1 | import _asap
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2 | from asap import rcParams
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3 | from asap import print_log
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4 | from asap import _n_bools
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5 |
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6 | class fitter:
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7 | """
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8 | The fitting class for ASAP.
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9 | """
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10 |
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11 | def __init__(self):
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12 | """
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13 | Create a fitter object. No state is set.
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14 | """
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15 | self.fitter = _asap.fitter()
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16 | self.x = None
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17 | self.y = None
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18 | self.mask = None
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19 | self.fitfunc = None
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20 | self.fitfuncs = None
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21 | self.fitted = False
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22 | self.data = None
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23 | self.components = 0
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24 | self._fittedrow = 0
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25 | self._p = None
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26 | self._selection = None
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27 | self.uselinear = False
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28 |
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29 | def set_data(self, xdat, ydat, mask=None):
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30 | """
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31 | Set the absissa and ordinate for the fit. Also set the mask
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32 | indicationg valid points.
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33 | This can be used for data vectors retrieved from a scantable.
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34 | For scantable fitting use 'fitter.set_scan(scan, mask)'.
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35 | Parameters:
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36 | xdat: the abcissa values
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37 | ydat: the ordinate values
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38 | mask: an optional mask
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39 |
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40 | """
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41 | self.fitted = False
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42 | self.x = xdat
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43 | self.y = ydat
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44 | if mask == None:
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45 | self.mask = _n_bools(len(xdat), True)
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46 | else:
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47 | self.mask = mask
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48 | return
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49 |
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50 | def set_scan(self, thescan=None, mask=None):
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51 | """
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52 | Set the 'data' (a scantable) of the fitter.
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53 | Parameters:
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54 | thescan: a scantable
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55 | mask: a msk retireved from the scantable
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56 | """
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57 | if not thescan:
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58 | msg = "Please give a correct scan"
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59 | if rcParams['verbose']:
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60 | print msg
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61 | return
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62 | else:
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63 | raise TypeError(msg)
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64 | self.fitted = False
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65 | self.data = thescan
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66 | self.mask = None
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67 | if mask is None:
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68 | self.mask = _n_bools(self.data.nchan(), True)
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69 | else:
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70 | self.mask = mask
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71 | return
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72 |
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73 | def set_function(self, **kwargs):
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74 | """
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75 | Set the function to be fit.
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76 | Parameters:
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77 | poly: use a polynomial of the order given with nonlinear least squares fit
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78 | lpoly: use polynomial of the order given with linear least squares fit
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79 | gauss: fit the number of gaussian specified
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80 | Example:
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81 | fitter.set_function(gauss=2) # will fit two gaussians
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82 | fitter.set_function(poly=3) # will fit a 3rd order polynomial via nonlinear method
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83 | fitter.set_function(lpoly=3) # will fit a 3rd order polynomial via linear method
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84 | """
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85 | #default poly order 0
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86 | n=0
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87 | if kwargs.has_key('poly'):
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88 | self.fitfunc = 'poly'
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89 | n = kwargs.get('poly')
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90 | self.components = [n]
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91 | self.uselinear = False
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92 | elif kwargs.has_key('lpoly'):
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93 | self.fitfunc = 'poly'
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94 | n = kwargs.get('lpoly')
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95 | self.components = [n]
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96 | self.uselinear = True
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97 | elif kwargs.has_key('gauss'):
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98 | n = kwargs.get('gauss')
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99 | self.fitfunc = 'gauss'
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100 | self.fitfuncs = [ 'gauss' for i in range(n) ]
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101 | self.components = [ 3 for i in range(n) ]
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102 | self.uselinear = False
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103 | else:
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104 | msg = "Invalid function type."
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105 | if rcParams['verbose']:
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106 | print msg
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107 | return
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108 | else:
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109 | raise TypeError(msg)
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110 |
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111 | self.fitter.setexpression(self.fitfunc,n)
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112 | self.fitted = False
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113 | return
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114 |
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115 | def fit(self, row=0, estimate=False):
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116 | """
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117 | Execute the actual fitting process. All the state has to be set.
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118 | Parameters:
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119 | row: specify the row in the scantable
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120 | estimate: auto-compute an initial parameter set (default False)
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121 | This can be used to compute estimates even if fit was
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122 | called before.
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123 | Example:
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124 | s = scantable('myscan.asap')
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125 | s.set_cursor(thepol=1) # select second pol
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126 | f = fitter()
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127 | f.set_scan(s)
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128 | f.set_function(poly=0)
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129 | f.fit(row=0) # fit first row
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130 | """
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131 | if ((self.x is None or self.y is None) and self.data is None) \
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132 | or self.fitfunc is None:
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133 | msg = "Fitter not yet initialised. Please set data & fit function"
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134 | if rcParams['verbose']:
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135 | print msg
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136 | return
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137 | else:
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138 | raise RuntimeError(msg)
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139 |
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140 | else:
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141 | if self.data is not None:
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142 | self.x = self.data._getabcissa(row)
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143 | self.y = self.data._getspectrum(row)
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144 | from asap import asaplog
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145 | asaplog.push("Fitting:")
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146 | i = row
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147 | 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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148 | asaplog.push(out,False)
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149 | self.fitter.setdata(self.x, self.y, self.mask)
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150 | if self.fitfunc == 'gauss':
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151 | ps = self.fitter.getparameters()
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152 | if len(ps) == 0 or estimate:
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153 | self.fitter.estimate()
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154 | try:
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155 | fxdpar = list(self.fitter.getfixedparameters())
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156 | if len(fxdpar) and fxdpar.count(0) == 0:
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157 | raise RuntimeError,"No point fitting, if all parameters are fixed."
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158 | if self.uselinear:
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159 | converged = self.fitter.lfit()
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160 | else:
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161 | converged = self.fitter.fit()
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162 | if not converged:
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163 | raise RuntimeError,"Fit didn't converge."
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164 | except RuntimeError, msg:
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165 | if rcParams['verbose']:
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166 | print msg
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167 | else:
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168 | raise
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169 | self._fittedrow = row
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170 | self.fitted = True
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171 | print_log()
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172 | return
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173 |
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174 | def store_fit(self, filename=None):
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175 | """
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176 | Save the fit parameters.
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177 | Parameters:
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178 | filename: if specified save as an ASCII file, if None (default)
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179 | store it in the scnatable
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180 | """
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181 | if self.fitted and self.data is not None:
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182 | pars = list(self.fitter.getparameters())
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183 | fixed = list(self.fitter.getfixedparameters())
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184 | from asap.asapfit import asapfit
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185 | fit = asapfit()
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186 | fit.setparameters(pars)
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187 | fit.setfixedparameters(fixed)
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188 | fit.setfunctions(self.fitfuncs)
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189 | fit.setcomponents(self.components)
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190 | fit.setframeinfo(self.data._getcoordinfo())
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191 | if filename is not None:
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192 | import os
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193 | filename = os.path.expandvars(os.path.expanduser(filename))
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194 | if os.path.exists(filename):
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195 | raise IOError("File '%s' exists." % filename)
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196 | fit.save(filename)
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197 | else:
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198 | self.data._addfit(fit,self._fittedrow)
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199 |
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200 | #def set_parameters(self, params, fixed=None, component=None):
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201 | def set_parameters(self,*args,**kwargs):
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202 | """
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203 | Set the parameters to be fitted.
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204 | Parameters:
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205 | params: a vector of parameters
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206 | fixed: a vector of which parameters are to be held fixed
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207 | (default is none)
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208 | component: in case of multiple gaussians, the index of the
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209 | component
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210 | """
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211 | component = None
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212 | fixed = None
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213 | params = None
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214 |
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215 | if len(args) and isinstance(args[0],dict):
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216 | kwargs = args[0]
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217 | if kwargs.has_key("fixed"): fixed = kwargs["fixed"]
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218 | if kwargs.has_key("params"): params = kwargs["params"]
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219 | if len(args) == 2 and isinstance(args[1], int):
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220 | component = args[1]
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221 | if self.fitfunc is None:
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222 | msg = "Please specify a fitting function first."
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223 | if rcParams['verbose']:
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224 | print msg
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225 | return
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226 | else:
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227 | raise RuntimeError(msg)
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228 | if self.fitfunc == "gauss" and component is not None:
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229 | if not self.fitted and sum(self.fitter.getparameters()) == 0:
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230 | pars = _n_bools(len(self.components)*3, False)
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231 | fxd = _n_bools(len(pars), False)
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232 | else:
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233 | pars = list(self.fitter.getparameters())
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234 | fxd = list(self.fitter.getfixedparameters())
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235 | i = 3*component
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236 | pars[i:i+3] = params
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237 | fxd[i:i+3] = fixed
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238 | params = pars
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239 | fixed = fxd
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240 | self.fitter.setparameters(params)
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241 | if fixed is not None:
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242 | self.fitter.setfixedparameters(fixed)
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243 | print_log()
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244 | return
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245 |
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246 | def set_gauss_parameters(self, peak, centre, fwhm,
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247 | peakfixed=0, centerfixed=0,
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248 | fwhmfixed=0,
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249 | component=0):
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250 | """
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251 | Set the Parameters of a 'Gaussian' component, set with set_function.
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252 | Parameters:
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253 | peak, centre, fwhm: The gaussian parameters
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254 | peakfixed,
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255 | centerfixed,
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256 | fwhmfixed: Optional parameters to indicate if
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257 | the paramters should be held fixed during
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258 | the fitting process. The default is to keep
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259 | all parameters flexible.
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260 | component: The number of the component (Default is the
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261 | component 0)
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262 | """
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263 | if self.fitfunc != "gauss":
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264 | msg = "Function only operates on Gaussian components."
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265 | if rcParams['verbose']:
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266 | print msg
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267 | return
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268 | else:
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269 | raise ValueError(msg)
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270 | if 0 <= component < len(self.components):
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271 | d = {'params':[peak, centre, fwhm],
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272 | 'fixed':[peakfixed, centerfixed, fwhmfixed]}
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273 | self.set_parameters(d, component)
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274 | else:
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275 | msg = "Please select a valid component."
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276 | if rcParams['verbose']:
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277 | print msg
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278 | return
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279 | else:
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280 | raise ValueError(msg)
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281 |
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282 | def get_area(self, component=None):
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283 | """
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284 | Return the area under the fitted gaussian component.
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285 | Parameters:
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286 | component: the gaussian component selection,
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287 | default (None) is the sum of all components
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288 | Note:
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289 | This will only work for gaussian fits.
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290 | """
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291 | if not self.fitted: return
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292 | if self.fitfunc == "gauss":
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293 | pars = list(self.fitter.getparameters())
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294 | from math import log,pi,sqrt
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295 | fac = sqrt(pi/log(16.0))
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296 | areas = []
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297 | for i in range(len(self.components)):
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298 | j = i*3
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299 | cpars = pars[j:j+3]
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300 | areas.append(fac * cpars[0] * cpars[2])
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301 | else:
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302 | return None
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303 | if component is not None:
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304 | return areas[component]
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305 | else:
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306 | return sum(areas)
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307 |
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308 | def get_errors(self, component=None):
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309 | """
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310 | Return the errors in the parameters.
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311 | Parameters:
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312 | component: get the errors for the specified component
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313 | only, default is all components
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314 | """
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315 | if not self.fitted:
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316 | msg = "Not yet fitted."
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317 | if rcParams['verbose']:
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318 | print msg
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319 | return
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320 | else:
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321 | raise RuntimeError(msg)
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322 | errs = list(self.fitter.geterrors())
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323 | cerrs = errs
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324 | if component is not None:
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325 | if self.fitfunc == "gauss":
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326 | i = 3*component
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327 | if i < len(errs):
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328 | cerrs = errs[i:i+3]
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329 | return cerrs
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330 |
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331 | def get_parameters(self, component=None, errors=False):
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332 | """
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333 | Return the fit paramters.
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334 | Parameters:
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335 | component: get the parameters for the specified component
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336 | only, default is all components
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337 | """
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338 | if not self.fitted:
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339 | msg = "Not yet fitted."
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340 | if rcParams['verbose']:
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341 | print msg
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342 | return
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343 | else:
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344 | raise RuntimeError(msg)
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345 | pars = list(self.fitter.getparameters())
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346 | fixed = list(self.fitter.getfixedparameters())
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347 | errs = list(self.fitter.geterrors())
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348 | area = []
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349 | if component is not None:
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350 | if self.fitfunc == "gauss":
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351 | i = 3*component
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352 | cpars = pars[i:i+3]
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353 | cfixed = fixed[i:i+3]
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354 | cerrs = errs[i:i+3]
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355 | a = self.get_area(component)
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356 | area = [a for i in range(3)]
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357 | else:
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358 | cpars = pars
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359 | cfixed = fixed
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360 | cerrs = errs
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361 | else:
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362 | cpars = pars
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363 | cfixed = fixed
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364 | cerrs = errs
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365 | if self.fitfunc == "gauss":
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366 | for c in range(len(self.components)):
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367 | a = self.get_area(c)
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368 | area += [a for i in range(3)]
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369 | fpars = self._format_pars(cpars, cfixed, errors and cerrs, area)
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370 | if rcParams['verbose']:
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371 | print fpars
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372 | return {'params':cpars, 'fixed':cfixed, 'formatted': fpars,
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373 | 'errors':cerrs}
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374 |
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375 | def _format_pars(self, pars, fixed, errors, area):
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376 | out = ''
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377 | if self.fitfunc == 'poly':
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378 | c = 0
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379 | for i in range(len(pars)):
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380 | fix = ""
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381 | if len(fixed) and fixed[i]: fix = "(fixed)"
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382 | if errors :
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383 | out += ' p%d%s= %3.6f (%1.6f),' % (c,fix,pars[i], errors[i])
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384 | else:
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385 | out += ' p%d%s= %3.6f,' % (c,fix,pars[i])
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386 | c+=1
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387 | out = out[:-1] # remove trailing ','
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388 | elif self.fitfunc == 'gauss':
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389 | i = 0
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390 | c = 0
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391 | aunit = ''
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392 | ounit = ''
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393 | if self.data:
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394 | aunit = self.data.get_unit()
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395 | ounit = self.data.get_fluxunit()
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396 | while i < len(pars):
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397 | if len(area):
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398 | out += ' %2d: peak = %3.3f %s , centre = %3.3f %s, FWHM = %3.3f %s\n area = %3.3f %s %s\n' % (c,pars[i],ounit,pars[i+1],aunit,pars[i+2],aunit, area[i],ounit,aunit)
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399 | else:
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400 | out += ' %2d: 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,ounit,aunit)
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401 | c+=1
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402 | i+=3
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403 | return out
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404 |
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405 | def get_estimate(self):
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406 | """
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407 | Return the parameter estimates (for non-linear functions).
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408 | """
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409 | pars = self.fitter.getestimate()
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410 | fixed = self.fitter.getfixedparameters()
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411 | if rcParams['verbose']:
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412 | print self._format_pars(pars,fixed,None)
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413 | return pars
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414 |
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415 | def get_residual(self):
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416 | """
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417 | Return the residual of the fit.
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418 | """
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419 | if not self.fitted:
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420 | msg = "Not yet fitted."
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421 | if rcParams['verbose']:
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422 | print msg
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423 | return
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424 | else:
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425 | raise RuntimeError(msg)
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426 | return self.fitter.getresidual()
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427 |
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428 | def get_chi2(self):
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429 | """
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430 | Return chi^2.
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431 | """
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432 | if not self.fitted:
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433 | msg = "Not yet fitted."
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434 | if rcParams['verbose']:
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435 | print msg
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436 | return
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437 | else:
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438 | raise RuntimeError(msg)
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439 | ch2 = self.fitter.getchi2()
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440 | if rcParams['verbose']:
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441 | print 'Chi^2 = %3.3f' % (ch2)
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442 | return ch2
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443 |
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444 | def get_fit(self):
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445 | """
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446 | Return the fitted ordinate values.
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447 | """
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448 | if not self.fitted:
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449 | msg = "Not yet fitted."
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450 | if rcParams['verbose']:
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451 | print msg
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452 | return
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453 | else:
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454 | raise RuntimeError(msg)
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455 | return self.fitter.getfit()
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456 |
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457 | def commit(self):
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458 | """
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459 | Return a new scan where the fits have been commited (subtracted)
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460 | """
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461 | if not self.fitted:
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462 | msg = "Not yet fitted."
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463 | if rcParams['verbose']:
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464 | print msg
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465 | return
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466 | else:
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467 | raise RuntimeError(msg)
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468 | from asap import scantable
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469 | if not isinstance(self.data, scantable):
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470 | msg = "Not a scantable"
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471 | if rcParams['verbose']:
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472 | print msg
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473 | return
|
---|
474 | else:
|
---|
475 | raise TypeError(msg)
|
---|
476 | scan = self.data.copy()
|
---|
477 | scan._setspectrum(self.fitter.getresidual())
|
---|
478 | print_log()
|
---|
479 | return scan
|
---|
480 |
|
---|
481 | def plot(self, residual=False, components=None, plotparms=False, filename=None):
|
---|
482 | """
|
---|
483 | Plot the last fit.
|
---|
484 | Parameters:
|
---|
485 | residual: an optional parameter indicating if the residual
|
---|
486 | should be plotted (default 'False')
|
---|
487 | components: a list of components to plot, e.g [0,1],
|
---|
488 | -1 plots the total fit. Default is to only
|
---|
489 | plot the total fit.
|
---|
490 | plotparms: Inidicates if the parameter values should be present
|
---|
491 | on the plot
|
---|
492 | """
|
---|
493 | if not self.fitted:
|
---|
494 | return
|
---|
495 | if not self._p or self._p.is_dead:
|
---|
496 | if rcParams['plotter.gui']:
|
---|
497 | from asap.asaplotgui import asaplotgui as asaplot
|
---|
498 | else:
|
---|
499 | from asap.asaplot import asaplot
|
---|
500 | self._p = asaplot()
|
---|
501 | self._p.hold()
|
---|
502 | self._p.clear()
|
---|
503 | self._p.set_panels()
|
---|
504 | self._p.palette(0)
|
---|
505 | tlab = 'Spectrum'
|
---|
506 | xlab = 'Abcissa'
|
---|
507 | ylab = 'Ordinate'
|
---|
508 | from matplotlib.numerix import ma,logical_not,logical_and,array
|
---|
509 | m = self.mask
|
---|
510 | if self.data:
|
---|
511 | tlab = self.data._getsourcename(self._fittedrow)
|
---|
512 | xlab = self.data._getabcissalabel(self._fittedrow)
|
---|
513 | m = logical_and(self.mask,
|
---|
514 | array(self.data._getmask(self._fittedrow),
|
---|
515 | copy=False))
|
---|
516 |
|
---|
517 | ylab = self.data._get_ordinate_label()
|
---|
518 |
|
---|
519 | colours = ["#777777","#dddddd","red","orange","purple","green","magenta", "cyan"]
|
---|
520 | self._p.palette(0,colours)
|
---|
521 | self._p.set_line(label='Spectrum')
|
---|
522 | y = ma.masked_array(self.y,mask=logical_not(m))
|
---|
523 | self._p.plot(self.x, y)
|
---|
524 | if residual:
|
---|
525 | self._p.palette(1)
|
---|
526 | self._p.set_line(label='Residual')
|
---|
527 | y = ma.masked_array(self.get_residual(),
|
---|
528 | mask=logical_not(m))
|
---|
529 | self._p.plot(self.x, y)
|
---|
530 | self._p.palette(2)
|
---|
531 | if components is not None:
|
---|
532 | cs = components
|
---|
533 | if isinstance(components,int): cs = [components]
|
---|
534 | if plotparms:
|
---|
535 | self._p.text(0.15,0.15,str(self.get_parameters()['formatted']),size=8)
|
---|
536 | n = len(self.components)
|
---|
537 | self._p.palette(3)
|
---|
538 | for c in cs:
|
---|
539 | if 0 <= c < n:
|
---|
540 | lab = self.fitfuncs[c]+str(c)
|
---|
541 | self._p.set_line(label=lab)
|
---|
542 | y = ma.masked_array(self.fitter.evaluate(c),
|
---|
543 | mask=logical_not(m))
|
---|
544 |
|
---|
545 | self._p.plot(self.x, y)
|
---|
546 | elif c == -1:
|
---|
547 | self._p.palette(2)
|
---|
548 | self._p.set_line(label="Total Fit")
|
---|
549 | y = ma.masked_array(self.fitter.getfit(),
|
---|
550 | mask=logical_not(m))
|
---|
551 | self._p.plot(self.x, y)
|
---|
552 | else:
|
---|
553 | self._p.palette(2)
|
---|
554 | self._p.set_line(label='Fit')
|
---|
555 | y = ma.masked_array(self.fitter.getfit(),
|
---|
556 | mask=logical_not(m))
|
---|
557 | self._p.plot(self.x, y)
|
---|
558 | xlim=[min(self.x),max(self.x)]
|
---|
559 | self._p.axes.set_xlim(xlim)
|
---|
560 | self._p.set_axes('xlabel',xlab)
|
---|
561 | self._p.set_axes('ylabel',ylab)
|
---|
562 | self._p.set_axes('title',tlab)
|
---|
563 | self._p.release()
|
---|
564 | if (not rcParams['plotter.gui']):
|
---|
565 | self._p.save(filename)
|
---|
566 | print_log()
|
---|
567 |
|
---|
568 | def auto_fit(self, insitu=None, plot=False):
|
---|
569 | """
|
---|
570 | Return a scan where the function is applied to all rows for
|
---|
571 | all Beams/IFs/Pols.
|
---|
572 |
|
---|
573 | """
|
---|
574 | from asap import scantable
|
---|
575 | if not isinstance(self.data, scantable) :
|
---|
576 | msg = "Data is not a scantable"
|
---|
577 | if rcParams['verbose']:
|
---|
578 | print msg
|
---|
579 | return
|
---|
580 | else:
|
---|
581 | raise TypeError(msg)
|
---|
582 | if insitu is None: insitu = rcParams['insitu']
|
---|
583 | if not insitu:
|
---|
584 | scan = self.data.copy()
|
---|
585 | else:
|
---|
586 | scan = self.data
|
---|
587 | rows = xrange(scan.nrow())
|
---|
588 | from asap import asaplog
|
---|
589 | asaplog.push("Fitting:")
|
---|
590 | for r in rows:
|
---|
591 | 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))
|
---|
592 | asaplog.push(out, False)
|
---|
593 | self.x = scan._getabcissa(r)
|
---|
594 | self.y = scan._getspectrum(r)
|
---|
595 | self.data = None
|
---|
596 | self.fit()
|
---|
597 | x = self.get_parameters()
|
---|
598 | if plot:
|
---|
599 | self.plot(residual=True)
|
---|
600 | x = raw_input("Accept fit ([y]/n): ")
|
---|
601 | if x.upper() == 'N':
|
---|
602 | continue
|
---|
603 | scan._setspectrum(self.fitter.getresidual(), r)
|
---|
604 | if plot:
|
---|
605 | self._p.unmap()
|
---|
606 | self._p = None
|
---|
607 | print_log()
|
---|
608 | return scan
|
---|
609 |
|
---|