[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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[1295] | 4 | from asap import _n_bools |
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[1603] | 5 | from asap import mask_and |
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[1614] | 6 | from asap import asaplog |
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[113] | 7 | |
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| 8 | class fitter: |
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| 9 | """ |
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| 10 | The fitting class for ASAP. |
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| 11 | """ |
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[723] | 12 | |
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[113] | 13 | def __init__(self): |
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| 14 | """ |
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| 15 | Create a fitter object. No state is set. |
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| 16 | """ |
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| 17 | self.fitter = _asap.fitter() |
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| 18 | self.x = None |
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| 19 | self.y = None |
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| 20 | self.mask = None |
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| 21 | self.fitfunc = None |
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[515] | 22 | self.fitfuncs = None |
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[113] | 23 | self.fitted = False |
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| 24 | self.data = None |
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[515] | 25 | self.components = 0 |
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| 26 | self._fittedrow = 0 |
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[113] | 27 | self._p = None |
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[515] | 28 | self._selection = None |
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[1389] | 29 | self.uselinear = False |
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[113] | 30 | |
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| 31 | def set_data(self, xdat, ydat, mask=None): |
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| 32 | """ |
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[158] | 33 | Set the absissa and ordinate for the fit. Also set the mask |
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[113] | 34 | indicationg valid points. |
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| 35 | This can be used for data vectors retrieved from a scantable. |
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| 36 | For scantable fitting use 'fitter.set_scan(scan, mask)'. |
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| 37 | Parameters: |
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[158] | 38 | xdat: the abcissa values |
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[113] | 39 | ydat: the ordinate values |
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| 40 | mask: an optional mask |
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[723] | 41 | |
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[113] | 42 | """ |
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| 43 | self.fitted = False |
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| 44 | self.x = xdat |
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| 45 | self.y = ydat |
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| 46 | if mask == None: |
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[1295] | 47 | self.mask = _n_bools(len(xdat), True) |
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[113] | 48 | else: |
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| 49 | self.mask = mask |
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| 50 | return |
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| 51 | |
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| 52 | def set_scan(self, thescan=None, mask=None): |
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| 53 | """ |
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| 54 | Set the 'data' (a scantable) of the fitter. |
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| 55 | Parameters: |
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| 56 | thescan: a scantable |
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[1603] | 57 | mask: a msk retrieved from the scantable |
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[113] | 58 | """ |
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| 59 | if not thescan: |
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[723] | 60 | msg = "Please give a correct scan" |
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| 61 | if rcParams['verbose']: |
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[1612] | 62 | #print msg |
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[1614] | 63 | asaplog.push(msg) |
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| 64 | print_log('ERROR') |
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[723] | 65 | return |
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| 66 | else: |
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| 67 | raise TypeError(msg) |
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[113] | 68 | self.fitted = False |
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| 69 | self.data = thescan |
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[1075] | 70 | self.mask = None |
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[113] | 71 | if mask is None: |
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[1295] | 72 | self.mask = _n_bools(self.data.nchan(), True) |
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[113] | 73 | else: |
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| 74 | self.mask = mask |
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| 75 | return |
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| 76 | |
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| 77 | def set_function(self, **kwargs): |
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| 78 | """ |
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| 79 | Set the function to be fit. |
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| 80 | Parameters: |
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[1389] | 81 | poly: use a polynomial of the order given with nonlinear least squares fit |
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| 82 | lpoly: use polynomial of the order given with linear least squares fit |
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[113] | 83 | gauss: fit the number of gaussian specified |
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| 84 | Example: |
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| 85 | fitter.set_function(gauss=2) # will fit two gaussians |
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[1389] | 86 | fitter.set_function(poly=3) # will fit a 3rd order polynomial via nonlinear method |
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| 87 | fitter.set_function(lpoly=3) # will fit a 3rd order polynomial via linear method |
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[113] | 88 | """ |
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[723] | 89 | #default poly order 0 |
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[515] | 90 | n=0 |
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[113] | 91 | if kwargs.has_key('poly'): |
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| 92 | self.fitfunc = 'poly' |
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| 93 | n = kwargs.get('poly') |
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[515] | 94 | self.components = [n] |
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[1389] | 95 | self.uselinear = False |
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| 96 | elif kwargs.has_key('lpoly'): |
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| 97 | self.fitfunc = 'poly' |
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| 98 | n = kwargs.get('lpoly') |
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| 99 | self.components = [n] |
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| 100 | self.uselinear = True |
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[113] | 101 | elif kwargs.has_key('gauss'): |
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| 102 | n = kwargs.get('gauss') |
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| 103 | self.fitfunc = 'gauss' |
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[515] | 104 | self.fitfuncs = [ 'gauss' for i in range(n) ] |
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| 105 | self.components = [ 3 for i in range(n) ] |
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[1389] | 106 | self.uselinear = False |
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[515] | 107 | else: |
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[723] | 108 | msg = "Invalid function type." |
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| 109 | if rcParams['verbose']: |
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[1612] | 110 | #print msg |
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[1614] | 111 | asaplog.push(msg) |
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| 112 | print_log('ERROR') |
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[723] | 113 | return |
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| 114 | else: |
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| 115 | raise TypeError(msg) |
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| 116 | |
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[113] | 117 | self.fitter.setexpression(self.fitfunc,n) |
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[1232] | 118 | self.fitted = False |
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[113] | 119 | return |
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[723] | 120 | |
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[1075] | 121 | def fit(self, row=0, estimate=False): |
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[113] | 122 | """ |
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| 123 | Execute the actual fitting process. All the state has to be set. |
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| 124 | Parameters: |
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[1075] | 125 | row: specify the row in the scantable |
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| 126 | estimate: auto-compute an initial parameter set (default False) |
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| 127 | This can be used to compute estimates even if fit was |
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| 128 | called before. |
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[113] | 129 | Example: |
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[515] | 130 | s = scantable('myscan.asap') |
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| 131 | s.set_cursor(thepol=1) # select second pol |
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[113] | 132 | f = fitter() |
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| 133 | f.set_scan(s) |
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| 134 | f.set_function(poly=0) |
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[723] | 135 | f.fit(row=0) # fit first row |
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[113] | 136 | """ |
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| 137 | if ((self.x is None or self.y is None) and self.data is None) \ |
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| 138 | or self.fitfunc is None: |
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[723] | 139 | msg = "Fitter not yet initialised. Please set data & fit function" |
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| 140 | if rcParams['verbose']: |
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[1612] | 141 | #print msg |
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[1614] | 142 | asaplog.push(msg) |
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| 143 | print_log('ERROR') |
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[723] | 144 | return |
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| 145 | else: |
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| 146 | raise RuntimeError(msg) |
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| 147 | |
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[113] | 148 | else: |
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| 149 | if self.data is not None: |
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[515] | 150 | self.x = self.data._getabcissa(row) |
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| 151 | self.y = self.data._getspectrum(row) |
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[1603] | 152 | self.mask = mask_and(self.mask, self.data._getmask(row)) |
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[723] | 153 | from asap import asaplog |
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| 154 | asaplog.push("Fitting:") |
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[943] | 155 | i = row |
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[1603] | 156 | out = "Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % (self.data.getscan(i), |
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| 157 | self.data.getbeam(i), |
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| 158 | self.data.getif(i), |
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| 159 | self.data.getpol(i), |
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| 160 | self.data.getcycle(i)) |
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[1075] | 161 | asaplog.push(out,False) |
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[515] | 162 | self.fitter.setdata(self.x, self.y, self.mask) |
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[113] | 163 | if self.fitfunc == 'gauss': |
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| 164 | ps = self.fitter.getparameters() |
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[1075] | 165 | if len(ps) == 0 or estimate: |
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[113] | 166 | self.fitter.estimate() |
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[1627] | 167 | try: fxdpar = list(self.fitter.getfixedparameters()) |
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[1232] | 168 | if len(fxdpar) and fxdpar.count(0) == 0: |
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| 169 | raise RuntimeError,"No point fitting, if all parameters are fixed." |
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[1389] | 170 | if self.uselinear: |
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| 171 | converged = self.fitter.lfit() |
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| 172 | else: |
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| 173 | converged = self.fitter.fit() |
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[1075] | 174 | if not converged: |
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| 175 | raise RuntimeError,"Fit didn't converge." |
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[626] | 176 | except RuntimeError, msg: |
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[723] | 177 | if rcParams['verbose']: |
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[1612] | 178 | #print msg |
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[1614] | 179 | print_log() |
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[1627] | 180 | asaplog.push(msg.message) |
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[1614] | 181 | print_log('ERROR') |
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[723] | 182 | else: |
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| 183 | raise |
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[515] | 184 | self._fittedrow = row |
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[113] | 185 | self.fitted = True |
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[723] | 186 | print_log() |
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[113] | 187 | return |
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| 188 | |
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[1232] | 189 | def store_fit(self, filename=None): |
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[526] | 190 | """ |
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[1232] | 191 | Save the fit parameters. |
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| 192 | Parameters: |
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| 193 | filename: if specified save as an ASCII file, if None (default) |
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| 194 | store it in the scnatable |
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[526] | 195 | """ |
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[515] | 196 | if self.fitted and self.data is not None: |
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| 197 | pars = list(self.fitter.getparameters()) |
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| 198 | fixed = list(self.fitter.getfixedparameters()) |
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[975] | 199 | from asap.asapfit import asapfit |
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| 200 | fit = asapfit() |
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| 201 | fit.setparameters(pars) |
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| 202 | fit.setfixedparameters(fixed) |
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| 203 | fit.setfunctions(self.fitfuncs) |
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| 204 | fit.setcomponents(self.components) |
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| 205 | fit.setframeinfo(self.data._getcoordinfo()) |
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[1232] | 206 | if filename is not None: |
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| 207 | import os |
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| 208 | filename = os.path.expandvars(os.path.expanduser(filename)) |
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| 209 | if os.path.exists(filename): |
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| 210 | raise IOError("File '%s' exists." % filename) |
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| 211 | fit.save(filename) |
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| 212 | else: |
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| 213 | self.data._addfit(fit,self._fittedrow) |
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[515] | 214 | |
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[1017] | 215 | #def set_parameters(self, params, fixed=None, component=None): |
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| 216 | def set_parameters(self,*args,**kwargs): |
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[526] | 217 | """ |
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| 218 | Set the parameters to be fitted. |
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| 219 | Parameters: |
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| 220 | params: a vector of parameters |
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| 221 | fixed: a vector of which parameters are to be held fixed |
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| 222 | (default is none) |
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| 223 | component: in case of multiple gaussians, the index of the |
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| 224 | component |
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[1017] | 225 | """ |
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| 226 | component = None |
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| 227 | fixed = None |
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| 228 | params = None |
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[1031] | 229 | |
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[1017] | 230 | if len(args) and isinstance(args[0],dict): |
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| 231 | kwargs = args[0] |
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| 232 | if kwargs.has_key("fixed"): fixed = kwargs["fixed"] |
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| 233 | if kwargs.has_key("params"): params = kwargs["params"] |
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| 234 | if len(args) == 2 and isinstance(args[1], int): |
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| 235 | component = args[1] |
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[515] | 236 | if self.fitfunc is None: |
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[723] | 237 | msg = "Please specify a fitting function first." |
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| 238 | if rcParams['verbose']: |
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[1612] | 239 | #print msg |
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[1614] | 240 | asaplog.push(msg) |
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| 241 | print_log('ERROR') |
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[723] | 242 | return |
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| 243 | else: |
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| 244 | raise RuntimeError(msg) |
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[515] | 245 | if self.fitfunc == "gauss" and component is not None: |
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[1017] | 246 | if not self.fitted and sum(self.fitter.getparameters()) == 0: |
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[1295] | 247 | pars = _n_bools(len(self.components)*3, False) |
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| 248 | fxd = _n_bools(len(pars), False) |
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[515] | 249 | else: |
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[723] | 250 | pars = list(self.fitter.getparameters()) |
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[515] | 251 | fxd = list(self.fitter.getfixedparameters()) |
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| 252 | i = 3*component |
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| 253 | pars[i:i+3] = params |
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| 254 | fxd[i:i+3] = fixed |
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| 255 | params = pars |
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[723] | 256 | fixed = fxd |
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[113] | 257 | self.fitter.setparameters(params) |
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| 258 | if fixed is not None: |
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| 259 | self.fitter.setfixedparameters(fixed) |
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[723] | 260 | print_log() |
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[113] | 261 | return |
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[515] | 262 | |
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[1217] | 263 | def set_gauss_parameters(self, peak, centre, fwhm, |
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[1603] | 264 | peakfixed=0, centrefixed=0, |
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[1217] | 265 | fwhmfixed=0, |
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[515] | 266 | component=0): |
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[113] | 267 | """ |
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[515] | 268 | Set the Parameters of a 'Gaussian' component, set with set_function. |
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| 269 | Parameters: |
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[1232] | 270 | peak, centre, fwhm: The gaussian parameters |
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[515] | 271 | peakfixed, |
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[1603] | 272 | centrefixed, |
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[1217] | 273 | fwhmfixed: Optional parameters to indicate if |
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[515] | 274 | the paramters should be held fixed during |
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| 275 | the fitting process. The default is to keep |
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| 276 | all parameters flexible. |
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[526] | 277 | component: The number of the component (Default is the |
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| 278 | component 0) |
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[515] | 279 | """ |
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| 280 | if self.fitfunc != "gauss": |
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[723] | 281 | msg = "Function only operates on Gaussian components." |
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| 282 | if rcParams['verbose']: |
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[1612] | 283 | #print msg |
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[1614] | 284 | asaplog.push(msg) |
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| 285 | print_log('ERROR') |
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[723] | 286 | return |
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| 287 | else: |
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| 288 | raise ValueError(msg) |
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[515] | 289 | if 0 <= component < len(self.components): |
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[1217] | 290 | d = {'params':[peak, centre, fwhm], |
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[1603] | 291 | 'fixed':[peakfixed, centrefixed, fwhmfixed]} |
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[1017] | 292 | self.set_parameters(d, component) |
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[515] | 293 | else: |
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[723] | 294 | msg = "Please select a valid component." |
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| 295 | if rcParams['verbose']: |
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[1612] | 296 | #print msg |
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[1614] | 297 | asaplog.push(msg) |
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| 298 | print_log('ERROR') |
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[723] | 299 | return |
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| 300 | else: |
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| 301 | raise ValueError(msg) |
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| 302 | |
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[975] | 303 | def get_area(self, component=None): |
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| 304 | """ |
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| 305 | Return the area under the fitted gaussian component. |
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| 306 | Parameters: |
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| 307 | component: the gaussian component selection, |
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| 308 | default (None) is the sum of all components |
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| 309 | Note: |
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| 310 | This will only work for gaussian fits. |
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| 311 | """ |
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| 312 | if not self.fitted: return |
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| 313 | if self.fitfunc == "gauss": |
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| 314 | pars = list(self.fitter.getparameters()) |
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| 315 | from math import log,pi,sqrt |
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| 316 | fac = sqrt(pi/log(16.0)) |
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| 317 | areas = [] |
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| 318 | for i in range(len(self.components)): |
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| 319 | j = i*3 |
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| 320 | cpars = pars[j:j+3] |
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| 321 | areas.append(fac * cpars[0] * cpars[2]) |
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| 322 | else: |
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| 323 | return None |
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| 324 | if component is not None: |
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| 325 | return areas[component] |
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| 326 | else: |
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| 327 | return sum(areas) |
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| 328 | |
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[1075] | 329 | def get_errors(self, component=None): |
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[515] | 330 | """ |
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[1075] | 331 | Return the errors in the parameters. |
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| 332 | Parameters: |
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| 333 | component: get the errors for the specified component |
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| 334 | only, default is all components |
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| 335 | """ |
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| 336 | if not self.fitted: |
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| 337 | msg = "Not yet fitted." |
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| 338 | if rcParams['verbose']: |
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[1612] | 339 | #print msg |
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[1614] | 340 | asaplog.push(msg) |
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| 341 | print_log('ERROR') |
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[1075] | 342 | return |
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| 343 | else: |
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| 344 | raise RuntimeError(msg) |
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| 345 | errs = list(self.fitter.geterrors()) |
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| 346 | cerrs = errs |
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| 347 | if component is not None: |
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| 348 | if self.fitfunc == "gauss": |
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| 349 | i = 3*component |
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| 350 | if i < len(errs): |
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| 351 | cerrs = errs[i:i+3] |
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| 352 | return cerrs |
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| 353 | |
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| 354 | def get_parameters(self, component=None, errors=False): |
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| 355 | """ |
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[113] | 356 | Return the fit paramters. |
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[526] | 357 | Parameters: |
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| 358 | component: get the parameters for the specified component |
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| 359 | only, default is all components |
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[113] | 360 | """ |
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| 361 | if not self.fitted: |
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[723] | 362 | msg = "Not yet fitted." |
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| 363 | if rcParams['verbose']: |
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[1612] | 364 | #print msg |
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[1614] | 365 | asaplog.push(msg) |
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| 366 | print_log('ERROR') |
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[723] | 367 | return |
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| 368 | else: |
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| 369 | raise RuntimeError(msg) |
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[113] | 370 | pars = list(self.fitter.getparameters()) |
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| 371 | fixed = list(self.fitter.getfixedparameters()) |
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[1075] | 372 | errs = list(self.fitter.geterrors()) |
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[1039] | 373 | area = [] |
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[723] | 374 | if component is not None: |
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[515] | 375 | if self.fitfunc == "gauss": |
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| 376 | i = 3*component |
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| 377 | cpars = pars[i:i+3] |
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| 378 | cfixed = fixed[i:i+3] |
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[1075] | 379 | cerrs = errs[i:i+3] |
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[1039] | 380 | a = self.get_area(component) |
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| 381 | area = [a for i in range(3)] |
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[515] | 382 | else: |
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| 383 | cpars = pars |
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[723] | 384 | cfixed = fixed |
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[1075] | 385 | cerrs = errs |
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[515] | 386 | else: |
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| 387 | cpars = pars |
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| 388 | cfixed = fixed |
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[1075] | 389 | cerrs = errs |
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[1039] | 390 | if self.fitfunc == "gauss": |
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| 391 | for c in range(len(self.components)): |
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| 392 | a = self.get_area(c) |
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| 393 | area += [a for i in range(3)] |
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[1088] | 394 | fpars = self._format_pars(cpars, cfixed, errors and cerrs, area) |
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[723] | 395 | if rcParams['verbose']: |
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[1612] | 396 | #print fpars |
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[1614] | 397 | asaplog.push(fpars) |
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| 398 | print_log() |
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[1075] | 399 | return {'params':cpars, 'fixed':cfixed, 'formatted': fpars, |
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| 400 | 'errors':cerrs} |
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[723] | 401 | |
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[1075] | 402 | def _format_pars(self, pars, fixed, errors, area): |
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[113] | 403 | out = '' |
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| 404 | if self.fitfunc == 'poly': |
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| 405 | c = 0 |
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[515] | 406 | for i in range(len(pars)): |
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| 407 | fix = "" |
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[1232] | 408 | if len(fixed) and fixed[i]: fix = "(fixed)" |
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[1088] | 409 | if errors : |
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| 410 | out += ' p%d%s= %3.6f (%1.6f),' % (c,fix,pars[i], errors[i]) |
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| 411 | else: |
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| 412 | out += ' p%d%s= %3.6f,' % (c,fix,pars[i]) |
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[113] | 413 | c+=1 |
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[515] | 414 | out = out[:-1] # remove trailing ',' |
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[113] | 415 | elif self.fitfunc == 'gauss': |
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| 416 | i = 0 |
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| 417 | c = 0 |
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[515] | 418 | aunit = '' |
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| 419 | ounit = '' |
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[113] | 420 | if self.data: |
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[515] | 421 | aunit = self.data.get_unit() |
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| 422 | ounit = self.data.get_fluxunit() |
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[113] | 423 | while i < len(pars): |
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[1039] | 424 | if len(area): |
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| 425 | 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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[1017] | 426 | else: |
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| 427 | 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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[113] | 428 | c+=1 |
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| 429 | i+=3 |
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| 430 | return out |
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[723] | 431 | |
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[113] | 432 | def get_estimate(self): |
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| 433 | """ |
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[515] | 434 | Return the parameter estimates (for non-linear functions). |
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[113] | 435 | """ |
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| 436 | pars = self.fitter.getestimate() |
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[943] | 437 | fixed = self.fitter.getfixedparameters() |
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[723] | 438 | if rcParams['verbose']: |
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[1612] | 439 | #print self._format_pars(pars,fixed,None) |
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[1614] | 440 | asaplog.push(self._format_pars(pars,fixed,None)) |
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| 441 | print_log() |
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[113] | 442 | return pars |
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| 443 | |
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| 444 | def get_residual(self): |
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| 445 | """ |
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| 446 | Return the residual of the fit. |
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| 447 | """ |
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| 448 | if not self.fitted: |
---|
[723] | 449 | msg = "Not yet fitted." |
---|
| 450 | if rcParams['verbose']: |
---|
[1612] | 451 | #print msg |
---|
[1614] | 452 | asaplog.push(msg) |
---|
| 453 | print_log('ERROR') |
---|
[723] | 454 | return |
---|
| 455 | else: |
---|
| 456 | raise RuntimeError(msg) |
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[113] | 457 | return self.fitter.getresidual() |
---|
| 458 | |
---|
| 459 | def get_chi2(self): |
---|
| 460 | """ |
---|
| 461 | Return chi^2. |
---|
| 462 | """ |
---|
| 463 | if not self.fitted: |
---|
[723] | 464 | msg = "Not yet fitted." |
---|
| 465 | if rcParams['verbose']: |
---|
[1612] | 466 | #print msg |
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[1614] | 467 | asaplog.push(msg) |
---|
| 468 | print_log('ERROR') |
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[723] | 469 | return |
---|
| 470 | else: |
---|
| 471 | raise RuntimeError(msg) |
---|
[113] | 472 | ch2 = self.fitter.getchi2() |
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[723] | 473 | if rcParams['verbose']: |
---|
[1612] | 474 | #print 'Chi^2 = %3.3f' % (ch2) |
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[1614] | 475 | asaplog.push( 'Chi^2 = %3.3f' % (ch2) ) |
---|
| 476 | print_log() |
---|
[723] | 477 | return ch2 |
---|
[113] | 478 | |
---|
| 479 | def get_fit(self): |
---|
| 480 | """ |
---|
| 481 | Return the fitted ordinate values. |
---|
| 482 | """ |
---|
| 483 | if not self.fitted: |
---|
[723] | 484 | msg = "Not yet fitted." |
---|
| 485 | if rcParams['verbose']: |
---|
[1612] | 486 | #print msg |
---|
[1614] | 487 | asaplog.push(msg) |
---|
| 488 | print_log('ERROR') |
---|
[723] | 489 | return |
---|
| 490 | else: |
---|
| 491 | raise RuntimeError(msg) |
---|
[113] | 492 | return self.fitter.getfit() |
---|
| 493 | |
---|
| 494 | def commit(self): |
---|
| 495 | """ |
---|
[526] | 496 | Return a new scan where the fits have been commited (subtracted) |
---|
[113] | 497 | """ |
---|
| 498 | if not self.fitted: |
---|
[723] | 499 | msg = "Not yet fitted." |
---|
| 500 | if rcParams['verbose']: |
---|
[1612] | 501 | #print msg |
---|
[1614] | 502 | asaplog.push(msg) |
---|
| 503 | print_log('ERROR') |
---|
[723] | 504 | return |
---|
| 505 | else: |
---|
| 506 | raise RuntimeError(msg) |
---|
[975] | 507 | from asap import scantable |
---|
| 508 | if not isinstance(self.data, scantable): |
---|
[723] | 509 | msg = "Not a scantable" |
---|
| 510 | if rcParams['verbose']: |
---|
[1612] | 511 | #print msg |
---|
[1614] | 512 | asaplog.push(msg) |
---|
| 513 | print_log('ERROR') |
---|
[723] | 514 | return |
---|
| 515 | else: |
---|
| 516 | raise TypeError(msg) |
---|
[113] | 517 | scan = self.data.copy() |
---|
[259] | 518 | scan._setspectrum(self.fitter.getresidual()) |
---|
[723] | 519 | print_log() |
---|
[1092] | 520 | return scan |
---|
[113] | 521 | |
---|
[723] | 522 | def plot(self, residual=False, components=None, plotparms=False, filename=None): |
---|
[113] | 523 | """ |
---|
| 524 | Plot the last fit. |
---|
| 525 | Parameters: |
---|
| 526 | residual: an optional parameter indicating if the residual |
---|
| 527 | should be plotted (default 'False') |
---|
[526] | 528 | components: a list of components to plot, e.g [0,1], |
---|
| 529 | -1 plots the total fit. Default is to only |
---|
| 530 | plot the total fit. |
---|
| 531 | plotparms: Inidicates if the parameter values should be present |
---|
| 532 | on the plot |
---|
[113] | 533 | """ |
---|
| 534 | if not self.fitted: |
---|
| 535 | return |
---|
[723] | 536 | if not self._p or self._p.is_dead: |
---|
| 537 | if rcParams['plotter.gui']: |
---|
| 538 | from asap.asaplotgui import asaplotgui as asaplot |
---|
| 539 | else: |
---|
| 540 | from asap.asaplot import asaplot |
---|
| 541 | self._p = asaplot() |
---|
| 542 | self._p.hold() |
---|
[113] | 543 | self._p.clear() |
---|
[515] | 544 | self._p.set_panels() |
---|
[652] | 545 | self._p.palette(0) |
---|
[113] | 546 | tlab = 'Spectrum' |
---|
[723] | 547 | xlab = 'Abcissa' |
---|
[1017] | 548 | ylab = 'Ordinate' |
---|
[1273] | 549 | from matplotlib.numerix import ma,logical_not,logical_and,array |
---|
| 550 | m = self.mask |
---|
[113] | 551 | if self.data: |
---|
[515] | 552 | tlab = self.data._getsourcename(self._fittedrow) |
---|
| 553 | xlab = self.data._getabcissalabel(self._fittedrow) |
---|
[1273] | 554 | m = logical_and(self.mask, |
---|
[1306] | 555 | array(self.data._getmask(self._fittedrow), |
---|
| 556 | copy=False)) |
---|
[1389] | 557 | |
---|
[626] | 558 | ylab = self.data._get_ordinate_label() |
---|
[515] | 559 | |
---|
[1075] | 560 | colours = ["#777777","#dddddd","red","orange","purple","green","magenta", "cyan"] |
---|
[1461] | 561 | nomask=True |
---|
| 562 | for i in range(len(m)): |
---|
| 563 | nomask = nomask and m[i] |
---|
| 564 | label0='Masked Region' |
---|
| 565 | label1='Spectrum' |
---|
| 566 | if ( nomask ): |
---|
| 567 | label0=label1 |
---|
| 568 | else: |
---|
| 569 | y = ma.masked_array( self.y, mask = m ) |
---|
| 570 | self._p.palette(1,colours) |
---|
| 571 | self._p.set_line( label = label1 ) |
---|
| 572 | self._p.plot( self.x, y ) |
---|
[652] | 573 | self._p.palette(0,colours) |
---|
[1461] | 574 | self._p.set_line(label=label0) |
---|
[1273] | 575 | y = ma.masked_array(self.y,mask=logical_not(m)) |
---|
[1088] | 576 | self._p.plot(self.x, y) |
---|
[113] | 577 | if residual: |
---|
[1461] | 578 | self._p.palette(7) |
---|
[515] | 579 | self._p.set_line(label='Residual') |
---|
[1116] | 580 | y = ma.masked_array(self.get_residual(), |
---|
[1273] | 581 | mask=logical_not(m)) |
---|
[1088] | 582 | self._p.plot(self.x, y) |
---|
[652] | 583 | self._p.palette(2) |
---|
[515] | 584 | if components is not None: |
---|
| 585 | cs = components |
---|
| 586 | if isinstance(components,int): cs = [components] |
---|
[526] | 587 | if plotparms: |
---|
[1031] | 588 | self._p.text(0.15,0.15,str(self.get_parameters()['formatted']),size=8) |
---|
[515] | 589 | n = len(self.components) |
---|
[652] | 590 | self._p.palette(3) |
---|
[515] | 591 | for c in cs: |
---|
| 592 | if 0 <= c < n: |
---|
| 593 | lab = self.fitfuncs[c]+str(c) |
---|
| 594 | self._p.set_line(label=lab) |
---|
[1116] | 595 | y = ma.masked_array(self.fitter.evaluate(c), |
---|
[1273] | 596 | mask=logical_not(m)) |
---|
[1088] | 597 | |
---|
| 598 | self._p.plot(self.x, y) |
---|
[515] | 599 | elif c == -1: |
---|
[652] | 600 | self._p.palette(2) |
---|
[515] | 601 | self._p.set_line(label="Total Fit") |
---|
[1116] | 602 | y = ma.masked_array(self.fitter.getfit(), |
---|
[1273] | 603 | mask=logical_not(m)) |
---|
[1088] | 604 | self._p.plot(self.x, y) |
---|
[515] | 605 | else: |
---|
[652] | 606 | self._p.palette(2) |
---|
[515] | 607 | self._p.set_line(label='Fit') |
---|
[1116] | 608 | y = ma.masked_array(self.fitter.getfit(), |
---|
[1273] | 609 | mask=logical_not(m)) |
---|
[1088] | 610 | self._p.plot(self.x, y) |
---|
[723] | 611 | xlim=[min(self.x),max(self.x)] |
---|
| 612 | self._p.axes.set_xlim(xlim) |
---|
[113] | 613 | self._p.set_axes('xlabel',xlab) |
---|
| 614 | self._p.set_axes('ylabel',ylab) |
---|
| 615 | self._p.set_axes('title',tlab) |
---|
| 616 | self._p.release() |
---|
[723] | 617 | if (not rcParams['plotter.gui']): |
---|
| 618 | self._p.save(filename) |
---|
| 619 | print_log() |
---|
[113] | 620 | |
---|
[1061] | 621 | def auto_fit(self, insitu=None, plot=False): |
---|
[113] | 622 | """ |
---|
[515] | 623 | Return a scan where the function is applied to all rows for |
---|
| 624 | all Beams/IFs/Pols. |
---|
[723] | 625 | |
---|
[113] | 626 | """ |
---|
| 627 | from asap import scantable |
---|
[515] | 628 | if not isinstance(self.data, scantable) : |
---|
[723] | 629 | msg = "Data is not a scantable" |
---|
| 630 | if rcParams['verbose']: |
---|
[1612] | 631 | #print msg |
---|
[1614] | 632 | asaplog.push(msg) |
---|
| 633 | print_log('ERROR') |
---|
[723] | 634 | return |
---|
| 635 | else: |
---|
| 636 | raise TypeError(msg) |
---|
[259] | 637 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 638 | if not insitu: |
---|
| 639 | scan = self.data.copy() |
---|
| 640 | else: |
---|
| 641 | scan = self.data |
---|
[880] | 642 | rows = xrange(scan.nrow()) |
---|
[1446] | 643 | # Save parameters of baseline fits as a class attribute. |
---|
| 644 | # NOTICE: This does not reflect changes in scantable! |
---|
| 645 | if len(rows) > 0: self.blpars=[] |
---|
[723] | 646 | from asap import asaplog |
---|
[876] | 647 | asaplog.push("Fitting:") |
---|
| 648 | for r in rows: |
---|
[1603] | 649 | out = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % (scan.getscan(r), |
---|
| 650 | scan.getbeam(r), |
---|
| 651 | scan.getif(r), |
---|
| 652 | scan.getpol(r), |
---|
| 653 | scan.getcycle(r)) |
---|
[880] | 654 | asaplog.push(out, False) |
---|
[876] | 655 | self.x = scan._getabcissa(r) |
---|
| 656 | self.y = scan._getspectrum(r) |
---|
[1603] | 657 | self.mask = mask_and(self.mask, scan._getmask(r)) |
---|
[876] | 658 | self.data = None |
---|
| 659 | self.fit() |
---|
[1603] | 660 | x = self.get_parameters() |
---|
[1446] | 661 | fpar = self.get_parameters() |
---|
[1061] | 662 | if plot: |
---|
| 663 | self.plot(residual=True) |
---|
| 664 | x = raw_input("Accept fit ([y]/n): ") |
---|
| 665 | if x.upper() == 'N': |
---|
[1446] | 666 | self.blpars.append(None) |
---|
[1061] | 667 | continue |
---|
[880] | 668 | scan._setspectrum(self.fitter.getresidual(), r) |
---|
[1446] | 669 | self.blpars.append(fpar) |
---|
[1061] | 670 | if plot: |
---|
| 671 | self._p.unmap() |
---|
| 672 | self._p = None |
---|
[876] | 673 | print_log() |
---|
| 674 | return scan |
---|
[794] | 675 | |
---|