| [113] | 1 | import _asap
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| [259] | 2 | from asap import rcParams
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| [723] | 3 | from asap import print_log
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| [113] | 4 |
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| 5 | class fitter:
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| 6 | """
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| 7 | The fitting class for ASAP.
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| 8 | """
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| [723] | 9 |
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| [113] | 10 | def __init__(self):
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| 11 | """
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| 12 | Create a fitter object. No state is set.
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| 13 | """
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| 14 | self.fitter = _asap.fitter()
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| 15 | self.x = None
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| 16 | self.y = None
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| 17 | self.mask = None
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| 18 | self.fitfunc = None
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| [515] | 19 | self.fitfuncs = None
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| [113] | 20 | self.fitted = False
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| 21 | self.data = None
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| [515] | 22 | self.components = 0
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| 23 | self._fittedrow = 0
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| [113] | 24 | self._p = None
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| [515] | 25 | self._selection = None
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| [113] | 26 |
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| 27 | def set_data(self, xdat, ydat, mask=None):
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| 28 | """
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| [158] | 29 | Set the absissa and ordinate for the fit. Also set the mask
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| [113] | 30 | indicationg valid points.
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| 31 | This can be used for data vectors retrieved from a scantable.
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| 32 | For scantable fitting use 'fitter.set_scan(scan, mask)'.
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| 33 | Parameters:
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| [158] | 34 | xdat: the abcissa values
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| [113] | 35 | ydat: the ordinate values
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| 36 | mask: an optional mask
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| [723] | 37 |
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| [113] | 38 | """
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| 39 | self.fitted = False
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| 40 | self.x = xdat
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| 41 | self.y = ydat
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| 42 | if mask == None:
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| 43 | from numarray import ones
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| 44 | self.mask = ones(len(xdat))
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| 45 | else:
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| 46 | self.mask = mask
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| 47 | return
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| 48 |
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| 49 | def set_scan(self, thescan=None, mask=None):
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| 50 | """
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| 51 | Set the 'data' (a scantable) of the fitter.
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| 52 | Parameters:
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| 53 | thescan: a scantable
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| 54 | mask: a msk retireved from the scantable
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| 55 | """
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| 56 | if not thescan:
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| [723] | 57 | msg = "Please give a correct scan"
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| 58 | if rcParams['verbose']:
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| 59 | print msg
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| 60 | return
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| 61 | else:
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| 62 | raise TypeError(msg)
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| [113] | 63 | self.fitted = False
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| 64 | self.data = thescan
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| 65 | if mask is None:
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| 66 | from numarray import ones
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| 67 | self.mask = ones(self.data.nchan())
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| 68 | else:
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| 69 | self.mask = mask
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| 70 | return
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| 71 |
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| 72 | def set_function(self, **kwargs):
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| 73 | """
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| 74 | Set the function to be fit.
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| 75 | Parameters:
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| 76 | poly: use a polynomial of the order given
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| 77 | gauss: fit the number of gaussian specified
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| 78 | Example:
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| 79 | fitter.set_function(gauss=2) # will fit two gaussians
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| 80 | fitter.set_function(poly=3) # will fit a 3rd order polynomial
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| 81 | """
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| [723] | 82 | #default poly order 0
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| [515] | 83 | n=0
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| [113] | 84 | if kwargs.has_key('poly'):
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| 85 | self.fitfunc = 'poly'
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| 86 | n = kwargs.get('poly')
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| [515] | 87 | self.components = [n]
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| [113] | 88 | elif kwargs.has_key('gauss'):
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| 89 | n = kwargs.get('gauss')
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| 90 | self.fitfunc = 'gauss'
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| [515] | 91 | self.fitfuncs = [ 'gauss' for i in range(n) ]
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| 92 | self.components = [ 3 for i in range(n) ]
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| 93 | else:
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| [723] | 94 | msg = "Invalid function type."
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| 95 | if rcParams['verbose']:
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| 96 | print msg
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| 97 | return
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| 98 | else:
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| 99 | raise TypeError(msg)
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| 100 |
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| [113] | 101 | self.fitter.setexpression(self.fitfunc,n)
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| 102 | return
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| [723] | 103 |
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| [515] | 104 | def fit(self, row=0):
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| [113] | 105 | """
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| 106 | Execute the actual fitting process. All the state has to be set.
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| 107 | Parameters:
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| [526] | 108 | row: specify the row in the scantable
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| [113] | 109 | Example:
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| [515] | 110 | s = scantable('myscan.asap')
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| 111 | s.set_cursor(thepol=1) # select second pol
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| [113] | 112 | f = fitter()
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| 113 | f.set_scan(s)
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| 114 | f.set_function(poly=0)
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| [723] | 115 | f.fit(row=0) # fit first row
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| [113] | 116 | """
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| 117 | if ((self.x is None or self.y is None) and self.data is None) \
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| 118 | or self.fitfunc is None:
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| [723] | 119 | msg = "Fitter not yet initialised. Please set data & fit function"
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| 120 | if rcParams['verbose']:
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| 121 | print msg
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| 122 | return
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| 123 | else:
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| 124 | raise RuntimeError(msg)
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| 125 |
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| [113] | 126 | else:
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| 127 | if self.data is not None:
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| [515] | 128 | self.x = self.data._getabcissa(row)
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| 129 | self.y = self.data._getspectrum(row)
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| [723] | 130 | from asap import asaplog
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| 131 | asaplog.push("Fitting:")
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| [943] | 132 | i = row
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| 133 | out = "Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % (self.data.getscan(i),self.data.getbeam(i),self.data.getif(i),self.data.getpol(i), self.data.getcycle(i))
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| [876] | 134 | asaplog.push(out)
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| [515] | 135 | self.fitter.setdata(self.x, self.y, self.mask)
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| [113] | 136 | if self.fitfunc == 'gauss':
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| 137 | ps = self.fitter.getparameters()
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| 138 | if len(ps) == 0:
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| 139 | self.fitter.estimate()
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| [626] | 140 | try:
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| 141 | self.fitter.fit()
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| 142 | except RuntimeError, msg:
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| [723] | 143 | if rcParams['verbose']:
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| 144 | print msg
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| 145 | else:
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| 146 | raise
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| [515] | 147 | self._fittedrow = row
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| [113] | 148 | self.fitted = True
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| [723] | 149 | print_log()
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| [113] | 150 | return
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| 151 |
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| [515] | 152 | def store_fit(self):
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| [526] | 153 | """
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| 154 | Store the fit parameters in the scantable.
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| 155 | """
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| [515] | 156 | if self.fitted and self.data is not None:
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| 157 | pars = list(self.fitter.getparameters())
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| 158 | fixed = list(self.fitter.getfixedparameters())
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| 159 | self.data._addfit(self._fittedrow, pars, fixed,
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| 160 | self.fitfuncs, self.components)
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| 161 |
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| 162 | def set_parameters(self, params, fixed=None, component=None):
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| [526] | 163 | """
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| 164 | Set the parameters to be fitted.
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| 165 | Parameters:
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| 166 | params: a vector of parameters
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| 167 | fixed: a vector of which parameters are to be held fixed
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| 168 | (default is none)
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| 169 | component: in case of multiple gaussians, the index of the
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| 170 | component
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| 171 | """
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| [515] | 172 | if self.fitfunc is None:
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| [723] | 173 | msg = "Please specify a fitting function first."
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| 174 | if rcParams['verbose']:
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| 175 | print msg
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| 176 | return
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| 177 | else:
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| 178 | raise RuntimeError(msg)
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| [515] | 179 | if self.fitfunc == "gauss" and component is not None:
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| 180 | if not self.fitted:
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| 181 | from numarray import zeros
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| 182 | pars = list(zeros(len(self.components)*3))
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| 183 | fxd = list(zeros(len(pars)))
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| 184 | else:
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| [723] | 185 | pars = list(self.fitter.getparameters())
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| [515] | 186 | fxd = list(self.fitter.getfixedparameters())
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| 187 | i = 3*component
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| 188 | pars[i:i+3] = params
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| 189 | fxd[i:i+3] = fixed
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| 190 | params = pars
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| [723] | 191 | fixed = fxd
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| [113] | 192 | self.fitter.setparameters(params)
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| 193 | if fixed is not None:
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| 194 | self.fitter.setfixedparameters(fixed)
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| [723] | 195 | print_log()
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| [113] | 196 | return
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| [515] | 197 |
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| 198 | def set_gauss_parameters(self, peak, centre, fhwm,
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| 199 | peakfixed=False, centerfixed=False,
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| 200 | fhwmfixed=False,
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| 201 | component=0):
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| [113] | 202 | """
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| [515] | 203 | Set the Parameters of a 'Gaussian' component, set with set_function.
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| 204 | Parameters:
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| 205 | peak, centre, fhwm: The gaussian parameters
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| 206 | peakfixed,
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| 207 | centerfixed,
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| 208 | fhwmfixed: Optional parameters to indicate if
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| 209 | the paramters should be held fixed during
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| 210 | the fitting process. The default is to keep
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| 211 | all parameters flexible.
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| [526] | 212 | component: The number of the component (Default is the
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| 213 | component 0)
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| [515] | 214 | """
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| 215 | if self.fitfunc != "gauss":
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| [723] | 216 | msg = "Function only operates on Gaussian components."
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| 217 | if rcParams['verbose']:
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| 218 | print msg
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| 219 | return
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| 220 | else:
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| 221 | raise ValueError(msg)
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| [515] | 222 | if 0 <= component < len(self.components):
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| 223 | self.set_parameters([peak, centre, fhwm],
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| 224 | [peakfixed, centerfixed, fhwmfixed],
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| 225 | component)
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| 226 | else:
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| [723] | 227 | msg = "Please select a valid component."
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| 228 | if rcParams['verbose']:
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| 229 | print msg
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| 230 | return
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| 231 | else:
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| 232 | raise ValueError(msg)
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| 233 |
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| [515] | 234 | def get_parameters(self, component=None):
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| 235 | """
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| [113] | 236 | Return the fit paramters.
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| [526] | 237 | Parameters:
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| 238 | component: get the parameters for the specified component
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| 239 | only, default is all components
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| [113] | 240 | """
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| 241 | if not self.fitted:
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| [723] | 242 | msg = "Not yet fitted."
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| 243 | if rcParams['verbose']:
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| 244 | print msg
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| 245 | return
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| 246 | else:
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| 247 | raise RuntimeError(msg)
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| [113] | 248 | pars = list(self.fitter.getparameters())
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| 249 | fixed = list(self.fitter.getfixedparameters())
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| [723] | 250 | if component is not None:
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| [515] | 251 | if self.fitfunc == "gauss":
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| 252 | i = 3*component
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| 253 | cpars = pars[i:i+3]
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| 254 | cfixed = fixed[i:i+3]
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| 255 | else:
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| 256 | cpars = pars
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| [723] | 257 | cfixed = fixed
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| [515] | 258 | else:
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| 259 | cpars = pars
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| 260 | cfixed = fixed
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| 261 | fpars = self._format_pars(cpars, cfixed)
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| [723] | 262 | if rcParams['verbose']:
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| [515] | 263 | print fpars
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| 264 | return cpars, cfixed, fpars
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| [723] | 265 |
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| [515] | 266 | def _format_pars(self, pars, fixed):
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| [113] | 267 | out = ''
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| 268 | if self.fitfunc == 'poly':
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| 269 | c = 0
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| [515] | 270 | for i in range(len(pars)):
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| 271 | fix = ""
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| 272 | if fixed[i]: fix = "(fixed)"
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| 273 | out += ' p%d%s= %3.3f,' % (c,fix,pars[i])
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| [113] | 274 | c+=1
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| [515] | 275 | out = out[:-1] # remove trailing ','
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| [113] | 276 | elif self.fitfunc == 'gauss':
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| 277 | i = 0
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| 278 | c = 0
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| [515] | 279 | aunit = ''
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| 280 | ounit = ''
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| [113] | 281 | if self.data:
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| [515] | 282 | aunit = self.data.get_unit()
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| 283 | ounit = self.data.get_fluxunit()
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| [113] | 284 | while i < len(pars):
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| [515] | 285 | 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] | 286 | c+=1
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| 287 | i+=3
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| 288 | return out
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| [723] | 289 |
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| [113] | 290 | def get_estimate(self):
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| 291 | """
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| [515] | 292 | Return the parameter estimates (for non-linear functions).
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| [113] | 293 | """
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| 294 | pars = self.fitter.getestimate()
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| [943] | 295 | fixed = self.fitter.getfixedparameters()
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| [723] | 296 | if rcParams['verbose']:
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| [943] | 297 | print self._format_pars(pars,fixed)
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| [113] | 298 | return pars
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| 299 |
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| 300 | def get_residual(self):
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| 301 | """
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| 302 | Return the residual of the fit.
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| 303 | """
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| 304 | if not self.fitted:
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| [723] | 305 | msg = "Not yet fitted."
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| 306 | if rcParams['verbose']:
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| 307 | print msg
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| 308 | return
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| 309 | else:
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| 310 | raise RuntimeError(msg)
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| [113] | 311 | return self.fitter.getresidual()
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| 312 |
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| 313 | def get_chi2(self):
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| 314 | """
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| 315 | Return chi^2.
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| 316 | """
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| 317 | if not self.fitted:
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| [723] | 318 | msg = "Not yet fitted."
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| 319 | if rcParams['verbose']:
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| 320 | print msg
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| 321 | return
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| 322 | else:
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| 323 | raise RuntimeError(msg)
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| [113] | 324 | ch2 = self.fitter.getchi2()
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| [723] | 325 | if rcParams['verbose']:
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| [113] | 326 | print 'Chi^2 = %3.3f' % (ch2)
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| [723] | 327 | return ch2
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| [113] | 328 |
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| 329 | def get_fit(self):
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| 330 | """
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| 331 | Return the fitted ordinate values.
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| 332 | """
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| 333 | if not self.fitted:
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| [723] | 334 | msg = "Not yet fitted."
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| 335 | if rcParams['verbose']:
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| 336 | print msg
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| 337 | return
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| 338 | else:
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| 339 | raise RuntimeError(msg)
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| [113] | 340 | return self.fitter.getfit()
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| 341 |
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| 342 | def commit(self):
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| 343 | """
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| [526] | 344 | Return a new scan where the fits have been commited (subtracted)
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| [113] | 345 | """
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| 346 | if not self.fitted:
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| 347 | print "Not yet fitted."
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| [723] | 348 | msg = "Not yet fitted."
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| 349 | if rcParams['verbose']:
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| 350 | print msg
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| 351 | return
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| 352 | else:
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| 353 | raise RuntimeError(msg)
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| [113] | 354 | if self.data is not scantable:
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| [723] | 355 | msg = "Not a scantable"
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| 356 | if rcParams['verbose']:
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| 357 | print msg
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| 358 | return
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| 359 | else:
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| 360 | raise TypeError(msg)
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| [113] | 361 | scan = self.data.copy()
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| [259] | 362 | scan._setspectrum(self.fitter.getresidual())
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| [723] | 363 | print_log()
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| [113] | 364 |
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| [723] | 365 | def plot(self, residual=False, components=None, plotparms=False, filename=None):
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| [113] | 366 | """
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| 367 | Plot the last fit.
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| 368 | Parameters:
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| 369 | residual: an optional parameter indicating if the residual
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| 370 | should be plotted (default 'False')
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| [526] | 371 | components: a list of components to plot, e.g [0,1],
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| 372 | -1 plots the total fit. Default is to only
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| 373 | plot the total fit.
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| 374 | plotparms: Inidicates if the parameter values should be present
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| 375 | on the plot
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| [113] | 376 | """
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| 377 | if not self.fitted:
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| 378 | return
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| [723] | 379 | if not self._p or self._p.is_dead:
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| 380 | if rcParams['plotter.gui']:
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| 381 | from asap.asaplotgui import asaplotgui as asaplot
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| 382 | else:
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| 383 | from asap.asaplot import asaplot
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| 384 | self._p = asaplot()
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| 385 | self._p.hold()
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| [113] | 386 | self._p.clear()
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| [515] | 387 | self._p.set_panels()
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| [652] | 388 | self._p.palette(0)
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| [113] | 389 | tlab = 'Spectrum'
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| [723] | 390 | xlab = 'Abcissa'
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| [515] | 391 | m = ()
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| [113] | 392 | if self.data:
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| [515] | 393 | tlab = self.data._getsourcename(self._fittedrow)
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| 394 | xlab = self.data._getabcissalabel(self._fittedrow)
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| 395 | m = self.data._getmask(self._fittedrow)
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| [626] | 396 | ylab = self.data._get_ordinate_label()
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| [515] | 397 |
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| [668] | 398 | colours = ["#777777","#bbbbbb","red","orange","purple","green","magenta", "cyan"]
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| [652] | 399 | self._p.palette(0,colours)
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| [515] | 400 | self._p.set_line(label='Spectrum')
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| [113] | 401 | self._p.plot(self.x, self.y, m)
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| 402 | if residual:
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| [652] | 403 | self._p.palette(1)
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| [515] | 404 | self._p.set_line(label='Residual')
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| [113] | 405 | self._p.plot(self.x, self.get_residual(), m)
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| [652] | 406 | self._p.palette(2)
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| [515] | 407 | if components is not None:
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| 408 | cs = components
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| 409 | if isinstance(components,int): cs = [components]
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| [526] | 410 | if plotparms:
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| 411 | self._p.text(0.15,0.15,str(self.get_parameters()[2]),size=8)
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| [515] | 412 | n = len(self.components)
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| [652] | 413 | self._p.palette(3)
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| [515] | 414 | for c in cs:
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| 415 | if 0 <= c < n:
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| 416 | lab = self.fitfuncs[c]+str(c)
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| 417 | self._p.set_line(label=lab)
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| 418 | self._p.plot(self.x, self.fitter.evaluate(c), m)
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| 419 | elif c == -1:
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| [652] | 420 | self._p.palette(2)
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| [515] | 421 | self._p.set_line(label="Total Fit")
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| [723] | 422 | self._p.plot(self.x, self.get_fit(), m)
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| [515] | 423 | else:
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| [652] | 424 | self._p.palette(2)
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| [515] | 425 | self._p.set_line(label='Fit')
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| 426 | self._p.plot(self.x, self.get_fit(), m)
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| [723] | 427 | xlim=[min(self.x),max(self.x)]
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| 428 | self._p.axes.set_xlim(xlim)
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| [113] | 429 | self._p.set_axes('xlabel',xlab)
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| 430 | self._p.set_axes('ylabel',ylab)
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| 431 | self._p.set_axes('title',tlab)
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| 432 | self._p.release()
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| [723] | 433 | if (not rcParams['plotter.gui']):
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| 434 | self._p.save(filename)
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| 435 | print_log()
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| [113] | 436 |
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| [876] | 437 | def auto_fit(self, insitu=None):
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| [113] | 438 | """
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| [515] | 439 | Return a scan where the function is applied to all rows for
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| 440 | all Beams/IFs/Pols.
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| [723] | 441 |
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| [113] | 442 | """
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| 443 | from asap import scantable
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| [515] | 444 | if not isinstance(self.data, scantable) :
|
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| [723] | 445 | msg = "Data is not a scantable"
|
|---|
| 446 | if rcParams['verbose']:
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|---|
| 447 | print msg
|
|---|
| 448 | return
|
|---|
| 449 | else:
|
|---|
| 450 | raise TypeError(msg)
|
|---|
| [259] | 451 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 452 | if not insitu:
|
|---|
| 453 | scan = self.data.copy()
|
|---|
| 454 | else:
|
|---|
| 455 | scan = self.data
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|---|
| [880] | 456 | rows = xrange(scan.nrow())
|
|---|
| [723] | 457 | from asap import asaplog
|
|---|
| [876] | 458 | asaplog.push("Fitting:")
|
|---|
| 459 | for r in rows:
|
|---|
| [880] | 460 | out = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % (scan.getscan(r),scan.getbeam(r),scan.getif(r),scan.getpol(r), scan.getcycle(r))
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|---|
| 461 | asaplog.push(out, False)
|
|---|
| [876] | 462 | self.x = scan._getabcissa(r)
|
|---|
| 463 | self.y = scan._getspectrum(r)
|
|---|
| 464 | self.data = None
|
|---|
| 465 | self.fit()
|
|---|
| 466 | x = self.get_parameters()
|
|---|
| [880] | 467 | scan._setspectrum(self.fitter.getresidual(), r)
|
|---|
| [876] | 468 | print_log()
|
|---|
| 469 | return scan
|
|---|
| [794] | 470 |
|
|---|
