| 1 | import _asap |
|---|
| 2 | from asap import rcParams |
|---|
| 3 | |
|---|
| 4 | class fitter: |
|---|
| 5 | """ |
|---|
| 6 | The fitting class for ASAP. |
|---|
| 7 | """ |
|---|
| 8 | def _verbose(self, *args): |
|---|
| 9 | """ |
|---|
| 10 | Set stdout output. |
|---|
| 11 | """ |
|---|
| 12 | if type(args[0]) is bool: |
|---|
| 13 | self._vb = args[0] |
|---|
| 14 | return |
|---|
| 15 | elif len(args) == 0: |
|---|
| 16 | return self._vb |
|---|
| 17 | |
|---|
| 18 | def __init__(self): |
|---|
| 19 | """ |
|---|
| 20 | Create a fitter object. No state is set. |
|---|
| 21 | """ |
|---|
| 22 | self.fitter = _asap.fitter() |
|---|
| 23 | self.x = None |
|---|
| 24 | self.y = None |
|---|
| 25 | self.mask = None |
|---|
| 26 | self.fitfunc = None |
|---|
| 27 | self.fitted = False |
|---|
| 28 | self.data = None |
|---|
| 29 | self._p = None |
|---|
| 30 | self._vb = True |
|---|
| 31 | |
|---|
| 32 | def set_data(self, xdat, ydat, mask=None): |
|---|
| 33 | """ |
|---|
| 34 | Set the absissa and ordinate for the fit. Also set the mask |
|---|
| 35 | indicationg valid points. |
|---|
| 36 | This can be used for data vectors retrieved from a scantable. |
|---|
| 37 | For scantable fitting use 'fitter.set_scan(scan, mask)'. |
|---|
| 38 | Parameters: |
|---|
| 39 | xdat: the abcissa values |
|---|
| 40 | ydat: the ordinate values |
|---|
| 41 | mask: an optional mask |
|---|
| 42 | |
|---|
| 43 | """ |
|---|
| 44 | self.fitted = False |
|---|
| 45 | self.x = xdat |
|---|
| 46 | self.y = ydat |
|---|
| 47 | if mask == None: |
|---|
| 48 | from numarray import ones |
|---|
| 49 | self.mask = ones(len(xdat)) |
|---|
| 50 | else: |
|---|
| 51 | self.mask = mask |
|---|
| 52 | return |
|---|
| 53 | |
|---|
| 54 | def set_scan(self, thescan=None, mask=None): |
|---|
| 55 | """ |
|---|
| 56 | Set the 'data' (a scantable) of the fitter. |
|---|
| 57 | Parameters: |
|---|
| 58 | thescan: a scantable |
|---|
| 59 | mask: a msk retireved from the scantable |
|---|
| 60 | """ |
|---|
| 61 | if not thescan: |
|---|
| 62 | print "Please give a correct scan" |
|---|
| 63 | self.fitted = False |
|---|
| 64 | self.data = thescan |
|---|
| 65 | if mask is None: |
|---|
| 66 | from numarray import ones |
|---|
| 67 | self.mask = ones(self.data.nchan()) |
|---|
| 68 | else: |
|---|
| 69 | self.mask = mask |
|---|
| 70 | return |
|---|
| 71 | |
|---|
| 72 | def set_function(self, **kwargs): |
|---|
| 73 | """ |
|---|
| 74 | Set the function to be fit. |
|---|
| 75 | Parameters: |
|---|
| 76 | poly: use a polynomial of the order given |
|---|
| 77 | gauss: fit the number of gaussian specified |
|---|
| 78 | Example: |
|---|
| 79 | fitter.set_function(gauss=2) # will fit two gaussians |
|---|
| 80 | fitter.set_function(poly=3) # will fit a 3rd order polynomial |
|---|
| 81 | """ |
|---|
| 82 | #default poly order 0 |
|---|
| 83 | |
|---|
| 84 | |
|---|
| 85 | if kwargs.has_key('poly'): |
|---|
| 86 | self.fitfunc = 'poly' |
|---|
| 87 | n = kwargs.get('poly') |
|---|
| 88 | elif kwargs.has_key('gauss'): |
|---|
| 89 | n = kwargs.get('gauss') |
|---|
| 90 | self.fitfunc = 'gauss' |
|---|
| 91 | |
|---|
| 92 | self.fitter.setexpression(self.fitfunc,n) |
|---|
| 93 | return |
|---|
| 94 | |
|---|
| 95 | def fit(self): |
|---|
| 96 | """ |
|---|
| 97 | Execute the actual fitting process. All the state has to be set. |
|---|
| 98 | Parameters: |
|---|
| 99 | none |
|---|
| 100 | Example: |
|---|
| 101 | s= scantable('myscan.asap') |
|---|
| 102 | f = fitter() |
|---|
| 103 | f.set_scan(s) |
|---|
| 104 | f.set_function(poly=0) |
|---|
| 105 | f.fit() |
|---|
| 106 | """ |
|---|
| 107 | if ((self.x is None or self.y is None) and self.data is None) \ |
|---|
| 108 | or self.fitfunc is None: |
|---|
| 109 | print "Fitter not yet initialised. Please set data & fit function" |
|---|
| 110 | return |
|---|
| 111 | else: |
|---|
| 112 | if self.data is not None: |
|---|
| 113 | self.x = self.data._getabcissa() |
|---|
| 114 | self.y = self.data._getspectrum() |
|---|
| 115 | print "Fitting:" |
|---|
| 116 | vb = self.data._vb |
|---|
| 117 | self.data._vb = True |
|---|
| 118 | s = self.data.get_cursor() |
|---|
| 119 | self.data._vb = vb |
|---|
| 120 | |
|---|
| 121 | self.fitter.setdata(self.x,self.y,self.mask) |
|---|
| 122 | if self.fitfunc == 'gauss': |
|---|
| 123 | ps = self.fitter.getparameters() |
|---|
| 124 | if len(ps) == 0: |
|---|
| 125 | self.fitter.estimate() |
|---|
| 126 | self.fitter.fit() |
|---|
| 127 | self.fitted = True |
|---|
| 128 | return |
|---|
| 129 | |
|---|
| 130 | def set_parameters(self, params, fixed=None): |
|---|
| 131 | self.fitter.setparameters(params) |
|---|
| 132 | if fixed is not None: |
|---|
| 133 | self.fitter.setfixedparameters(fixed) |
|---|
| 134 | return |
|---|
| 135 | |
|---|
| 136 | def get_parameters(self): |
|---|
| 137 | """ |
|---|
| 138 | Return the fit paramters. |
|---|
| 139 | |
|---|
| 140 | """ |
|---|
| 141 | if not self.fitted: |
|---|
| 142 | print "Not yet fitted." |
|---|
| 143 | pars = list(self.fitter.getparameters()) |
|---|
| 144 | fixed = list(self.fitter.getfixedparameters()) |
|---|
| 145 | if self._vb: |
|---|
| 146 | print self._format_pars(pars) |
|---|
| 147 | return pars,fixed |
|---|
| 148 | |
|---|
| 149 | def _format_pars(self, pars): |
|---|
| 150 | out = '' |
|---|
| 151 | if self.fitfunc == 'poly': |
|---|
| 152 | c = 0 |
|---|
| 153 | for i in pars: |
|---|
| 154 | out += ' p%d = %3.3f, ' % (c,i) |
|---|
| 155 | c+=1 |
|---|
| 156 | elif self.fitfunc == 'gauss': |
|---|
| 157 | i = 0 |
|---|
| 158 | c = 0 |
|---|
| 159 | unit = '' |
|---|
| 160 | if self.data: |
|---|
| 161 | unit = self.data.get_unit() |
|---|
| 162 | while i < len(pars): |
|---|
| 163 | out += ' %d: peak = %3.3f , centre = %3.3f %s, FWHM = %3.3f %s \n' % (c,pars[i],pars[i+1],unit,pars[i+2],unit) |
|---|
| 164 | c+=1 |
|---|
| 165 | i+=3 |
|---|
| 166 | return out |
|---|
| 167 | |
|---|
| 168 | def get_estimate(self): |
|---|
| 169 | """ |
|---|
| 170 | Return the paramter estimates (for non-linear functions). |
|---|
| 171 | """ |
|---|
| 172 | pars = self.fitter.getestimate() |
|---|
| 173 | if self._vb: |
|---|
| 174 | print self._format_pars(pars) |
|---|
| 175 | return pars |
|---|
| 176 | |
|---|
| 177 | |
|---|
| 178 | def get_residual(self): |
|---|
| 179 | """ |
|---|
| 180 | Return the residual of the fit. |
|---|
| 181 | """ |
|---|
| 182 | if not self.fitted: |
|---|
| 183 | print "Not yet fitted." |
|---|
| 184 | return self.fitter.getresidual() |
|---|
| 185 | |
|---|
| 186 | def get_chi2(self): |
|---|
| 187 | """ |
|---|
| 188 | Return chi^2. |
|---|
| 189 | """ |
|---|
| 190 | |
|---|
| 191 | if not self.fitted: |
|---|
| 192 | print "Not yet fitted." |
|---|
| 193 | ch2 = self.fitter.getchi2() |
|---|
| 194 | if self._vb: |
|---|
| 195 | print 'Chi^2 = %3.3f' % (ch2) |
|---|
| 196 | return ch2 |
|---|
| 197 | |
|---|
| 198 | def get_fit(self): |
|---|
| 199 | """ |
|---|
| 200 | Return the fitted ordinate values. |
|---|
| 201 | """ |
|---|
| 202 | if not self.fitted: |
|---|
| 203 | print "Not yet fitted." |
|---|
| 204 | return self.fitter.getfit() |
|---|
| 205 | |
|---|
| 206 | def commit(self): |
|---|
| 207 | """ |
|---|
| 208 | Return a new scan where teh fits have been commited. |
|---|
| 209 | """ |
|---|
| 210 | if not self.fitted: |
|---|
| 211 | print "Not yet fitted." |
|---|
| 212 | if self.data is not scantable: |
|---|
| 213 | print "Only works with scantables" |
|---|
| 214 | return |
|---|
| 215 | scan = self.data.copy() |
|---|
| 216 | scan._setspectrum(self.fitter.getresidual()) |
|---|
| 217 | |
|---|
| 218 | def plot(self, residual=False): |
|---|
| 219 | """ |
|---|
| 220 | Plot the last fit. |
|---|
| 221 | Parameters: |
|---|
| 222 | residual: an optional parameter indicating if the residual |
|---|
| 223 | should be plotted (default 'False') |
|---|
| 224 | """ |
|---|
| 225 | if not self.fitted: |
|---|
| 226 | return |
|---|
| 227 | if not self._p: |
|---|
| 228 | from asap.asaplot import ASAPlot |
|---|
| 229 | self._p = ASAPlot() |
|---|
| 230 | if self._p.is_dead: |
|---|
| 231 | from asap.asaplot import ASAPlot |
|---|
| 232 | self._p = ASAPlot() |
|---|
| 233 | self._p.clear() |
|---|
| 234 | tlab = 'Spectrum' |
|---|
| 235 | xlab = 'Abcissa' |
|---|
| 236 | if self.data: |
|---|
| 237 | tlab = self.data._getsourcename(0) |
|---|
| 238 | xlab = self.data._getabcissalabel(0) |
|---|
| 239 | ylab = r'Flux' |
|---|
| 240 | m = self.data._getmask(0) |
|---|
| 241 | self._p.set_line(colour='blue',label='Spectrum') |
|---|
| 242 | self._p.plot(self.x, self.y, m) |
|---|
| 243 | if residual: |
|---|
| 244 | self._p.set_line(colour='green',label='Residual') |
|---|
| 245 | self._p.plot(self.x, self.get_residual(), m) |
|---|
| 246 | self._p.set_line(colour='red',label='Fit') |
|---|
| 247 | self._p.plot(self.x, self.get_fit(), m) |
|---|
| 248 | |
|---|
| 249 | self._p.set_axes('xlabel',xlab) |
|---|
| 250 | self._p.set_axes('ylabel',ylab) |
|---|
| 251 | self._p.set_axes('title',tlab) |
|---|
| 252 | self._p.release() |
|---|
| 253 | |
|---|
| 254 | |
|---|
| 255 | def auto_fit(self, insitu=None): |
|---|
| 256 | """ |
|---|
| 257 | Return a scan where the function is applied to all rows for all Beams/IFs/Pols. |
|---|
| 258 | |
|---|
| 259 | """ |
|---|
| 260 | from asap import scantable |
|---|
| 261 | if not isinstance(self.data,scantable) : |
|---|
| 262 | print "Only works with scantables" |
|---|
| 263 | return |
|---|
| 264 | if insitu is None: insitu = rcParams['insitu'] |
|---|
| 265 | if not insitu: |
|---|
| 266 | scan = self.data.copy() |
|---|
| 267 | else: |
|---|
| 268 | scan = self.data |
|---|
| 269 | vb = scan._vb |
|---|
| 270 | scan._vb = False |
|---|
| 271 | sel = scan.get_cursor() |
|---|
| 272 | rows = range(scan.nrow()) |
|---|
| 273 | for i in range(scan.nbeam()): |
|---|
| 274 | scan.setbeam(i) |
|---|
| 275 | for j in range(scan.nif()): |
|---|
| 276 | scan.setif(j) |
|---|
| 277 | for k in range(scan.npol()): |
|---|
| 278 | scan.setpol(k) |
|---|
| 279 | if self._vb: |
|---|
| 280 | print "Fitting:" |
|---|
| 281 | print 'Beam[%d], IF[%d], Pol[%d]' % (i,j,k) |
|---|
| 282 | for iRow in rows: |
|---|
| 283 | self.x = scan._getabcissa(iRow) |
|---|
| 284 | self.y = scan._getspectrum(iRow) |
|---|
| 285 | self.data = None |
|---|
| 286 | self.fit() |
|---|
| 287 | x = self.get_parameters() |
|---|
| 288 | scan._setspectrum(self.fitter.getresidual(),iRow) |
|---|
| 289 | scan.set_cursor(sel[0],sel[1],sel[2]) |
|---|
| 290 | scan._vb = vb |
|---|
| 291 | if not insitu: |
|---|
| 292 | return scan |
|---|
