| 210 |
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| 211 | def get_parameters(self, component=None):
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| 212 | """
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| [113] | 213 | Return the fit paramters.
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| [526] | 214 | Parameters:
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| 215 | component: get the parameters for the specified component
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| 216 | only, default is all components
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| [113] | 217 | """
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| 218 | if not self.fitted:
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| 219 | print "Not yet fitted."
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| 220 | pars = list(self.fitter.getparameters())
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| 221 | fixed = list(self.fitter.getfixedparameters())
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| [515] | 222 | if component is not None:
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| 223 | if self.fitfunc == "gauss":
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| 224 | i = 3*component
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| 225 | cpars = pars[i:i+3]
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| 226 | cfixed = fixed[i:i+3]
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| 227 | else:
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| 228 | cpars = pars
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| 229 | cfixed = fixed
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| 230 | else:
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| 231 | cpars = pars
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| 232 | cfixed = fixed
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| 233 | fpars = self._format_pars(cpars, cfixed)
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| [113] | 234 | if self._vb:
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| [515] | 235 | print fpars
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| 236 | return cpars, cfixed, fpars
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| [113] | 237 |
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| [515] | 238 | def _format_pars(self, pars, fixed):
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| [113] | 239 | out = ''
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| 240 | if self.fitfunc == 'poly':
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| 241 | c = 0
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| [515] | 242 | for i in range(len(pars)):
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| 243 | fix = ""
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| 244 | if fixed[i]: fix = "(fixed)"
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| 245 | out += ' p%d%s= %3.3f,' % (c,fix,pars[i])
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| [113] | 246 | c+=1
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| [515] | 247 | out = out[:-1] # remove trailing ','
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| [113] | 248 | elif self.fitfunc == 'gauss':
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| 249 | i = 0
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| 250 | c = 0
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| [515] | 251 | aunit = ''
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| 252 | ounit = ''
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| [113] | 253 | if self.data:
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| [515] | 254 | aunit = self.data.get_unit()
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| 255 | ounit = self.data.get_fluxunit()
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| [113] | 256 | while i < len(pars):
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| [515] | 257 | out += ' %d: peak = %3.3f %s , centre = %3.3f %s, FWHM = %3.3f %s \n' % (c,pars[i],ounit,pars[i+1],aunit,pars[i+2],aunit)
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| [113] | 258 | c+=1
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| 259 | i+=3
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| 260 | return out
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| 261 |
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| 262 | def get_estimate(self):
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| 263 | """
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| [515] | 264 | Return the parameter estimates (for non-linear functions).
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| [113] | 265 | """
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| 266 | pars = self.fitter.getestimate()
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| 267 | if self._vb:
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| 268 | print self._format_pars(pars)
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| 269 | return pars
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| 270 |
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| 271 |
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| 272 | def get_residual(self):
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| 273 | """
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| 274 | Return the residual of the fit.
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| 275 | """
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| 276 | if not self.fitted:
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| 277 | print "Not yet fitted."
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| 278 | return self.fitter.getresidual()
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| 279 |
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| 280 | def get_chi2(self):
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| 281 | """
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| 282 | Return chi^2.
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| 283 | """
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| 284 | if not self.fitted:
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| 285 | print "Not yet fitted."
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| 286 | ch2 = self.fitter.getchi2()
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| 287 | if self._vb:
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| 288 | print 'Chi^2 = %3.3f' % (ch2)
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| 289 | return ch2
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| 290 |
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| 291 | def get_fit(self):
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| 292 | """
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| 293 | Return the fitted ordinate values.
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| 294 | """
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| 295 | if not self.fitted:
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| 296 | print "Not yet fitted."
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| 297 | return self.fitter.getfit()
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| 298 |
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| 299 | def commit(self):
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| 300 | """
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| [526] | 301 | Return a new scan where the fits have been commited (subtracted)
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| [113] | 302 | """
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| 303 | if not self.fitted:
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| 304 | print "Not yet fitted."
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| 305 | if self.data is not scantable:
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| 306 | print "Only works with scantables"
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| 307 | return
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| 308 | scan = self.data.copy()
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| [259] | 309 | scan._setspectrum(self.fitter.getresidual())
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| [113] | 310 |
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| [526] | 311 | def plot(self, residual=False, components=None, plotparms=False):
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| [113] | 312 | """
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| 313 | Plot the last fit.
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| 314 | Parameters:
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| 315 | residual: an optional parameter indicating if the residual
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| 316 | should be plotted (default 'False')
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| [526] | 317 | components: a list of components to plot, e.g [0,1],
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| 318 | -1 plots the total fit. Default is to only
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| 319 | plot the total fit.
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| 320 | plotparms: Inidicates if the parameter values should be present
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| 321 | on the plot
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| [113] | 322 | """
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| 323 | if not self.fitted:
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| 324 | return
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| 325 | if not self._p:
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| 326 | from asap.asaplot import ASAPlot
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| 327 | self._p = ASAPlot()
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| [298] | 328 | if self._p.is_dead:
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| [190] | 329 | from asap.asaplot import ASAPlot
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| 330 | self._p = ASAPlot()
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| [113] | 331 | self._p.clear()
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| [515] | 332 | self._p.set_panels()
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| [652] | 333 | self._p.palette(0)
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| [113] | 334 | tlab = 'Spectrum'
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| [515] | 335 | xlab = 'Abcissa'
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| 336 | m = ()
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| [113] | 337 | if self.data:
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| [515] | 338 | tlab = self.data._getsourcename(self._fittedrow)
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| 339 | xlab = self.data._getabcissalabel(self._fittedrow)
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| 340 | m = self.data._getmask(self._fittedrow)
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| [626] | 341 | ylab = self.data._get_ordinate_label()
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| [515] | 342 |
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| [668] | 343 | colours = ["#777777","#bbbbbb","red","orange","purple","green","magenta", "cyan"]
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| [652] | 344 | self._p.palette(0,colours)
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| [515] | 345 | self._p.set_line(label='Spectrum')
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| [113] | 346 | self._p.plot(self.x, self.y, m)
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| 347 | if residual:
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| [652] | 348 | self._p.palette(1)
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| [515] | 349 | self._p.set_line(label='Residual')
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| [113] | 350 | self._p.plot(self.x, self.get_residual(), m)
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| [652] | 351 | self._p.palette(2)
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| [515] | 352 | if components is not None:
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| 353 | cs = components
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| 354 | if isinstance(components,int): cs = [components]
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| [526] | 355 | if plotparms:
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| 356 | self._p.text(0.15,0.15,str(self.get_parameters()[2]),size=8)
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| [515] | 357 | n = len(self.components)
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| [652] | 358 | self._p.palette(3)
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| [515] | 359 | for c in cs:
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| 360 | if 0 <= c < n:
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| 361 | lab = self.fitfuncs[c]+str(c)
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| 362 | self._p.set_line(label=lab)
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| 363 | self._p.plot(self.x, self.fitter.evaluate(c), m)
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| 364 | elif c == -1:
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| [652] | 365 | self._p.palette(2)
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| [515] | 366 | self._p.set_line(label="Total Fit")
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| 367 | self._p.plot(self.x, self.get_fit(), m)
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| 368 | else:
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| [652] | 369 | self._p.palette(2)
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| [515] | 370 | self._p.set_line(label='Fit')
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| 371 | self._p.plot(self.x, self.get_fit(), m)
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| [113] | 372 | self._p.set_axes('xlabel',xlab)
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| 373 | self._p.set_axes('ylabel',ylab)
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| 374 | self._p.set_axes('title',tlab)
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| 375 | self._p.release()
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| 376 |
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| [259] | 377 | def auto_fit(self, insitu=None):
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| [113] | 378 | """
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| [515] | 379 | Return a scan where the function is applied to all rows for
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| 380 | all Beams/IFs/Pols.
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| [113] | 381 |
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| 382 | """
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| 383 | from asap import scantable
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| [515] | 384 | if not isinstance(self.data, scantable) :
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| [113] | 385 | print "Only works with scantables"
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| 386 | return
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| [259] | 387 | if insitu is None: insitu = rcParams['insitu']
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| 388 | if not insitu:
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| 389 | scan = self.data.copy()
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| 390 | else:
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| 391 | scan = self.data
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| 392 | vb = scan._vb
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| 393 | scan._vb = False
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| 394 | sel = scan.get_cursor()
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| [159] | 395 | rows = range(scan.nrow())
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| [113] | 396 | for i in range(scan.nbeam()):
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| 397 | scan.setbeam(i)
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| 398 | for j in range(scan.nif()):
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| 399 | scan.setif(j)
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| 400 | for k in range(scan.npol()):
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| 401 | scan.setpol(k)
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| 402 | if self._vb:
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| 403 | print "Fitting:"
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| 404 | print 'Beam[%d], IF[%d], Pol[%d]' % (i,j,k)
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| [159] | 405 | for iRow in rows:
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| [259] | 406 | self.x = scan._getabcissa(iRow)
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| 407 | self.y = scan._getspectrum(iRow)
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| [159] | 408 | self.data = None
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| 409 | self.fit()
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| [113] | 410 | x = self.get_parameters()
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| [259] | 411 | scan._setspectrum(self.fitter.getresidual(),iRow)
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| 412 | scan.set_cursor(sel[0],sel[1],sel[2])
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| 413 | scan._vb = vb
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| 414 | if not insitu:
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| 415 | return scan
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