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annotate fit.py @ 69:fba792d5f83b draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
author rv43
date Fri, 10 Mar 2023 16:02:04 +0000
parents f31ef7bfb430
children 1cf15b61cd83
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1 #!/usr/bin/env python3
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3 # -*- coding: utf-8 -*-
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4 """
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5 Created on Mon Dec 6 15:36:22 2021
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7 @author: rv43
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8 """
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10 import logging
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12 from asteval import Interpreter, get_ast_names
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13 from copy import deepcopy
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14 from lmfit import Model, Parameters
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15 from lmfit.model import ModelResult
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16 from lmfit.models import ConstantModel, LinearModel, QuadraticModel, PolynomialModel,\
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17 ExponentialModel, StepModel, RectangleModel, ExpressionModel, GaussianModel,\
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18 LorentzianModel
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19 import numpy as np
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20 from os import cpu_count, getpid, listdir, mkdir, path
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21 from re import compile, sub
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22 from shutil import rmtree
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23 from sympy import diff, simplify
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24 try:
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25 from joblib import Parallel, delayed
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26 have_joblib = True
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27 except:
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28 have_joblib = False
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29 try:
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30 import xarray as xr
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31 have_xarray = True
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32 except:
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33 have_xarray = False
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34
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35 from .general import illegal_value, is_int, is_dict_series, is_index, index_nearest, \
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36 almost_equal, quick_plot #, eval_expr
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37 #from sys import path as syspath
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38 #syspath.append(f'/nfs/chess/user/rv43/msnctools/msnctools')
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39 #from general import illegal_value, is_int, is_dict_series, is_index, index_nearest, \
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40 # almost_equal, quick_plot #, eval_expr
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42 from sys import float_info
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43 float_min = float_info.min
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44 float_max = float_info.max
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46 # sigma = fwhm_factor*fwhm
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47 fwhm_factor = {
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48 'gaussian': f'fwhm/(2*sqrt(2*log(2)))',
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49 'lorentzian': f'0.5*fwhm',
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50 'splitlorentzian': f'0.5*fwhm', # sigma = sigma_r
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51 'voight': f'0.2776*fwhm', # sigma = gamma
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52 'pseudovoight': f'0.5*fwhm'} # fraction = 0.5
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53
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54 # amplitude = height_factor*height*fwhm
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55 height_factor = {
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56 'gaussian': f'height*fwhm*0.5*sqrt(pi/log(2))',
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57 'lorentzian': f'height*fwhm*0.5*pi',
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58 'splitlorentzian': f'height*fwhm*0.5*pi', # sigma = sigma_r
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59 'voight': f'3.334*height*fwhm', # sigma = gamma
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60 'pseudovoight': f'1.268*height*fwhm'} # fraction = 0.5
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61
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62 class Fit:
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63 """Wrapper class for lmfit
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64 """
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65 def __init__(self, y, x=None, models=None, normalize=True, **kwargs):
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66 if not isinstance(normalize, bool):
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67 raise ValueError(f'Invalid parameter normalize ({normalize})')
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68 self._mask = None
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69 self._model = None
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70 self._norm = None
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71 self._normalized = False
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72 self._parameters = Parameters()
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73 self._parameter_bounds = None
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74 self._parameter_norms = {}
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75 self._linear_parameters = []
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76 self._nonlinear_parameters = []
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77 self._result = None
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78 self._try_linear_fit = True
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79 self._y = None
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80 self._y_norm = None
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81 self._y_range = None
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82 if 'try_linear_fit' in kwargs:
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83 try_linear_fit = kwargs.pop('try_linear_fit')
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84 if not isinstance(try_linear_fit, bool):
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85 illegal_value(try_linear_fit, 'try_linear_fit', 'Fit.fit', raise_error=True)
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86 self._try_linear_fit = try_linear_fit
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87 if y is not None:
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88 if isinstance(y, (tuple, list, np.ndarray)):
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89 self._x = np.asarray(x)
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90 elif have_xarray and isinstance(y, xr.DataArray):
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91 if x is not None:
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92 logging.warning('Ignoring superfluous input x ({x}) in Fit.__init__')
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93 if y.ndim != 1:
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94 illegal_value(y.ndim, 'DataArray dimensions', 'Fit:__init__', raise_error=True)
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95 self._x = np.asarray(y[y.dims[0]])
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96 else:
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97 illegal_value(y, 'y', 'Fit:__init__', raise_error=True)
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98 self._y = y
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99 if self._x.ndim != 1:
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100 raise ValueError(f'Invalid dimension for input x ({self._x.ndim})')
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101 if self._x.size != self._y.size:
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102 raise ValueError(f'Inconsistent x and y dimensions ({self._x.size} vs '+
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103 f'{self._y.size})')
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104 if 'mask' in kwargs:
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105 self._mask = kwargs.pop('mask')
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106 if self._mask is None:
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107 y_min = float(self._y.min())
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108 self._y_range = float(self._y.max())-y_min
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109 if normalize and self._y_range > 0.0:
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110 self._norm = (y_min, self._y_range)
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111 else:
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112 self._mask = np.asarray(self._mask).astype(bool)
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113 if self._x.size != self._mask.size:
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114 raise ValueError(f'Inconsistent x and mask dimensions ({self._x.size} vs '+
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115 f'{self._mask.size})')
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116 y_masked = np.asarray(self._y)[~self._mask]
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117 y_min = float(y_masked.min())
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118 self._y_range = float(y_masked.max())-y_min
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119 if normalize and self._y_range > 0.0:
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120 if normalize and self._y_range > 0.0:
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121 self._norm = (y_min, self._y_range)
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122 if models is not None:
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123 if callable(models) or isinstance(models, str):
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124 kwargs = self.add_model(models, **kwargs)
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125 elif isinstance(models, (tuple, list)):
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126 for model in models:
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127 kwargs = self.add_model(model, **kwargs)
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128 self.fit(**kwargs)
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129
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130 @classmethod
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131 def fit_data(cls, y, models, x=None, normalize=True, **kwargs):
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132 return(cls(y, x=x, models=models, normalize=normalize, **kwargs))
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133
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134 @property
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135 def best_errors(self):
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136 if self._result is None:
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137 return(None)
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138 return({name:self._result.params[name].stderr for name in sorted(self._result.params)
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139 if name != 'tmp_normalization_offset_c'})
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140
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141 @property
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142 def best_fit(self):
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143 if self._result is None:
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144 return(None)
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145 return(self._result.best_fit)
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146
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147 @property
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148 def best_parameters(self):
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149 if self._result is None:
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150 return(None)
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151 parameters = {}
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152 for name in sorted(self._result.params):
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153 if name != 'tmp_normalization_offset_c':
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154 par = self._result.params[name]
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155 parameters[name] = {'value': par.value, 'error': par.stderr,
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156 'init_value': par.init_value, 'min': par.min, 'max': par.max,
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157 'vary': par.vary, 'expr': par.expr}
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158 return(parameters)
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159
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160 @property
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161 def best_results(self):
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162 """Convert the input data array to a data set and add the fit results.
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163 """
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164 if self._result is None:
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165 return(None)
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166 if isinstance(self._y, xr.DataArray):
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167 best_results = self._y.to_dataset()
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168 dims = self._y.dims
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169 fit_name = f'{self._y.name}_fit'
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170 else:
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171 coords = {'x': (['x'], self._x)}
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172 dims = ('x')
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173 best_results = xr.Dataset(coords=coords)
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174 best_results['y'] = (dims, self._y)
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175 fit_name = 'y_fit'
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176 best_results[fit_name] = (dims, self.best_fit)
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177 if self._mask is not None:
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178 best_results['mask'] = self._mask
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179 best_results.coords['par_names'] = ('peak', [name for name in self.best_values.keys()])
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180 best_results['best_values'] = (['par_names'], [v for v in self.best_values.values()])
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181 best_results['best_errors'] = (['par_names'], [v for v in self.best_errors.values()])
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182 best_results.attrs['components'] = self.components
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183 return(best_results)
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184
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185 @property
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186 def best_values(self):
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187 if self._result is None:
69
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188 return(None)
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189 return({name:self._result.params[name].value for name in sorted(self._result.params)
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190 if name != 'tmp_normalization_offset_c'})
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191
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192 @property
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193 def chisqr(self):
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194 if self._result is None:
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195 return(None)
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196 return(self._result.chisqr)
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197
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198 @property
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199 def components(self):
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200 components = {}
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201 if self._result is None:
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202 logging.warning('Unable to collect components in Fit.components')
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203 return(components)
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204 for component in self._result.components:
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205 if 'tmp_normalization_offset_c' in component.param_names:
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206 continue
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207 parameters = {}
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208 for name in component.param_names:
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209 par = self._parameters[name]
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210 parameters[name] = {'free': par.vary, 'value': self._result.params[name].value}
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211 if par.expr is not None:
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212 parameters[name]['expr'] = par.expr
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213 expr = None
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214 if isinstance(component, ExpressionModel):
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215 name = component._name
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216 if name[-1] == '_':
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217 name = name[:-1]
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218 expr = component.expr
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219 else:
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220 prefix = component.prefix
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221 if len(prefix):
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222 if prefix[-1] == '_':
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223 prefix = prefix[:-1]
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224 name = f'{prefix} ({component._name})'
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225 else:
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226 name = f'{component._name}'
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227 if expr is None:
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228 components[name] = {'parameters': parameters}
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229 else:
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230 components[name] = {'expr': expr, 'parameters': parameters}
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231 return(components)
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232
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233 @property
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234 def covar(self):
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235 if self._result is None:
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236 return(None)
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237 return(self._result.covar)
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238
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239 @property
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240 def init_parameters(self):
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241 if self._result is None or self._result.init_params is None:
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242 return(None)
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243 parameters = {}
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244 for name in sorted(self._result.init_params):
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245 if name != 'tmp_normalization_offset_c':
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246 par = self._result.init_params[name]
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247 parameters[name] = {'value': par.value, 'min': par.min, 'max': par.max,
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248 'vary': par.vary, 'expr': par.expr}
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249 return(parameters)
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250
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251 @property
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252 def init_values(self):
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253 if self._result is None or self._result.init_params is None:
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254 return(None)
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255 return({name:self._result.init_params[name].value for name in
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256 sorted(self._result.init_params) if name != 'tmp_normalization_offset_c'})
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257
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258 @property
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259 def normalization_offset(self):
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260 if self._result is None:
69
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261 return(None)
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262 if self._norm is None:
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263 return(0.0)
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264 else:
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265 if self._result.init_params is not None:
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266 normalization_offset = self._result.init_params['tmp_normalization_offset_c']
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267 else:
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268 normalization_offset = self._result.params['tmp_normalization_offset_c']
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269 return(normalization_offset)
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270
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271 @property
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272 def num_func_eval(self):
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273 if self._result is None:
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274 return(None)
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275 return(self._result.nfev)
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276
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277 @property
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278 def parameters(self):
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279 return({name:{'min': par.min, 'max': par.max, 'vary': par.vary, 'expr': par.expr}
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280 for name, par in self._parameters.items() if name != 'tmp_normalization_offset_c'})
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281
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282 @property
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283 def redchi(self):
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284 if self._result is None:
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285 return(None)
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286 return(self._result.redchi)
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287
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288 @property
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289 def residual(self):
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290 if self._result is None:
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291 return(None)
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292 return(self._result.residual)
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293
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294 @property
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295 def success(self):
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296 if self._result is None:
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297 return(None)
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298 if not self._result.success:
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299 # print(f'ier = {self._result.ier}')
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300 # print(f'lmdif_message = {self._result.lmdif_message}')
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301 # print(f'message = {self._result.message}')
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302 # print(f'nfev = {self._result.nfev}')
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303 # print(f'redchi = {self._result.redchi}')
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304 # print(f'success = {self._result.success}')
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305 if self._result.ier == 0 or self._result.ier == 5:
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306 logging.warning(f'ier = {self._result.ier}: {self._result.message}')
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307 else:
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308 logging.warning(f'ier = {self._result.ier}: {self._result.message}')
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309 return(True)
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310 # self.print_fit_report()
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311 # self.plot()
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312 return(self._result.success)
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313
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314 @property
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315 def var_names(self):
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316 """Intended to be used with covar
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317 """
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318 if self._result is None:
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319 return(None)
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320 return(getattr(self._result, 'var_names', None))
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321
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322 @property
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323 def x(self):
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324 return(self._x)
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325
69
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326 @property
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327 def y(self):
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328 return(self._y)
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329
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330 def print_fit_report(self, result=None, show_correl=False):
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331 if result is None:
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332 result = self._result
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333 if result is not None:
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334 print(result.fit_report(show_correl=show_correl))
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335
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336 def add_parameter(self, **parameter):
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337 if not isinstance(parameter, dict):
69
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338 raise ValueError(f'Invalid parameter ({parameter})')
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339 if parameter.get('expr') is not None:
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340 raise KeyError(f'Illegal "expr" key in parameter {parameter}')
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341 name = parameter['name']
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342 if not isinstance(name, str):
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343 raise ValueError(f'Illegal "name" value ({name}) in parameter {parameter}')
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344 if parameter.get('norm') is None:
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345 self._parameter_norms[name] = False
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346 else:
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347 norm = parameter.pop('norm')
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348 if self._norm is None:
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349 logging.warning(f'Ignoring norm in parameter {name} in '+
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350 f'Fit.add_parameter (normalization is turned off)')
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351 self._parameter_norms[name] = False
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352 else:
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353 if not isinstance(norm, bool):
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354 raise ValueError(f'Illegal "norm" value ({norm}) in parameter {parameter}')
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355 self._parameter_norms[name] = norm
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356 vary = parameter.get('vary')
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357 if vary is not None:
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358 if not isinstance(vary, bool):
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359 raise ValueError(f'Illegal "vary" value ({vary}) in parameter {parameter}')
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360 if not vary:
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361 if 'min' in parameter:
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362 logging.warning(f'Ignoring min in parameter {name} in '+
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363 f'Fit.add_parameter (vary = {vary})')
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364 parameter.pop('min')
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365 if 'max' in parameter:
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366 logging.warning(f'Ignoring max in parameter {name} in '+
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367 f'Fit.add_parameter (vary = {vary})')
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368 parameter.pop('max')
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369 if self._norm is not None and name not in self._parameter_norms:
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370 raise ValueError(f'Missing parameter normalization type for paremeter {name}')
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371 self._parameters.add(**parameter)
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372
69
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373 def add_model(self, model, prefix=None, parameters=None, parameter_norms=None, **kwargs):
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374 # Create the new model
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375 # print(f'at start add_model:\nself._parameters:\n{self._parameters}')
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376 # print(f'at start add_model: kwargs = {kwargs}')
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377 # print(f'parameters = {parameters}')
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378 # print(f'parameter_norms = {parameter_norms}')
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379 # if len(self._parameters.keys()):
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380 # print('\nAt start adding model:')
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381 # self._parameters.pretty_print()
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382 # print(f'parameter_norms:\n{self._parameter_norms}')
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383 if prefix is not None and not isinstance(prefix, str):
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384 logging.warning('Ignoring illegal prefix: {model} {type(model)}')
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385 prefix = None
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386 if prefix is None:
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387 pprefix = ''
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388 else:
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389 pprefix = prefix
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390 if parameters is not None:
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391 if isinstance(parameters, dict):
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392 parameters = (parameters, )
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393 elif not is_dict_series(parameters):
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394 illegal_value(parameters, 'parameters', 'Fit.add_model', raise_error=True)
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395 parameters = deepcopy(parameters)
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396 if parameter_norms is not None:
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397 if isinstance(parameter_norms, dict):
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398 parameter_norms = (parameter_norms, )
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399 if not is_dict_series(parameter_norms):
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400 illegal_value(parameter_norms, 'parameter_norms', 'Fit.add_model', raise_error=True)
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401 new_parameter_norms = {}
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402 if callable(model):
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403 # Linear fit not yet implemented for callable models
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404 self._try_linear_fit = False
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405 if parameter_norms is None:
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406 if parameters is None:
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407 raise ValueError('Either "parameters" or "parameter_norms" is required in '+
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408 f'{model}')
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409 for par in parameters:
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410 name = par['name']
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411 if not isinstance(name, str):
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412 raise ValueError(f'Illegal "name" value ({name}) in input parameters')
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413 if par.get('norm') is not None:
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414 norm = par.pop('norm')
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415 if not isinstance(norm, bool):
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416 raise ValueError(f'Illegal "norm" value ({norm}) in input parameters')
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417 new_parameter_norms[f'{pprefix}{name}'] = norm
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418 else:
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419 for par in parameter_norms:
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420 name = par['name']
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421 if not isinstance(name, str):
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422 raise ValueError(f'Illegal "name" value ({name}) in input parameters')
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423 norm = par.get('norm')
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424 if norm is None or not isinstance(norm, bool):
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425 raise ValueError(f'Illegal "norm" value ({norm}) in input parameters')
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426 new_parameter_norms[f'{pprefix}{name}'] = norm
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427 if parameters is not None:
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428 for par in parameters:
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429 if par.get('expr') is not None:
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430 raise KeyError(f'Illegal "expr" key ({par.get("expr")}) in parameter '+
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431 f'{name} for a callable model {model}')
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432 name = par['name']
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433 if not isinstance(name, str):
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434 raise ValueError(f'Illegal "name" value ({name}) in input parameters')
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435 # RV FIX callable model will need partial deriv functions for any linear pars to get the linearized matrix, so for now skip linear solution option
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436 newmodel = Model(model, prefix=prefix)
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437 elif isinstance(model, str):
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438 if model == 'constant': # Par: c
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439 newmodel = ConstantModel(prefix=prefix)
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440 new_parameter_norms[f'{pprefix}c'] = True
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441 self._linear_parameters.append(f'{pprefix}c')
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442 elif model == 'linear': # Par: slope, intercept
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443 newmodel = LinearModel(prefix=prefix)
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444 new_parameter_norms[f'{pprefix}slope'] = True
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445 new_parameter_norms[f'{pprefix}intercept'] = True
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446 self._linear_parameters.append(f'{pprefix}slope')
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447 self._linear_parameters.append(f'{pprefix}intercept')
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448 elif model == 'quadratic': # Par: a, b, c
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449 newmodel = QuadraticModel(prefix=prefix)
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450 new_parameter_norms[f'{pprefix}a'] = True
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451 new_parameter_norms[f'{pprefix}b'] = True
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452 new_parameter_norms[f'{pprefix}c'] = True
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453 self._linear_parameters.append(f'{pprefix}a')
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454 self._linear_parameters.append(f'{pprefix}b')
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455 self._linear_parameters.append(f'{pprefix}c')
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456 elif model == 'gaussian': # Par: amplitude, center, sigma (fwhm, height)
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457 newmodel = GaussianModel(prefix=prefix)
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458 new_parameter_norms[f'{pprefix}amplitude'] = True
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459 new_parameter_norms[f'{pprefix}center'] = False
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460 new_parameter_norms[f'{pprefix}sigma'] = False
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461 self._linear_parameters.append(f'{pprefix}amplitude')
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462 self._nonlinear_parameters.append(f'{pprefix}center')
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463 self._nonlinear_parameters.append(f'{pprefix}sigma')
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464 # parameter norms for height and fwhm are needed to get correct errors
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465 new_parameter_norms[f'{pprefix}height'] = True
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466 new_parameter_norms[f'{pprefix}fwhm'] = False
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467 elif model == 'lorentzian': # Par: amplitude, center, sigma (fwhm, height)
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468 newmodel = LorentzianModel(prefix=prefix)
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469 new_parameter_norms[f'{pprefix}amplitude'] = True
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470 new_parameter_norms[f'{pprefix}center'] = False
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471 new_parameter_norms[f'{pprefix}sigma'] = False
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472 self._linear_parameters.append(f'{pprefix}amplitude')
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473 self._nonlinear_parameters.append(f'{pprefix}center')
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474 self._nonlinear_parameters.append(f'{pprefix}sigma')
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475 # parameter norms for height and fwhm are needed to get correct errors
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476 new_parameter_norms[f'{pprefix}height'] = True
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477 new_parameter_norms[f'{pprefix}fwhm'] = False
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478 elif model == 'exponential': # Par: amplitude, decay
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479 newmodel = ExponentialModel(prefix=prefix)
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480 new_parameter_norms[f'{pprefix}amplitude'] = True
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481 new_parameter_norms[f'{pprefix}decay'] = False
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482 self._linear_parameters.append(f'{pprefix}amplitude')
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483 self._nonlinear_parameters.append(f'{pprefix}decay')
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484 elif model == 'step': # Par: amplitude, center, sigma
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485 form = kwargs.get('form')
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486 if form is not None:
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487 kwargs.pop('form')
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488 if form is None or form not in ('linear', 'atan', 'arctan', 'erf', 'logistic'):
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489 raise ValueError(f'Invalid parameter form for build-in step model ({form})')
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490 newmodel = StepModel(prefix=prefix, form=form)
69
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491 new_parameter_norms[f'{pprefix}amplitude'] = True
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492 new_parameter_norms[f'{pprefix}center'] = False
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493 new_parameter_norms[f'{pprefix}sigma'] = False
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494 self._linear_parameters.append(f'{pprefix}amplitude')
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495 self._nonlinear_parameters.append(f'{pprefix}center')
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diff changeset
496 self._nonlinear_parameters.append(f'{pprefix}sigma')
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497 elif model == 'rectangle': # Par: amplitude, center1, center2, sigma1, sigma2
49
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498 form = kwargs.get('form')
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499 if form is not None:
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500 kwargs.pop('form')
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501 if form is None or form not in ('linear', 'atan', 'arctan', 'erf', 'logistic'):
69
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diff changeset
502 raise ValueError('Invalid parameter form for build-in rectangle model '+
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diff changeset
503 f'({form})')
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diff changeset
504 newmodel = RectangleModel(prefix=prefix, form=form)
69
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diff changeset
505 new_parameter_norms[f'{pprefix}amplitude'] = True
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diff changeset
506 new_parameter_norms[f'{pprefix}center1'] = False
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507 new_parameter_norms[f'{pprefix}center2'] = False
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diff changeset
508 new_parameter_norms[f'{pprefix}sigma1'] = False
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509 new_parameter_norms[f'{pprefix}sigma2'] = False
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diff changeset
510 self._linear_parameters.append(f'{pprefix}amplitude')
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511 self._nonlinear_parameters.append(f'{pprefix}center1')
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diff changeset
512 self._nonlinear_parameters.append(f'{pprefix}center2')
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513 self._nonlinear_parameters.append(f'{pprefix}sigma1')
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514 self._nonlinear_parameters.append(f'{pprefix}sigma2')
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515 elif model == 'expression': # Par: by expression
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516 expr = kwargs['expr']
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517 if not isinstance(expr, str):
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518 raise ValueError(f'Illegal "expr" value ({expr}) in {model}')
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519 kwargs.pop('expr')
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520 if parameter_norms is not None:
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diff changeset
521 logging.warning('Ignoring parameter_norms (normalization determined from '+
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522 'linearity)}')
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523 if parameters is not None:
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diff changeset
524 for par in parameters:
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525 if par.get('expr') is not None:
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526 raise KeyError(f'Illegal "expr" key ({par.get("expr")}) in parameter '+
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527 f'({par}) for an expression model')
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528 if par.get('norm') is not None:
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529 logging.warning(f'Ignoring "norm" key in parameter ({par}) '+
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530 '(normalization determined from linearity)}')
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diff changeset
531 par.pop('norm')
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532 name = par['name']
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533 if not isinstance(name, str):
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534 raise ValueError(f'Illegal "name" value ({name}) in input parameters')
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diff changeset
535 ast = Interpreter()
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diff changeset
536 expr_parameters = [name for name in get_ast_names(ast.parse(expr))
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diff changeset
537 if name != 'x' and name not in self._parameters
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diff changeset
538 and name not in ast.symtable]
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diff changeset
539 # print(f'\nexpr_parameters: {expr_parameters}')
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540 # print(f'expr = {expr}')
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diff changeset
541 if prefix is None:
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542 newmodel = ExpressionModel(expr=expr)
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543 else:
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diff changeset
544 for name in expr_parameters:
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545 expr = sub(rf'\b{name}\b', f'{prefix}{name}', expr)
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diff changeset
546 expr_parameters = [f'{prefix}{name}' for name in expr_parameters]
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diff changeset
547 # print(f'\nexpr_parameters: {expr_parameters}')
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548 # print(f'expr = {expr}')
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549 newmodel = ExpressionModel(expr=expr, name=name)
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diff changeset
550 # print(f'\nnewmodel = {newmodel.__dict__}')
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551 # print(f'params_names = {newmodel._param_names}')
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552 # print(f'params_names = {newmodel.param_names}')
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553 # Remove already existing names
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diff changeset
554 for name in newmodel.param_names.copy():
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555 if name not in expr_parameters:
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556 newmodel._func_allargs.remove(name)
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diff changeset
557 newmodel._param_names.remove(name)
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diff changeset
558 # print(f'params_names = {newmodel._param_names}')
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diff changeset
559 # print(f'params_names = {newmodel.param_names}')
49
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diff changeset
560 else:
69
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diff changeset
561 raise ValueError(f'Unknown build-in fit model ({model})')
49
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diff changeset
562 else:
69
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diff changeset
563 illegal_value(model, 'model', 'Fit.add_model', raise_error=True)
49
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diff changeset
564
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diff changeset
565 # Add the new model to the current one
69
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diff changeset
566 # print('\nBefore adding model:')
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567 # print(f'\nnewmodel = {newmodel.__dict__}')
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diff changeset
568 # if len(self._parameters):
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diff changeset
569 # self._parameters.pretty_print()
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570 if self._model is None:
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diff changeset
571 self._model = newmodel
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diff changeset
572 else:
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diff changeset
573 self._model += newmodel
69
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diff changeset
574 new_parameters = newmodel.make_params()
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diff changeset
575 self._parameters += new_parameters
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diff changeset
576 # print('\nAfter adding model:')
69
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diff changeset
577 # print(f'\nnewmodel = {newmodel.__dict__}')
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diff changeset
578 # print(f'\nnew_parameters = {new_parameters}')
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diff changeset
579 # self._parameters.pretty_print()
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diff changeset
580
69
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diff changeset
581 # Check linearity of expression model paremeters
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diff changeset
582 if isinstance(newmodel, ExpressionModel):
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diff changeset
583 for name in newmodel.param_names:
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diff changeset
584 if not diff(newmodel.expr, name, name):
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diff changeset
585 if name not in self._linear_parameters:
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586 self._linear_parameters.append(name)
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587 new_parameter_norms[name] = True
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588 # print(f'\nADDING {name} TO LINEAR')
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589 else:
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590 if name not in self._nonlinear_parameters:
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591 self._nonlinear_parameters.append(name)
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592 new_parameter_norms[name] = False
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593 # print(f'\nADDING {name} TO NONLINEAR')
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594 # print(f'new_parameter_norms:\n{new_parameter_norms}')
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595
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596 # Scale the default initial model parameters
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597 if self._norm is not None:
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598 for name, norm in new_parameter_norms.copy().items():
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599 par = self._parameters.get(name)
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600 if par is None:
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601 new_parameter_norms.pop(name)
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602 continue
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603 if par.expr is None and norm:
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604 value = par.value*self._norm[1]
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605 _min = par.min
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606 _max = par.max
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607 if not np.isinf(_min) and abs(_min) != float_min:
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608 _min *= self._norm[1]
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609 if not np.isinf(_max) and abs(_max) != float_min:
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610 _max *= self._norm[1]
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611 par.set(value=value, min=_min, max=_max)
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612 # print('\nAfter norm defaults:')
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613 # self._parameters.pretty_print()
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614 # print(f'parameters:\n{parameters}')
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615 # print(f'all_parameters:\n{list(self.parameters)}')
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616 # print(f'new_parameter_norms:\n{new_parameter_norms}')
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617 # print(f'parameter_norms:\n{self._parameter_norms}')
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618
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619 # Initialize the model parameters from parameters
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620 if prefix is None:
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621 prefix = ""
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622 if parameters is not None:
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623 for parameter in parameters:
69
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624 name = parameter['name']
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625 if not isinstance(name, str):
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626 raise ValueError(f'Illegal "name" value ({name}) in input parameters')
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627 if name not in new_parameters:
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628 name = prefix+name
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629 parameter['name'] = name
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630 if name not in new_parameters:
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631 logging.warning(f'Ignoring superfluous parameter info for {name}')
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632 continue
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633 if name in self._parameters:
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634 parameter.pop('name')
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635 if 'norm' in parameter:
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636 if not isinstance(parameter['norm'], bool):
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637 illegal_value(parameter['norm'], 'norm', 'Fit.add_model',
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638 raise_error=True)
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639 new_parameter_norms[name] = parameter['norm']
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640 parameter.pop('norm')
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641 if parameter.get('expr') is not None:
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642 if 'value' in parameter:
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643 logging.warning(f'Ignoring value in parameter {name} '+
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644 f'(set by expression: {parameter["expr"]})')
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645 parameter.pop('value')
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646 if 'vary' in parameter:
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647 logging.warning(f'Ignoring vary in parameter {name} '+
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648 f'(set by expression: {parameter["expr"]})')
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649 parameter.pop('vary')
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650 if 'min' in parameter:
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651 logging.warning(f'Ignoring min in parameter {name} '+
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652 f'(set by expression: {parameter["expr"]})')
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653 parameter.pop('min')
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654 if 'max' in parameter:
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655 logging.warning(f'Ignoring max in parameter {name} '+
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656 f'(set by expression: {parameter["expr"]})')
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657 parameter.pop('max')
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658 if 'vary' in parameter:
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659 if not isinstance(parameter['vary'], bool):
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660 illegal_value(parameter['vary'], 'vary', 'Fit.add_model',
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661 raise_error=True)
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662 if not parameter['vary']:
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663 if 'min' in parameter:
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664 logging.warning(f'Ignoring min in parameter {name} in '+
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665 f'Fit.add_model (vary = {parameter["vary"]})')
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666 parameter.pop('min')
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667 if 'max' in parameter:
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668 logging.warning(f'Ignoring max in parameter {name} in '+
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669 f'Fit.add_model (vary = {parameter["vary"]})')
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670 parameter.pop('max')
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671 self._parameters[name].set(**parameter)
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672 parameter['name'] = name
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673 else:
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674 illegal_value(parameter, 'parameter name', 'Fit.model', raise_error=True)
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675 self._parameter_norms = {**self._parameter_norms, **new_parameter_norms}
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676 # print('\nAfter parameter init:')
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677 # self._parameters.pretty_print()
69
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678 # print(f'parameters:\n{parameters}')
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679 # print(f'new_parameter_norms:\n{new_parameter_norms}')
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680 # print(f'parameter_norms:\n{self._parameter_norms}')
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681 # print(f'kwargs:\n{kwargs}')
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diff changeset
682
69
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683 # Initialize the model parameters from kwargs
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684 for name, value in {**kwargs}.items():
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685 full_name = f'{pprefix}{name}'
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686 if full_name in new_parameter_norms and isinstance(value, (int, float)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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687 kwargs.pop(name)
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688 if self._parameters[full_name].expr is None:
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689 self._parameters[full_name].set(value=value)
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690 else:
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691 logging.warning(f'Ignoring parameter {name} in Fit.fit (set by expression: '+
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692 f'{self._parameters[full_name].expr})')
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693 # print('\nAfter kwargs init:')
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694 # self._parameters.pretty_print()
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695 # print(f'parameter_norms:\n{self._parameter_norms}')
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696 # print(f'kwargs:\n{kwargs}')
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diff changeset
697
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diff changeset
698 # Check parameter norms (also need it for expressions to renormalize the errors)
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699 if self._norm is not None and (callable(model) or model == 'expression'):
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diff changeset
700 missing_norm = False
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701 for name in new_parameters.valuesdict():
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702 if name not in self._parameter_norms:
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diff changeset
703 print(f'new_parameters:\n{new_parameters.valuesdict()}')
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704 print(f'self._parameter_norms:\n{self._parameter_norms}')
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diff changeset
705 logging.error(f'Missing parameter normalization type for {name} in {model}')
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diff changeset
706 missing_norm = True
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707 if missing_norm:
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diff changeset
708 raise ValueError
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diff changeset
709
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diff changeset
710 # print(f'at end add_model:\nself._parameters:\n{list(self.parameters)}')
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711 # print(f'at end add_model: kwargs = {kwargs}')
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712 # print(f'\nat end add_model: newmodel:\n{newmodel.__dict__}\n')
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713 return(kwargs)
49
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diff changeset
714
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diff changeset
715 def fit(self, interactive=False, guess=False, **kwargs):
69
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716 # Check inputs
49
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diff changeset
717 if self._model is None:
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diff changeset
718 logging.error('Undefined fit model')
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diff changeset
719 return
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
720 if not isinstance(interactive, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
721 illegal_value(interactive, 'interactive', 'Fit.fit', raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
722 if not isinstance(guess, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
723 illegal_value(guess, 'guess', 'Fit.fit', raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
724 if 'try_linear_fit' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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725 try_linear_fit = kwargs.pop('try_linear_fit')
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diff changeset
726 if not isinstance(try_linear_fit, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
727 illegal_value(try_linear_fit, 'try_linear_fit', 'Fit.fit', raise_error=True)
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diff changeset
728 if not self._try_linear_fit:
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diff changeset
729 logging.warning('Ignore superfluous keyword argument "try_linear_fit" (not '+
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diff changeset
730 'yet supported for callable models)')
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diff changeset
731 else:
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diff changeset
732 self._try_linear_fit = try_linear_fit
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
733 # if self._result is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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734 # if 'parameters' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
735 # raise ValueError('Invalid parameter parameters ({kwargs["parameters"]})')
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736 # else:
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737 if self._result is not None:
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diff changeset
738 if guess:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
739 logging.warning('Ignoring input parameter guess in Fit.fit during refitting')
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740 guess = False
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diff changeset
741
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
742 # Check for circular expressions
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
743 # FIX TODO
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744 # for name1, par1 in self._parameters.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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745 # if par1.expr is not None:
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diff changeset
746
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diff changeset
747 # Apply mask if supplied:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
748 if 'mask' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
749 self._mask = kwargs.pop('mask')
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diff changeset
750 if self._mask is not None:
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diff changeset
751 self._mask = np.asarray(self._mask).astype(bool)
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diff changeset
752 if self._x.size != self._mask.size:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
753 raise ValueError(f'Inconsistent x and mask dimensions ({self._x.size} vs '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
754 f'{self._mask.size})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
755
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
756 # Estimate initial parameters with build-in lmfit guess method (only for a single model)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
757 # print(f'\nat start fit: kwargs = {kwargs}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
758 #RV print('\nAt start of fit:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
759 #RV self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
760 # print(f'parameter_norms:\n{self._parameter_norms}')
49
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diff changeset
761 if guess:
69
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diff changeset
762 if self._mask is None:
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diff changeset
763 self._parameters = self._model.guess(self._y, x=self._x)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
764 else:
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diff changeset
765 self._parameters = self._model.guess(np.asarray(self._y)[~self._mask],
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
766 x=self._x[~self._mask])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
767 # print('\nAfter guess:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
768 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
769
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
770 # Add constant offset for a normalized model
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771 if self._result is None and self._norm is not None and self._norm[0]:
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772 self.add_model('constant', prefix='tmp_normalization_offset_', parameters={'name': 'c',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
773 'value': -self._norm[0], 'vary': False, 'norm': True})
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
774 #'value': -self._norm[0]/self._norm[1], 'vary': False, 'norm': False})
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
775
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
776 # Adjust existing parameters for refit:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
777 if 'parameters' in kwargs:
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diff changeset
778 parameters = kwargs.pop('parameters')
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779 if isinstance(parameters, dict):
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diff changeset
780 parameters = (parameters, )
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diff changeset
781 elif not is_dict_series(parameters):
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diff changeset
782 illegal_value(parameters, 'parameters', 'Fit.fit', raise_error=True)
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783 for par in parameters:
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784 name = par['name']
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785 if name not in self._parameters:
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786 raise ValueError(f'Unable to match {name} parameter {par} to an existing one')
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787 if self._parameters[name].expr is not None:
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788 raise ValueError(f'Unable to modify {name} parameter {par} (currently an '+
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789 'expression)')
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790 if par.get('expr') is not None:
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791 raise KeyError(f'Illegal "expr" key in {name} parameter {par}')
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792 self._parameters[name].set(vary=par.get('vary'))
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793 self._parameters[name].set(min=par.get('min'))
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794 self._parameters[name].set(max=par.get('max'))
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795 self._parameters[name].set(value=par.get('value'))
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796 #RV print('\nAfter adjust:')
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797 #RV self._parameters.pretty_print()
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798
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diff changeset
799 # Apply parameter updates through keyword arguments
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800 # print(f'kwargs = {kwargs}')
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801 # print(f'parameter_norms = {self._parameter_norms}')
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802 for name in set(self._parameters) & set(kwargs):
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803 value = kwargs.pop(name)
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804 if self._parameters[name].expr is None:
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805 self._parameters[name].set(value=value)
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806 else:
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807 logging.warning(f'Ignoring parameter {name} in Fit.fit (set by expression: '+
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808 f'{self._parameters[name].expr})')
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809
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810 # Check for uninitialized parameters
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811 for name, par in self._parameters.items():
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812 if par.expr is None:
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813 value = par.value
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814 if value is None or np.isinf(value) or np.isnan(value):
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815 if interactive:
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816 value = input_num(f'Enter an initial value for {name}', default=1.0)
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817 else:
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818 value = 1.0
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819 if self._norm is None or name not in self._parameter_norms:
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820 self._parameters[name].set(value=value)
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821 elif self._parameter_norms[name]:
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822 self._parameters[name].set(value=value*self._norm[1])
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
823
69
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824 # Check if model is linear
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825 try:
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826 linear_model = self._check_linearity_model()
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827 except:
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828 linear_model = False
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829 # print(f'\n\n--------> linear_model = {linear_model}\n')
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830 if kwargs.get('check_only_linearity') is not None:
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831 return(linear_model)
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832
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diff changeset
833 # Normalize the data and initial parameters
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834 #RV print('\nBefore normalization:')
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835 #RV self._parameters.pretty_print()
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836 # print(f'parameter_norms:\n{self._parameter_norms}')
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837 self._normalize()
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838 # print(f'norm = {self._norm}')
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839 #RV print('\nAfter normalization:')
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840 #RV self._parameters.pretty_print()
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841 # self.print_fit_report()
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842 # print(f'parameter_norms:\n{self._parameter_norms}')
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diff changeset
843
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diff changeset
844 if linear_model:
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845 # Perform a linear fit by direct matrix solution with numpy
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846 try:
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847 if self._mask is None:
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diff changeset
848 self._fit_linear_model(self._x, self._y_norm)
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849 else:
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850 self._fit_linear_model(self._x[~self._mask],
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851 np.asarray(self._y_norm)[~self._mask])
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diff changeset
852 except:
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diff changeset
853 linear_model = False
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854 if not linear_model:
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diff changeset
855 # Perform a non-linear fit with lmfit
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856 # Prevent initial values from sitting at boundaries
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857 self._parameter_bounds = {name:{'min': par.min, 'max': par.max} for name, par in
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858 self._parameters.items() if par.vary}
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859 for par in self._parameters.values():
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860 if par.vary:
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861 par.set(value=self._reset_par_at_boundary(par, par.value))
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862 # print('\nAfter checking boundaries:')
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863 # self._parameters.pretty_print()
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864
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diff changeset
865 # Perform the fit
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866 # fit_kws = None
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867 # if 'Dfun' in kwargs:
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868 # fit_kws = {'Dfun': kwargs.pop('Dfun')}
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869 # self._result = self._model.fit(self._y_norm, self._parameters, x=self._x,
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870 # fit_kws=fit_kws, **kwargs)
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871 if self._mask is None:
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872 self._result = self._model.fit(self._y_norm, self._parameters, x=self._x, **kwargs)
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diff changeset
873 else:
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diff changeset
874 self._result = self._model.fit(np.asarray(self._y_norm)[~self._mask],
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875 self._parameters, x=self._x[~self._mask], **kwargs)
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diff changeset
876 #RV print('\nAfter fit:')
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diff changeset
877 # print(f'\nself._result ({self._result}):\n\t{self._result.__dict__}')
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diff changeset
878 #RV self._parameters.pretty_print()
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879 # self.print_fit_report()
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diff changeset
880
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
881 # Set internal parameter values to fit results upon success
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882 if self.success:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
883 for name, par in self._parameters.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
884 if par.expr is None and par.vary:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
885 par.set(value=self._result.params[name].value)
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diff changeset
886 # print('\nAfter update parameter values:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
887 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
888
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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diff changeset
889 # Renormalize the data and results
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
890 self._renormalize()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
891 #RV print('\nAfter renormalization:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
892 #RV self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
893 # self.print_fit_report()
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diff changeset
894
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
895 def plot(self, y=None, y_title=None, result=None, skip_init=False, plot_comp_legends=False,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
896 plot_residual=False, plot_masked_data=True, **kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
897 if result is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
898 result = self._result
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
899 if result is None:
49
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parents:
diff changeset
900 return
69
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diff changeset
901 plots = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
902 legend = []
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diff changeset
903 if self._mask is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
904 mask = np.zeros(self._x.size).astype(bool)
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diff changeset
905 plot_masked_data = False
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diff changeset
906 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
907 mask = self._mask
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
908 if y is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
909 if not isinstance(y, (tuple, list, np.ndarray)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
910 illegal_value(y, 'y', 'Fit.plot')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
911 if len(y) != len(self._x):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
912 logging.warning('Ignoring parameter y in Fit.plot (wrong dimension)')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
913 y = None
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diff changeset
914 if y is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
915 if y_title is None or not isinstance(y_title, str):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
916 y_title = 'data'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
917 plots += [(self._x, y, '.')]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
918 legend += [y_title]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
919 if self._y is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
920 plots += [(self._x, np.asarray(self._y), 'b.')]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
921 legend += ['data']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
922 if plot_masked_data:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
923 plots += [(self._x[mask], np.asarray(self._y)[mask], 'bx')]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
924 legend += ['masked data']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
925 if isinstance(plot_residual, bool) and plot_residual:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
926 plots += [(self._x[~mask], result.residual, 'k-')]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
927 legend += ['residual']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
928 plots += [(self._x[~mask], result.best_fit, 'k-')]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
929 legend += ['best fit']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
930 if not skip_init and hasattr(result, 'init_fit'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
931 plots += [(self._x[~mask], result.init_fit, 'g-')]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
932 legend += ['init']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
933 components = result.eval_components(x=self._x[~mask])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
934 num_components = len(components)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
935 if 'tmp_normalization_offset_' in components:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
936 num_components -= 1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
937 if num_components > 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
938 eval_index = 0
49
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rv43
parents:
diff changeset
939 for modelname, y in components.items():
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
940 if modelname == 'tmp_normalization_offset_':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
941 continue
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
942 if modelname == '_eval':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
943 modelname = f'eval{eval_index}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
944 if len(modelname) > 20:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
945 modelname = f'{modelname[0:16]} ...'
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
946 if isinstance(y, (int, float)):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
947 y *= np.ones(self._x[~mask].size)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
948 plots += [(self._x[~mask], y, '--')]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
949 if plot_comp_legends:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
950 if modelname[-1] == '_':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
951 legend.append(modelname[:-1])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
952 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
953 legend.append(modelname)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
954 title = kwargs.get('title')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
955 if title is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
956 kwargs.pop('title')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
957 quick_plot(tuple(plots), legend=legend, title=title, block=True, **kwargs)
49
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rv43
parents:
diff changeset
958
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
959 @staticmethod
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
960 def guess_init_peak(x, y, *args, center_guess=None, use_max_for_center=True):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
961 """ Return a guess for the initial height, center and fwhm for a peak
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
962 """
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
963 # print(f'\n\nargs = {args}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
964 # print(f'center_guess = {center_guess}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
965 # quick_plot(x, y, vlines=center_guess, block=True)
49
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rv43
parents:
diff changeset
966 center_guesses = None
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
967 x = np.asarray(x)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
968 y = np.asarray(y)
49
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parents:
diff changeset
969 if len(x) != len(y):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
970 logging.error(f'Invalid x and y lengths ({len(x)}, {len(y)}), skip initial guess')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
971 return(None, None, None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
972 if isinstance(center_guess, (int, float)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
973 if len(args):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
974 logging.warning('Ignoring additional arguments for single center_guess value')
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
975 center_guesses = [center_guess]
49
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parents:
diff changeset
976 elif isinstance(center_guess, (tuple, list, np.ndarray)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
977 if len(center_guess) == 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
978 logging.warning('Ignoring additional arguments for single center_guess value')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
979 if not isinstance(center_guess[0], (int, float)):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
980 raise ValueError(f'Invalid parameter center_guess ({type(center_guess[0])})')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
981 center_guess = center_guess[0]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
982 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
983 if len(args) != 1:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
984 raise ValueError(f'Invalid number of arguments ({len(args)})')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
985 n = args[0]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
986 if not is_index(n, 0, len(center_guess)):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
987 raise ValueError('Invalid argument')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
988 center_guesses = center_guess
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
989 center_guess = center_guesses[n]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
990 elif center_guess is not None:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
991 raise ValueError(f'Invalid center_guess type ({type(center_guess)})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
992 # print(f'x = {x}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
993 # print(f'y = {y}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
994 # print(f'center_guess = {center_guess}')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
995
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
996 # Sort the inputs
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
997 index = np.argsort(x)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
998 x = x[index]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
999 y = y[index]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1000 miny = y.min()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1001 # print(f'miny = {miny}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1002 # print(f'x_range = {x[0]} {x[-1]} {len(x)}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1003 # print(f'y_range = {y[0]} {y[-1]} {len(y)}')
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1004 # quick_plot(x, y, vlines=center_guess, block=True)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1005
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1006 # xx = x
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1007 # yy = y
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1008 # Set range for current peak
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1009 # print(f'n = {n}')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1010 # print(f'center_guesses = {center_guesses}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1011 if center_guesses is not None:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1012 if len(center_guesses) > 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1013 index = np.argsort(center_guesses)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1014 n = list(index).index(n)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1015 # print(f'n = {n}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1016 # print(f'index = {index}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1017 center_guesses = np.asarray(center_guesses)[index]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1018 # print(f'center_guesses = {center_guesses}')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1019 if n == 0:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1020 low = 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1021 upp = index_nearest(x, (center_guesses[0]+center_guesses[1])/2)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1022 elif n == len(center_guesses)-1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1023 low = index_nearest(x, (center_guesses[n-1]+center_guesses[n])/2)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1024 upp = len(x)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1025 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1026 low = index_nearest(x, (center_guesses[n-1]+center_guesses[n])/2)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1027 upp = index_nearest(x, (center_guesses[n]+center_guesses[n+1])/2)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1028 # print(f'low = {low}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1029 # print(f'upp = {upp}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1030 x = x[low:upp]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1031 y = y[low:upp]
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1032 # quick_plot(x, y, vlines=(x[0], center_guess, x[-1]), block=True)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1033
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1034 # Estimate FHHM
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1035 maxy = y.max()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1036 # print(f'x_range = {x[0]} {x[-1]} {len(x)}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1037 # print(f'y_range = {y[0]} {y[-1]} {len(y)} {miny} {maxy}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1038 # print(f'center_guess = {center_guess}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1039 if center_guess is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1040 center_index = np.argmax(y)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1041 center = x[center_index]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1042 height = maxy-miny
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1043 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1044 if use_max_for_center:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1045 center_index = np.argmax(y)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1046 center = x[center_index]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1047 if center_index < 0.1*len(x) or center_index > 0.9*len(x):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1048 center_index = index_nearest(x, center_guess)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1049 center = center_guess
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1050 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1051 center_index = index_nearest(x, center_guess)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1052 center = center_guess
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1053 height = y[center_index]-miny
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1054 # print(f'center_index = {center_index}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1055 # print(f'center = {center}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1056 # print(f'height = {height}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1057 half_height = miny+0.5*height
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1058 # print(f'half_height = {half_height}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1059 fwhm_index1 = 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1060 for i in range(center_index, fwhm_index1, -1):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1061 if y[i] < half_height:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1062 fwhm_index1 = i
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1063 break
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1064 # print(f'fwhm_index1 = {fwhm_index1} {x[fwhm_index1]}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1065 fwhm_index2 = len(x)-1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1066 for i in range(center_index, fwhm_index2):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1067 if y[i] < half_height:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1068 fwhm_index2 = i
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1069 break
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1070 # print(f'fwhm_index2 = {fwhm_index2} {x[fwhm_index2]}')
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1071 # quick_plot((x,y,'o'), vlines=(x[fwhm_index1], center, x[fwhm_index2]), block=True)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1072 if fwhm_index1 == 0 and fwhm_index2 < len(x)-1:
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1073 fwhm = 2*(x[fwhm_index2]-center)
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1074 elif fwhm_index1 > 0 and fwhm_index2 == len(x)-1:
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diff changeset
1075 fwhm = 2*(center-x[fwhm_index1])
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1076 else:
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1077 fwhm = x[fwhm_index2]-x[fwhm_index1]
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diff changeset
1078 # print(f'fwhm_index1 = {fwhm_index1} {x[fwhm_index1]}')
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1079 # print(f'fwhm_index2 = {fwhm_index2} {x[fwhm_index2]}')
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1080 # print(f'fwhm = {fwhm}')
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1081
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diff changeset
1082 # Return height, center and FWHM
69
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1083 # quick_plot((x,y,'o'), (xx,yy), vlines=(x[fwhm_index1], center, x[fwhm_index2]), block=True)
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1084 return(height, center, fwhm)
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1085
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1086 def _check_linearity_model(self):
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1087 """Identify the linearity of all model parameters and check if the model is linear or not
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1088 """
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1089 if not self._try_linear_fit:
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1090 logging.info('Skip linearity check (not yet supported for callable models)')
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1091 return(False)
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1092 free_parameters = [name for name, par in self._parameters.items() if par.vary]
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1093 for component in self._model.components:
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1094 if 'tmp_normalization_offset_c' in component.param_names:
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1095 continue
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1096 if isinstance(component, ExpressionModel):
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1097 for name in free_parameters:
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1098 if diff(component.expr, name, name):
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1099 # print(f'\t\t{component.expr} is non-linear in {name}')
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1100 self._nonlinear_parameters.append(name)
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1101 if name in self._linear_parameters:
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1102 self._linear_parameters.remove(name)
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1103 else:
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1104 model_parameters = component.param_names.copy()
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1105 for basename, hint in component.param_hints.items():
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1106 name = f'{component.prefix}{basename}'
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1107 if hint.get('expr') is not None:
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1108 model_parameters.remove(name)
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1109 for name in model_parameters:
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diff changeset
1110 expr = self._parameters[name].expr
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1111 if expr is not None:
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1112 for nname in free_parameters:
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1113 if name in self._nonlinear_parameters:
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1114 if diff(expr, nname):
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1115 # print(f'\t\t{component} is non-linear in {nname} (through {name} = "{expr}")')
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1116 self._nonlinear_parameters.append(nname)
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1117 if nname in self._linear_parameters:
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1118 self._linear_parameters.remove(nname)
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1119 else:
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diff changeset
1120 assert(name in self._linear_parameters)
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1121 # print(f'\n\nexpr ({type(expr)}) = {expr}\nnname ({type(nname)}) = {nname}\n\n')
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1122 if diff(expr, nname, nname):
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1123 # print(f'\t\t{component} is non-linear in {nname} (through {name} = "{expr}")')
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1124 self._nonlinear_parameters.append(nname)
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1125 if nname in self._linear_parameters:
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1126 self._linear_parameters.remove(nname)
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1127 # print(f'\nfree parameters:\n\t{free_parameters}')
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1128 # print(f'linear parameters:\n\t{self._linear_parameters}')
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1129 # print(f'nonlinear parameters:\n\t{self._nonlinear_parameters}\n')
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1130 if any(True for name in self._nonlinear_parameters if self._parameters[name].vary):
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1131 return(False)
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1132 return(True)
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1133
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1134 def _fit_linear_model(self, x, y):
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1135 """Perform a linear fit by direct matrix solution with numpy
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1136 """
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1137 # Construct the matrix and the free parameter vector
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1138 # print(f'\nparameters:')
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1139 # self._parameters.pretty_print()
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1140 # print(f'\nparameter_norms:\n\t{self._parameter_norms}')
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1141 # print(f'\nlinear_parameters:\n\t{self._linear_parameters}')
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1142 # print(f'nonlinear_parameters:\n\t{self._nonlinear_parameters}')
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1143 free_parameters = [name for name, par in self._parameters.items() if par.vary]
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1144 # print(f'free parameters:\n\t{free_parameters}\n')
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1145 expr_parameters = {name:par.expr for name, par in self._parameters.items()
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1146 if par.expr is not None}
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1147 model_parameters = []
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1148 for component in self._model.components:
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1149 if 'tmp_normalization_offset_c' in component.param_names:
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diff changeset
1150 continue
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diff changeset
1151 model_parameters += component.param_names
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diff changeset
1152 for basename, hint in component.param_hints.items():
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diff changeset
1153 name = f'{component.prefix}{basename}'
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1154 if hint.get('expr') is not None:
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diff changeset
1155 expr_parameters.pop(name)
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diff changeset
1156 model_parameters.remove(name)
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1157 # print(f'expr parameters:\n{expr_parameters}')
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1158 # print(f'model parameters:\n\t{model_parameters}\n')
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diff changeset
1159 norm = 1.0
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diff changeset
1160 if self._normalized:
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1161 norm = self._norm[1]
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1162 # print(f'\n\nself._normalized = {self._normalized}\nnorm = {norm}\nself._norm = {self._norm}\n')
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diff changeset
1163 # Add expression parameters to asteval
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diff changeset
1164 ast = Interpreter()
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1165 # print(f'Adding to asteval sym table:')
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diff changeset
1166 for name, expr in expr_parameters.items():
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diff changeset
1167 # print(f'\tadding {name} {expr}')
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1168 ast.symtable[name] = expr
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1169 # Add constant parameters to asteval
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1170 # (renormalize to use correctly in evaluation of expression models)
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1171 for name, par in self._parameters.items():
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1172 if par.expr is None and not par.vary:
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1173 if self._parameter_norms[name]:
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1174 # print(f'\tadding {name} {par.value*norm}')
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1175 ast.symtable[name] = par.value*norm
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1176 else:
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1177 # print(f'\tadding {name} {par.value}')
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diff changeset
1178 ast.symtable[name] = par.value
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diff changeset
1179 A = np.zeros((len(x), len(free_parameters)), dtype='float64')
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diff changeset
1180 y_const = np.zeros(len(x), dtype='float64')
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diff changeset
1181 have_expression_model = False
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diff changeset
1182 for component in self._model.components:
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1183 if isinstance(component, ConstantModel):
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1184 name = component.param_names[0]
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1185 # print(f'\nConstant model: {name} {self._parameters[name]}\n')
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1186 if name in free_parameters:
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1187 # print(f'\t\t{name} is a free constant set matrix column {free_parameters.index(name)} to 1.0')
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1188 A[:,free_parameters.index(name)] = 1.0
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1189 else:
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1190 if self._parameter_norms[name]:
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1191 delta_y_const = self._parameters[name]*np.ones(len(x))
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1192 else:
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1193 delta_y_const = (self._parameters[name]*norm)*np.ones(len(x))
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1194 y_const += delta_y_const
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1195 # print(f'\ndelta_y_const ({type(delta_y_const)}):\n{delta_y_const}\n')
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1196 elif isinstance(component, ExpressionModel):
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1197 have_expression_model = True
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1198 const_expr = component.expr
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1199 # print(f'\nExpression model:\nconst_expr: {const_expr}\n')
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1200 for name in free_parameters:
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1201 dexpr_dname = diff(component.expr, name)
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diff changeset
1202 if dexpr_dname:
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diff changeset
1203 const_expr = f'{const_expr}-({str(dexpr_dname)})*{name}'
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diff changeset
1204 # print(f'\tconst_expr: {const_expr}')
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diff changeset
1205 if not self._parameter_norms[name]:
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diff changeset
1206 dexpr_dname = f'({dexpr_dname})/{norm}'
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1207 # print(f'\t{component.expr} is linear in {name}\n\t\tadd "{str(dexpr_dname)}" to matrix as column {free_parameters.index(name)}')
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diff changeset
1208 fx = [(lambda _: ast.eval(str(dexpr_dname)))(ast(f'x={v}')) for v in x]
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diff changeset
1209 # print(f'\tfx:\n{fx}')
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diff changeset
1210 if len(ast.error):
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diff changeset
1211 raise ValueError(f'Unable to evaluate {dexpr_dname}')
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diff changeset
1212 A[:,free_parameters.index(name)] += fx
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diff changeset
1213 # if self._parameter_norms[name]:
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1214 # print(f'\t\t{component.expr} is linear in {name} add "{str(dexpr_dname)}" to matrix as column {free_parameters.index(name)}')
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diff changeset
1215 # A[:,free_parameters.index(name)] += fx
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diff changeset
1216 # else:
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diff changeset
1217 # print(f'\t\t{component.expr} is linear in {name} add "({str(dexpr_dname)})/{norm}" to matrix as column {free_parameters.index(name)}')
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diff changeset
1218 # A[:,free_parameters.index(name)] += np.asarray(fx)/norm
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diff changeset
1219 # FIX: find another solution if expr not supported by simplify
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diff changeset
1220 const_expr = str(simplify(f'({const_expr})/{norm}'))
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diff changeset
1221 # print(f'\nconst_expr: {const_expr}')
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diff changeset
1222 delta_y_const = [(lambda _: ast.eval(const_expr))(ast(f'x = {v}')) for v in x]
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diff changeset
1223 y_const += delta_y_const
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diff changeset
1224 # print(f'\ndelta_y_const ({type(delta_y_const)}):\n{delta_y_const}\n')
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diff changeset
1225 if len(ast.error):
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diff changeset
1226 raise ValueError(f'Unable to evaluate {const_expr}')
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diff changeset
1227 else:
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diff changeset
1228 free_model_parameters = [name for name in component.param_names
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diff changeset
1229 if name in free_parameters or name in expr_parameters]
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diff changeset
1230 # print(f'\nBuild-in model ({component}):\nfree_model_parameters: {free_model_parameters}\n')
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diff changeset
1231 if not len(free_model_parameters):
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diff changeset
1232 y_const += component.eval(params=self._parameters, x=x)
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diff changeset
1233 elif isinstance(component, LinearModel):
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diff changeset
1234 if f'{component.prefix}slope' in free_model_parameters:
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diff changeset
1235 A[:,free_parameters.index(f'{component.prefix}slope')] = x
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diff changeset
1236 else:
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diff changeset
1237 y_const += self._parameters[f'{component.prefix}slope'].value*x
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diff changeset
1238 if f'{component.prefix}intercept' in free_model_parameters:
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diff changeset
1239 A[:,free_parameters.index(f'{component.prefix}intercept')] = 1.0
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diff changeset
1240 else:
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diff changeset
1241 y_const += self._parameters[f'{component.prefix}intercept'].value* \
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diff changeset
1242 np.ones(len(x))
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1243 elif isinstance(component, QuadraticModel):
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diff changeset
1244 if f'{component.prefix}a' in free_model_parameters:
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diff changeset
1245 A[:,free_parameters.index(f'{component.prefix}a')] = x**2
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diff changeset
1246 else:
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diff changeset
1247 y_const += self._parameters[f'{component.prefix}a'].value*x**2
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diff changeset
1248 if f'{component.prefix}b' in free_model_parameters:
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diff changeset
1249 A[:,free_parameters.index(f'{component.prefix}b')] = x
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diff changeset
1250 else:
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diff changeset
1251 y_const += self._parameters[f'{component.prefix}b'].value*x
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diff changeset
1252 if f'{component.prefix}c' in free_model_parameters:
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diff changeset
1253 A[:,free_parameters.index(f'{component.prefix}c')] = 1.0
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diff changeset
1254 else:
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diff changeset
1255 y_const += self._parameters[f'{component.prefix}c'].value*np.ones(len(x))
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diff changeset
1256 else:
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diff changeset
1257 # At this point each build-in model must be strictly proportional to each linear
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diff changeset
1258 # model parameter. Without this assumption, the model equation is needed
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1259 # For the current build-in lmfit models, this can only ever be the amplitude
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1260 assert(len(free_model_parameters) == 1)
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1261 name = f'{component.prefix}amplitude'
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1262 assert(free_model_parameters[0] == name)
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diff changeset
1263 assert(self._parameter_norms[name])
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1264 expr = self._parameters[name].expr
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1265 if expr is None:
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diff changeset
1266 # print(f'\t{component} is linear in {name} add to matrix as column {free_parameters.index(name)}')
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diff changeset
1267 parameters = deepcopy(self._parameters)
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diff changeset
1268 parameters[name].set(value=1.0)
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diff changeset
1269 index = free_parameters.index(name)
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diff changeset
1270 A[:,free_parameters.index(name)] += component.eval(params=parameters, x=x)
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1271 else:
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diff changeset
1272 const_expr = expr
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1273 # print(f'\tconst_expr: {const_expr}')
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diff changeset
1274 parameters = deepcopy(self._parameters)
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diff changeset
1275 parameters[name].set(value=1.0)
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diff changeset
1276 dcomp_dname = component.eval(params=parameters, x=x)
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1277 # print(f'\tdcomp_dname ({type(dcomp_dname)}):\n{dcomp_dname}')
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diff changeset
1278 for nname in free_parameters:
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1279 dexpr_dnname = diff(expr, nname)
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1280 if dexpr_dnname:
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1281 assert(self._parameter_norms[name])
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1282 # print(f'\t\td({expr})/d{nname} = {dexpr_dnname}')
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1283 # print(f'\t\t{component} is linear in {nname} (through {name} = "{expr}", add to matrix as column {free_parameters.index(nname)})')
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diff changeset
1284 fx = np.asarray(dexpr_dnname*dcomp_dname, dtype='float64')
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1285 # print(f'\t\tfx ({type(fx)}): {fx}')
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1286 # print(f'free_parameters.index({nname}): {free_parameters.index(nname)}')
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1287 if self._parameter_norms[nname]:
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1288 A[:,free_parameters.index(nname)] += fx
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1289 else:
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1290 A[:,free_parameters.index(nname)] += fx/norm
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1291 const_expr = f'{const_expr}-({dexpr_dnname})*{nname}'
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1292 # print(f'\t\tconst_expr: {const_expr}')
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1293 const_expr = str(simplify(f'({const_expr})/{norm}'))
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1294 # print(f'\tconst_expr: {const_expr}')
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1295 fx = [(lambda _: ast.eval(const_expr))(ast(f'x = {v}')) for v in x]
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1296 # print(f'\tfx: {fx}')
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1297 delta_y_const = np.multiply(fx, dcomp_dname)
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1298 y_const += delta_y_const
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1299 # print(f'\ndelta_y_const ({type(delta_y_const)}):\n{delta_y_const}\n')
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1300 # print(A)
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1301 # print(y_const)
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1302 solution, residual, rank, s = np.linalg.lstsq(A, y-y_const, rcond=None)
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1303 # print(f'\nsolution ({type(solution)} {solution.shape}):\n\t{solution}')
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1304 # print(f'\nresidual ({type(residual)} {residual.shape}):\n\t{residual}')
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1305 # print(f'\nrank ({type(rank)} {rank.shape}):\n\t{rank}')
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1306 # print(f'\ns ({type(s)} {s.shape}):\n\t{s}\n')
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diff changeset
1307
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1308 # Assemble result (compensate for normalization in expression models)
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1309 for name, value in zip(free_parameters, solution):
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1310 self._parameters[name].set(value=value)
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1311 if self._normalized and (have_expression_model or len(expr_parameters)):
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1312 for name, norm in self._parameter_norms.items():
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1313 par = self._parameters[name]
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1314 if par.expr is None and norm:
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1315 self._parameters[name].set(value=par.value*self._norm[1])
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1316 # self._parameters.pretty_print()
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1317 # print(f'\nself._parameter_norms:\n\t{self._parameter_norms}')
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1318 self._result = ModelResult(self._model, deepcopy(self._parameters))
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1319 self._result.best_fit = self._model.eval(params=self._parameters, x=x)
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diff changeset
1320 if self._normalized and (have_expression_model or len(expr_parameters)):
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1321 if 'tmp_normalization_offset_c' in self._parameters:
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1322 offset = self._parameters['tmp_normalization_offset_c']
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1323 else:
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diff changeset
1324 offset = 0.0
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1325 self._result.best_fit = (self._result.best_fit-offset-self._norm[0])/self._norm[1]
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diff changeset
1326 if self._normalized:
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1327 for name, norm in self._parameter_norms.items():
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1328 par = self._parameters[name]
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1329 if par.expr is None and norm:
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1330 value = par.value/self._norm[1]
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1331 self._parameters[name].set(value=value)
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1332 self._result.params[name].set(value=value)
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1333 # self._parameters.pretty_print()
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1334 self._result.residual = self._result.best_fit-y
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1335 self._result.components = self._model.components
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1336 self._result.init_params = None
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1337 # quick_plot((x, y, '.'), (x, y_const, 'g'), (x, self._result.best_fit, 'k'), (x, self._result.residual, 'r'), block=True)
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1338
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1339 def _normalize(self):
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1340 """Normalize the data and initial parameters
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1341 """
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1342 if self._normalized:
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1343 return
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1344 if self._norm is None:
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1345 if self._y is not None and self._y_norm is None:
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1346 self._y_norm = np.asarray(self._y)
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1347 else:
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1348 if self._y is not None and self._y_norm is None:
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1349 self._y_norm = (np.asarray(self._y)-self._norm[0])/self._norm[1]
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1350 self._y_range = 1.0
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1351 for name, norm in self._parameter_norms.items():
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diff changeset
1352 par = self._parameters[name]
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diff changeset
1353 if par.expr is None and norm:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1354 value = par.value/self._norm[1]
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diff changeset
1355 _min = par.min
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diff changeset
1356 _max = par.max
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diff changeset
1357 if not np.isinf(_min) and abs(_min) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1358 _min /= self._norm[1]
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diff changeset
1359 if not np.isinf(_max) and abs(_max) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1360 _max /= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1361 par.set(value=value, min=_min, max=_max)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1362 self._normalized = True
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diff changeset
1363
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diff changeset
1364 def _renormalize(self):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1365 """Renormalize the data and results
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1366 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1367 if self._norm is None or not self._normalized:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1368 return
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1369 self._normalized = False
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diff changeset
1370 for name, norm in self._parameter_norms.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1371 par = self._parameters[name]
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diff changeset
1372 if par.expr is None and norm:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1373 value = par.value*self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1374 _min = par.min
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diff changeset
1375 _max = par.max
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diff changeset
1376 if not np.isinf(_min) and abs(_min) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1377 _min *= self._norm[1]
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diff changeset
1378 if not np.isinf(_max) and abs(_max) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1379 _max *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1380 par.set(value=value, min=_min, max=_max)
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diff changeset
1381 if self._result is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1382 return
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diff changeset
1383 self._result.best_fit = self._result.best_fit*self._norm[1]+self._norm[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1384 for name, par in self._result.params.items():
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diff changeset
1385 if self._parameter_norms.get(name, False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1386 if par.stderr is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1387 par.stderr *= self._norm[1]
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diff changeset
1388 if par.expr is None:
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diff changeset
1389 _min = par.min
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parents: 65
diff changeset
1390 _max = par.max
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1391 value = par.value*self._norm[1]
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diff changeset
1392 if par.init_value is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1393 par.init_value *= self._norm[1]
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parents: 65
diff changeset
1394 if not np.isinf(_min) and abs(_min) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1395 _min *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1396 if not np.isinf(_max) and abs(_max) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1397 _max *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1398 par.set(value=value, min=_min, max=_max)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1399 if hasattr(self._result, 'init_fit'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1400 self._result.init_fit = self._result.init_fit*self._norm[1]+self._norm[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1401 if hasattr(self._result, 'init_values'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1402 init_values = {}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1403 for name, value in self._result.init_values.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1404 if name not in self._parameter_norms or self._parameters[name].expr is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1405 init_values[name] = value
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diff changeset
1406 elif self._parameter_norms[name]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1407 init_values[name] = value*self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1408 self._result.init_values = init_values
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diff changeset
1409 for name, par in self._result.init_params.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1410 if par.expr is None and self._parameter_norms.get(name, False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1411 value = par.value
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1412 _min = par.min
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1413 _max = par.max
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1414 value *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1415 if not np.isinf(_min) and abs(_min) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1416 _min *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1417 if not np.isinf(_max) and abs(_max) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1418 _max *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1419 par.set(value=value, min=_min, max=_max)
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diff changeset
1420 par.init_value = par.value
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1421 # Don't renormalize chisqr, it has no useful meaning in physical units
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1422 #self._result.chisqr *= self._norm[1]*self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1423 if self._result.covar is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1424 for i, name in enumerate(self._result.var_names):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1425 if self._parameter_norms.get(name, False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1426 for j in range(len(self._result.var_names)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1427 if self._result.covar[i,j] is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1428 self._result.covar[i,j] *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1429 if self._result.covar[j,i] is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1430 self._result.covar[j,i] *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1431 # Don't renormalize redchi, it has no useful meaning in physical units
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1432 #self._result.redchi *= self._norm[1]*self._norm[1]
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diff changeset
1433 if self._result.residual is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1434 self._result.residual *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1435
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1436 def _reset_par_at_boundary(self, par, value):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1437 assert(par.vary)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1438 name = par.name
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1439 _min = self._parameter_bounds[name]['min']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1440 _max = self._parameter_bounds[name]['max']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1441 if np.isinf(_min):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1442 if not np.isinf(_max):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1443 if self._parameter_norms.get(name, False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1444 upp = _max-0.1*self._y_range
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1445 elif _max == 0.0:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1446 upp = _max-0.1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1447 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1448 upp = _max-0.1*abs(_max)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1449 if value >= upp:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1450 return(upp)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1451 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1452 if np.isinf(_max):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1453 if self._parameter_norms.get(name, False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1454 low = _min+0.1*self._y_range
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1455 elif _min == 0.0:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1456 low = _min+0.1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1457 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1458 low = _min+0.1*abs(_min)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1459 if value <= low:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1460 return(low)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1461 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1462 low = 0.9*_min+0.1*_max
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1463 upp = 0.1*_min+0.9*_max
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1464 if value <= low:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1465 return(low)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1466 elif value >= upp:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1467 return(upp)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1468 return(value)
49
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rv43
parents:
diff changeset
1469
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1470
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1471 class FitMultipeak(Fit):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1472 """Fit data with multiple peaks
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1473 """
69
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diff changeset
1474 def __init__(self, y, x=None, normalize=True):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1475 super().__init__(y, x=x, normalize=normalize)
49
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parents:
diff changeset
1476 self._fwhm_max = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1477 self._sigma_max = None
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rv43
parents:
diff changeset
1478
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1479 @classmethod
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1480 def fit_multipeak(cls, y, centers, x=None, normalize=True, peak_models='gaussian',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1481 center_exprs=None, fit_type=None, background_order=None, background_exp=False,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1482 fwhm_max=None, plot_components=False):
49
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rv43
parents:
diff changeset
1483 """Make sure that centers and fwhm_max are in the correct units and consistent with expr
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1484 for a uniform fit (fit_type == 'uniform')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1485 """
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1486 fit = cls(y, x=x, normalize=normalize)
49
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rv43
parents:
diff changeset
1487 success = fit.fit(centers, fit_type=fit_type, peak_models=peak_models, fwhm_max=fwhm_max,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1488 center_exprs=center_exprs, background_order=background_order,
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1489 background_exp=background_exp, plot_components=plot_components)
49
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rv43
parents:
diff changeset
1490 if success:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1491 return(fit.best_fit, fit.residual, fit.best_values, fit.best_errors, fit.redchi, \
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1492 fit.success)
49
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rv43
parents:
diff changeset
1493 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1494 return(np.array([]), np.array([]), {}, {}, float_max, False)
49
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rv43
parents:
diff changeset
1495
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1496 def fit(self, centers, fit_type=None, peak_models=None, center_exprs=None, fwhm_max=None,
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1497 background_order=None, background_exp=False, plot_components=False,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1498 param_constraint=False):
49
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rv43
parents:
diff changeset
1499 self._fwhm_max = fwhm_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1500 # Create the multipeak model
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parents:
diff changeset
1501 self._create_model(centers, fit_type, peak_models, center_exprs, background_order,
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1502 background_exp, param_constraint)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1503
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1504 # RV: Obsolete Normalize the data and results
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parents: 65
diff changeset
1505 # print('\nBefore fit before normalization in FitMultipeak:')
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parents: 65
diff changeset
1506 # self._parameters.pretty_print()
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parents: 65
diff changeset
1507 # self._normalize()
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parents: 65
diff changeset
1508 # print('\nBefore fit after normalization in FitMultipeak:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1509 # self._parameters.pretty_print()
49
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rv43
parents:
diff changeset
1510
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1511 # Perform the fit
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1512 try:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1513 if param_constraint:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1514 super().fit(fit_kws={'xtol': 1.e-5, 'ftol': 1.e-5, 'gtol': 1.e-5})
49
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rv43
parents:
diff changeset
1515 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1516 super().fit()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1517 except:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1518 return(False)
49
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rv43
parents:
diff changeset
1519
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1520 # Check for valid fit parameter results
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1521 fit_failure = self._check_validity()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1522 success = True
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1523 if fit_failure:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1524 if param_constraint:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1525 logging.warning(' -> Should not happen with param_constraint set, fail the fit')
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parents:
diff changeset
1526 success = False
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rv43
parents:
diff changeset
1527 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1528 logging.info(' -> Retry fitting with constraints')
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parents:
diff changeset
1529 self.fit(centers, fit_type, peak_models, center_exprs, fwhm_max=fwhm_max,
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1530 background_order=background_order, background_exp=background_exp,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1531 plot_components=plot_components, param_constraint=True)
49
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parents:
diff changeset
1532 else:
69
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parents: 65
diff changeset
1533 # RV: Obsolete Renormalize the data and results
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1534 # print('\nAfter fit before renormalization in FitMultipeak:')
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parents: 65
diff changeset
1535 # self._parameters.pretty_print()
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diff changeset
1536 # self.print_fit_report()
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diff changeset
1537 # self._renormalize()
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diff changeset
1538 # print('\nAfter fit after renormalization in FitMultipeak:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1539 # self._parameters.pretty_print()
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diff changeset
1540 # self.print_fit_report()
49
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parents:
diff changeset
1541
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1542 # Print report and plot components if requested
69
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diff changeset
1543 if plot_components:
49
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parents:
diff changeset
1544 self.print_fit_report()
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parents:
diff changeset
1545 self.plot()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1546
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1547 return(success)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1548
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1549 def _create_model(self, centers, fit_type=None, peak_models=None, center_exprs=None,
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1550 background_order=None, background_exp=False, param_constraint=False):
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1551 """Create the multipeak model
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1552 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1553 if isinstance(centers, (int, float)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1554 centers = [centers]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1555 num_peaks = len(centers)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1556 if peak_models is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1557 peak_models = num_peaks*['gaussian']
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1558 elif isinstance(peak_models, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1559 peak_models = num_peaks*[peak_models]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1560 if len(peak_models) != num_peaks:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1561 raise ValueError(f'Inconsistent number of peaks in peak_models ({len(peak_models)} vs '+
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1562 f'{num_peaks})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1563 if num_peaks == 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1564 if fit_type is not None:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1565 logging.debug('Ignoring fit_type input for fitting one peak')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1566 fit_type = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1567 if center_exprs is not None:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1568 logging.debug('Ignoring center_exprs input for fitting one peak')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1569 center_exprs = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1570 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1571 if fit_type == 'uniform':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1572 if center_exprs is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1573 center_exprs = [f'scale_factor*{cen}' for cen in centers]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1574 if len(center_exprs) != num_peaks:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1575 raise ValueError(f'Inconsistent number of peaks in center_exprs '+
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1576 f'({len(center_exprs)} vs {num_peaks})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1577 elif fit_type == 'unconstrained' or fit_type is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1578 if center_exprs is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1579 logging.warning('Ignoring center_exprs input for unconstrained fit')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1580 center_exprs = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1581 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1582 raise ValueError(f'Invalid fit_type in fit_multigaussian {fit_type}')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1583 self._sigma_max = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1584 if param_constraint:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1585 min_value = float_min
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1586 if self._fwhm_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1587 self._sigma_max = np.zeros(num_peaks)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1588 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1589 min_value = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1590
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1591 # Reset the fit
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1592 self._model = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1593 self._parameters = Parameters()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1594 self._result = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1595
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1596 # Add background model
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1597 if background_order is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1598 if background_order == 0:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1599 self.add_model('constant', prefix='background', parameters=
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1600 {'name': 'c', 'value': float_min, 'min': min_value})
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1601 elif background_order == 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1602 self.add_model('linear', prefix='background', slope=0.0, intercept=0.0)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1603 elif background_order == 2:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1604 self.add_model('quadratic', prefix='background', a=0.0, b=0.0, c=0.0)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1605 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1606 raise ValueError(f'Invalid parameter background_order ({background_order})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1607 if background_exp:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1608 self.add_model('exponential', prefix='background', parameters=(
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1609 {'name': 'amplitude', 'value': float_min, 'min': min_value},
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1610 {'name': 'decay', 'value': float_min, 'min': min_value}))
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1611
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1612 # Add peaks and guess initial fit parameters
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1613 ast = Interpreter()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1614 if num_peaks == 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1615 height_init, cen_init, fwhm_init = self.guess_init_peak(self._x, self._y)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1616 if self._fwhm_max is not None and fwhm_init > self._fwhm_max:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1617 fwhm_init = self._fwhm_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1618 ast(f'fwhm = {fwhm_init}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1619 ast(f'height = {height_init}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1620 sig_init = ast(fwhm_factor[peak_models[0]])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1621 amp_init = ast(height_factor[peak_models[0]])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1622 sig_max = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1623 if self._sigma_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1624 ast(f'fwhm = {self._fwhm_max}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1625 sig_max = ast(fwhm_factor[peak_models[0]])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1626 self._sigma_max[0] = sig_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1627 self.add_model(peak_models[0], parameters=(
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1628 {'name': 'amplitude', 'value': amp_init, 'min': min_value},
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1629 {'name': 'center', 'value': cen_init, 'min': min_value},
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1630 {'name': 'sigma', 'value': sig_init, 'min': min_value, 'max': sig_max}))
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1631 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1632 if fit_type == 'uniform':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1633 self.add_parameter(name='scale_factor', value=1.0)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1634 for i in range(num_peaks):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1635 height_init, cen_init, fwhm_init = self.guess_init_peak(self._x, self._y, i,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1636 center_guess=centers)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1637 if self._fwhm_max is not None and fwhm_init > self._fwhm_max:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1638 fwhm_init = self._fwhm_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1639 ast(f'fwhm = {fwhm_init}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1640 ast(f'height = {height_init}')
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parents:
diff changeset
1641 sig_init = ast(fwhm_factor[peak_models[i]])
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parents:
diff changeset
1642 amp_init = ast(height_factor[peak_models[i]])
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parents:
diff changeset
1643 sig_max = None
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parents:
diff changeset
1644 if self._sigma_max is not None:
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parents:
diff changeset
1645 ast(f'fwhm = {self._fwhm_max}')
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parents:
diff changeset
1646 sig_max = ast(fwhm_factor[peak_models[i]])
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parents:
diff changeset
1647 self._sigma_max[i] = sig_max
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parents:
diff changeset
1648 if fit_type == 'uniform':
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parents:
diff changeset
1649 self.add_model(peak_models[i], prefix=f'peak{i+1}_', parameters=(
69
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diff changeset
1650 {'name': 'amplitude', 'value': amp_init, 'min': min_value},
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1651 {'name': 'center', 'expr': center_exprs[i]},
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diff changeset
1652 {'name': 'sigma', 'value': sig_init, 'min': min_value,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1653 'max': sig_max}))
49
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parents:
diff changeset
1654 else:
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parents:
diff changeset
1655 self.add_model('gaussian', prefix=f'peak{i+1}_', parameters=(
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1656 {'name': 'amplitude', 'value': amp_init, 'min': min_value},
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1657 {'name': 'center', 'value': cen_init, 'min': min_value},
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parents: 65
diff changeset
1658 {'name': 'sigma', 'value': sig_init, 'min': min_value,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1659 'max': sig_max}))
49
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parents:
diff changeset
1660
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parents:
diff changeset
1661 def _check_validity(self):
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parents:
diff changeset
1662 """Check for valid fit parameter results
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parents:
diff changeset
1663 """
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parents:
diff changeset
1664 fit_failure = False
69
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diff changeset
1665 index = compile(r'\d+')
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diff changeset
1666 for name, par in self.best_parameters.items():
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parents: 65
diff changeset
1667 if 'background' in name:
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parents: 65
diff changeset
1668 # if ((name == 'backgroundc' and par['value'] <= 0.0) or
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parents: 65
diff changeset
1669 # (name.endswith('amplitude') and par['value'] <= 0.0) or
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parents: 65
diff changeset
1670 if ((name.endswith('amplitude') and par['value'] <= 0.0) or
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1671 (name.endswith('decay') and par['value'] <= 0.0)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1672 logging.info(f'Invalid fit result for {name} ({par["value"]})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1673 fit_failure = True
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parents: 65
diff changeset
1674 elif (((name.endswith('amplitude') or name.endswith('height')) and
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parents: 65
diff changeset
1675 par['value'] <= 0.0) or
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1676 ((name.endswith('sigma') or name.endswith('fwhm')) and par['value'] <= 0.0) or
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1677 (name.endswith('center') and par['value'] <= 0.0) or
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parents: 65
diff changeset
1678 (name == 'scale_factor' and par['value'] <= 0.0)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1679 logging.info(f'Invalid fit result for {name} ({par["value"]})')
49
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parents:
diff changeset
1680 fit_failure = True
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1681 if name.endswith('sigma') and self._sigma_max is not None:
49
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parents:
diff changeset
1682 if name == 'sigma':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1683 sigma_max = self._sigma_max[0]
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parents:
diff changeset
1684 else:
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rv43
parents:
diff changeset
1685 sigma_max = self._sigma_max[int(index.search(name).group())-1]
69
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parents: 65
diff changeset
1686 if par['value'] > sigma_max:
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parents: 65
diff changeset
1687 logging.info(f'Invalid fit result for {name} ({par["value"]})')
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parents: 65
diff changeset
1688 fit_failure = True
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parents: 65
diff changeset
1689 elif par['value'] == sigma_max:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1690 logging.warning(f'Edge result on for {name} ({par["value"]})')
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parents: 65
diff changeset
1691 if name.endswith('fwhm') and self._fwhm_max is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1692 if par['value'] > self._fwhm_max:
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parents: 65
diff changeset
1693 logging.info(f'Invalid fit result for {name} ({par["value"]})')
49
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rv43
parents:
diff changeset
1694 fit_failure = True
69
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parents: 65
diff changeset
1695 elif par['value'] == self._fwhm_max:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1696 logging.warning(f'Edge result on for {name} ({par["value"]})')
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parents: 65
diff changeset
1697 return(fit_failure)
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parents: 65
diff changeset
1698
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parents: 65
diff changeset
1699
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1700 class FitMap(Fit):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1701 """Fit a map of data
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parents: 65
diff changeset
1702 """
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diff changeset
1703 def __init__(self, ymap, x=None, models=None, normalize=True, transpose=None, **kwargs):
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parents: 65
diff changeset
1704 super().__init__(None)
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parents: 65
diff changeset
1705 self._best_errors = None
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parents: 65
diff changeset
1706 self._best_fit = None
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parents: 65
diff changeset
1707 self._best_parameters = None
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parents: 65
diff changeset
1708 self._best_values = None
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parents: 65
diff changeset
1709 self._inv_transpose = None
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parents: 65
diff changeset
1710 self._max_nfev = None
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parents: 65
diff changeset
1711 self._memfolder = None
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parents: 65
diff changeset
1712 self._new_parameters = None
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diff changeset
1713 self._out_of_bounds = None
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parents: 65
diff changeset
1714 self._plot = False
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parents: 65
diff changeset
1715 self._print_report = False
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parents: 65
diff changeset
1716 self._redchi = None
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diff changeset
1717 self._redchi_cutoff = 0.1
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diff changeset
1718 self._skip_init = True
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diff changeset
1719 self._success = None
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parents: 65
diff changeset
1720 self._transpose = None
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diff changeset
1721 self._try_no_bounds = True
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parents: 65
diff changeset
1722
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1723 # At this point the fastest index should always be the signal dimension so that the slowest
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diff changeset
1724 # ndim-1 dimensions are the map dimensions
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parents: 65
diff changeset
1725 if isinstance(ymap, (tuple, list, np.ndarray)):
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diff changeset
1726 self._x = np.asarray(x)
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parents: 65
diff changeset
1727 elif have_xarray and isinstance(ymap, xr.DataArray):
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parents: 65
diff changeset
1728 if x is not None:
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diff changeset
1729 logging.warning('Ignoring superfluous input x ({x}) in Fit.__init__')
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diff changeset
1730 self._x = np.asarray(ymap[ymap.dims[-1]])
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diff changeset
1731 else:
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diff changeset
1732 illegal_value(ymap, 'ymap', 'FitMap:__init__', raise_error=True)
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diff changeset
1733 self._ymap = ymap
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diff changeset
1734
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diff changeset
1735 # Verify the input parameters
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diff changeset
1736 if self._x.ndim != 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1737 raise ValueError(f'Invalid dimension for input x {self._x.ndim}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1738 if self._ymap.ndim < 2:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1739 raise ValueError('Invalid number of dimension of the input dataset '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1740 f'{self._ymap.ndim}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1741 if self._x.size != self._ymap.shape[-1]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1742 raise ValueError(f'Inconsistent x and y dimensions ({self._x.size} vs '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1743 f'{self._ymap.shape[-1]})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1744 if not isinstance(normalize, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1745 logging.warning(f'Invalid value for normalize ({normalize}) in Fit.__init__: '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1746 'setting normalize to True')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1747 normalize = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1748 if isinstance(transpose, bool) and not transpose:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1749 transpose = None
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diff changeset
1750 if transpose is not None and self._ymap.ndim < 3:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1751 logging.warning(f'Transpose meaningless for {self._ymap.ndim-1}D data maps: ignoring '+
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diff changeset
1752 'transpose')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1753 if transpose is not None:
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diff changeset
1754 if self._ymap.ndim == 3 and isinstance(transpose, bool) and transpose:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1755 self._transpose = (1, 0)
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diff changeset
1756 elif not isinstance(transpose, (tuple, list)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1757 logging.warning(f'Invalid data type for transpose ({transpose}, '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1758 f'{type(transpose)}) in Fit.__init__: setting transpose to False')
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diff changeset
1759 elif len(transpose) != self._ymap.ndim-1:
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diff changeset
1760 logging.warning(f'Invalid dimension for transpose ({transpose}, must be equal to '+
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diff changeset
1761 f'{self._ymap.ndim-1}) in Fit.__init__: setting transpose to False')
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diff changeset
1762 elif any(i not in transpose for i in range(len(transpose))):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1763 logging.warning(f'Invalid index in transpose ({transpose}) '+
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diff changeset
1764 f'in Fit.__init__: setting transpose to False')
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diff changeset
1765 elif not all(i==transpose[i] for i in range(self._ymap.ndim-1)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1766 self._transpose = transpose
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diff changeset
1767 if self._transpose is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1768 self._inv_transpose = tuple(self._transpose.index(i)
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diff changeset
1769 for i in range(len(self._transpose)))
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diff changeset
1770
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diff changeset
1771 # Flatten the map (transpose if requested)
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diff changeset
1772 # Store the flattened map in self._ymap_norm, whether normalized or not
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diff changeset
1773 if self._transpose is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1774 self._ymap_norm = np.transpose(np.asarray(self._ymap), list(self._transpose)+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1775 [len(self._transpose)])
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diff changeset
1776 else:
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diff changeset
1777 self._ymap_norm = np.asarray(self._ymap)
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diff changeset
1778 self._map_dim = int(self._ymap_norm.size/self._x.size)
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diff changeset
1779 self._map_shape = self._ymap_norm.shape[:-1]
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diff changeset
1780 self._ymap_norm = np.reshape(self._ymap_norm, (self._map_dim, self._x.size))
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diff changeset
1781
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diff changeset
1782 # Check if a mask is provided
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diff changeset
1783 if 'mask' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1784 self._mask = kwargs.pop('mask')
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diff changeset
1785 if self._mask is None:
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diff changeset
1786 ymap_min = float(self._ymap_norm.min())
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diff changeset
1787 ymap_max = float(self._ymap_norm.max())
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diff changeset
1788 else:
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diff changeset
1789 self._mask = np.asarray(self._mask).astype(bool)
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diff changeset
1790 if self._x.size != self._mask.size:
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diff changeset
1791 raise ValueError(f'Inconsistent mask dimension ({self._x.size} vs '+
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diff changeset
1792 f'{self._mask.size})')
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diff changeset
1793 ymap_masked = np.asarray(self._ymap_norm)[:,~self._mask]
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diff changeset
1794 ymap_min = float(ymap_masked.min())
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diff changeset
1795 ymap_max = float(ymap_masked.max())
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diff changeset
1796
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diff changeset
1797 # Normalize the data
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diff changeset
1798 self._y_range = ymap_max-ymap_min
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diff changeset
1799 if normalize and self._y_range > 0.0:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1800 self._norm = (ymap_min, self._y_range)
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diff changeset
1801 self._ymap_norm = (self._ymap_norm-self._norm[0])/self._norm[1]
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diff changeset
1802 else:
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diff changeset
1803 self._redchi_cutoff *= self._y_range**2
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diff changeset
1804 if models is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1805 if callable(models) or isinstance(models, str):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1806 kwargs = self.add_model(models, **kwargs)
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diff changeset
1807 elif isinstance(models, (tuple, list)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1808 for model in models:
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diff changeset
1809 kwargs = self.add_model(model, **kwargs)
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diff changeset
1810 self.fit(**kwargs)
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diff changeset
1811
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diff changeset
1812 @classmethod
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diff changeset
1813 def fit_map(cls, x, ymap, models, normalize=True, **kwargs):
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diff changeset
1814 return(cls(x, ymap, models, normalize=normalize, **kwargs))
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diff changeset
1815
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diff changeset
1816 @property
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diff changeset
1817 def best_errors(self):
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diff changeset
1818 return(self._best_errors)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1819
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diff changeset
1820 @property
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1821 def best_fit(self):
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diff changeset
1822 return(self._best_fit)
49
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diff changeset
1823
69
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diff changeset
1824 @property
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1825 def best_results(self):
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diff changeset
1826 """Convert the input data array to a data set and add the fit results.
49
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diff changeset
1827 """
69
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diff changeset
1828 if self.best_values is None or self.best_errors is None or self.best_fit is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1829 return(None)
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diff changeset
1830 if not have_xarray:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1831 logging.warning('Unable to load xarray module')
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diff changeset
1832 return(None)
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diff changeset
1833 best_values = self.best_values
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diff changeset
1834 best_errors = self.best_errors
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1835 if isinstance(self._ymap, xr.DataArray):
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diff changeset
1836 best_results = self._ymap.to_dataset()
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diff changeset
1837 dims = self._ymap.dims
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diff changeset
1838 fit_name = f'{self._ymap.name}_fit'
49
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diff changeset
1839 else:
69
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diff changeset
1840 coords = {f'dim{n}_index':([f'dim{n}_index'], range(self._ymap.shape[n]))
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diff changeset
1841 for n in range(self._ymap.ndim-1)}
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diff changeset
1842 coords['x'] = (['x'], self._x)
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diff changeset
1843 dims = list(coords.keys())
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diff changeset
1844 best_results = xr.Dataset(coords=coords)
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diff changeset
1845 best_results['y'] = (dims, self._ymap)
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diff changeset
1846 fit_name = 'y_fit'
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diff changeset
1847 best_results[fit_name] = (dims, self.best_fit)
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diff changeset
1848 if self._mask is not None:
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diff changeset
1849 best_results['mask'] = self._mask
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diff changeset
1850 for n in range(best_values.shape[0]):
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diff changeset
1851 best_results[f'{self._best_parameters[n]}_values'] = (dims[:-1], best_values[n])
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diff changeset
1852 best_results[f'{self._best_parameters[n]}_errors'] = (dims[:-1], best_errors[n])
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diff changeset
1853 best_results.attrs['components'] = self.components
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diff changeset
1854 return(best_results)
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diff changeset
1855
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diff changeset
1856 @property
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diff changeset
1857 def best_values(self):
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diff changeset
1858 return(self._best_values)
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diff changeset
1859
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diff changeset
1860 @property
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diff changeset
1861 def chisqr(self):
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diff changeset
1862 logging.warning('property chisqr not defined for fit.FitMap')
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diff changeset
1863 return(None)
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diff changeset
1864
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1865 @property
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diff changeset
1866 def components(self):
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diff changeset
1867 components = {}
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diff changeset
1868 if self._result is None:
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diff changeset
1869 logging.warning('Unable to collect components in FitMap.components')
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diff changeset
1870 return(components)
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diff changeset
1871 for component in self._result.components:
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diff changeset
1872 if 'tmp_normalization_offset_c' in component.param_names:
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diff changeset
1873 continue
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diff changeset
1874 parameters = {}
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diff changeset
1875 for name in component.param_names:
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diff changeset
1876 if self._parameters[name].vary:
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diff changeset
1877 parameters[name] = {'free': True}
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diff changeset
1878 elif self._parameters[name].expr is not None:
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diff changeset
1879 parameters[name] = {'free': False, 'expr': self._parameters[name].expr}
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diff changeset
1880 else:
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diff changeset
1881 parameters[name] = {'free': False, 'value': self.init_parameters[name]['value']}
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diff changeset
1882 expr = None
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diff changeset
1883 if isinstance(component, ExpressionModel):
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diff changeset
1884 name = component._name
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diff changeset
1885 if name[-1] == '_':
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diff changeset
1886 name = name[:-1]
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diff changeset
1887 expr = component.expr
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diff changeset
1888 else:
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diff changeset
1889 prefix = component.prefix
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diff changeset
1890 if len(prefix):
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diff changeset
1891 if prefix[-1] == '_':
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diff changeset
1892 prefix = prefix[:-1]
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diff changeset
1893 name = f'{prefix} ({component._name})'
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diff changeset
1894 else:
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diff changeset
1895 name = f'{component._name}'
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diff changeset
1896 if expr is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1897 components[name] = {'parameters': parameters}
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diff changeset
1898 else:
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diff changeset
1899 components[name] = {'expr': expr, 'parameters': parameters}
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diff changeset
1900 return(components)
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diff changeset
1901
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diff changeset
1902 @property
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diff changeset
1903 def covar(self):
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diff changeset
1904 logging.warning('property covar not defined for fit.FitMap')
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diff changeset
1905 return(None)
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diff changeset
1906
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diff changeset
1907 @property
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diff changeset
1908 def max_nfev(self):
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diff changeset
1909 return(self._max_nfev)
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diff changeset
1910
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diff changeset
1911 @property
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diff changeset
1912 def num_func_eval(self):
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diff changeset
1913 logging.warning('property num_func_eval not defined for fit.FitMap')
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diff changeset
1914 return(None)
49
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parents:
diff changeset
1915
69
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diff changeset
1916 @property
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diff changeset
1917 def out_of_bounds(self):
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diff changeset
1918 return(self._out_of_bounds)
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diff changeset
1919
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diff changeset
1920 @property
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diff changeset
1921 def redchi(self):
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diff changeset
1922 return(self._redchi)
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diff changeset
1923
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diff changeset
1924 @property
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diff changeset
1925 def residual(self):
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diff changeset
1926 if self.best_fit is None:
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diff changeset
1927 return(None)
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diff changeset
1928 if self._mask is None:
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diff changeset
1929 return(np.asarray(self._ymap)-self.best_fit)
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diff changeset
1930 else:
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diff changeset
1931 ymap_flat = np.reshape(np.asarray(self._ymap), (self._map_dim, self._x.size))
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1932 ymap_flat_masked = ymap_flat[:,~self._mask]
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1933 ymap_masked = np.reshape(ymap_flat_masked,
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1934 list(self._map_shape)+[ymap_flat_masked.shape[-1]])
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1935 return(ymap_masked-self.best_fit)
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1936
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diff changeset
1937 @property
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1938 def success(self):
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1939 return(self._success)
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1940
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1941 @property
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1942 def var_names(self):
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1943 logging.warning('property var_names not defined for fit.FitMap')
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1944 return(None)
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1945
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1946 @property
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1947 def y(self):
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1948 logging.warning('property y not defined for fit.FitMap')
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1949 return(None)
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1950
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1951 @property
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1952 def ymap(self):
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1953 return(self._ymap)
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1954
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1955 def best_parameters(self, dims=None):
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1956 if dims is None:
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1957 return(self._best_parameters)
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1958 if not isinstance(dims, (list, tuple)) or len(dims) != len(self._map_shape):
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1959 illegal_value(dims, 'dims', 'FitMap.best_parameters', raise_error=True)
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1960 if self.best_values is None or self.best_errors is None:
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1961 logging.warning(f'Unable to obtain best parameter values for dims = {dims} in '+
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1962 'FitMap.best_parameters')
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1963 return({})
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1964 # Create current parameters
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1965 parameters = deepcopy(self._parameters)
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1966 for n, name in enumerate(self._best_parameters):
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1967 if self._parameters[name].vary:
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1968 parameters[name].set(value=self.best_values[n][dims])
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1969 parameters[name].stderr = self.best_errors[n][dims]
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1970 parameters_dict = {}
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1971 for name in sorted(parameters):
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1972 if name != 'tmp_normalization_offset_c':
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1973 par = parameters[name]
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1974 parameters_dict[name] = {'value': par.value, 'error': par.stderr,
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1975 'init_value': self.init_parameters[name]['value'], 'min': par.min,
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1976 'max': par.max, 'vary': par.vary, 'expr': par.expr}
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1977 return(parameters_dict)
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1978
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1979 def freemem(self):
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1980 if self._memfolder is None:
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1981 return
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1982 try:
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1983 rmtree(self._memfolder)
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1984 self._memfolder = None
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diff changeset
1985 except:
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1986 logging.warning('Could not clean-up automatically.')
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1987
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diff changeset
1988 def plot(self, dims, y_title=None, plot_residual=False, plot_comp_legends=False,
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diff changeset
1989 plot_masked_data=True):
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1990 if not isinstance(dims, (list, tuple)) or len(dims) != len(self._map_shape):
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1991 illegal_value(dims, 'dims', 'FitMap.plot', raise_error=True)
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1992 if self._result is None or self.best_fit is None or self.best_values is None:
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1993 logging.warning(f'Unable to plot fit for dims = {dims} in FitMap.plot')
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diff changeset
1994 return
69
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1995 if y_title is None or not isinstance(y_title, str):
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1996 y_title = 'data'
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1997 if self._mask is None:
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1998 mask = np.zeros(self._x.size).astype(bool)
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1999 plot_masked_data = False
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2000 else:
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2001 mask = self._mask
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2002 plots = [(self._x, np.asarray(self._ymap[dims]), 'b.')]
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2003 legend = [y_title]
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2004 if plot_masked_data:
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2005 plots += [(self._x[mask], np.asarray(self._ymap)[(*dims,mask)], 'bx')]
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2006 legend += ['masked data']
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2007 plots += [(self._x[~mask], self.best_fit[dims], 'k-')]
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2008 legend += ['best fit']
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2009 if plot_residual:
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2010 plots += [(self._x[~mask], self.residual[dims], 'k--')]
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2011 legend += ['residual']
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2012 # Create current parameters
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2013 parameters = deepcopy(self._parameters)
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2014 for name in self._best_parameters:
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2015 if self._parameters[name].vary:
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2016 parameters[name].set(value=
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2017 self.best_values[self._best_parameters.index(name)][dims])
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2018 for component in self._result.components:
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2019 if 'tmp_normalization_offset_c' in component.param_names:
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parents:
diff changeset
2020 continue
69
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2021 if isinstance(component, ExpressionModel):
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2022 prefix = component._name
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2023 if prefix[-1] == '_':
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2024 prefix = prefix[:-1]
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2025 modelname = f'{prefix}: {component.expr}'
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diff changeset
2026 else:
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2027 prefix = component.prefix
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diff changeset
2028 if len(prefix):
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diff changeset
2029 if prefix[-1] == '_':
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parents: 65
diff changeset
2030 prefix = prefix[:-1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2031 modelname = f'{prefix} ({component._name})'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2032 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2033 modelname = f'{component._name}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2034 if len(modelname) > 20:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2035 modelname = f'{modelname[0:16]} ...'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2036 y = component.eval(params=parameters, x=self._x[~mask])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2037 if isinstance(y, (int, float)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2038 y *= np.ones(self._x[~mask].size)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2039 plots += [(self._x[~mask], y, '--')]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2040 if plot_comp_legends:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2041 legend.append(modelname)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2042 quick_plot(tuple(plots), legend=legend, title=str(dims), block=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2043
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2044 def fit(self, **kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2045 # t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2046 # Check input parameters
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2047 if self._model is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2048 logging.error('Undefined fit model')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2049 if 'num_proc' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2050 num_proc = kwargs.pop('num_proc')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2051 if not is_int(num_proc, ge=1):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2052 illegal_value(num_proc, 'num_proc', 'FitMap.fit', raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2053 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2054 num_proc = cpu_count()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2055 if num_proc > 1 and not have_joblib:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2056 logging.warning(f'Missing joblib in the conda environment, running FitMap serially')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2057 num_proc = 1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2058 if num_proc > cpu_count():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2059 logging.warning(f'The requested number of processors ({num_proc}) exceeds the maximum '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2060 f'number of processors, num_proc reduced to ({cpu_count()})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2061 num_proc = cpu_count()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2062 if 'try_no_bounds' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2063 self._try_no_bounds = kwargs.pop('try_no_bounds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2064 if not isinstance(self._try_no_bounds, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2065 illegal_value(self._try_no_bounds, 'try_no_bounds', 'FitMap.fit', raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2066 if 'redchi_cutoff' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2067 self._redchi_cutoff = kwargs.pop('redchi_cutoff')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2068 if not is_num(self._redchi_cutoff, gt=0):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2069 illegal_value(self._redchi_cutoff, 'redchi_cutoff', 'FitMap.fit', raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2070 if 'print_report' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2071 self._print_report = kwargs.pop('print_report')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2072 if not isinstance(self._print_report, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2073 illegal_value(self._print_report, 'print_report', 'FitMap.fit', raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2074 if 'plot' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2075 self._plot = kwargs.pop('plot')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2076 if not isinstance(self._plot, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2077 illegal_value(self._plot, 'plot', 'FitMap.fit', raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2078 if 'skip_init' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2079 self._skip_init = kwargs.pop('skip_init')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2080 if not isinstance(self._skip_init, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2081 illegal_value(self._skip_init, 'skip_init', 'FitMap.fit', raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2082
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2083 # Apply mask if supplied:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2084 if 'mask' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2085 self._mask = kwargs.pop('mask')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2086 if self._mask is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2087 self._mask = np.asarray(self._mask).astype(bool)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2088 if self._x.size != self._mask.size:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2089 raise ValueError(f'Inconsistent x and mask dimensions ({self._x.size} vs '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2090 f'{self._mask.size})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2091
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2092 # Add constant offset for a normalized single component model
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2093 if self._result is None and self._norm is not None and self._norm[0]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2094 self.add_model('constant', prefix='tmp_normalization_offset_', parameters={'name': 'c',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2095 'value': -self._norm[0], 'vary': False, 'norm': True})
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2096 #'value': -self._norm[0]/self._norm[1], 'vary': False, 'norm': False})
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2097
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2098 # Adjust existing parameters for refit:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2099 if 'parameters' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2100 # print('\nIn FitMap before adjusting existing parameters for refit:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2101 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2102 # if self._result is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2103 # raise ValueError('Invalid parameter parameters ({parameters})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2104 # if self._best_values is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2105 # raise ValueError('Valid self._best_values required for refitting in FitMap.fit')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2106 parameters = kwargs.pop('parameters')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2107 # print(f'\nparameters:\n{parameters}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2108 if isinstance(parameters, dict):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2109 parameters = (parameters, )
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2110 elif not is_dict_series(parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2111 illegal_value(parameters, 'parameters', 'Fit.fit', raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2112 for par in parameters:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2113 name = par['name']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2114 if name not in self._parameters:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2115 raise ValueError(f'Unable to match {name} parameter {par} to an existing one')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2116 if self._parameters[name].expr is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2117 raise ValueError(f'Unable to modify {name} parameter {par} (currently an '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2118 'expression)')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2119 value = par.get('value')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2120 vary = par.get('vary')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2121 if par.get('expr') is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2122 raise KeyError(f'Illegal "expr" key in {name} parameter {par}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2123 self._parameters[name].set(value=value, vary=vary, min=par.get('min'),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2124 max=par.get('max'))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2125 # Overwrite existing best values for fixed parameters when a value is specified
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diff changeset
2126 # print(f'best values befored resetting:\n{self._best_values}')
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diff changeset
2127 if isinstance(value, (int, float)) and vary is False:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2128 for i, nname in enumerate(self._best_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2129 if nname == name:
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diff changeset
2130 self._best_values[i] = value
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2131 # print(f'best values after resetting (value={value}, vary={vary}):\n{self._best_values}')
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diff changeset
2132 #RV print('\nIn FitMap after adjusting existing parameters for refit:')
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diff changeset
2133 #RV self._parameters.pretty_print()
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diff changeset
2134
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diff changeset
2135 # Check for uninitialized parameters
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diff changeset
2136 for name, par in self._parameters.items():
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diff changeset
2137 if par.expr is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2138 value = par.value
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diff changeset
2139 if value is None or np.isinf(value) or np.isnan(value):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2140 value = 1.0
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diff changeset
2141 if self._norm is None or name not in self._parameter_norms:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2142 self._parameters[name].set(value=value)
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diff changeset
2143 elif self._parameter_norms[name]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2144 self._parameters[name].set(value=value*self._norm[1])
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diff changeset
2145
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diff changeset
2146 # Create the best parameter list, consisting of all varying parameters plus the expression
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2147 # parameters in order to collect their errors
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diff changeset
2148 if self._result is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2149 # Initial fit
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diff changeset
2150 assert(self._best_parameters is None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2151 self._best_parameters = [name for name, par in self._parameters.items()
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diff changeset
2152 if par.vary or par.expr is not None]
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diff changeset
2153 num_new_parameters = 0
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diff changeset
2154 else:
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diff changeset
2155 # Refit
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diff changeset
2156 assert(len(self._best_parameters))
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diff changeset
2157 self._new_parameters = [name for name, par in self._parameters.items()
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diff changeset
2158 if name != 'tmp_normalization_offset_c' and name not in self._best_parameters and
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2159 (par.vary or par.expr is not None)]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2160 num_new_parameters = len(self._new_parameters)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2161 num_best_parameters = len(self._best_parameters)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2162
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diff changeset
2163 # Flatten and normalize the best values of the previous fit, remove the remaining results
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diff changeset
2164 # of the previous fit
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diff changeset
2165 if self._result is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2166 # print('\nBefore flatten and normalize:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2167 # print(f'self._best_values:\n{self._best_values}')
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diff changeset
2168 self._out_of_bounds = None
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diff changeset
2169 self._max_nfev = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2170 self._redchi = None
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diff changeset
2171 self._success = None
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diff changeset
2172 self._best_fit = None
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diff changeset
2173 self._best_errors = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2174 assert(self._best_values is not None)
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diff changeset
2175 assert(self._best_values.shape[0] == num_best_parameters)
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diff changeset
2176 assert(self._best_values.shape[1:] == self._map_shape)
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diff changeset
2177 if self._transpose is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2178 self._best_values = np.transpose(self._best_values,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2179 [0]+[i+1 for i in self._transpose])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2180 self._best_values = [np.reshape(self._best_values[i], self._map_dim)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2181 for i in range(num_best_parameters)]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2182 if self._norm is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2183 for i, name in enumerate(self._best_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2184 if self._parameter_norms.get(name, False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2185 self._best_values[i] /= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2186 #RV print('\nAfter flatten and normalize:')
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diff changeset
2187 #RV print(f'self._best_values:\n{self._best_values}')
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diff changeset
2188
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diff changeset
2189 # Normalize the initial parameters (and best values for a refit)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2190 # print('\nIn FitMap before normalize:')
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diff changeset
2191 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2192 # print(f'\nparameter_norms:\n{self._parameter_norms}\n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2193 self._normalize()
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diff changeset
2194 # print('\nIn FitMap after normalize:')
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diff changeset
2195 # self._parameters.pretty_print()
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diff changeset
2196 # print(f'\nparameter_norms:\n{self._parameter_norms}\n')
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diff changeset
2197
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diff changeset
2198 # Prevent initial values from sitting at boundaries
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diff changeset
2199 self._parameter_bounds = {name:{'min': par.min, 'max': par.max}
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diff changeset
2200 for name, par in self._parameters.items() if par.vary}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2201 for name, par in self._parameters.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2202 if par.vary:
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diff changeset
2203 par.set(value=self._reset_par_at_boundary(par, par.value))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2204 # print('\nAfter checking boundaries:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2205 # self._parameters.pretty_print()
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diff changeset
2206
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diff changeset
2207 # Set parameter bounds to unbound (only use bounds when fit fails)
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diff changeset
2208 if self._try_no_bounds:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2209 for name in self._parameter_bounds.keys():
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diff changeset
2210 self._parameters[name].set(min=-np.inf, max=np.inf)
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diff changeset
2211
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2212 # Allocate memory to store fit results
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diff changeset
2213 if self._mask is None:
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diff changeset
2214 x_size = self._x.size
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2215 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2216 x_size = self._x[~self._mask].size
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2217 if num_proc == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2218 self._out_of_bounds_flat = np.zeros(self._map_dim, dtype=bool)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2219 self._max_nfev_flat = np.zeros(self._map_dim, dtype=bool)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2220 self._redchi_flat = np.zeros(self._map_dim, dtype=np.float64)
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diff changeset
2221 self._success_flat = np.zeros(self._map_dim, dtype=bool)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2222 self._best_fit_flat = np.zeros((self._map_dim, x_size),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2223 dtype=self._ymap_norm.dtype)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2224 self._best_errors_flat = [np.zeros(self._map_dim, dtype=np.float64)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2225 for _ in range(num_best_parameters+num_new_parameters)]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2226 if self._result is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2227 self._best_values_flat = [np.zeros(self._map_dim, dtype=np.float64)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2228 for _ in range(num_best_parameters)]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2229 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2230 self._best_values_flat = self._best_values
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2231 self._best_values_flat += [np.zeros(self._map_dim, dtype=np.float64)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2232 for _ in range(num_new_parameters)]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2233 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2234 self._memfolder = './joblib_memmap'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2235 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2236 mkdir(self._memfolder)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2237 except FileExistsError:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2238 pass
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2239 filename_memmap = path.join(self._memfolder, 'out_of_bounds_memmap')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2240 self._out_of_bounds_flat = np.memmap(filename_memmap, dtype=bool,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2241 shape=(self._map_dim), mode='w+')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2242 filename_memmap = path.join(self._memfolder, 'max_nfev_memmap')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2243 self._max_nfev_flat = np.memmap(filename_memmap, dtype=bool,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2244 shape=(self._map_dim), mode='w+')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2245 filename_memmap = path.join(self._memfolder, 'redchi_memmap')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2246 self._redchi_flat = np.memmap(filename_memmap, dtype=np.float64,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2247 shape=(self._map_dim), mode='w+')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2248 filename_memmap = path.join(self._memfolder, 'success_memmap')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2249 self._success_flat = np.memmap(filename_memmap, dtype=bool,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2250 shape=(self._map_dim), mode='w+')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2251 filename_memmap = path.join(self._memfolder, 'best_fit_memmap')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2252 self._best_fit_flat = np.memmap(filename_memmap, dtype=self._ymap_norm.dtype,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2253 shape=(self._map_dim, x_size), mode='w+')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2254 self._best_errors_flat = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2255 for i in range(num_best_parameters+num_new_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2256 filename_memmap = path.join(self._memfolder, f'best_errors_memmap_{i}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2257 self._best_errors_flat.append(np.memmap(filename_memmap, dtype=np.float64,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2258 shape=self._map_dim, mode='w+'))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2259 self._best_values_flat = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2260 for i in range(num_best_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2261 filename_memmap = path.join(self._memfolder, f'best_values_memmap_{i}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2262 self._best_values_flat.append(np.memmap(filename_memmap, dtype=np.float64,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2263 shape=self._map_dim, mode='w+'))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2264 if self._result is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2265 self._best_values_flat[i][:] = self._best_values[i][:]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2266 for i in range(num_new_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2267 filename_memmap = path.join(self._memfolder,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2268 f'best_values_memmap_{i+num_best_parameters}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2269 self._best_values_flat.append(np.memmap(filename_memmap, dtype=np.float64,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2270 shape=self._map_dim, mode='w+'))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2271
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2272 # Update the best parameter list
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2273 if num_new_parameters:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2274 self._best_parameters += self._new_parameters
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2275
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2276 # Perform the first fit to get model component info and initial parameters
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2277 current_best_values = {}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2278 # print(f'0 before:\n{current_best_values}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2279 # t1 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2280 self._result = self._fit(0, current_best_values, return_result=True, **kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2281 # t2 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2282 # print(f'0 after:\n{current_best_values}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2283 # print('\nAfter the first fit:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2284 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2285 # print(self._result.fit_report(show_correl=False))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2286
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2287 # Remove all irrelevant content from self._result
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2288 for attr in ('_abort', 'aborted', 'aic', 'best_fit', 'best_values', 'bic', 'calc_covar',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2289 'call_kws', 'chisqr', 'ci_out', 'col_deriv', 'covar', 'data', 'errorbars',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2290 'flatchain', 'ier', 'init_vals', 'init_fit', 'iter_cb', 'jacfcn', 'kws',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2291 'last_internal_values', 'lmdif_message', 'message', 'method', 'nan_policy',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2292 'ndata', 'nfev', 'nfree', 'params', 'redchi', 'reduce_fcn', 'residual', 'result',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2293 'scale_covar', 'show_candidates', 'calc_covar', 'success', 'userargs', 'userfcn',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2294 'userkws', 'values', 'var_names', 'weights', 'user_options'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2295 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2296 delattr(self._result, attr)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2297 except AttributeError:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2298 # logging.warning(f'Unknown attribute {attr} in fit.FtMap._cleanup_result')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2299 pass
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2300
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2301 # t3 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2302 if num_proc == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2303 # Perform the remaining fits serially
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2304 for n in range(1, self._map_dim):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2305 # print(f'{n} before:\n{current_best_values}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2306 self._fit(n, current_best_values, **kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2307 # print(f'{n} after:\n{current_best_values}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2308 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2309 # Perform the remaining fits in parallel
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2310 num_fit = self._map_dim-1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2311 # print(f'num_fit = {num_fit}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2312 if num_proc > num_fit:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2313 logging.warning(f'The requested number of processors ({num_proc}) exceeds the '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2314 f'number of fits, num_proc reduced to ({num_fit})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2315 num_proc = num_fit
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2316 num_fit_per_proc = 1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2317 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2318 num_fit_per_proc = round((num_fit)/num_proc)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2319 if num_proc*num_fit_per_proc < num_fit:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2320 num_fit_per_proc +=1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2321 # print(f'num_fit_per_proc = {num_fit_per_proc}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2322 num_fit_batch = min(num_fit_per_proc, 40)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2323 # print(f'num_fit_batch = {num_fit_batch}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2324 with Parallel(n_jobs=num_proc) as parallel:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2325 parallel(delayed(self._fit_parallel)(current_best_values, num_fit_batch,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2326 n_start, **kwargs) for n_start in range(1, self._map_dim, num_fit_batch))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2327 # t4 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2328
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2329 # Renormalize the initial parameters for external use
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2330 if self._norm is not None and self._normalized:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2331 init_values = {}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2332 for name, value in self._result.init_values.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2333 if name not in self._parameter_norms or self._parameters[name].expr is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2334 init_values[name] = value
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2335 elif self._parameter_norms[name]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2336 init_values[name] = value*self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2337 self._result.init_values = init_values
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2338 for name, par in self._result.init_params.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2339 if par.expr is None and self._parameter_norms.get(name, False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2340 _min = par.min
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2341 _max = par.max
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2342 value = par.value*self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2343 if not np.isinf(_min) and abs(_min) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2344 _min *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2345 if not np.isinf(_max) and abs(_max) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2346 _max *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2347 par.set(value=value, min=_min, max=_max)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2348 par.init_value = par.value
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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diff changeset
2349
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2350 # Remap the best results
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2351 # t5 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2352 self._out_of_bounds = np.copy(np.reshape(self._out_of_bounds_flat, self._map_shape))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2353 self._max_nfev = np.copy(np.reshape(self._max_nfev_flat, self._map_shape))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2354 self._redchi = np.copy(np.reshape(self._redchi_flat, self._map_shape))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2355 self._success = np.copy(np.reshape(self._success_flat, self._map_shape))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2356 self._best_fit = np.copy(np.reshape(self._best_fit_flat,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2357 list(self._map_shape)+[x_size]))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2358 self._best_values = np.asarray([np.reshape(par, list(self._map_shape))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2359 for par in self._best_values_flat])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2360 self._best_errors = np.asarray([np.reshape(par, list(self._map_shape))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2361 for par in self._best_errors_flat])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2362 if self._inv_transpose is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2363 self._out_of_bounds = np.transpose(self._out_of_bounds, self._inv_transpose)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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diff changeset
2364 self._max_nfev = np.transpose(self._max_nfev, self._inv_transpose)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2365 self._redchi = np.transpose(self._redchi, self._inv_transpose)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2366 self._success = np.transpose(self._success, self._inv_transpose)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2367 self._best_fit = np.transpose(self._best_fit,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2368 list(self._inv_transpose)+[len(self._inv_transpose)])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2369 self._best_values = np.transpose(self._best_values,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2370 [0]+[i+1 for i in self._inv_transpose])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2371 self._best_errors = np.transpose(self._best_errors,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2372 [0]+[i+1 for i in self._inv_transpose])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2373 del self._out_of_bounds_flat
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2374 del self._max_nfev_flat
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2375 del self._redchi_flat
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2376 del self._success_flat
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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diff changeset
2377 del self._best_fit_flat
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2378 del self._best_values_flat
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2379 del self._best_errors_flat
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2380 # t6 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2381
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2382 # Restore parameter bounds and renormalize the parameters
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2383 for name, par in self._parameter_bounds.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2384 self._parameters[name].set(min=par['min'], max=par['max'])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2385 self._normalized = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2386 if self._norm is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2387 for name, norm in self._parameter_norms.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2388 par = self._parameters[name]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2389 if par.expr is None and norm:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2390 value = par.value*self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2391 _min = par.min
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2392 _max = par.max
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2393 if not np.isinf(_min) and abs(_min) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2394 _min *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2395 if not np.isinf(_max) and abs(_max) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2396 _max *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2397 par.set(value=value, min=_min, max=_max)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2398 # t7 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2399 # print(f'total run time in fit: {t7-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2400 # print(f'run time first fit: {t2-t1:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2401 # print(f'run time remaining fits: {t4-t3:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2402 # print(f'run time remapping results: {t6-t5:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2403
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2404 # print('\n\nAt end fit:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2405 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2406 # print(f'self._best_values:\n{self._best_values}\n\n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2407
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2408 # Free the shared memory
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parents: 65
diff changeset
2409 self.freemem()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2410
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2411 def _fit_parallel(self, current_best_values, num, n_start, **kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2412 num = min(num, self._map_dim-n_start)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2413 for n in range(num):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2414 # print(f'{n_start+n} before:\n{current_best_values}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2415 self._fit(n_start+n, current_best_values, **kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2416 # print(f'{n_start+n} after:\n{current_best_values}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2417
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diff changeset
2418 def _fit(self, n, current_best_values, return_result=False, **kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2419 #RV print(f'\n\nstart FitMap._fit {n}\n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2420 #RV print(f'current_best_values = {current_best_values}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2421 #RV print(f'self._best_parameters = {self._best_parameters}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2422 #RV print(f'self._new_parameters = {self._new_parameters}\n\n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2423 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2424 # Set parameters to current best values, but prevent them from sitting at boundaries
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2425 if self._new_parameters is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2426 # Initial fit
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2427 for name, value in current_best_values.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2428 par = self._parameters[name]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2429 par.set(value=self._reset_par_at_boundary(par, value))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2430 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2431 # Refit
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2432 for i, name in enumerate(self._best_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2433 par = self._parameters[name]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2434 if name in self._new_parameters:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2435 if name in current_best_values:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2436 par.set(value=self._reset_par_at_boundary(par, current_best_values[name]))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2437 elif par.expr is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2438 par.set(value=self._best_values[i][n])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2439 #RV print(f'\nbefore fit {n}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2440 #RV self._parameters.pretty_print()
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parents: 65
diff changeset
2441 if self._mask is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2442 result = self._model.fit(self._ymap_norm[n], self._parameters, x=self._x, **kwargs)
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parents: 65
diff changeset
2443 else:
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rv43
parents: 65
diff changeset
2444 result = self._model.fit(self._ymap_norm[n][~self._mask], self._parameters,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2445 x=self._x[~self._mask], **kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2446 # print(f'\nafter fit {n}')
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parents: 65
diff changeset
2447 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2448 # print(result.fit_report(show_correl=False))
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parents: 65
diff changeset
2449 out_of_bounds = False
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rv43
parents: 65
diff changeset
2450 for name, par in self._parameter_bounds.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2451 value = result.params[name].value
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2452 if not np.isinf(par['min']) and value < par['min']:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2453 out_of_bounds = True
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parents: 65
diff changeset
2454 break
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2455 if not np.isinf(par['max']) and value > par['max']:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2456 out_of_bounds = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2457 break
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2458 self._out_of_bounds_flat[n] = out_of_bounds
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2459 if self._try_no_bounds and out_of_bounds:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2460 # Rerun fit with parameter bounds in place
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2461 for name, par in self._parameter_bounds.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2462 self._parameters[name].set(min=par['min'], max=par['max'])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2463 # Set parameters to current best values, but prevent them from sitting at boundaries
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parents: 65
diff changeset
2464 if self._new_parameters is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2465 # Initial fit
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2466 for name, value in current_best_values.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2467 par = self._parameters[name]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2468 par.set(value=self._reset_par_at_boundary(par, value))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2469 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2470 # Refit
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parents: 65
diff changeset
2471 for i, name in enumerate(self._best_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2472 par = self._parameters[name]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2473 if name in self._new_parameters:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2474 if name in current_best_values:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2475 par.set(value=self._reset_par_at_boundary(par,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2476 current_best_values[name]))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2477 elif par.expr is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2478 par.set(value=self._best_values[i][n])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2479 # print('\nbefore fit')
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parents: 65
diff changeset
2480 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2481 # print(result.fit_report(show_correl=False))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2482 if self._mask is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2483 result = self._model.fit(self._ymap_norm[n], self._parameters, x=self._x, **kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2484 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2485 result = self._model.fit(self._ymap_norm[n][~self._mask], self._parameters,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2486 x=self._x[~self._mask], **kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2487 # print(f'\nafter fit {n}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2488 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2489 # print(result.fit_report(show_correl=False))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2490 out_of_bounds = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2491 for name, par in self._parameter_bounds.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2492 value = result.params[name].value
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2493 if not np.isinf(par['min']) and value < par['min']:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2494 out_of_bounds = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2495 break
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2496 if not np.isinf(par['max']) and value > par['max']:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2497 out_of_bounds = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2498 break
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2499 # print(f'{n} redchi < redchi_cutoff = {result.redchi < self._redchi_cutoff} success = {result.success} out_of_bounds = {out_of_bounds}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2500 # Reset parameters back to unbound
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2501 for name in self._parameter_bounds.keys():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2502 self._parameters[name].set(min=-np.inf, max=np.inf)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2503 assert(not out_of_bounds)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2504 if result.redchi >= self._redchi_cutoff:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2505 result.success = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2506 if result.nfev == result.max_nfev:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2507 # print(f'Maximum number of function evaluations reached for n = {n}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2508 # logging.warning(f'Maximum number of function evaluations reached for n = {n}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2509 if result.redchi < self._redchi_cutoff:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2510 result.success = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2511 self._max_nfev_flat[n] = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2512 if result.success:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2513 assert(all(True for par in current_best_values if par in result.params.values()))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2514 for par in result.params.values():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2515 if par.vary:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2516 current_best_values[par.name] = par.value
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2517 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2518 logging.warning(f'Fit for n = {n} failed: {result.lmdif_message}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2519 # Renormalize the data and results
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2520 self._renormalize(n, result)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2521 if self._print_report:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2522 print(result.fit_report(show_correl=False))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2523 if self._plot:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2524 dims = np.unravel_index(n, self._map_shape)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2525 if self._inv_transpose is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2526 dims= tuple(dims[self._inv_transpose[i]] for i in range(len(dims)))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2527 super().plot(result=result, y=np.asarray(self._ymap[dims]), plot_comp_legends=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2528 skip_init=self._skip_init, title=str(dims))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2529 #RV print(f'\n\nend FitMap._fit {n}\n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2530 #RV print(f'current_best_values = {current_best_values}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2531 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2532 # print(result.fit_report(show_correl=False))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2533 #RV print(f'\nself._best_values_flat:\n{self._best_values_flat}\n\n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2534 if return_result:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2535 return(result)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2536
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2537 def _renormalize(self, n, result):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2538 self._redchi_flat[n] = np.float64(result.redchi)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2539 self._success_flat[n] = result.success
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2540 if self._norm is None or not self._normalized:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2541 self._best_fit_flat[n] = result.best_fit
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2542 for i, name in enumerate(self._best_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2543 self._best_values_flat[i][n] = np.float64(result.params[name].value)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2544 self._best_errors_flat[i][n] = np.float64(result.params[name].stderr)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2545 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2546 pars = set(self._parameter_norms) & set(self._best_parameters)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2547 for name, par in result.params.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2548 if name in pars and self._parameter_norms[name]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2549 if par.stderr is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2550 par.stderr *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2551 if par.expr is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2552 par.value *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2553 if self._print_report:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2554 if par.init_value is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2555 par.init_value *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2556 if not np.isinf(par.min) and abs(par.min) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2557 par.min *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2558 if not np.isinf(par.max) and abs(par.max) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2559 par.max *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2560 self._best_fit_flat[n] = result.best_fit*self._norm[1]+self._norm[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2561 for i, name in enumerate(self._best_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2562 self._best_values_flat[i][n] = np.float64(result.params[name].value)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2563 self._best_errors_flat[i][n] = np.float64(result.params[name].stderr)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2564 if self._plot:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2565 if not self._skip_init:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2566 result.init_fit = result.init_fit*self._norm[1]+self._norm[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2567 result.best_fit = np.copy(self._best_fit_flat[n])