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annotate fit.py @ 49:26f99fdd8d61 draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
author rv43
date Thu, 28 Jul 2022 16:05:24 +0000
parents
children 98a83f03d91b
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49
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1 #!/usr/bin/env python3
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2
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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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9
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10 import sys
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11 import re
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12 import logging
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13 import numpy as np
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14
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15 from asteval import Interpreter
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16 from copy import deepcopy
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17 #from lmfit import Minimizer
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18 from lmfit import Model, Parameters
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19 from lmfit.models import ConstantModel, LinearModel, QuadraticModel, PolynomialModel,\
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20 StepModel, RectangleModel, GaussianModel, LorentzianModel
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22 #from .general import *
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23 from general import is_index, index_nearest, quickPlot
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24
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25 # sigma = fwhm_factor*fwhm
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26 fwhm_factor = {
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27 'gaussian' : f'fwhm/(2*sqrt(2*log(2)))',
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28 'lorentzian' : f'0.5*fwhm',
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29 'splitlorentzian' : f'0.5*fwhm', # sigma = sigma_r
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30 'voight' : f'0.2776*fwhm', # sigma = gamma
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31 'pseudovoight' : f'0.5*fwhm'} # fraction = 0.5
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32
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33 # amplitude = height_factor*height*fwhm
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34 height_factor = {
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35 'gaussian' : f'height*fwhm*0.5*sqrt(pi/log(2))',
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36 'lorentzian' : f'height*fwhm*0.5*pi',
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37 'splitlorentzian' : f'height*fwhm*0.5*pi', # sigma = sigma_r
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38 'voight' : f'3.334*height*fwhm', # sigma = gamma
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39 'pseudovoight' : f'1.268*height*fwhm'} # fraction = 0.5
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40
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41 class Fit:
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42 """Wrapper class for lmfit
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43 """
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44 def __init__(self, x, y, models=None, **kwargs):
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45 self._x = x
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46 self._y = y
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47 self._model = None
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48 self._parameters = Parameters()
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49 self._result = None
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50 if models is not None:
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51 if callable(models) or isinstance(models, str):
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52 kwargs = self.add_model(models, **kwargs)
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53 elif isinstance(models, (tuple, list)):
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54 for model in models:
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55 kwargs = self.add_model(model, **kwargs)
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56 self.fit(**kwargs)
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57
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58 @classmethod
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59 def fit_data(cls, x, y, models, **kwargs):
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60 return cls(x, y, models, **kwargs)
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61
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62 @property
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63 def best_errors(self):
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64 if self._result is None:
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65 return None
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66 errors = {}
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67 names = sorted(self._result.params)
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68 for name in names:
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69 par = self._result.params[name]
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70 errors[name] = par.stderr
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71 return errors
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72
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73 @property
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74 def best_fit(self):
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75 if self._result is None:
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76 return None
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77 return self._result.best_fit
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78
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79 @property
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80 def best_parameters(self):
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81 if self._result is None:
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82 return None
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83 parameters = []
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84 names = sorted(self._result.params)
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85 for name in names:
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86 par = self._result.params[name]
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87 parameters.append({'name' : par.name, 'value' : par.value, 'error' : par.stderr,
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88 'init_value' : par.init_value, 'min' : par.min, 'max' : par.max,
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89 'vary' : par.vary, 'expr' : par.expr})
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90 return parameters
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91
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92 @property
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93 def best_values(self):
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94 if self._result is None:
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95 return None
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96 return self._result.params.valuesdict()
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97
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98 @property
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99 def chisqr(self):
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100 return self._result.chisqr
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101
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102 @property
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103 def covar(self):
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104 return self._result.covar
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105
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106 @property
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107 def init_values(self):
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108 if self._result is None:
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109 return None
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110 return self._result.init_values
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111
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112 @property
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113 def num_func_eval(self):
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114 return self._result.nfev
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115
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116 @property
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117 def redchi(self):
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118 return self._result.redchi
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119
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120 @property
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121 def residual(self):
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122 return self._result.residual
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123
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124 @property
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125 def success(self):
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126 if not self._result.success:
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127 # print(f'ier = {self._result.ier}')
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128 # print(f'lmdif_message = {self._result.lmdif_message}')
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129 # print(f'message = {self._result.message}')
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130 # print(f'nfev = {self._result.nfev}')
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131 # print(f'redchi = {self._result.redchi}')
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132 # print(f'success = {self._result.success}')
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133 if self._result.ier == 0 or self._result.ier == 5:
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134 logging.warning(f'ier = {self._result.ier}: {self._result.message}')
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135 else:
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136 logging.warning(f'ier = {self._result.ier}: {self._result.message}')
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137 return True
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138 # self.print_fit_report()
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139 # self.plot()
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140 return self._result.success
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141
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142 @property
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143 def var_names(self):
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144 """Intended to be used with covar
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145 """
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146 if self._result is None:
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147 return None
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148 return self._result.var_names
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149
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150 def print_fit_report(self, show_correl=False):
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151 if self._result is not None:
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152 print(self._result.fit_report(show_correl=show_correl))
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153
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154 def add_parameter(self, **parameter):
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155 if not isinstance(parameter, dict):
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156 illegal_value(parameter, 'parameter', 'add_parameter')
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157 return
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158 self._parameters.add(**parameter)
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159
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160 def add_model(self, model, prefix=None, parameters=None, **kwargs):
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161 # Create the new model
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162 # print('\nAt start adding model:')
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163 # self._parameters.pretty_print()
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164 if prefix is not None and not isinstance(prefix, str):
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165 logging.warning('Ignoring illegal prefix: {model} {type(model)}')
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166 prefix = None
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167 if callable(model):
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168 newmodel = Model(model, prefix=prefix)
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169 elif isinstance(model, str):
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170 if model == 'constant':
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171 newmodel = ConstantModel(prefix=prefix)
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172 elif model == 'linear':
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173 newmodel = LinearModel(prefix=prefix)
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174 elif model == 'quadratic':
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175 newmodel = QuadraticModel(prefix=prefix)
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176 elif model == 'gaussian':
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177 newmodel = GaussianModel(prefix=prefix)
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178 elif model == 'step':
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179 form = kwargs.get('form')
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180 if form is not None:
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181 del kwargs['form']
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182 if form is None or form not in ('linear', 'atan', 'arctan', 'erf', 'logistic'):
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183 logging.error(f'Illegal form parameter for build-in step model ({form})')
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184 return kwargs
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185 newmodel = StepModel(prefix=prefix, form=form)
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186 elif model == 'rectangle':
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187 form = kwargs.get('form')
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188 if form is not None:
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189 del kwargs['form']
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190 if form is None or form not in ('linear', 'atan', 'arctan', 'erf', 'logistic'):
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191 logging.error(f'Illegal form parameter for build-in rectangle model ({form})')
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192 return kwargs
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193 newmodel = RectangleModel(prefix=prefix, form=form)
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194 else:
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195 logging.error('Unknown build-in fit model')
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196 return kwargs
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197 else:
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198 illegal_value(model, 'model', 'add_model')
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199 return kwargs
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200
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201 # Add the new model to the current one
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202 if self._model is None:
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203 self._model = newmodel
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204 else:
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205 self._model += newmodel
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206 if self._parameters is None:
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207 self._parameters = newmodel.make_params()
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208 else:
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209 self._parameters += newmodel.make_params()
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210 # print('\nAfter adding model:')
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211 # self._parameters.pretty_print()
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212
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213 # Initialize the model parameters
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214 if prefix is None:
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215 prefix = ""
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216 if parameters is not None:
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217 if not isinstance(parameters, (tuple, list)):
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218 illegal_value(parameters, 'parameters', 'add_model')
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219 return kwargs
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220 for parameter in parameters:
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221 if not isinstance(parameter, dict):
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222 illegal_value(parameter, 'parameter in parameters', 'add_model')
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223 return kwargs
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224 parameter['name'] = prefix+parameter['name']
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225 self._parameters.add(**parameter)
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226 for name, value in kwargs.items():
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227 if isinstance(value, (int, float)):
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228 self._parameters.add(prefix+name, value=value)
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229 # print('\nAt end add_model:')
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230 # self._parameters.pretty_print()
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231
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232 return kwargs
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233
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234 def fit(self, interactive=False, guess=False, **kwargs):
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235 if self._model is None:
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236 logging.error('Undefined fit model')
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237 return
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238 # Current parameter values
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239 pars = self._parameters.valuesdict()
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240 # Apply parameter updates through keyword arguments
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241 for par in set(pars) & set(kwargs):
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242 pars[par] = kwargs.pop(par)
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243 self._parameters[par].set(value=pars[par])
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244 # Check for uninitialized parameters
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245 for par, value in pars.items():
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246 if value is None or np.isinf(value) or np.isnan(value):
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247 if interactive:
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248 self._parameters[par].set(value=
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249 input_num(f'Enter an initial value for {par}: '))
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250 else:
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251 self._parameters[par].set(value=1.0)
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252 # print('\nAt start actual fit:')
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253 # print(f'kwargs = {kwargs}')
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254 # self._parameters.pretty_print()
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255 # print(f'parameters:\n{self._parameters}')
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256 # print(f'x = {self._x}')
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257 # print(f'len(x) = {len(self._x)}')
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258 # print(f'y = {self._y}')
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259 # print(f'len(y) = {len(self._y)}')
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260 if guess:
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261 self._parameters = self._model.guess(self._y, x=self._x)
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262 self._result = self._model.fit(self._y, self._parameters, x=self._x, **kwargs)
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263 # print('\nAt end actual fit:')
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264 # print(f'var_names:\n{self._result.var_names}')
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265 # print(f'stderr:\n{np.sqrt(np.diagonal(self._result.covar))}')
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266 # self._parameters.pretty_print()
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267 # print(f'parameters:\n{self._parameters}')
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268
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269 def plot(self):
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270 if self._result is None:
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271 return
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272 components = self._result.eval_components()
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273 plots = ((self._x, self._y, '.'), (self._x, self._result.best_fit, 'k-'),
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274 (self._x, self._result.init_fit, 'g-'))
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275 legend = ['data', 'best fit', 'init']
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276 if len(components) > 1:
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277 for modelname, y in components.items():
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278 if isinstance(y, (int, float)):
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279 y *= np.ones(len(self._x))
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280 plots += ((self._x, y, '--'),)
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281 # if modelname[-1] == '_':
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282 # legend.append(modelname[:-1])
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283 # else:
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284 # legend.append(modelname)
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285 quickPlot(plots, legend=legend, block=True)
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286
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287 @staticmethod
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288 def guess_init_peak(x, y, *args, center_guess=None, use_max_for_center=True):
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289 """ Return a guess for the initial height, center and fwhm for a peak
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290 """
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291 center_guesses = None
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292 if len(x) != len(y):
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293 logging.error(f'Illegal x and y lengths ({len(x)}, {len(y)}), skip initial guess')
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294 return None, None, None
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295 if isinstance(center_guess, (int, float)):
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296 if len(args):
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297 logging.warning('Ignoring additional arguments for single center_guess value')
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diff changeset
298 elif isinstance(center_guess, (tuple, list, np.ndarray)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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299 if len(center_guess) == 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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300 logging.warning('Ignoring additional arguments for single center_guess value')
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diff changeset
301 if not isinstance(center_guess[0], (int, float)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
302 raise ValueError(f'Illegal center_guess type ({type(center_guess[0])})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
303 center_guess = center_guess[0]
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diff changeset
304 else:
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diff changeset
305 if len(args) != 1:
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306 raise ValueError(f'Illegal number of arguments ({len(args)})')
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diff changeset
307 n = args[0]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
308 if not is_index(n, 0, len(center_guess)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
309 raise ValueError('Illegal argument')
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310 center_guesses = center_guess
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diff changeset
311 center_guess = center_guesses[n]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
312 elif center_guess is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
313 raise ValueError(f'Illegal center_guess type ({type(center_guess)})')
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diff changeset
314
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
315 # Sort the inputs
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
316 index = np.argsort(x)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
317 x = x[index]
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diff changeset
318 y = y[index]
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diff changeset
319 miny = y.min()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
320 # print(f'miny = {miny}')
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diff changeset
321 # print(f'x_range = {x[0]} {x[-1]} {len(x)}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
322 # print(f'y_range = {y[0]} {y[-1]} {len(y)}')
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parents:
diff changeset
323
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
324 # xx = x
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
325 # yy = y
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parents:
diff changeset
326 # Set range for current peak
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
327 # print(f'center_guesses = {center_guesses}')
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parents:
diff changeset
328 if center_guesses is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
329 if n == 0:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
330 low = 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
331 upp = index_nearest(x, (center_guesses[0]+center_guesses[1])/2)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
332 elif n == len(center_guesses)-1:
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parents:
diff changeset
333 low = index_nearest(x, (center_guesses[n-1]+center_guesses[n])/2)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
334 upp = len(x)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
335 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
336 low = index_nearest(x, (center_guesses[n-1]+center_guesses[n])/2)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
337 upp = index_nearest(x, (center_guesses[n]+center_guesses[n+1])/2)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
338 # print(f'low = {low}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
339 # print(f'upp = {upp}')
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parents:
diff changeset
340 x = x[low:upp]
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parents:
diff changeset
341 y = y[low:upp]
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diff changeset
342 # quickPlot(x, y, vlines=(x[0], center_guess, x[-1]), block=True)
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diff changeset
343
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diff changeset
344 # Estimate FHHM
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diff changeset
345 maxy = y.max()
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diff changeset
346 # print(f'x_range = {x[0]} {x[-1]} {len(x)}')
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diff changeset
347 # print(f'y_range = {y[0]} {y[-1]} {len(y)} {miny} {maxy}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
348 # print(f'center_guess = {center_guess}')
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diff changeset
349 if center_guess is None:
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diff changeset
350 center_index = np.argmax(y)
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diff changeset
351 center = x[center_index]
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diff changeset
352 height = maxy-miny
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diff changeset
353 else:
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parents:
diff changeset
354 if use_max_for_center:
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parents:
diff changeset
355 center_index = np.argmax(y)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
356 center = x[center_index]
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parents:
diff changeset
357 if center_index < 0.1*len(x) or center_index > 0.9*len(x):
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parents:
diff changeset
358 center_index = index_nearest(x, center_guess)
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parents:
diff changeset
359 center = center_guess
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parents:
diff changeset
360 else:
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parents:
diff changeset
361 center_index = index_nearest(x, center_guess)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
362 center = center_guess
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parents:
diff changeset
363 height = y[center_index]-miny
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
364 # print(f'center_index = {center_index}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
365 # print(f'center = {center}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
366 # print(f'height = {height}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
367 half_height = miny+0.5*height
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
368 # print(f'half_height = {half_height}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
369 fwhm_index1 = 0
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parents:
diff changeset
370 for i in range(center_index, fwhm_index1, -1):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
371 if y[i] < half_height:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
372 fwhm_index1 = i
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
373 break
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
374 # print(f'fwhm_index1 = {fwhm_index1} {x[fwhm_index1]}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
375 fwhm_index2 = len(x)-1
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parents:
diff changeset
376 for i in range(center_index, fwhm_index2):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
377 if y[i] < half_height:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
378 fwhm_index2 = i
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parents:
diff changeset
379 break
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parents:
diff changeset
380 # print(f'fwhm_index2 = {fwhm_index2} {x[fwhm_index2]}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
381 # quickPlot((x,y,'o'), vlines=(x[fwhm_index1], center, x[fwhm_index2]), block=True)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
382 if fwhm_index1 == 0 and fwhm_index2 < len(x)-1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
383 fwhm = 2*(x[fwhm_index2]-center)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
384 elif fwhm_index1 > 0 and fwhm_index2 == len(x)-1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
385 fwhm = 2*(center-x[fwhm_index1])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
386 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
387 fwhm = x[fwhm_index2]-x[fwhm_index1]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
388 # print(f'fwhm_index1 = {fwhm_index1} {x[fwhm_index1]}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
389 # print(f'fwhm_index2 = {fwhm_index2} {x[fwhm_index2]}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
390 # print(f'fwhm = {fwhm}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
391
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
392 # Return height, center and FWHM
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
393 # quickPlot((x,y,'o'), (xx,yy), vlines=(x[fwhm_index1], center, x[fwhm_index2]), block=True)
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diff changeset
394 return height, center, fwhm
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
395
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
396
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
397 class FitMultipeak(Fit):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
398 """Fit data with multiple peaks
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
399 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
400 def __init__(self, x, y, normalize=True):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
401 super().__init__(x, deepcopy(y))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
402 self._norm = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
403 self._fwhm_max = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
404 self._sigma_max = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
405 if normalize:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
406 self._normalize()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
407 #quickPlot((self._x,self._y), block=True)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
408
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
409 @classmethod
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
410 def fit_multipeak(cls, x, y, centers, peak_models='gaussian', center_exprs=None, fit_type=None,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
411 background_order=None, fwhm_max=None, plot_components=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
412 """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"
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parents:
diff changeset
413 for a uniform fit (fit_type == 'uniform')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
414 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
415 fit = cls(x, y)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
416 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"
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parents:
diff changeset
417 center_exprs=center_exprs, background_order=background_order,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
418 plot_components=plot_components)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
419 if success:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
420 return fit.best_fit, fit.residual, fit.best_values, fit.best_errors, fit.redchi, \
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
421 fit.success
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
422 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
423 return np.array([]), np.array([]), {}, {}, sys.float_info.max, False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
424
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
425 def fit(self, centers, fit_type=None, peak_models=None, center_exprs=None, fwhm_max=None,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
426 background_order=None, plot_components=None, param_constraint=False):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
427 self._fwhm_max = fwhm_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
428 # Create the multipeak model
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
429 self._create_model(centers, fit_type, peak_models, center_exprs, background_order,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
430 param_constraint)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
431
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
432 # Perform the fit
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
433 try:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
434 if param_constraint:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
435 super().fit(fit_kws={'xtol' : 1.e-5, 'ftol' : 1.e-5, 'gtol' : 1.e-5})
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
436 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
437 super().fit()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
438 except:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
439 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
440
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
441 # Check for valid fit parameter results
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
442 fit_failure = self._check_validity()
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parents:
diff changeset
443 success = True
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parents:
diff changeset
444 if fit_failure:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
445 if param_constraint:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
446 logging.warning(' -> Should not happen with param_constraint set, fail the fit')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
447 success = False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
448 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
449 logging.info(' -> Retry fitting with constraints')
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parents:
diff changeset
450 self.fit(centers, fit_type, peak_models, center_exprs, fwhm_max=fwhm_max,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
451 background_order=background_order, plot_components=plot_components,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
452 param_constraint=True)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
453 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
454 # Renormalize the data and results
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
455 self._renormalize()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
456
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
457 # Print report and plot components if requested
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
458 if plot_components is not None:
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parents:
diff changeset
459 self.print_fit_report()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
460 self.plot()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
461
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
462 return success
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
463
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
464 def _create_model(self, centers, fit_type=None, peak_models=None, center_exprs=None,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
465 background_order=None, param_constraint=False):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
466 """Create the multipeak model
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
467 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
468 if isinstance(centers, (int, float)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
469 centers = [centers]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
470 num_peaks = len(centers)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
471 if peak_models is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
472 peak_models = num_peaks*['gaussian']
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
473 elif isinstance(peak_models, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
474 peak_models = num_peaks*[peak_models]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
475 if len(peak_models) != num_peaks:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
476 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"
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parents:
diff changeset
477 f'{num_peaks})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
478 if num_peaks == 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
479 if fit_type is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
480 logging.warning('Ignoring fit_type input for fitting one peak')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
481 fit_type = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
482 if center_exprs is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
483 logging.warning('Ignoring center_exprs input for fitting one peak')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
484 center_exprs = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
485 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
486 if fit_type == 'uniform':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
487 if center_exprs is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
488 center_exprs = [f'scale_factor*{cen}' for cen in centers]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
489 if len(center_exprs) != num_peaks:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
490 raise ValueError(f'Inconsistent number of peaks in center_exprs '+
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
491 f'({len(center_exprs)} vs {num_peaks})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
492 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
493 if center_exprs is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
494 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
495 center_exprs = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
496 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
497 raise ValueError(f'Illegal fit_type in fit_multigaussian {fit_type}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
498 self._sigma_max = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
499 if param_constraint:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
500 min_value = sys.float_info.min
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
501 if self._fwhm_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
502 self._sigma_max = np.zeros(num_peaks)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
503 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
504 min_value = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
505
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
506 # Reset the fit
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
507 self._model = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
508 self._parameters = Parameters()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
509 self._result = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
510
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
511 # Add background model
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
512 if background_order is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
513 if background_order == 0:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
514 self.add_model('constant', prefix='background', c=0.0)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
515 elif background_order == 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
516 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
517 elif background_order == 2:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
518 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
519 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
520 raise ValueError(f'background_order = {background_order}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
521
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
522 # Add peaks and guess initial fit parameters
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
523 ast = Interpreter()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
524 if num_peaks == 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
525 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
526 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
527 fwhm_init = self._fwhm_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
528 ast(f'fwhm = {fwhm_init}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
529 ast(f'height = {height_init}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
530 sig_init = ast(fwhm_factor[peak_models[0]])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
531 amp_init = ast(height_factor[peak_models[0]])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
532 sig_max = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
533 if self._sigma_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
534 ast(f'fwhm = {self._fwhm_max}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
535 sig_max = ast(fwhm_factor[peak_models[0]])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
536 self._sigma_max[0] = sig_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
537 self.add_model(peak_models[0], parameters=(
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
538 {'name' : 'amplitude', 'value' : amp_init, 'min' : min_value},
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
539 {'name' : 'center', 'value' : cen_init, 'min' : min_value},
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
540 {'name' : 'sigma', 'value' : sig_init, 'min' : min_value, 'max' : sig_max}))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
541 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
542 if fit_type == 'uniform':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
543 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
544 for i in range(num_peaks):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
545 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
546 center_guess=centers)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
547 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
548 fwhm_init = self._fwhm_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
549 ast(f'fwhm = {fwhm_init}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
550 ast(f'height = {height_init}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
551 sig_init = ast(fwhm_factor[peak_models[i]])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
552 amp_init = ast(height_factor[peak_models[i]])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
553 sig_max = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
554 if self._sigma_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
555 ast(f'fwhm = {self._fwhm_max}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
556 sig_max = ast(fwhm_factor[peak_models[i]])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
557 self._sigma_max[i] = sig_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
558 if fit_type == 'uniform':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
559 self.add_model(peak_models[i], prefix=f'peak{i+1}_', parameters=(
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
560 {'name' : 'amplitude', 'value' : amp_init, 'min' : min_value},
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
561 {'name' : 'center', 'expr' : center_exprs[i], 'min' : min_value},
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
562 {'name' : 'sigma', 'value' : sig_init, 'min' : min_value,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
563 'max' : sig_max}))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
564 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
565 self.add_model('gaussian', prefix=f'peak{i+1}_', parameters=(
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
566 {'name' : 'amplitude', 'value' : amp_init, 'min' : min_value},
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
567 {'name' : 'center', 'value' : cen_init, 'min' : min_value},
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
568 {'name' : 'sigma', 'value' : sig_init, 'min' : min_value,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
569 'max' : sig_max}))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
570
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
571 def _check_validity(self):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
572 """Check for valid fit parameter results
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
573 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
574 fit_failure = False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
575 index = re.compile(r'\d+')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
576 for parameter in self.best_parameters:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
577 name = parameter['name']
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
578 if ((('amplitude' in name or 'height' in name) and parameter['value'] <= 0.0) or
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
579 (('sigma' in name or 'fwhm' in name) and parameter['value'] <= 0.0) or
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
580 ('center' in name and parameter['value'] <= 0.0) or
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
581 (name == 'scale_factor' and parameter['value'] <= 0.0)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
582 logging.info(f'Invalid fit result for {name} ({parameter["value"]})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
583 fit_failure = True
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
584 if 'sigma' in name and self._sigma_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
585 if name == 'sigma':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
586 sigma_max = self._sigma_max[0]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
587 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
588 sigma_max = self._sigma_max[int(index.search(name).group())-1]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
589 i = int(index.search(name).group())-1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
590 if parameter['value'] > sigma_max:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
591 logging.info(f'Invalid fit result for {name} ({parameter["value"]})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
592 fit_failure = True
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
593 elif parameter['value'] == sigma_max:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
594 logging.warning(f'Edge result on for {name} ({parameter["value"]})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
595 if 'fwhm' in name and self._fwhm_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
596 if parameter['value'] > self._fwhm_max:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
597 logging.info(f'Invalid fit result for {name} ({parameter["value"]})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
598 fit_failure = True
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
599 elif parameter['value'] == self._fwhm_max:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
600 logging.warning(f'Edge result on for {name} ({parameter["value"]})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
601 return fit_failure
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
602
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
603 def _normalize(self):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
604 """Normalize the data
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
605 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
606 y_min = self._y.min()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
607 self._norm = (y_min, self._y.max()-y_min)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
608 if self._norm[1] == 0.0:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
609 self._norm = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
610 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
611 self._y = (self._y-self._norm[0])/self._norm[1]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
612
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
613 def _renormalize(self):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
614 """Renormalize the data and results
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
615 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
616 if self._norm is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
617 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
618 self._y = self._norm[0]+self._norm[1]*self._y
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
619 self._result.best_fit = self._norm[0]+self._norm[1]*self._result.best_fit
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
620 for name in self._result.params:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
621 par = self._result.params[name]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
622 if 'amplitude' in name or 'height' in name or 'background' in name:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
623 par.value *= self._norm[1]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
624 if par.stderr is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
625 par.stderr *= self._norm[1]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
626 if par.init_value is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
627 par.init_value *= self._norm[1]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
628 if par.min is not None and not np.isinf(par.min):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
629 par.min *= self._norm[1]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
630 if par.max is not None and not np.isinf(par.max):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
631 par.max *= self._norm[1]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
632 if 'intercept' in name or 'backgroundc' in name:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
633 par.value += self._norm[0]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
634 if par.init_value is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
635 par.init_value += self._norm[0]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
636 if par.min is not None and not np.isinf(par.min):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
637 par.min += self._norm[0]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
638 if par.max is not None and not np.isinf(par.max):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
639 par.max += self._norm[0]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
640 self._result.init_fit = self._norm[0]+self._norm[1]*self._result.init_fit
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
641 init_values = {}
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
642 for name in self._result.init_values:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
643 init_values[name] = self._result.init_values[name]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
644 if init_values[name] is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
645 continue
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
646 if 'amplitude' in name or 'height' in name or 'background' in name:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
647 init_values[name] *= self._norm[1]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
648 if 'intercept' in name or 'backgroundc' in name:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
649 init_values[name] += self._norm[0]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
650 self._result.init_values = init_values
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
651 # Don't renormalized chisqr, it has no useful meaning in physical units
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
652 #self._result.chisqr *= self._norm[1]*self._norm[1]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
653 if self._result.covar is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
654 for i, name in enumerate(self._result.var_names):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
655 if 'amplitude' in name or 'height' in name or 'background' in name:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
656 for j in range(len(self._result.var_names)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
657 if self._result.covar[i,j] is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
658 self._result.covar[i,j] *= self._norm[1]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
659 if self._result.covar[j,i] is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
660 self._result.covar[j,i] *= self._norm[1]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
661 # Don't renormalized redchi, it has no useful meaning in physical units
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
662 #self._result.redchi *= self._norm[1]*self._norm[1]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
663 self._result.residual *= self._norm[1]