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annotate fit.py @ 71:1cf15b61cd83 draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213
author rv43
date Mon, 20 Mar 2023 13:56:57 +0000
parents fba792d5f83b
children d5e1d4ea2b7e
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1 #!/usr/bin/env python3
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3 # -*- coding: utf-8 -*-
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4 """
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5 Created on Mon Dec 6 15:36:22 2021
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7 @author: rv43
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8 """
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10 import logging
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11
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12 from asteval import Interpreter, get_ast_names
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13 from copy import deepcopy
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14 from lmfit import Model, Parameters
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15 from lmfit.model import ModelResult
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16 from lmfit.models import ConstantModel, LinearModel, QuadraticModel, PolynomialModel,\
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17 ExponentialModel, StepModel, RectangleModel, ExpressionModel, GaussianModel,\
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18 LorentzianModel
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19 import numpy as np
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20 from os import cpu_count, getpid, listdir, mkdir, path
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21 from re import compile, sub
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22 from shutil import rmtree
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23 try:
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24 from sympy import diff, simplify
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25 except:
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26 pass
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27 try:
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28 from joblib import Parallel, delayed
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29 have_joblib = True
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30 except:
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31 have_joblib = False
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32 try:
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33 import xarray as xr
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34 have_xarray = True
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35 except:
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36 have_xarray = False
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37
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38 #try:
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39 # from .general import illegal_value, is_int, is_dict_series, is_index, index_nearest, \
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40 # almost_equal, quick_plot #, eval_expr
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41 #except:
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42 # try:
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43 # from sys import path as syspath
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44 # syspath.append(f'/nfs/chess/user/rv43/msnctools/msnctools')
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45 # from general import illegal_value, is_int, is_dict_series, is_index, index_nearest, \
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46 # almost_equal, quick_plot #, eval_expr
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47 # except:
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48 # from general import illegal_value, is_int, is_dict_series, is_index, index_nearest, \
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49 # almost_equal, quick_plot #, eval_expr
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50 from general import illegal_value, is_int, is_dict_series, is_index, index_nearest, \
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51 almost_equal, quick_plot #, eval_expr
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52
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53 from sys import float_info
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54 float_min = float_info.min
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55 float_max = float_info.max
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57 # sigma = fwhm_factor*fwhm
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58 fwhm_factor = {
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59 'gaussian': f'fwhm/(2*sqrt(2*log(2)))',
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60 'lorentzian': f'0.5*fwhm',
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61 'splitlorentzian': f'0.5*fwhm', # sigma = sigma_r
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62 'voight': f'0.2776*fwhm', # sigma = gamma
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63 'pseudovoight': f'0.5*fwhm'} # fraction = 0.5
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64
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65 # amplitude = height_factor*height*fwhm
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66 height_factor = {
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67 'gaussian': f'height*fwhm*0.5*sqrt(pi/log(2))',
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68 'lorentzian': f'height*fwhm*0.5*pi',
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69 'splitlorentzian': f'height*fwhm*0.5*pi', # sigma = sigma_r
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70 'voight': f'3.334*height*fwhm', # sigma = gamma
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71 'pseudovoight': f'1.268*height*fwhm'} # fraction = 0.5
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72
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73 class Fit:
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74 """Wrapper class for lmfit
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75 """
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76 def __init__(self, y, x=None, models=None, normalize=True, **kwargs):
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77 if not isinstance(normalize, bool):
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78 raise ValueError(f'Invalid parameter normalize ({normalize})')
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79 self._mask = None
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80 self._model = None
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81 self._norm = None
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82 self._normalized = False
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83 self._parameters = Parameters()
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84 self._parameter_bounds = None
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85 self._parameter_norms = {}
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86 self._linear_parameters = []
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87 self._nonlinear_parameters = []
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88 self._result = None
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89 self._try_linear_fit = True
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90 self._y = None
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91 self._y_norm = None
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92 self._y_range = None
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93 if 'try_linear_fit' in kwargs:
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94 try_linear_fit = kwargs.pop('try_linear_fit')
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95 if not isinstance(try_linear_fit, bool):
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96 illegal_value(try_linear_fit, 'try_linear_fit', 'Fit.fit', raise_error=True)
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97 self._try_linear_fit = try_linear_fit
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98 if y is not None:
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99 if isinstance(y, (tuple, list, np.ndarray)):
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100 self._x = np.asarray(x)
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101 elif have_xarray and isinstance(y, xr.DataArray):
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102 if x is not None:
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103 logging.warning('Ignoring superfluous input x ({x}) in Fit.__init__')
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104 if y.ndim != 1:
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105 illegal_value(y.ndim, 'DataArray dimensions', 'Fit:__init__', raise_error=True)
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106 self._x = np.asarray(y[y.dims[0]])
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107 else:
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108 illegal_value(y, 'y', 'Fit:__init__', raise_error=True)
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109 self._y = y
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110 if self._x.ndim != 1:
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111 raise ValueError(f'Invalid dimension for input x ({self._x.ndim})')
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112 if self._x.size != self._y.size:
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113 raise ValueError(f'Inconsistent x and y dimensions ({self._x.size} vs '+
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114 f'{self._y.size})')
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115 if 'mask' in kwargs:
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116 self._mask = kwargs.pop('mask')
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117 if self._mask is None:
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118 y_min = float(self._y.min())
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119 self._y_range = float(self._y.max())-y_min
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120 if normalize and self._y_range > 0.0:
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121 self._norm = (y_min, self._y_range)
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122 else:
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123 self._mask = np.asarray(self._mask).astype(bool)
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124 if self._x.size != self._mask.size:
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125 raise ValueError(f'Inconsistent x and mask dimensions ({self._x.size} vs '+
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126 f'{self._mask.size})')
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127 y_masked = np.asarray(self._y)[~self._mask]
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128 y_min = float(y_masked.min())
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129 self._y_range = float(y_masked.max())-y_min
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130 if normalize and self._y_range > 0.0:
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131 if normalize and self._y_range > 0.0:
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132 self._norm = (y_min, self._y_range)
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133 if models is not None:
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134 if callable(models) or isinstance(models, str):
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135 kwargs = self.add_model(models, **kwargs)
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136 elif isinstance(models, (tuple, list)):
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137 for model in models:
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138 kwargs = self.add_model(model, **kwargs)
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139 self.fit(**kwargs)
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140
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141 @classmethod
69
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142 def fit_data(cls, y, models, x=None, normalize=True, **kwargs):
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143 return(cls(y, x=x, models=models, normalize=normalize, **kwargs))
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144
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145 @property
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146 def best_errors(self):
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147 if self._result is None:
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148 return(None)
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149 return({name:self._result.params[name].stderr for name in sorted(self._result.params)
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150 if name != 'tmp_normalization_offset_c'})
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151
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152 @property
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153 def best_fit(self):
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154 if self._result is None:
69
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155 return(None)
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156 return(self._result.best_fit)
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157
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158 @property
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159 def best_parameters(self):
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160 if self._result is None:
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161 return(None)
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162 parameters = {}
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163 for name in sorted(self._result.params):
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164 if name != 'tmp_normalization_offset_c':
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165 par = self._result.params[name]
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166 parameters[name] = {'value': par.value, 'error': par.stderr,
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167 'init_value': par.init_value, 'min': par.min, 'max': par.max,
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168 'vary': par.vary, 'expr': par.expr}
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169 return(parameters)
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170
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171 @property
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172 def best_results(self):
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173 """Convert the input data array to a data set and add the fit results.
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174 """
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175 if self._result is None:
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176 return(None)
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177 if isinstance(self._y, xr.DataArray):
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178 best_results = self._y.to_dataset()
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179 dims = self._y.dims
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180 fit_name = f'{self._y.name}_fit'
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181 else:
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182 coords = {'x': (['x'], self._x)}
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183 dims = ('x')
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184 best_results = xr.Dataset(coords=coords)
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185 best_results['y'] = (dims, self._y)
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186 fit_name = 'y_fit'
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187 best_results[fit_name] = (dims, self.best_fit)
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188 if self._mask is not None:
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189 best_results['mask'] = self._mask
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190 best_results.coords['par_names'] = ('peak', [name for name in self.best_values.keys()])
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191 best_results['best_values'] = (['par_names'], [v for v in self.best_values.values()])
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192 best_results['best_errors'] = (['par_names'], [v for v in self.best_errors.values()])
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193 best_results.attrs['components'] = self.components
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194 return(best_results)
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195
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196 @property
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197 def best_values(self):
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198 if self._result is None:
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199 return(None)
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200 return({name:self._result.params[name].value for name in sorted(self._result.params)
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201 if name != 'tmp_normalization_offset_c'})
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202
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203 @property
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204 def chisqr(self):
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205 if self._result is None:
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206 return(None)
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207 return(self._result.chisqr)
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208
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209 @property
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210 def components(self):
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211 components = {}
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212 if self._result is None:
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213 logging.warning('Unable to collect components in Fit.components')
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214 return(components)
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215 for component in self._result.components:
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216 if 'tmp_normalization_offset_c' in component.param_names:
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217 continue
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218 parameters = {}
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219 for name in component.param_names:
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220 par = self._parameters[name]
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221 parameters[name] = {'free': par.vary, 'value': self._result.params[name].value}
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222 if par.expr is not None:
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223 parameters[name]['expr'] = par.expr
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224 expr = None
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225 if isinstance(component, ExpressionModel):
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226 name = component._name
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227 if name[-1] == '_':
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228 name = name[:-1]
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229 expr = component.expr
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230 else:
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231 prefix = component.prefix
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232 if len(prefix):
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233 if prefix[-1] == '_':
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234 prefix = prefix[:-1]
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235 name = f'{prefix} ({component._name})'
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236 else:
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237 name = f'{component._name}'
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238 if expr is None:
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239 components[name] = {'parameters': parameters}
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240 else:
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241 components[name] = {'expr': expr, 'parameters': parameters}
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242 return(components)
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243
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244 @property
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245 def covar(self):
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246 if self._result is None:
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247 return(None)
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248 return(self._result.covar)
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249
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250 @property
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251 def init_parameters(self):
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252 if self._result is None or self._result.init_params is None:
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253 return(None)
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254 parameters = {}
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255 for name in sorted(self._result.init_params):
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256 if name != 'tmp_normalization_offset_c':
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257 par = self._result.init_params[name]
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258 parameters[name] = {'value': par.value, 'min': par.min, 'max': par.max,
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259 'vary': par.vary, 'expr': par.expr}
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260 return(parameters)
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261
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262 @property
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263 def init_values(self):
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264 if self._result is None or self._result.init_params is None:
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265 return(None)
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266 return({name:self._result.init_params[name].value for name in
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267 sorted(self._result.init_params) if name != 'tmp_normalization_offset_c'})
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268
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269 @property
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270 def normalization_offset(self):
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271 if self._result is None:
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272 return(None)
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273 if self._norm is None:
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274 return(0.0)
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275 else:
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276 if self._result.init_params is not None:
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277 normalization_offset = self._result.init_params['tmp_normalization_offset_c']
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278 else:
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279 normalization_offset = self._result.params['tmp_normalization_offset_c']
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280 return(normalization_offset)
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281
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282 @property
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283 def num_func_eval(self):
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284 if self._result is None:
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285 return(None)
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286 return(self._result.nfev)
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287
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288 @property
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289 def parameters(self):
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290 return({name:{'min': par.min, 'max': par.max, 'vary': par.vary, 'expr': par.expr}
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291 for name, par in self._parameters.items() if name != 'tmp_normalization_offset_c'})
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292
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293 @property
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294 def redchi(self):
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295 if self._result is None:
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296 return(None)
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297 return(self._result.redchi)
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298
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299 @property
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300 def residual(self):
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301 if self._result is None:
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302 return(None)
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303 return(self._result.residual)
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304
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305 @property
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306 def success(self):
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307 if self._result is None:
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308 return(None)
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309 if not self._result.success:
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310 # print(f'ier = {self._result.ier}')
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311 # print(f'lmdif_message = {self._result.lmdif_message}')
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312 # print(f'message = {self._result.message}')
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313 # print(f'nfev = {self._result.nfev}')
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314 # print(f'redchi = {self._result.redchi}')
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315 # print(f'success = {self._result.success}')
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316 if self._result.ier == 0 or self._result.ier == 5:
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317 logging.warning(f'ier = {self._result.ier}: {self._result.message}')
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318 else:
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319 logging.warning(f'ier = {self._result.ier}: {self._result.message}')
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320 return(True)
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321 # self.print_fit_report()
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322 # self.plot()
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323 return(self._result.success)
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324
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325 @property
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326 def var_names(self):
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327 """Intended to be used with covar
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328 """
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329 if self._result is None:
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330 return(None)
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331 return(getattr(self._result, 'var_names', None))
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332
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333 @property
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334 def x(self):
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335 return(self._x)
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336
69
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337 @property
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338 def y(self):
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339 return(self._y)
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340
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341 def print_fit_report(self, result=None, show_correl=False):
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342 if result is None:
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343 result = self._result
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344 if result is not None:
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345 print(result.fit_report(show_correl=show_correl))
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346
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347 def add_parameter(self, **parameter):
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348 if not isinstance(parameter, dict):
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349 raise ValueError(f'Invalid parameter ({parameter})')
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350 if parameter.get('expr') is not None:
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351 raise KeyError(f'Illegal "expr" key in parameter {parameter}')
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352 name = parameter['name']
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353 if not isinstance(name, str):
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354 raise ValueError(f'Illegal "name" value ({name}) in parameter {parameter}')
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355 if parameter.get('norm') is None:
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356 self._parameter_norms[name] = False
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357 else:
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358 norm = parameter.pop('norm')
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359 if self._norm is None:
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360 logging.warning(f'Ignoring norm in parameter {name} in '+
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361 f'Fit.add_parameter (normalization is turned off)')
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362 self._parameter_norms[name] = False
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363 else:
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364 if not isinstance(norm, bool):
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365 raise ValueError(f'Illegal "norm" value ({norm}) in parameter {parameter}')
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366 self._parameter_norms[name] = norm
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367 vary = parameter.get('vary')
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368 if vary is not None:
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369 if not isinstance(vary, bool):
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370 raise ValueError(f'Illegal "vary" value ({vary}) in parameter {parameter}')
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371 if not vary:
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372 if 'min' in parameter:
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373 logging.warning(f'Ignoring min in parameter {name} in '+
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374 f'Fit.add_parameter (vary = {vary})')
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375 parameter.pop('min')
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376 if 'max' in parameter:
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377 logging.warning(f'Ignoring max in parameter {name} in '+
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378 f'Fit.add_parameter (vary = {vary})')
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379 parameter.pop('max')
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380 if self._norm is not None and name not in self._parameter_norms:
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381 raise ValueError(f'Missing parameter normalization type for paremeter {name}')
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382 self._parameters.add(**parameter)
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383
69
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384 def add_model(self, model, prefix=None, parameters=None, parameter_norms=None, **kwargs):
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385 # Create the new model
69
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386 # print(f'at start add_model:\nself._parameters:\n{self._parameters}')
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387 # print(f'at start add_model: kwargs = {kwargs}')
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388 # print(f'parameters = {parameters}')
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389 # print(f'parameter_norms = {parameter_norms}')
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390 # if len(self._parameters.keys()):
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391 # print('\nAt start adding model:')
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392 # self._parameters.pretty_print()
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393 # print(f'parameter_norms:\n{self._parameter_norms}')
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394 if prefix is not None and not isinstance(prefix, str):
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395 logging.warning('Ignoring illegal prefix: {model} {type(model)}')
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396 prefix = None
69
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397 if prefix is None:
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398 pprefix = ''
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399 else:
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400 pprefix = prefix
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401 if parameters is not None:
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402 if isinstance(parameters, dict):
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403 parameters = (parameters, )
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404 elif not is_dict_series(parameters):
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405 illegal_value(parameters, 'parameters', 'Fit.add_model', raise_error=True)
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406 parameters = deepcopy(parameters)
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407 if parameter_norms is not None:
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408 if isinstance(parameter_norms, dict):
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409 parameter_norms = (parameter_norms, )
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410 if not is_dict_series(parameter_norms):
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411 illegal_value(parameter_norms, 'parameter_norms', 'Fit.add_model', raise_error=True)
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412 new_parameter_norms = {}
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413 if callable(model):
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414 # Linear fit not yet implemented for callable models
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415 self._try_linear_fit = False
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416 if parameter_norms is None:
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417 if parameters is None:
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418 raise ValueError('Either "parameters" or "parameter_norms" is required in '+
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419 f'{model}')
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420 for par in parameters:
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421 name = par['name']
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422 if not isinstance(name, str):
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423 raise ValueError(f'Illegal "name" value ({name}) in input parameters')
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424 if par.get('norm') is not None:
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425 norm = par.pop('norm')
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426 if not isinstance(norm, bool):
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427 raise ValueError(f'Illegal "norm" value ({norm}) in input parameters')
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428 new_parameter_norms[f'{pprefix}{name}'] = norm
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429 else:
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430 for par in parameter_norms:
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431 name = par['name']
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432 if not isinstance(name, str):
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433 raise ValueError(f'Illegal "name" value ({name}) in input parameters')
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434 norm = par.get('norm')
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435 if norm is None or not isinstance(norm, bool):
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436 raise ValueError(f'Illegal "norm" value ({norm}) in input parameters')
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437 new_parameter_norms[f'{pprefix}{name}'] = norm
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438 if parameters is not None:
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439 for par in parameters:
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440 if par.get('expr') is not None:
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441 raise KeyError(f'Illegal "expr" key ({par.get("expr")}) in parameter '+
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442 f'{name} for a callable model {model}')
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443 name = par['name']
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444 if not isinstance(name, str):
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445 raise ValueError(f'Illegal "name" value ({name}) in input parameters')
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446 # RV FIX callable model will need partial deriv functions for any linear pars to get the linearized matrix, so for now skip linear solution option
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447 newmodel = Model(model, prefix=prefix)
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448 elif isinstance(model, str):
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449 if model == 'constant': # Par: c
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450 newmodel = ConstantModel(prefix=prefix)
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451 new_parameter_norms[f'{pprefix}c'] = True
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452 self._linear_parameters.append(f'{pprefix}c')
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453 elif model == 'linear': # Par: slope, intercept
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454 newmodel = LinearModel(prefix=prefix)
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455 new_parameter_norms[f'{pprefix}slope'] = True
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456 new_parameter_norms[f'{pprefix}intercept'] = True
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457 self._linear_parameters.append(f'{pprefix}slope')
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458 self._linear_parameters.append(f'{pprefix}intercept')
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459 elif model == 'quadratic': # Par: a, b, c
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460 newmodel = QuadraticModel(prefix=prefix)
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461 new_parameter_norms[f'{pprefix}a'] = True
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462 new_parameter_norms[f'{pprefix}b'] = True
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463 new_parameter_norms[f'{pprefix}c'] = True
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464 self._linear_parameters.append(f'{pprefix}a')
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465 self._linear_parameters.append(f'{pprefix}b')
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466 self._linear_parameters.append(f'{pprefix}c')
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467 elif model == 'gaussian': # Par: amplitude, center, sigma (fwhm, height)
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468 newmodel = GaussianModel(prefix=prefix)
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469 new_parameter_norms[f'{pprefix}amplitude'] = True
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470 new_parameter_norms[f'{pprefix}center'] = False
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471 new_parameter_norms[f'{pprefix}sigma'] = False
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472 self._linear_parameters.append(f'{pprefix}amplitude')
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473 self._nonlinear_parameters.append(f'{pprefix}center')
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474 self._nonlinear_parameters.append(f'{pprefix}sigma')
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475 # parameter norms for height and fwhm are needed to get correct errors
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476 new_parameter_norms[f'{pprefix}height'] = True
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477 new_parameter_norms[f'{pprefix}fwhm'] = False
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478 elif model == 'lorentzian': # Par: amplitude, center, sigma (fwhm, height)
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479 newmodel = LorentzianModel(prefix=prefix)
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480 new_parameter_norms[f'{pprefix}amplitude'] = True
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481 new_parameter_norms[f'{pprefix}center'] = False
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482 new_parameter_norms[f'{pprefix}sigma'] = False
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483 self._linear_parameters.append(f'{pprefix}amplitude')
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484 self._nonlinear_parameters.append(f'{pprefix}center')
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485 self._nonlinear_parameters.append(f'{pprefix}sigma')
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486 # parameter norms for height and fwhm are needed to get correct errors
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487 new_parameter_norms[f'{pprefix}height'] = True
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488 new_parameter_norms[f'{pprefix}fwhm'] = False
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489 elif model == 'exponential': # Par: amplitude, decay
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490 newmodel = ExponentialModel(prefix=prefix)
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491 new_parameter_norms[f'{pprefix}amplitude'] = True
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492 new_parameter_norms[f'{pprefix}decay'] = False
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493 self._linear_parameters.append(f'{pprefix}amplitude')
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494 self._nonlinear_parameters.append(f'{pprefix}decay')
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495 elif model == 'step': # Par: amplitude, center, sigma
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496 form = kwargs.get('form')
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497 if form is not None:
69
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498 kwargs.pop('form')
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499 if form is None or form not in ('linear', 'atan', 'arctan', 'erf', 'logistic'):
69
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500 raise ValueError(f'Invalid parameter form for build-in step model ({form})')
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501 newmodel = StepModel(prefix=prefix, form=form)
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diff changeset
502 new_parameter_norms[f'{pprefix}amplitude'] = True
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503 new_parameter_norms[f'{pprefix}center'] = False
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504 new_parameter_norms[f'{pprefix}sigma'] = False
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505 self._linear_parameters.append(f'{pprefix}amplitude')
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506 self._nonlinear_parameters.append(f'{pprefix}center')
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507 self._nonlinear_parameters.append(f'{pprefix}sigma')
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508 elif model == 'rectangle': # Par: amplitude, center1, center2, sigma1, sigma2
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509 form = kwargs.get('form')
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510 if form is not None:
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511 kwargs.pop('form')
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512 if form is None or form not in ('linear', 'atan', 'arctan', 'erf', 'logistic'):
69
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513 raise ValueError('Invalid parameter form for build-in rectangle model '+
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514 f'({form})')
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515 newmodel = RectangleModel(prefix=prefix, form=form)
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516 new_parameter_norms[f'{pprefix}amplitude'] = True
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517 new_parameter_norms[f'{pprefix}center1'] = False
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518 new_parameter_norms[f'{pprefix}center2'] = False
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519 new_parameter_norms[f'{pprefix}sigma1'] = False
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520 new_parameter_norms[f'{pprefix}sigma2'] = False
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521 self._linear_parameters.append(f'{pprefix}amplitude')
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522 self._nonlinear_parameters.append(f'{pprefix}center1')
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523 self._nonlinear_parameters.append(f'{pprefix}center2')
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524 self._nonlinear_parameters.append(f'{pprefix}sigma1')
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525 self._nonlinear_parameters.append(f'{pprefix}sigma2')
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526 elif model == 'expression': # Par: by expression
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527 expr = kwargs['expr']
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528 if not isinstance(expr, str):
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529 raise ValueError(f'Illegal "expr" value ({expr}) in {model}')
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530 kwargs.pop('expr')
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diff changeset
531 if parameter_norms is not None:
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532 logging.warning('Ignoring parameter_norms (normalization determined from '+
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533 'linearity)}')
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534 if parameters is not None:
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535 for par in parameters:
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536 if par.get('expr') is not None:
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537 raise KeyError(f'Illegal "expr" key ({par.get("expr")}) in parameter '+
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diff changeset
538 f'({par}) for an expression model')
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539 if par.get('norm') is not None:
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diff changeset
540 logging.warning(f'Ignoring "norm" key in parameter ({par}) '+
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diff changeset
541 '(normalization determined from linearity)}')
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diff changeset
542 par.pop('norm')
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543 name = par['name']
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544 if not isinstance(name, str):
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545 raise ValueError(f'Illegal "name" value ({name}) in input parameters')
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546 ast = Interpreter()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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547 expr_parameters = [name for name in get_ast_names(ast.parse(expr))
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diff changeset
548 if name != 'x' and name not in self._parameters
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diff changeset
549 and name not in ast.symtable]
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diff changeset
550 # print(f'\nexpr_parameters: {expr_parameters}')
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551 # print(f'expr = {expr}')
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552 if prefix is None:
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553 newmodel = ExpressionModel(expr=expr)
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554 else:
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diff changeset
555 for name in expr_parameters:
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diff changeset
556 expr = sub(rf'\b{name}\b', f'{prefix}{name}', expr)
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diff changeset
557 expr_parameters = [f'{prefix}{name}' for name in expr_parameters]
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diff changeset
558 # print(f'\nexpr_parameters: {expr_parameters}')
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diff changeset
559 # print(f'expr = {expr}')
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diff changeset
560 newmodel = ExpressionModel(expr=expr, name=name)
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diff changeset
561 # print(f'\nnewmodel = {newmodel.__dict__}')
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diff changeset
562 # print(f'params_names = {newmodel._param_names}')
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diff changeset
563 # print(f'params_names = {newmodel.param_names}')
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diff changeset
564 # Remove already existing names
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diff changeset
565 for name in newmodel.param_names.copy():
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diff changeset
566 if name not in expr_parameters:
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diff changeset
567 newmodel._func_allargs.remove(name)
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diff changeset
568 newmodel._param_names.remove(name)
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diff changeset
569 # print(f'params_names = {newmodel._param_names}')
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diff changeset
570 # print(f'params_names = {newmodel.param_names}')
49
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diff changeset
571 else:
69
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diff changeset
572 raise ValueError(f'Unknown build-in fit model ({model})')
49
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diff changeset
573 else:
69
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diff changeset
574 illegal_value(model, 'model', 'Fit.add_model', raise_error=True)
49
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diff changeset
575
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diff changeset
576 # Add the new model to the current one
69
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diff changeset
577 # print('\nBefore adding model:')
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diff changeset
578 # print(f'\nnewmodel = {newmodel.__dict__}')
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diff changeset
579 # if len(self._parameters):
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580 # self._parameters.pretty_print()
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diff changeset
581 if self._model is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
582 self._model = newmodel
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diff changeset
583 else:
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diff changeset
584 self._model += newmodel
69
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diff changeset
585 new_parameters = newmodel.make_params()
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diff changeset
586 self._parameters += new_parameters
49
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diff changeset
587 # print('\nAfter adding model:')
69
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588 # print(f'\nnewmodel = {newmodel.__dict__}')
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589 # print(f'\nnew_parameters = {new_parameters}')
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590 # self._parameters.pretty_print()
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591
69
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592 # Check linearity of expression model paremeters
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593 if isinstance(newmodel, ExpressionModel):
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594 for name in newmodel.param_names:
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595 if not diff(newmodel.expr, name, name):
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596 if name not in self._linear_parameters:
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597 self._linear_parameters.append(name)
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598 new_parameter_norms[name] = True
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599 # print(f'\nADDING {name} TO LINEAR')
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600 else:
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601 if name not in self._nonlinear_parameters:
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602 self._nonlinear_parameters.append(name)
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603 new_parameter_norms[name] = False
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604 # print(f'\nADDING {name} TO NONLINEAR')
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605 # print(f'new_parameter_norms:\n{new_parameter_norms}')
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606
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607 # Scale the default initial model parameters
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608 if self._norm is not None:
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609 for name, norm in new_parameter_norms.copy().items():
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610 par = self._parameters.get(name)
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611 if par is None:
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612 new_parameter_norms.pop(name)
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613 continue
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614 if par.expr is None and norm:
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615 value = par.value*self._norm[1]
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616 _min = par.min
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617 _max = par.max
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618 if not np.isinf(_min) and abs(_min) != float_min:
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619 _min *= self._norm[1]
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620 if not np.isinf(_max) and abs(_max) != float_min:
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621 _max *= self._norm[1]
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622 par.set(value=value, min=_min, max=_max)
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623 # print('\nAfter norm defaults:')
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624 # self._parameters.pretty_print()
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625 # print(f'parameters:\n{parameters}')
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626 # print(f'all_parameters:\n{list(self.parameters)}')
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627 # print(f'new_parameter_norms:\n{new_parameter_norms}')
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628 # print(f'parameter_norms:\n{self._parameter_norms}')
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629
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630 # Initialize the model parameters from parameters
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631 if prefix is None:
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632 prefix = ""
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633 if parameters is not None:
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634 for parameter in parameters:
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635 name = parameter['name']
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636 if not isinstance(name, str):
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637 raise ValueError(f'Illegal "name" value ({name}) in input parameters')
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638 if name not in new_parameters:
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639 name = prefix+name
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640 parameter['name'] = name
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641 if name not in new_parameters:
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642 logging.warning(f'Ignoring superfluous parameter info for {name}')
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643 continue
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644 if name in self._parameters:
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645 parameter.pop('name')
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646 if 'norm' in parameter:
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647 if not isinstance(parameter['norm'], bool):
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648 illegal_value(parameter['norm'], 'norm', 'Fit.add_model',
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649 raise_error=True)
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650 new_parameter_norms[name] = parameter['norm']
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651 parameter.pop('norm')
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652 if parameter.get('expr') is not None:
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653 if 'value' in parameter:
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654 logging.warning(f'Ignoring value in parameter {name} '+
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655 f'(set by expression: {parameter["expr"]})')
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656 parameter.pop('value')
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657 if 'vary' in parameter:
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658 logging.warning(f'Ignoring vary in parameter {name} '+
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659 f'(set by expression: {parameter["expr"]})')
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660 parameter.pop('vary')
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661 if 'min' in parameter:
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662 logging.warning(f'Ignoring min in parameter {name} '+
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663 f'(set by expression: {parameter["expr"]})')
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664 parameter.pop('min')
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665 if 'max' in parameter:
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666 logging.warning(f'Ignoring max in parameter {name} '+
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667 f'(set by expression: {parameter["expr"]})')
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668 parameter.pop('max')
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669 if 'vary' in parameter:
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670 if not isinstance(parameter['vary'], bool):
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671 illegal_value(parameter['vary'], 'vary', 'Fit.add_model',
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672 raise_error=True)
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673 if not parameter['vary']:
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674 if 'min' in parameter:
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675 logging.warning(f'Ignoring min in parameter {name} in '+
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676 f'Fit.add_model (vary = {parameter["vary"]})')
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677 parameter.pop('min')
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678 if 'max' in parameter:
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679 logging.warning(f'Ignoring max in parameter {name} in '+
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680 f'Fit.add_model (vary = {parameter["vary"]})')
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diff changeset
681 parameter.pop('max')
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682 self._parameters[name].set(**parameter)
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683 parameter['name'] = name
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684 else:
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685 illegal_value(parameter, 'parameter name', 'Fit.model', raise_error=True)
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686 self._parameter_norms = {**self._parameter_norms, **new_parameter_norms}
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687 # print('\nAfter parameter init:')
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688 # self._parameters.pretty_print()
69
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689 # print(f'parameters:\n{parameters}')
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690 # print(f'new_parameter_norms:\n{new_parameter_norms}')
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691 # print(f'parameter_norms:\n{self._parameter_norms}')
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692 # print(f'kwargs:\n{kwargs}')
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693
69
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694 # Initialize the model parameters from kwargs
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695 for name, value in {**kwargs}.items():
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696 full_name = f'{pprefix}{name}'
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697 if full_name in new_parameter_norms and isinstance(value, (int, float)):
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698 kwargs.pop(name)
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699 if self._parameters[full_name].expr is None:
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700 self._parameters[full_name].set(value=value)
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701 else:
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702 logging.warning(f'Ignoring parameter {name} in Fit.fit (set by expression: '+
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703 f'{self._parameters[full_name].expr})')
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704 # print('\nAfter kwargs init:')
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705 # self._parameters.pretty_print()
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706 # print(f'parameter_norms:\n{self._parameter_norms}')
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707 # print(f'kwargs:\n{kwargs}')
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708
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diff changeset
709 # Check parameter norms (also need it for expressions to renormalize the errors)
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710 if self._norm is not None and (callable(model) or model == 'expression'):
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711 missing_norm = False
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712 for name in new_parameters.valuesdict():
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713 if name not in self._parameter_norms:
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diff changeset
714 print(f'new_parameters:\n{new_parameters.valuesdict()}')
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715 print(f'self._parameter_norms:\n{self._parameter_norms}')
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716 logging.error(f'Missing parameter normalization type for {name} in {model}')
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717 missing_norm = True
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718 if missing_norm:
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diff changeset
719 raise ValueError
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diff changeset
720
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diff changeset
721 # print(f'at end add_model:\nself._parameters:\n{list(self.parameters)}')
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722 # print(f'at end add_model: kwargs = {kwargs}')
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723 # print(f'\nat end add_model: newmodel:\n{newmodel.__dict__}\n')
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724 return(kwargs)
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diff changeset
725
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diff changeset
726 def fit(self, interactive=False, guess=False, **kwargs):
69
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727 # Check inputs
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728 if self._model is None:
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diff changeset
729 logging.error('Undefined fit model')
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730 return
69
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731 if not isinstance(interactive, bool):
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732 illegal_value(interactive, 'interactive', 'Fit.fit', raise_error=True)
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733 if not isinstance(guess, bool):
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diff changeset
734 illegal_value(guess, 'guess', 'Fit.fit', raise_error=True)
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diff changeset
735 if 'try_linear_fit' in kwargs:
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736 try_linear_fit = kwargs.pop('try_linear_fit')
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737 if not isinstance(try_linear_fit, bool):
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738 illegal_value(try_linear_fit, 'try_linear_fit', 'Fit.fit', raise_error=True)
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739 if not self._try_linear_fit:
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740 logging.warning('Ignore superfluous keyword argument "try_linear_fit" (not '+
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741 'yet supported for callable models)')
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742 else:
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743 self._try_linear_fit = try_linear_fit
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744 # if self._result is None:
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diff changeset
745 # if 'parameters' in kwargs:
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746 # raise ValueError('Invalid parameter parameters ({kwargs["parameters"]})')
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747 # else:
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748 if self._result is not None:
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diff changeset
749 if guess:
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750 logging.warning('Ignoring input parameter guess in Fit.fit during refitting')
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751 guess = False
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diff changeset
752
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diff changeset
753 # Check for circular expressions
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diff changeset
754 # FIX TODO
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755 # for name1, par1 in self._parameters.items():
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756 # if par1.expr is not None:
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diff changeset
757
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diff changeset
758 # Apply mask if supplied:
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759 if 'mask' in kwargs:
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760 self._mask = kwargs.pop('mask')
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761 if self._mask is not None:
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diff changeset
762 self._mask = np.asarray(self._mask).astype(bool)
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763 if self._x.size != self._mask.size:
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diff changeset
764 raise ValueError(f'Inconsistent x and mask dimensions ({self._x.size} vs '+
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765 f'{self._mask.size})')
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diff changeset
766
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diff changeset
767 # Estimate initial parameters with build-in lmfit guess method (only for a single model)
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768 # print(f'\nat start fit: kwargs = {kwargs}')
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769 #RV print('\nAt start of fit:')
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diff changeset
770 #RV self._parameters.pretty_print()
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771 # print(f'parameter_norms:\n{self._parameter_norms}')
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diff changeset
772 if guess:
69
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diff changeset
773 if self._mask is None:
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774 self._parameters = self._model.guess(self._y, x=self._x)
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diff changeset
775 else:
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776 self._parameters = self._model.guess(np.asarray(self._y)[~self._mask],
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777 x=self._x[~self._mask])
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diff changeset
778 # print('\nAfter guess:')
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779 # self._parameters.pretty_print()
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diff changeset
780
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diff changeset
781 # Add constant offset for a normalized model
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782 if self._result is None and self._norm is not None and self._norm[0]:
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diff changeset
783 self.add_model('constant', prefix='tmp_normalization_offset_', parameters={'name': 'c',
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784 'value': -self._norm[0], 'vary': False, 'norm': True})
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785 #'value': -self._norm[0]/self._norm[1], 'vary': False, 'norm': False})
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diff changeset
786
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diff changeset
787 # Adjust existing parameters for refit:
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788 if 'parameters' in kwargs:
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diff changeset
789 parameters = kwargs.pop('parameters')
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790 if isinstance(parameters, dict):
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791 parameters = (parameters, )
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792 elif not is_dict_series(parameters):
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793 illegal_value(parameters, 'parameters', 'Fit.fit', raise_error=True)
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794 for par in parameters:
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795 name = par['name']
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796 if name not in self._parameters:
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797 raise ValueError(f'Unable to match {name} parameter {par} to an existing one')
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798 if self._parameters[name].expr is not None:
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diff changeset
799 raise ValueError(f'Unable to modify {name} parameter {par} (currently an '+
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800 'expression)')
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801 if par.get('expr') is not None:
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802 raise KeyError(f'Illegal "expr" key in {name} parameter {par}')
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803 self._parameters[name].set(vary=par.get('vary'))
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diff changeset
804 self._parameters[name].set(min=par.get('min'))
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diff changeset
805 self._parameters[name].set(max=par.get('max'))
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diff changeset
806 self._parameters[name].set(value=par.get('value'))
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807 #RV print('\nAfter adjust:')
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diff changeset
808 #RV self._parameters.pretty_print()
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diff changeset
809
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diff changeset
810 # Apply parameter updates through keyword arguments
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811 # print(f'kwargs = {kwargs}')
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812 # print(f'parameter_norms = {self._parameter_norms}')
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813 for name in set(self._parameters) & set(kwargs):
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814 value = kwargs.pop(name)
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815 if self._parameters[name].expr is None:
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diff changeset
816 self._parameters[name].set(value=value)
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817 else:
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diff changeset
818 logging.warning(f'Ignoring parameter {name} in Fit.fit (set by expression: '+
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819 f'{self._parameters[name].expr})')
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diff changeset
820
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diff changeset
821 # Check for uninitialized parameters
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diff changeset
822 for name, par in self._parameters.items():
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823 if par.expr is None:
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824 value = par.value
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825 if value is None or np.isinf(value) or np.isnan(value):
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826 if interactive:
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827 value = input_num(f'Enter an initial value for {name}', default=1.0)
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828 else:
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diff changeset
829 value = 1.0
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830 if self._norm is None or name not in self._parameter_norms:
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diff changeset
831 self._parameters[name].set(value=value)
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832 elif self._parameter_norms[name]:
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833 self._parameters[name].set(value=value*self._norm[1])
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
834
69
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diff changeset
835 # Check if model is linear
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diff changeset
836 try:
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837 linear_model = self._check_linearity_model()
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diff changeset
838 except:
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diff changeset
839 linear_model = False
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840 # print(f'\n\n--------> linear_model = {linear_model}\n')
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841 if kwargs.get('check_only_linearity') is not None:
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diff changeset
842 return(linear_model)
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843
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diff changeset
844 # Normalize the data and initial parameters
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845 #RV print('\nBefore normalization:')
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846 #RV self._parameters.pretty_print()
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847 # print(f'parameter_norms:\n{self._parameter_norms}')
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848 self._normalize()
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849 # print(f'norm = {self._norm}')
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850 #RV print('\nAfter normalization:')
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851 #RV self._parameters.pretty_print()
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852 # self.print_fit_report()
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853 # print(f'parameter_norms:\n{self._parameter_norms}')
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diff changeset
854
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855 if linear_model:
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diff changeset
856 # Perform a linear fit by direct matrix solution with numpy
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diff changeset
857 try:
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858 if self._mask is None:
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diff changeset
859 self._fit_linear_model(self._x, self._y_norm)
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860 else:
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861 self._fit_linear_model(self._x[~self._mask],
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862 np.asarray(self._y_norm)[~self._mask])
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diff changeset
863 except:
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diff changeset
864 linear_model = False
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865 if not linear_model:
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866 # Perform a non-linear fit with lmfit
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867 # Prevent initial values from sitting at boundaries
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868 self._parameter_bounds = {name:{'min': par.min, 'max': par.max} for name, par in
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869 self._parameters.items() if par.vary}
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870 for par in self._parameters.values():
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871 if par.vary:
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872 par.set(value=self._reset_par_at_boundary(par, par.value))
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873 # print('\nAfter checking boundaries:')
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874 # self._parameters.pretty_print()
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diff changeset
875
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diff changeset
876 # Perform the fit
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diff changeset
877 # fit_kws = None
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878 # if 'Dfun' in kwargs:
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879 # fit_kws = {'Dfun': kwargs.pop('Dfun')}
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880 # self._result = self._model.fit(self._y_norm, self._parameters, x=self._x,
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diff changeset
881 # fit_kws=fit_kws, **kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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882 if self._mask is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
883 self._result = self._model.fit(self._y_norm, self._parameters, x=self._x, **kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
884 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
885 self._result = self._model.fit(np.asarray(self._y_norm)[~self._mask],
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
886 self._parameters, x=self._x[~self._mask], **kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
887 #RV print('\nAfter fit:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
888 # print(f'\nself._result ({self._result}):\n\t{self._result.__dict__}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
889 #RV self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
890 # self.print_fit_report()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
891
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
892 # Set internal parameter values to fit results upon success
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
893 if self.success:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
894 for name, par in self._parameters.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
895 if par.expr is None and par.vary:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
896 par.set(value=self._result.params[name].value)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
897 # print('\nAfter update parameter values:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
898 # self._parameters.pretty_print()
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diff changeset
899
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
900 # Renormalize the data and results
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
901 self._renormalize()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
902 #RV print('\nAfter renormalization:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
903 #RV self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
904 # self.print_fit_report()
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diff changeset
905
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
906 def plot(self, y=None, y_title=None, result=None, skip_init=False, plot_comp_legends=False,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
907 plot_residual=False, plot_masked_data=True, **kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
908 if result is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
909 result = self._result
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diff changeset
910 if result is None:
49
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parents:
diff changeset
911 return
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
912 plots = []
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parents: 65
diff changeset
913 legend = []
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diff changeset
914 if self._mask is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
915 mask = np.zeros(self._x.size).astype(bool)
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diff changeset
916 plot_masked_data = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
917 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
918 mask = self._mask
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
919 if y is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
920 if not isinstance(y, (tuple, list, np.ndarray)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
921 illegal_value(y, 'y', 'Fit.plot')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
922 if len(y) != len(self._x):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
923 logging.warning('Ignoring parameter y in Fit.plot (wrong dimension)')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
924 y = None
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diff changeset
925 if y is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
926 if y_title is None or not isinstance(y_title, str):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
927 y_title = 'data'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
928 plots += [(self._x, y, '.')]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
929 legend += [y_title]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
930 if self._y is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
931 plots += [(self._x, np.asarray(self._y), 'b.')]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
932 legend += ['data']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
933 if plot_masked_data:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
934 plots += [(self._x[mask], np.asarray(self._y)[mask], 'bx')]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
935 legend += ['masked data']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
936 if isinstance(plot_residual, bool) and plot_residual:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
937 plots += [(self._x[~mask], result.residual, 'k-')]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
938 legend += ['residual']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
939 plots += [(self._x[~mask], result.best_fit, 'k-')]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
940 legend += ['best fit']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
941 if not skip_init and hasattr(result, 'init_fit'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
942 plots += [(self._x[~mask], result.init_fit, 'g-')]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
943 legend += ['init']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
944 components = result.eval_components(x=self._x[~mask])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
945 num_components = len(components)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
946 if 'tmp_normalization_offset_' in components:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
947 num_components -= 1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
948 if num_components > 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
949 eval_index = 0
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
950 for modelname, y in components.items():
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
951 if modelname == 'tmp_normalization_offset_':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
952 continue
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
953 if modelname == '_eval':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
954 modelname = f'eval{eval_index}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
955 if len(modelname) > 20:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
956 modelname = f'{modelname[0:16]} ...'
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
957 if isinstance(y, (int, float)):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
958 y *= np.ones(self._x[~mask].size)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
959 plots += [(self._x[~mask], y, '--')]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
960 if plot_comp_legends:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
961 if modelname[-1] == '_':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
962 legend.append(modelname[:-1])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
963 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
964 legend.append(modelname)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
965 title = kwargs.get('title')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
966 if title is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
967 kwargs.pop('title')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
968 quick_plot(tuple(plots), legend=legend, title=title, block=True, **kwargs)
49
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rv43
parents:
diff changeset
969
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
970 @staticmethod
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
971 def guess_init_peak(x, y, *args, center_guess=None, use_max_for_center=True):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
972 """ Return a guess for the initial height, center and fwhm for a peak
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
973 """
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
974 # print(f'\n\nargs = {args}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
975 # print(f'center_guess = {center_guess}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
976 # quick_plot(x, y, vlines=center_guess, block=True)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
977 center_guesses = None
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
978 x = np.asarray(x)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
979 y = np.asarray(y)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
980 if len(x) != len(y):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
981 logging.error(f'Invalid x and y lengths ({len(x)}, {len(y)}), skip initial guess')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
982 return(None, None, None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
983 if isinstance(center_guess, (int, float)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
984 if len(args):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
985 logging.warning('Ignoring additional arguments for single center_guess value')
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
986 center_guesses = [center_guess]
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
987 elif isinstance(center_guess, (tuple, list, np.ndarray)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
988 if len(center_guess) == 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
989 logging.warning('Ignoring additional arguments for single center_guess value')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
990 if not isinstance(center_guess[0], (int, float)):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
991 raise ValueError(f'Invalid parameter center_guess ({type(center_guess[0])})')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
992 center_guess = center_guess[0]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
993 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
994 if len(args) != 1:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
995 raise ValueError(f'Invalid number of arguments ({len(args)})')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
996 n = args[0]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
997 if not is_index(n, 0, len(center_guess)):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
998 raise ValueError('Invalid argument')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
999 center_guesses = center_guess
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1000 center_guess = center_guesses[n]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1001 elif center_guess is not None:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1002 raise ValueError(f'Invalid center_guess type ({type(center_guess)})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1003 # print(f'x = {x}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1004 # print(f'y = {y}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1005 # print(f'center_guess = {center_guess}')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1006
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1007 # Sort the inputs
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1008 index = np.argsort(x)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1009 x = x[index]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1010 y = y[index]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1011 miny = y.min()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1012 # print(f'miny = {miny}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1013 # print(f'x_range = {x[0]} {x[-1]} {len(x)}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1014 # print(f'y_range = {y[0]} {y[-1]} {len(y)}')
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1015 # quick_plot(x, y, vlines=center_guess, block=True)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1016
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1017 # xx = x
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1018 # yy = y
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1019 # Set range for current peak
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1020 # print(f'n = {n}')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1021 # print(f'center_guesses = {center_guesses}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1022 if center_guesses is not None:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1023 if len(center_guesses) > 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1024 index = np.argsort(center_guesses)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1025 n = list(index).index(n)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1026 # print(f'n = {n}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1027 # print(f'index = {index}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1028 center_guesses = np.asarray(center_guesses)[index]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1029 # print(f'center_guesses = {center_guesses}')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1030 if n == 0:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1031 low = 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1032 upp = index_nearest(x, (center_guesses[0]+center_guesses[1])/2)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1033 elif n == len(center_guesses)-1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1034 low = index_nearest(x, (center_guesses[n-1]+center_guesses[n])/2)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1035 upp = len(x)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1036 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1037 low = index_nearest(x, (center_guesses[n-1]+center_guesses[n])/2)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1038 upp = index_nearest(x, (center_guesses[n]+center_guesses[n+1])/2)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1039 # print(f'low = {low}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1040 # print(f'upp = {upp}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1041 x = x[low:upp]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1042 y = y[low:upp]
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1043 # quick_plot(x, y, vlines=(x[0], center_guess, x[-1]), block=True)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1044
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1045 # Estimate FHHM
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1046 maxy = y.max()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1047 # print(f'x_range = {x[0]} {x[-1]} {len(x)}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1048 # print(f'y_range = {y[0]} {y[-1]} {len(y)} {miny} {maxy}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1049 # print(f'center_guess = {center_guess}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1050 if center_guess is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1051 center_index = np.argmax(y)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1052 center = x[center_index]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1053 height = maxy-miny
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1054 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1055 if use_max_for_center:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1056 center_index = np.argmax(y)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1057 center = x[center_index]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1058 if center_index < 0.1*len(x) or center_index > 0.9*len(x):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1059 center_index = index_nearest(x, center_guess)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1060 center = center_guess
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1061 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1062 center_index = index_nearest(x, center_guess)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1063 center = center_guess
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1064 height = y[center_index]-miny
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1065 # print(f'center_index = {center_index}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1066 # print(f'center = {center}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1067 # print(f'height = {height}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1068 half_height = miny+0.5*height
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1069 # print(f'half_height = {half_height}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1070 fwhm_index1 = 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1071 for i in range(center_index, fwhm_index1, -1):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1072 if y[i] < half_height:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1073 fwhm_index1 = i
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parents:
diff changeset
1074 break
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diff changeset
1075 # print(f'fwhm_index1 = {fwhm_index1} {x[fwhm_index1]}')
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diff changeset
1076 fwhm_index2 = len(x)-1
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diff changeset
1077 for i in range(center_index, fwhm_index2):
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diff changeset
1078 if y[i] < half_height:
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diff changeset
1079 fwhm_index2 = i
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parents:
diff changeset
1080 break
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diff changeset
1081 # print(f'fwhm_index2 = {fwhm_index2} {x[fwhm_index2]}')
69
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1082 # quick_plot((x,y,'o'), vlines=(x[fwhm_index1], center, x[fwhm_index2]), block=True)
49
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diff changeset
1083 if fwhm_index1 == 0 and fwhm_index2 < len(x)-1:
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diff changeset
1084 fwhm = 2*(x[fwhm_index2]-center)
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1085 elif fwhm_index1 > 0 and fwhm_index2 == len(x)-1:
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parents:
diff changeset
1086 fwhm = 2*(center-x[fwhm_index1])
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1087 else:
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diff changeset
1088 fwhm = x[fwhm_index2]-x[fwhm_index1]
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diff changeset
1089 # print(f'fwhm_index1 = {fwhm_index1} {x[fwhm_index1]}')
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diff changeset
1090 # print(f'fwhm_index2 = {fwhm_index2} {x[fwhm_index2]}')
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diff changeset
1091 # print(f'fwhm = {fwhm}')
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diff changeset
1092
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diff changeset
1093 # Return height, center and FWHM
69
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1094 # quick_plot((x,y,'o'), (xx,yy), vlines=(x[fwhm_index1], center, x[fwhm_index2]), block=True)
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1095 return(height, center, fwhm)
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1096
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1097 def _check_linearity_model(self):
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1098 """Identify the linearity of all model parameters and check if the model is linear or not
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1099 """
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1100 if not self._try_linear_fit:
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1101 logging.info('Skip linearity check (not yet supported for callable models)')
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1102 return(False)
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1103 free_parameters = [name for name, par in self._parameters.items() if par.vary]
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1104 for component in self._model.components:
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1105 if 'tmp_normalization_offset_c' in component.param_names:
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1106 continue
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1107 if isinstance(component, ExpressionModel):
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1108 for name in free_parameters:
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1109 if diff(component.expr, name, name):
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1110 # print(f'\t\t{component.expr} is non-linear in {name}')
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1111 self._nonlinear_parameters.append(name)
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1112 if name in self._linear_parameters:
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1113 self._linear_parameters.remove(name)
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1114 else:
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1115 model_parameters = component.param_names.copy()
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1116 for basename, hint in component.param_hints.items():
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1117 name = f'{component.prefix}{basename}'
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1118 if hint.get('expr') is not None:
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1119 model_parameters.remove(name)
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1120 for name in model_parameters:
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1121 expr = self._parameters[name].expr
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1122 if expr is not None:
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1123 for nname in free_parameters:
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1124 if name in self._nonlinear_parameters:
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1125 if diff(expr, nname):
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1126 # print(f'\t\t{component} is non-linear in {nname} (through {name} = "{expr}")')
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1127 self._nonlinear_parameters.append(nname)
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1128 if nname in self._linear_parameters:
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1129 self._linear_parameters.remove(nname)
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1130 else:
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diff changeset
1131 assert(name in self._linear_parameters)
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1132 # print(f'\n\nexpr ({type(expr)}) = {expr}\nnname ({type(nname)}) = {nname}\n\n')
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1133 if diff(expr, nname, nname):
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1134 # print(f'\t\t{component} is non-linear in {nname} (through {name} = "{expr}")')
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1135 self._nonlinear_parameters.append(nname)
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1136 if nname in self._linear_parameters:
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1137 self._linear_parameters.remove(nname)
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1138 # print(f'\nfree parameters:\n\t{free_parameters}')
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1139 # print(f'linear parameters:\n\t{self._linear_parameters}')
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1140 # print(f'nonlinear parameters:\n\t{self._nonlinear_parameters}\n')
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1141 if any(True for name in self._nonlinear_parameters if self._parameters[name].vary):
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1142 return(False)
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1143 return(True)
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1144
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1145 def _fit_linear_model(self, x, y):
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1146 """Perform a linear fit by direct matrix solution with numpy
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1147 """
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1148 # Construct the matrix and the free parameter vector
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1149 # print(f'\nparameters:')
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1150 # self._parameters.pretty_print()
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1151 # print(f'\nparameter_norms:\n\t{self._parameter_norms}')
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1152 # print(f'\nlinear_parameters:\n\t{self._linear_parameters}')
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1153 # print(f'nonlinear_parameters:\n\t{self._nonlinear_parameters}')
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1154 free_parameters = [name for name, par in self._parameters.items() if par.vary]
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1155 # print(f'free parameters:\n\t{free_parameters}\n')
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1156 expr_parameters = {name:par.expr for name, par in self._parameters.items()
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diff changeset
1157 if par.expr is not None}
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diff changeset
1158 model_parameters = []
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1159 for component in self._model.components:
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1160 if 'tmp_normalization_offset_c' in component.param_names:
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diff changeset
1161 continue
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1162 model_parameters += component.param_names
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1163 for basename, hint in component.param_hints.items():
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1164 name = f'{component.prefix}{basename}'
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1165 if hint.get('expr') is not None:
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1166 expr_parameters.pop(name)
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diff changeset
1167 model_parameters.remove(name)
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1168 # print(f'expr parameters:\n{expr_parameters}')
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1169 # print(f'model parameters:\n\t{model_parameters}\n')
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1170 norm = 1.0
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1171 if self._normalized:
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1172 norm = self._norm[1]
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1173 # print(f'\n\nself._normalized = {self._normalized}\nnorm = {norm}\nself._norm = {self._norm}\n')
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1174 # Add expression parameters to asteval
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1175 ast = Interpreter()
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1176 # print(f'Adding to asteval sym table:')
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1177 for name, expr in expr_parameters.items():
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1178 # print(f'\tadding {name} {expr}')
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1179 ast.symtable[name] = expr
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1180 # Add constant parameters to asteval
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1181 # (renormalize to use correctly in evaluation of expression models)
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1182 for name, par in self._parameters.items():
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1183 if par.expr is None and not par.vary:
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1184 if self._parameter_norms[name]:
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1185 # print(f'\tadding {name} {par.value*norm}')
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1186 ast.symtable[name] = par.value*norm
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1187 else:
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1188 # print(f'\tadding {name} {par.value}')
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1189 ast.symtable[name] = par.value
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1190 A = np.zeros((len(x), len(free_parameters)), dtype='float64')
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1191 y_const = np.zeros(len(x), dtype='float64')
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1192 have_expression_model = False
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1193 for component in self._model.components:
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1194 if isinstance(component, ConstantModel):
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1195 name = component.param_names[0]
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1196 # print(f'\nConstant model: {name} {self._parameters[name]}\n')
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1197 if name in free_parameters:
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1198 # print(f'\t\t{name} is a free constant set matrix column {free_parameters.index(name)} to 1.0')
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1199 A[:,free_parameters.index(name)] = 1.0
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1200 else:
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diff changeset
1201 if self._parameter_norms[name]:
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diff changeset
1202 delta_y_const = self._parameters[name]*np.ones(len(x))
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1203 else:
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diff changeset
1204 delta_y_const = (self._parameters[name]*norm)*np.ones(len(x))
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diff changeset
1205 y_const += delta_y_const
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1206 # print(f'\ndelta_y_const ({type(delta_y_const)}):\n{delta_y_const}\n')
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1207 elif isinstance(component, ExpressionModel):
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diff changeset
1208 have_expression_model = True
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diff changeset
1209 const_expr = component.expr
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1210 # print(f'\nExpression model:\nconst_expr: {const_expr}\n')
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diff changeset
1211 for name in free_parameters:
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1212 dexpr_dname = diff(component.expr, name)
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diff changeset
1213 if dexpr_dname:
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diff changeset
1214 const_expr = f'{const_expr}-({str(dexpr_dname)})*{name}'
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diff changeset
1215 # print(f'\tconst_expr: {const_expr}')
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diff changeset
1216 if not self._parameter_norms[name]:
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diff changeset
1217 dexpr_dname = f'({dexpr_dname})/{norm}'
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diff changeset
1218 # print(f'\t{component.expr} is linear in {name}\n\t\tadd "{str(dexpr_dname)}" to matrix as column {free_parameters.index(name)}')
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diff changeset
1219 fx = [(lambda _: ast.eval(str(dexpr_dname)))(ast(f'x={v}')) for v in x]
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diff changeset
1220 # print(f'\tfx:\n{fx}')
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diff changeset
1221 if len(ast.error):
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diff changeset
1222 raise ValueError(f'Unable to evaluate {dexpr_dname}')
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diff changeset
1223 A[:,free_parameters.index(name)] += fx
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diff changeset
1224 # if self._parameter_norms[name]:
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diff changeset
1225 # print(f'\t\t{component.expr} is linear in {name} add "{str(dexpr_dname)}" to matrix as column {free_parameters.index(name)}')
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diff changeset
1226 # A[:,free_parameters.index(name)] += fx
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diff changeset
1227 # else:
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diff changeset
1228 # print(f'\t\t{component.expr} is linear in {name} add "({str(dexpr_dname)})/{norm}" to matrix as column {free_parameters.index(name)}')
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diff changeset
1229 # A[:,free_parameters.index(name)] += np.asarray(fx)/norm
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diff changeset
1230 # FIX: find another solution if expr not supported by simplify
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diff changeset
1231 const_expr = str(simplify(f'({const_expr})/{norm}'))
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diff changeset
1232 # print(f'\nconst_expr: {const_expr}')
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diff changeset
1233 delta_y_const = [(lambda _: ast.eval(const_expr))(ast(f'x = {v}')) for v in x]
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diff changeset
1234 y_const += delta_y_const
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diff changeset
1235 # print(f'\ndelta_y_const ({type(delta_y_const)}):\n{delta_y_const}\n')
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diff changeset
1236 if len(ast.error):
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diff changeset
1237 raise ValueError(f'Unable to evaluate {const_expr}')
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diff changeset
1238 else:
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diff changeset
1239 free_model_parameters = [name for name in component.param_names
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diff changeset
1240 if name in free_parameters or name in expr_parameters]
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diff changeset
1241 # print(f'\nBuild-in model ({component}):\nfree_model_parameters: {free_model_parameters}\n')
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1242 if not len(free_model_parameters):
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diff changeset
1243 y_const += component.eval(params=self._parameters, x=x)
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diff changeset
1244 elif isinstance(component, LinearModel):
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diff changeset
1245 if f'{component.prefix}slope' in free_model_parameters:
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diff changeset
1246 A[:,free_parameters.index(f'{component.prefix}slope')] = x
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diff changeset
1247 else:
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diff changeset
1248 y_const += self._parameters[f'{component.prefix}slope'].value*x
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diff changeset
1249 if f'{component.prefix}intercept' in free_model_parameters:
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diff changeset
1250 A[:,free_parameters.index(f'{component.prefix}intercept')] = 1.0
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diff changeset
1251 else:
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diff changeset
1252 y_const += self._parameters[f'{component.prefix}intercept'].value* \
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diff changeset
1253 np.ones(len(x))
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1254 elif isinstance(component, QuadraticModel):
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diff changeset
1255 if f'{component.prefix}a' in free_model_parameters:
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diff changeset
1256 A[:,free_parameters.index(f'{component.prefix}a')] = x**2
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diff changeset
1257 else:
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diff changeset
1258 y_const += self._parameters[f'{component.prefix}a'].value*x**2
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diff changeset
1259 if f'{component.prefix}b' in free_model_parameters:
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diff changeset
1260 A[:,free_parameters.index(f'{component.prefix}b')] = x
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1261 else:
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diff changeset
1262 y_const += self._parameters[f'{component.prefix}b'].value*x
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diff changeset
1263 if f'{component.prefix}c' in free_model_parameters:
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diff changeset
1264 A[:,free_parameters.index(f'{component.prefix}c')] = 1.0
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1265 else:
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diff changeset
1266 y_const += self._parameters[f'{component.prefix}c'].value*np.ones(len(x))
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1267 else:
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diff changeset
1268 # At this point each build-in model must be strictly proportional to each linear
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diff changeset
1269 # model parameter. Without this assumption, the model equation is needed
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diff changeset
1270 # For the current build-in lmfit models, this can only ever be the amplitude
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diff changeset
1271 assert(len(free_model_parameters) == 1)
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diff changeset
1272 name = f'{component.prefix}amplitude'
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1273 assert(free_model_parameters[0] == name)
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diff changeset
1274 assert(self._parameter_norms[name])
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1275 expr = self._parameters[name].expr
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1276 if expr is None:
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1277 # print(f'\t{component} is linear in {name} add to matrix as column {free_parameters.index(name)}')
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1278 parameters = deepcopy(self._parameters)
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1279 parameters[name].set(value=1.0)
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1280 index = free_parameters.index(name)
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1281 A[:,free_parameters.index(name)] += component.eval(params=parameters, x=x)
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1282 else:
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1283 const_expr = expr
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1284 # print(f'\tconst_expr: {const_expr}')
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1285 parameters = deepcopy(self._parameters)
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1286 parameters[name].set(value=1.0)
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1287 dcomp_dname = component.eval(params=parameters, x=x)
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1288 # print(f'\tdcomp_dname ({type(dcomp_dname)}):\n{dcomp_dname}')
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diff changeset
1289 for nname in free_parameters:
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1290 dexpr_dnname = diff(expr, nname)
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1291 if dexpr_dnname:
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1292 assert(self._parameter_norms[name])
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1293 # print(f'\t\td({expr})/d{nname} = {dexpr_dnname}')
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1294 # print(f'\t\t{component} is linear in {nname} (through {name} = "{expr}", add to matrix as column {free_parameters.index(nname)})')
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diff changeset
1295 fx = np.asarray(dexpr_dnname*dcomp_dname, dtype='float64')
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1296 # print(f'\t\tfx ({type(fx)}): {fx}')
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1297 # print(f'free_parameters.index({nname}): {free_parameters.index(nname)}')
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diff changeset
1298 if self._parameter_norms[nname]:
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1299 A[:,free_parameters.index(nname)] += fx
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1300 else:
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1301 A[:,free_parameters.index(nname)] += fx/norm
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1302 const_expr = f'{const_expr}-({dexpr_dnname})*{nname}'
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1303 # print(f'\t\tconst_expr: {const_expr}')
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1304 const_expr = str(simplify(f'({const_expr})/{norm}'))
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1305 # print(f'\tconst_expr: {const_expr}')
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diff changeset
1306 fx = [(lambda _: ast.eval(const_expr))(ast(f'x = {v}')) for v in x]
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1307 # print(f'\tfx: {fx}')
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1308 delta_y_const = np.multiply(fx, dcomp_dname)
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1309 y_const += delta_y_const
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1310 # print(f'\ndelta_y_const ({type(delta_y_const)}):\n{delta_y_const}\n')
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1311 # print(A)
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1312 # print(y_const)
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1313 solution, residual, rank, s = np.linalg.lstsq(A, y-y_const, rcond=None)
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1314 # print(f'\nsolution ({type(solution)} {solution.shape}):\n\t{solution}')
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1315 # print(f'\nresidual ({type(residual)} {residual.shape}):\n\t{residual}')
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1316 # print(f'\nrank ({type(rank)} {rank.shape}):\n\t{rank}')
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1317 # print(f'\ns ({type(s)} {s.shape}):\n\t{s}\n')
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1318
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1319 # Assemble result (compensate for normalization in expression models)
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1320 for name, value in zip(free_parameters, solution):
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1321 self._parameters[name].set(value=value)
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1322 if self._normalized and (have_expression_model or len(expr_parameters)):
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1323 for name, norm in self._parameter_norms.items():
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1324 par = self._parameters[name]
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1325 if par.expr is None and norm:
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1326 self._parameters[name].set(value=par.value*self._norm[1])
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1327 # self._parameters.pretty_print()
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1328 # print(f'\nself._parameter_norms:\n\t{self._parameter_norms}')
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1329 self._result = ModelResult(self._model, deepcopy(self._parameters))
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1330 self._result.best_fit = self._model.eval(params=self._parameters, x=x)
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diff changeset
1331 if self._normalized and (have_expression_model or len(expr_parameters)):
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1332 if 'tmp_normalization_offset_c' in self._parameters:
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1333 offset = self._parameters['tmp_normalization_offset_c']
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1334 else:
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1335 offset = 0.0
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1336 self._result.best_fit = (self._result.best_fit-offset-self._norm[0])/self._norm[1]
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diff changeset
1337 if self._normalized:
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1338 for name, norm in self._parameter_norms.items():
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1339 par = self._parameters[name]
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1340 if par.expr is None and norm:
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1341 value = par.value/self._norm[1]
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1342 self._parameters[name].set(value=value)
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1343 self._result.params[name].set(value=value)
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1344 # self._parameters.pretty_print()
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1345 self._result.residual = self._result.best_fit-y
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1346 self._result.components = self._model.components
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1347 self._result.init_params = None
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1348 # quick_plot((x, y, '.'), (x, y_const, 'g'), (x, self._result.best_fit, 'k'), (x, self._result.residual, 'r'), block=True)
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1349
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1350 def _normalize(self):
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1351 """Normalize the data and initial parameters
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diff changeset
1352 """
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diff changeset
1353 if self._normalized:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1354 return
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diff changeset
1355 if self._norm is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1356 if self._y is not None and self._y_norm is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1357 self._y_norm = np.asarray(self._y)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1358 else:
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diff changeset
1359 if self._y is not None and self._y_norm is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1360 self._y_norm = (np.asarray(self._y)-self._norm[0])/self._norm[1]
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diff changeset
1361 self._y_range = 1.0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1362 for name, norm in self._parameter_norms.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1363 par = self._parameters[name]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1364 if par.expr is None and norm:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1365 value = par.value/self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1366 _min = par.min
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1367 _max = par.max
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diff changeset
1368 if not np.isinf(_min) and abs(_min) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1369 _min /= self._norm[1]
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diff changeset
1370 if not np.isinf(_max) and abs(_max) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1371 _max /= self._norm[1]
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diff changeset
1372 par.set(value=value, min=_min, max=_max)
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diff changeset
1373 self._normalized = True
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diff changeset
1374
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diff changeset
1375 def _renormalize(self):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1376 """Renormalize the data and results
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diff changeset
1377 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1378 if self._norm is None or not self._normalized:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1379 return
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diff changeset
1380 self._normalized = False
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parents: 65
diff changeset
1381 for name, norm in self._parameter_norms.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1382 par = self._parameters[name]
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diff changeset
1383 if par.expr is None and norm:
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diff changeset
1384 value = par.value*self._norm[1]
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diff changeset
1385 _min = par.min
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diff changeset
1386 _max = par.max
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diff changeset
1387 if not np.isinf(_min) and abs(_min) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1388 _min *= self._norm[1]
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diff changeset
1389 if not np.isinf(_max) and abs(_max) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1390 _max *= self._norm[1]
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diff changeset
1391 par.set(value=value, min=_min, max=_max)
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diff changeset
1392 if self._result is None:
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diff changeset
1393 return
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diff changeset
1394 self._result.best_fit = self._result.best_fit*self._norm[1]+self._norm[0]
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diff changeset
1395 for name, par in self._result.params.items():
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diff changeset
1396 if self._parameter_norms.get(name, False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1397 if par.stderr is not None:
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diff changeset
1398 par.stderr *= self._norm[1]
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diff changeset
1399 if par.expr is None:
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diff changeset
1400 _min = par.min
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parents: 65
diff changeset
1401 _max = par.max
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diff changeset
1402 value = par.value*self._norm[1]
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diff changeset
1403 if par.init_value is not None:
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diff changeset
1404 par.init_value *= self._norm[1]
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parents: 65
diff changeset
1405 if not np.isinf(_min) and abs(_min) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1406 _min *= self._norm[1]
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parents: 65
diff changeset
1407 if not np.isinf(_max) and abs(_max) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1408 _max *= self._norm[1]
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diff changeset
1409 par.set(value=value, min=_min, max=_max)
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diff changeset
1410 if hasattr(self._result, 'init_fit'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1411 self._result.init_fit = self._result.init_fit*self._norm[1]+self._norm[0]
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diff changeset
1412 if hasattr(self._result, 'init_values'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1413 init_values = {}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1414 for name, value in self._result.init_values.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1415 if name not in self._parameter_norms or self._parameters[name].expr is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1416 init_values[name] = value
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diff changeset
1417 elif self._parameter_norms[name]:
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diff changeset
1418 init_values[name] = value*self._norm[1]
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diff changeset
1419 self._result.init_values = init_values
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diff changeset
1420 for name, par in self._result.init_params.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1421 if par.expr is None and self._parameter_norms.get(name, False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1422 value = par.value
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diff changeset
1423 _min = par.min
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1424 _max = par.max
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diff changeset
1425 value *= self._norm[1]
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diff changeset
1426 if not np.isinf(_min) and abs(_min) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1427 _min *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1428 if not np.isinf(_max) and abs(_max) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1429 _max *= self._norm[1]
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diff changeset
1430 par.set(value=value, min=_min, max=_max)
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diff changeset
1431 par.init_value = par.value
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diff changeset
1432 # Don't renormalize chisqr, it has no useful meaning in physical units
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diff changeset
1433 #self._result.chisqr *= self._norm[1]*self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1434 if self._result.covar is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1435 for i, name in enumerate(self._result.var_names):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1436 if self._parameter_norms.get(name, False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1437 for j in range(len(self._result.var_names)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1438 if self._result.covar[i,j] is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1439 self._result.covar[i,j] *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1440 if self._result.covar[j,i] is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1441 self._result.covar[j,i] *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1442 # Don't renormalize redchi, it has no useful meaning in physical units
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1443 #self._result.redchi *= self._norm[1]*self._norm[1]
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diff changeset
1444 if self._result.residual is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1445 self._result.residual *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1446
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1447 def _reset_par_at_boundary(self, par, value):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1448 assert(par.vary)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1449 name = par.name
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1450 _min = self._parameter_bounds[name]['min']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1451 _max = self._parameter_bounds[name]['max']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1452 if np.isinf(_min):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1453 if not np.isinf(_max):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1454 if self._parameter_norms.get(name, False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1455 upp = _max-0.1*self._y_range
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1456 elif _max == 0.0:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1457 upp = _max-0.1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1458 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1459 upp = _max-0.1*abs(_max)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1460 if value >= upp:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1461 return(upp)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1462 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1463 if np.isinf(_max):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1464 if self._parameter_norms.get(name, False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1465 low = _min+0.1*self._y_range
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1466 elif _min == 0.0:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1467 low = _min+0.1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1468 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1469 low = _min+0.1*abs(_min)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1470 if value <= low:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1471 return(low)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1472 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1473 low = 0.9*_min+0.1*_max
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1474 upp = 0.1*_min+0.9*_max
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1475 if value <= low:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1476 return(low)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1477 elif value >= upp:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1478 return(upp)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1479 return(value)
49
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rv43
parents:
diff changeset
1480
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1481
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1482 class FitMultipeak(Fit):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1483 """Fit data with multiple peaks
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1484 """
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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diff changeset
1485 def __init__(self, y, x=None, normalize=True):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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diff changeset
1486 super().__init__(y, x=x, normalize=normalize)
49
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rv43
parents:
diff changeset
1487 self._fwhm_max = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1488 self._sigma_max = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1489
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1490 @classmethod
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1491 def fit_multipeak(cls, y, centers, x=None, normalize=True, peak_models='gaussian',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1492 center_exprs=None, fit_type=None, background_order=None, background_exp=False,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1493 fwhm_max=None, plot_components=False):
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1494 """Make sure that centers and fwhm_max are in the correct units and consistent with expr
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1495 for a uniform fit (fit_type == 'uniform')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1496 """
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1497 fit = cls(y, x=x, normalize=normalize)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1498 success = fit.fit(centers, fit_type=fit_type, peak_models=peak_models, fwhm_max=fwhm_max,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1499 center_exprs=center_exprs, background_order=background_order,
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1500 background_exp=background_exp, plot_components=plot_components)
49
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rv43
parents:
diff changeset
1501 if success:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1502 return(fit.best_fit, fit.residual, fit.best_values, fit.best_errors, fit.redchi, \
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1503 fit.success)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1504 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1505 return(np.array([]), np.array([]), {}, {}, float_max, False)
49
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rv43
parents:
diff changeset
1506
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1507 def fit(self, centers, fit_type=None, peak_models=None, center_exprs=None, fwhm_max=None,
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1508 background_order=None, background_exp=False, plot_components=False,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1509 param_constraint=False):
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1510 self._fwhm_max = fwhm_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1511 # Create the multipeak model
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1512 self._create_model(centers, fit_type, peak_models, center_exprs, background_order,
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1513 background_exp, param_constraint)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1514
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1515 # RV: Obsolete Normalize the data and results
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1516 # print('\nBefore fit before normalization in FitMultipeak:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1517 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1518 # self._normalize()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1519 # print('\nBefore fit after normalization in FitMultipeak:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1520 # self._parameters.pretty_print()
49
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rv43
parents:
diff changeset
1521
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1522 # Perform the fit
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1523 try:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1524 if param_constraint:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1525 super().fit(fit_kws={'xtol': 1.e-5, 'ftol': 1.e-5, 'gtol': 1.e-5})
49
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rv43
parents:
diff changeset
1526 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1527 super().fit()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1528 except:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1529 return(False)
49
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rv43
parents:
diff changeset
1530
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1531 # Check for valid fit parameter results
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1532 fit_failure = self._check_validity()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1533 success = True
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1534 if fit_failure:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1535 if param_constraint:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1536 logging.warning(' -> Should not happen with param_constraint set, fail the fit')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1537 success = False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1538 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1539 logging.info(' -> Retry fitting with constraints')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1540 self.fit(centers, fit_type, peak_models, center_exprs, fwhm_max=fwhm_max,
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1541 background_order=background_order, background_exp=background_exp,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1542 plot_components=plot_components, param_constraint=True)
49
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rv43
parents:
diff changeset
1543 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1544 # RV: Obsolete Renormalize the data and results
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1545 # print('\nAfter fit before renormalization in FitMultipeak:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1546 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1547 # self.print_fit_report()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1548 # self._renormalize()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1549 # print('\nAfter fit after renormalization in FitMultipeak:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1550 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1551 # self.print_fit_report()
49
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rv43
parents:
diff changeset
1552
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1553 # Print report and plot components if requested
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1554 if plot_components:
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1555 self.print_fit_report()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1556 self.plot()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1557
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1558 return(success)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1559
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1560 def _create_model(self, centers, fit_type=None, peak_models=None, center_exprs=None,
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1561 background_order=None, background_exp=False, param_constraint=False):
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1562 """Create the multipeak model
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1563 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1564 if isinstance(centers, (int, float)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1565 centers = [centers]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1566 num_peaks = len(centers)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1567 if peak_models is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1568 peak_models = num_peaks*['gaussian']
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1569 elif isinstance(peak_models, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1570 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
1571 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
1572 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
1573 f'{num_peaks})')
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parents:
diff changeset
1574 if num_peaks == 1:
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parents:
diff changeset
1575 if fit_type is not None:
69
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diff changeset
1576 logging.debug('Ignoring fit_type input for fitting one peak')
49
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parents:
diff changeset
1577 fit_type = None
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parents:
diff changeset
1578 if center_exprs is not None:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1579 logging.debug('Ignoring center_exprs input for fitting one peak')
49
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parents:
diff changeset
1580 center_exprs = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1581 else:
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parents:
diff changeset
1582 if fit_type == 'uniform':
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parents:
diff changeset
1583 if center_exprs is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1584 center_exprs = [f'scale_factor*{cen}' for cen in centers]
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rv43
parents:
diff changeset
1585 if len(center_exprs) != num_peaks:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1586 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
1587 f'({len(center_exprs)} vs {num_peaks})')
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rv43
parents:
diff changeset
1588 elif fit_type == 'unconstrained' or fit_type is None:
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rv43
parents:
diff changeset
1589 if center_exprs is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1590 logging.warning('Ignoring center_exprs input for unconstrained fit')
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rv43
parents:
diff changeset
1591 center_exprs = None
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parents:
diff changeset
1592 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1593 raise ValueError(f'Invalid fit_type in fit_multigaussian {fit_type}')
49
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rv43
parents:
diff changeset
1594 self._sigma_max = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1595 if param_constraint:
69
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diff changeset
1596 min_value = float_min
49
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rv43
parents:
diff changeset
1597 if self._fwhm_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1598 self._sigma_max = np.zeros(num_peaks)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1599 else:
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rv43
parents:
diff changeset
1600 min_value = None
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rv43
parents:
diff changeset
1601
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1602 # Reset the fit
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parents:
diff changeset
1603 self._model = None
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rv43
parents:
diff changeset
1604 self._parameters = Parameters()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1605 self._result = None
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rv43
parents:
diff changeset
1606
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1607 # Add background model
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1608 if background_order is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1609 if background_order == 0:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1610 self.add_model('constant', prefix='background', parameters=
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1611 {'name': 'c', 'value': float_min, 'min': min_value})
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1612 elif background_order == 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1613 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
1614 elif background_order == 2:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1615 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"
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parents:
diff changeset
1616 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1617 raise ValueError(f'Invalid parameter background_order ({background_order})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1618 if background_exp:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1619 self.add_model('exponential', prefix='background', parameters=(
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1620 {'name': 'amplitude', 'value': float_min, 'min': min_value},
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1621 {'name': 'decay', 'value': float_min, 'min': min_value}))
49
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rv43
parents:
diff changeset
1622
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1623 # Add peaks and guess initial fit parameters
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1624 ast = Interpreter()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1625 if num_peaks == 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1626 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
1627 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
1628 fwhm_init = self._fwhm_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1629 ast(f'fwhm = {fwhm_init}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1630 ast(f'height = {height_init}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1631 sig_init = ast(fwhm_factor[peak_models[0]])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1632 amp_init = ast(height_factor[peak_models[0]])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1633 sig_max = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1634 if self._sigma_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1635 ast(f'fwhm = {self._fwhm_max}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1636 sig_max = ast(fwhm_factor[peak_models[0]])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1637 self._sigma_max[0] = sig_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1638 self.add_model(peak_models[0], parameters=(
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1639 {'name': 'amplitude', 'value': amp_init, 'min': min_value},
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1640 {'name': 'center', 'value': cen_init, 'min': min_value},
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1641 {'name': 'sigma', 'value': sig_init, 'min': min_value, 'max': sig_max}))
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1642 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1643 if fit_type == 'uniform':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1644 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
1645 for i in range(num_peaks):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1646 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
1647 center_guess=centers)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1648 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
1649 fwhm_init = self._fwhm_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1650 ast(f'fwhm = {fwhm_init}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1651 ast(f'height = {height_init}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1652 sig_init = ast(fwhm_factor[peak_models[i]])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1653 amp_init = ast(height_factor[peak_models[i]])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1654 sig_max = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1655 if self._sigma_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1656 ast(f'fwhm = {self._fwhm_max}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1657 sig_max = ast(fwhm_factor[peak_models[i]])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1658 self._sigma_max[i] = sig_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1659 if fit_type == 'uniform':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1660 self.add_model(peak_models[i], prefix=f'peak{i+1}_', parameters=(
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1661 {'name': 'amplitude', 'value': amp_init, 'min': min_value},
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1662 {'name': 'center', 'expr': center_exprs[i]},
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1663 {'name': 'sigma', 'value': sig_init, 'min': min_value,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1664 'max': sig_max}))
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1665 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1666 self.add_model('gaussian', prefix=f'peak{i+1}_', parameters=(
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1667 {'name': 'amplitude', 'value': amp_init, 'min': min_value},
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1668 {'name': 'center', 'value': cen_init, 'min': min_value},
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1669 {'name': 'sigma', 'value': sig_init, 'min': min_value,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1670 'max': sig_max}))
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1671
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1672 def _check_validity(self):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1673 """Check for valid fit parameter results
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1674 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1675 fit_failure = False
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1676 index = compile(r'\d+')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1677 for name, par in self.best_parameters.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1678 if 'background' in name:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1679 # if ((name == 'backgroundc' and par['value'] <= 0.0) or
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1680 # (name.endswith('amplitude') and par['value'] <= 0.0) or
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1681 if ((name.endswith('amplitude') and par['value'] <= 0.0) or
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1682 (name.endswith('decay') and par['value'] <= 0.0)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1683 logging.info(f'Invalid fit result for {name} ({par["value"]})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1684 fit_failure = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1685 elif (((name.endswith('amplitude') or name.endswith('height')) and
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1686 par['value'] <= 0.0) or
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1687 ((name.endswith('sigma') or name.endswith('fwhm')) and par['value'] <= 0.0) or
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1688 (name.endswith('center') and par['value'] <= 0.0) or
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1689 (name == 'scale_factor' and par['value'] <= 0.0)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1690 logging.info(f'Invalid fit result for {name} ({par["value"]})')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1691 fit_failure = True
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1692 if name.endswith('sigma') and self._sigma_max is not None:
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1693 if name == 'sigma':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1694 sigma_max = self._sigma_max[0]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1695 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1696 sigma_max = self._sigma_max[int(index.search(name).group())-1]
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1697 if par['value'] > sigma_max:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1698 logging.info(f'Invalid fit result for {name} ({par["value"]})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1699 fit_failure = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1700 elif par['value'] == sigma_max:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1701 logging.warning(f'Edge result on for {name} ({par["value"]})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1702 if name.endswith('fwhm') and self._fwhm_max is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1703 if par['value'] > self._fwhm_max:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1704 logging.info(f'Invalid fit result for {name} ({par["value"]})')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1705 fit_failure = True
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1706 elif par['value'] == self._fwhm_max:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1707 logging.warning(f'Edge result on for {name} ({par["value"]})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1708 return(fit_failure)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1709
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1710
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1711 class FitMap(Fit):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1712 """Fit a map of data
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1713 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1714 def __init__(self, ymap, x=None, models=None, normalize=True, transpose=None, **kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1715 super().__init__(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1716 self._best_errors = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1717 self._best_fit = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1718 self._best_parameters = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1719 self._best_values = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1720 self._inv_transpose = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1721 self._max_nfev = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1722 self._memfolder = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1723 self._new_parameters = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1724 self._out_of_bounds = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1725 self._plot = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1726 self._print_report = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1727 self._redchi = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1728 self._redchi_cutoff = 0.1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1729 self._skip_init = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1730 self._success = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1731 self._transpose = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1732 self._try_no_bounds = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
1733
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1734 # At this point the fastest index should always be the signal dimension so that the slowest
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1735 # ndim-1 dimensions are the map dimensions
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parents: 65
diff changeset
1736 if isinstance(ymap, (tuple, list, np.ndarray)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1737 self._x = np.asarray(x)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1738 elif have_xarray and isinstance(ymap, xr.DataArray):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1739 if x is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1740 logging.warning('Ignoring superfluous input x ({x}) in Fit.__init__')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1741 self._x = np.asarray(ymap[ymap.dims[-1]])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1742 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1743 illegal_value(ymap, 'ymap', 'FitMap:__init__', raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1744 self._ymap = ymap
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1745
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1746 # Verify the input parameters
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diff changeset
1747 if self._x.ndim != 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1748 raise ValueError(f'Invalid dimension for input x {self._x.ndim}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1749 if self._ymap.ndim < 2:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
1750 raise ValueError('Invalid number of dimension of the input dataset '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1751 f'{self._ymap.ndim}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1752 if self._x.size != self._ymap.shape[-1]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1753 raise ValueError(f'Inconsistent x and y dimensions ({self._x.size} vs '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1754 f'{self._ymap.shape[-1]})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1755 if not isinstance(normalize, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1756 logging.warning(f'Invalid value for normalize ({normalize}) in Fit.__init__: '+
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diff changeset
1757 'setting normalize to True')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1758 normalize = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1759 if isinstance(transpose, bool) and not transpose:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1760 transpose = None
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diff changeset
1761 if transpose is not None and self._ymap.ndim < 3:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1762 logging.warning(f'Transpose meaningless for {self._ymap.ndim-1}D data maps: ignoring '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1763 'transpose')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1764 if transpose is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1765 if self._ymap.ndim == 3 and isinstance(transpose, bool) and transpose:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1766 self._transpose = (1, 0)
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diff changeset
1767 elif not isinstance(transpose, (tuple, list)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1768 logging.warning(f'Invalid data type for transpose ({transpose}, '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1769 f'{type(transpose)}) in Fit.__init__: setting transpose to False')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1770 elif len(transpose) != self._ymap.ndim-1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1771 logging.warning(f'Invalid dimension for transpose ({transpose}, must be equal to '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1772 f'{self._ymap.ndim-1}) in Fit.__init__: setting transpose to False')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1773 elif any(i not in transpose for i in range(len(transpose))):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1774 logging.warning(f'Invalid index in transpose ({transpose}) '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1775 f'in Fit.__init__: setting transpose to False')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1776 elif not all(i==transpose[i] for i in range(self._ymap.ndim-1)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1777 self._transpose = transpose
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1778 if self._transpose is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1779 self._inv_transpose = tuple(self._transpose.index(i)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1780 for i in range(len(self._transpose)))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1781
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diff changeset
1782 # Flatten the map (transpose if requested)
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diff changeset
1783 # Store the flattened map in self._ymap_norm, whether normalized or not
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1784 if self._transpose is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1785 self._ymap_norm = np.transpose(np.asarray(self._ymap), list(self._transpose)+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1786 [len(self._transpose)])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1787 else:
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diff changeset
1788 self._ymap_norm = np.asarray(self._ymap)
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diff changeset
1789 self._map_dim = int(self._ymap_norm.size/self._x.size)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1790 self._map_shape = self._ymap_norm.shape[:-1]
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diff changeset
1791 self._ymap_norm = np.reshape(self._ymap_norm, (self._map_dim, self._x.size))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1792
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1793 # Check if a mask is provided
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1794 if 'mask' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1795 self._mask = kwargs.pop('mask')
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diff changeset
1796 if self._mask is None:
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diff changeset
1797 ymap_min = float(self._ymap_norm.min())
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1798 ymap_max = float(self._ymap_norm.max())
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diff changeset
1799 else:
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diff changeset
1800 self._mask = np.asarray(self._mask).astype(bool)
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diff changeset
1801 if self._x.size != self._mask.size:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1802 raise ValueError(f'Inconsistent mask dimension ({self._x.size} vs '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1803 f'{self._mask.size})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1804 ymap_masked = np.asarray(self._ymap_norm)[:,~self._mask]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1805 ymap_min = float(ymap_masked.min())
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1806 ymap_max = float(ymap_masked.max())
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1807
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1808 # Normalize the data
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diff changeset
1809 self._y_range = ymap_max-ymap_min
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1810 if normalize and self._y_range > 0.0:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1811 self._norm = (ymap_min, self._y_range)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1812 self._ymap_norm = (self._ymap_norm-self._norm[0])/self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1813 else:
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diff changeset
1814 self._redchi_cutoff *= self._y_range**2
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1815 if models is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1816 if callable(models) or isinstance(models, str):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1817 kwargs = self.add_model(models, **kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1818 elif isinstance(models, (tuple, list)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1819 for model in models:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1820 kwargs = self.add_model(model, **kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1821 self.fit(**kwargs)
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diff changeset
1822
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1823 @classmethod
71
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diff changeset
1824 def fit_map(cls, ymap, models, x=None, normalize=True, **kwargs):
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diff changeset
1825 return(cls(ymap, x=x, models=models, normalize=normalize, **kwargs))
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1826
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1827 @property
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1828 def best_errors(self):
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diff changeset
1829 return(self._best_errors)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1830
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diff changeset
1831 @property
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1832 def best_fit(self):
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1833 return(self._best_fit)
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diff changeset
1834
69
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diff changeset
1835 @property
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1836 def best_results(self):
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1837 """Convert the input data array to a data set and add the fit results.
49
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diff changeset
1838 """
69
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1839 if self.best_values is None or self.best_errors is None or self.best_fit is None:
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diff changeset
1840 return(None)
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1841 if not have_xarray:
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1842 logging.warning('Unable to load xarray module')
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1843 return(None)
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1844 best_values = self.best_values
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1845 best_errors = self.best_errors
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1846 if isinstance(self._ymap, xr.DataArray):
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1847 best_results = self._ymap.to_dataset()
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1848 dims = self._ymap.dims
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1849 fit_name = f'{self._ymap.name}_fit'
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1850 else:
69
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1851 coords = {f'dim{n}_index':([f'dim{n}_index'], range(self._ymap.shape[n]))
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1852 for n in range(self._ymap.ndim-1)}
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1853 coords['x'] = (['x'], self._x)
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diff changeset
1854 dims = list(coords.keys())
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1855 best_results = xr.Dataset(coords=coords)
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diff changeset
1856 best_results['y'] = (dims, self._ymap)
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diff changeset
1857 fit_name = 'y_fit'
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diff changeset
1858 best_results[fit_name] = (dims, self.best_fit)
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1859 if self._mask is not None:
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diff changeset
1860 best_results['mask'] = self._mask
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diff changeset
1861 for n in range(best_values.shape[0]):
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diff changeset
1862 best_results[f'{self._best_parameters[n]}_values'] = (dims[:-1], best_values[n])
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diff changeset
1863 best_results[f'{self._best_parameters[n]}_errors'] = (dims[:-1], best_errors[n])
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diff changeset
1864 best_results.attrs['components'] = self.components
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diff changeset
1865 return(best_results)
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diff changeset
1866
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diff changeset
1867 @property
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diff changeset
1868 def best_values(self):
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diff changeset
1869 return(self._best_values)
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diff changeset
1870
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diff changeset
1871 @property
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diff changeset
1872 def chisqr(self):
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diff changeset
1873 logging.warning('property chisqr not defined for fit.FitMap')
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diff changeset
1874 return(None)
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diff changeset
1875
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diff changeset
1876 @property
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diff changeset
1877 def components(self):
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diff changeset
1878 components = {}
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diff changeset
1879 if self._result is None:
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diff changeset
1880 logging.warning('Unable to collect components in FitMap.components')
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diff changeset
1881 return(components)
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diff changeset
1882 for component in self._result.components:
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diff changeset
1883 if 'tmp_normalization_offset_c' in component.param_names:
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diff changeset
1884 continue
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diff changeset
1885 parameters = {}
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diff changeset
1886 for name in component.param_names:
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diff changeset
1887 if self._parameters[name].vary:
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diff changeset
1888 parameters[name] = {'free': True}
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diff changeset
1889 elif self._parameters[name].expr is not None:
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diff changeset
1890 parameters[name] = {'free': False, 'expr': self._parameters[name].expr}
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diff changeset
1891 else:
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diff changeset
1892 parameters[name] = {'free': False, 'value': self.init_parameters[name]['value']}
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diff changeset
1893 expr = None
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diff changeset
1894 if isinstance(component, ExpressionModel):
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diff changeset
1895 name = component._name
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diff changeset
1896 if name[-1] == '_':
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diff changeset
1897 name = name[:-1]
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diff changeset
1898 expr = component.expr
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diff changeset
1899 else:
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diff changeset
1900 prefix = component.prefix
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diff changeset
1901 if len(prefix):
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diff changeset
1902 if prefix[-1] == '_':
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diff changeset
1903 prefix = prefix[:-1]
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diff changeset
1904 name = f'{prefix} ({component._name})'
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diff changeset
1905 else:
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diff changeset
1906 name = f'{component._name}'
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diff changeset
1907 if expr is None:
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diff changeset
1908 components[name] = {'parameters': parameters}
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1909 else:
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diff changeset
1910 components[name] = {'expr': expr, 'parameters': parameters}
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diff changeset
1911 return(components)
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diff changeset
1912
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diff changeset
1913 @property
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1914 def covar(self):
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diff changeset
1915 logging.warning('property covar not defined for fit.FitMap')
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diff changeset
1916 return(None)
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diff changeset
1917
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diff changeset
1918 @property
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diff changeset
1919 def max_nfev(self):
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diff changeset
1920 return(self._max_nfev)
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diff changeset
1921
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diff changeset
1922 @property
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diff changeset
1923 def num_func_eval(self):
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diff changeset
1924 logging.warning('property num_func_eval not defined for fit.FitMap')
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diff changeset
1925 return(None)
49
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parents:
diff changeset
1926
69
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diff changeset
1927 @property
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diff changeset
1928 def out_of_bounds(self):
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diff changeset
1929 return(self._out_of_bounds)
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diff changeset
1930
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1931 @property
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1932 def redchi(self):
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1933 return(self._redchi)
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1934
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1935 @property
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1936 def residual(self):
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1937 if self.best_fit is None:
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1938 return(None)
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1939 if self._mask is None:
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1940 return(np.asarray(self._ymap)-self.best_fit)
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1941 else:
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1942 ymap_flat = np.reshape(np.asarray(self._ymap), (self._map_dim, self._x.size))
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1943 ymap_flat_masked = ymap_flat[:,~self._mask]
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1944 ymap_masked = np.reshape(ymap_flat_masked,
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1945 list(self._map_shape)+[ymap_flat_masked.shape[-1]])
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1946 return(ymap_masked-self.best_fit)
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1947
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1948 @property
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1949 def success(self):
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1950 return(self._success)
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1951
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1952 @property
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1953 def var_names(self):
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1954 logging.warning('property var_names not defined for fit.FitMap')
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1955 return(None)
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1956
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1957 @property
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1958 def y(self):
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1959 logging.warning('property y not defined for fit.FitMap')
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1960 return(None)
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1961
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1962 @property
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1963 def ymap(self):
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1964 return(self._ymap)
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1965
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1966 def best_parameters(self, dims=None):
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1967 if dims is None:
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1968 return(self._best_parameters)
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1969 if not isinstance(dims, (list, tuple)) or len(dims) != len(self._map_shape):
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1970 illegal_value(dims, 'dims', 'FitMap.best_parameters', raise_error=True)
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1971 if self.best_values is None or self.best_errors is None:
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1972 logging.warning(f'Unable to obtain best parameter values for dims = {dims} in '+
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1973 'FitMap.best_parameters')
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1974 return({})
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1975 # Create current parameters
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1976 parameters = deepcopy(self._parameters)
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1977 for n, name in enumerate(self._best_parameters):
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1978 if self._parameters[name].vary:
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1979 parameters[name].set(value=self.best_values[n][dims])
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1980 parameters[name].stderr = self.best_errors[n][dims]
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1981 parameters_dict = {}
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1982 for name in sorted(parameters):
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1983 if name != 'tmp_normalization_offset_c':
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1984 par = parameters[name]
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1985 parameters_dict[name] = {'value': par.value, 'error': par.stderr,
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1986 'init_value': self.init_parameters[name]['value'], 'min': par.min,
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1987 'max': par.max, 'vary': par.vary, 'expr': par.expr}
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1988 return(parameters_dict)
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1989
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1990 def freemem(self):
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1991 if self._memfolder is None:
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1992 return
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1993 try:
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1994 rmtree(self._memfolder)
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1995 self._memfolder = None
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diff changeset
1996 except:
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1997 logging.warning('Could not clean-up automatically.')
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1998
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1999 def plot(self, dims, y_title=None, plot_residual=False, plot_comp_legends=False,
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diff changeset
2000 plot_masked_data=True):
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2001 if not isinstance(dims, (list, tuple)) or len(dims) != len(self._map_shape):
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2002 illegal_value(dims, 'dims', 'FitMap.plot', raise_error=True)
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2003 if self._result is None or self.best_fit is None or self.best_values is None:
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2004 logging.warning(f'Unable to plot fit for dims = {dims} in FitMap.plot')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
2005 return
69
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2006 if y_title is None or not isinstance(y_title, str):
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2007 y_title = 'data'
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2008 if self._mask is None:
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2009 mask = np.zeros(self._x.size).astype(bool)
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2010 plot_masked_data = False
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2011 else:
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2012 mask = self._mask
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2013 plots = [(self._x, np.asarray(self._ymap[dims]), 'b.')]
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2014 legend = [y_title]
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2015 if plot_masked_data:
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2016 plots += [(self._x[mask], np.asarray(self._ymap)[(*dims,mask)], 'bx')]
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2017 legend += ['masked data']
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2018 plots += [(self._x[~mask], self.best_fit[dims], 'k-')]
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2019 legend += ['best fit']
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2020 if plot_residual:
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2021 plots += [(self._x[~mask], self.residual[dims], 'k--')]
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2022 legend += ['residual']
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diff changeset
2023 # Create current parameters
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2024 parameters = deepcopy(self._parameters)
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2025 for name in self._best_parameters:
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2026 if self._parameters[name].vary:
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diff changeset
2027 parameters[name].set(value=
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2028 self.best_values[self._best_parameters.index(name)][dims])
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diff changeset
2029 for component in self._result.components:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2030 if 'tmp_normalization_offset_c' in component.param_names:
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
2031 continue
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2032 if isinstance(component, ExpressionModel):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2033 prefix = component._name
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2034 if prefix[-1] == '_':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2035 prefix = prefix[:-1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2036 modelname = f'{prefix}: {component.expr}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2037 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2038 prefix = component.prefix
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2039 if len(prefix):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2040 if prefix[-1] == '_':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2041 prefix = prefix[:-1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2042 modelname = f'{prefix} ({component._name})'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2043 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2044 modelname = f'{component._name}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2045 if len(modelname) > 20:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2046 modelname = f'{modelname[0:16]} ...'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2047 y = component.eval(params=parameters, x=self._x[~mask])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2048 if isinstance(y, (int, float)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2049 y *= np.ones(self._x[~mask].size)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2050 plots += [(self._x[~mask], y, '--')]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2051 if plot_comp_legends:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2052 legend.append(modelname)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2053 quick_plot(tuple(plots), legend=legend, title=str(dims), block=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2054
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2055 def fit(self, **kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2056 # t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2057 # Check input parameters
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2058 if self._model is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2059 logging.error('Undefined fit model')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2060 if 'num_proc' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2061 num_proc = kwargs.pop('num_proc')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2062 if not is_int(num_proc, ge=1):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2063 illegal_value(num_proc, 'num_proc', 'FitMap.fit', raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2064 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2065 num_proc = cpu_count()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2066 if num_proc > 1 and not have_joblib:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2067 logging.warning(f'Missing joblib in the conda environment, running FitMap serially')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2068 num_proc = 1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2069 if num_proc > cpu_count():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2070 logging.warning(f'The requested number of processors ({num_proc}) exceeds the maximum '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2071 f'number of processors, num_proc reduced to ({cpu_count()})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2072 num_proc = cpu_count()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2073 if 'try_no_bounds' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2074 self._try_no_bounds = kwargs.pop('try_no_bounds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2075 if not isinstance(self._try_no_bounds, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2076 illegal_value(self._try_no_bounds, 'try_no_bounds', 'FitMap.fit', raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2077 if 'redchi_cutoff' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2078 self._redchi_cutoff = kwargs.pop('redchi_cutoff')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2079 if not is_num(self._redchi_cutoff, gt=0):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2080 illegal_value(self._redchi_cutoff, 'redchi_cutoff', 'FitMap.fit', raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2081 if 'print_report' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2082 self._print_report = kwargs.pop('print_report')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2083 if not isinstance(self._print_report, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2084 illegal_value(self._print_report, 'print_report', 'FitMap.fit', raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2085 if 'plot' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2086 self._plot = kwargs.pop('plot')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2087 if not isinstance(self._plot, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2088 illegal_value(self._plot, 'plot', 'FitMap.fit', raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2089 if 'skip_init' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2090 self._skip_init = kwargs.pop('skip_init')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2091 if not isinstance(self._skip_init, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2092 illegal_value(self._skip_init, 'skip_init', 'FitMap.fit', raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2093
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2094 # Apply mask if supplied:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2095 if 'mask' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2096 self._mask = kwargs.pop('mask')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2097 if self._mask is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2098 self._mask = np.asarray(self._mask).astype(bool)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2099 if self._x.size != self._mask.size:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2100 raise ValueError(f'Inconsistent x and mask dimensions ({self._x.size} vs '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2101 f'{self._mask.size})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2102
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2103 # Add constant offset for a normalized single component model
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2104 if self._result is None and self._norm is not None and self._norm[0]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2105 self.add_model('constant', prefix='tmp_normalization_offset_', parameters={'name': 'c',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2106 'value': -self._norm[0], 'vary': False, 'norm': True})
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2107 #'value': -self._norm[0]/self._norm[1], 'vary': False, 'norm': False})
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2108
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2109 # Adjust existing parameters for refit:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2110 if 'parameters' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2111 # print('\nIn FitMap before adjusting existing parameters for refit:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2112 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2113 # if self._result is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2114 # raise ValueError('Invalid parameter parameters ({parameters})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2115 # if self._best_values is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2116 # raise ValueError('Valid self._best_values required for refitting in FitMap.fit')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2117 parameters = kwargs.pop('parameters')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2118 # print(f'\nparameters:\n{parameters}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2119 if isinstance(parameters, dict):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2120 parameters = (parameters, )
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2121 elif not is_dict_series(parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2122 illegal_value(parameters, 'parameters', 'Fit.fit', raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2123 for par in parameters:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2124 name = par['name']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2125 if name not in self._parameters:
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diff changeset
2126 raise ValueError(f'Unable to match {name} parameter {par} to an existing one')
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diff changeset
2127 if self._parameters[name].expr is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2128 raise ValueError(f'Unable to modify {name} parameter {par} (currently an '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2129 'expression)')
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diff changeset
2130 value = par.get('value')
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diff changeset
2131 vary = par.get('vary')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2132 if par.get('expr') is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2133 raise KeyError(f'Illegal "expr" key in {name} parameter {par}')
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diff changeset
2134 self._parameters[name].set(value=value, vary=vary, min=par.get('min'),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2135 max=par.get('max'))
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diff changeset
2136 # Overwrite existing best values for fixed parameters when a value is specified
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diff changeset
2137 # print(f'best values befored resetting:\n{self._best_values}')
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diff changeset
2138 if isinstance(value, (int, float)) and vary is False:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2139 for i, nname in enumerate(self._best_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2140 if nname == name:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2141 self._best_values[i] = value
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diff changeset
2142 # print(f'best values after resetting (value={value}, vary={vary}):\n{self._best_values}')
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diff changeset
2143 #RV print('\nIn FitMap after adjusting existing parameters for refit:')
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diff changeset
2144 #RV self._parameters.pretty_print()
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diff changeset
2145
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diff changeset
2146 # Check for uninitialized parameters
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diff changeset
2147 for name, par in self._parameters.items():
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diff changeset
2148 if par.expr is None:
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diff changeset
2149 value = par.value
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diff changeset
2150 if value is None or np.isinf(value) or np.isnan(value):
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diff changeset
2151 value = 1.0
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diff changeset
2152 if self._norm is None or name not in self._parameter_norms:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2153 self._parameters[name].set(value=value)
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diff changeset
2154 elif self._parameter_norms[name]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2155 self._parameters[name].set(value=value*self._norm[1])
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diff changeset
2156
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diff changeset
2157 # Create the best parameter list, consisting of all varying parameters plus the expression
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2158 # parameters in order to collect their errors
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diff changeset
2159 if self._result is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2160 # Initial fit
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2161 assert(self._best_parameters is None)
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diff changeset
2162 self._best_parameters = [name for name, par in self._parameters.items()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2163 if par.vary or par.expr is not None]
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diff changeset
2164 num_new_parameters = 0
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diff changeset
2165 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2166 # Refit
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diff changeset
2167 assert(len(self._best_parameters))
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diff changeset
2168 self._new_parameters = [name for name, par in self._parameters.items()
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diff changeset
2169 if name != 'tmp_normalization_offset_c' and name not in self._best_parameters and
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2170 (par.vary or par.expr is not None)]
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parents: 65
diff changeset
2171 num_new_parameters = len(self._new_parameters)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2172 num_best_parameters = len(self._best_parameters)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2173
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diff changeset
2174 # Flatten and normalize the best values of the previous fit, remove the remaining results
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2175 # of the previous fit
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2176 if self._result is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2177 # print('\nBefore flatten and normalize:')
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diff changeset
2178 # print(f'self._best_values:\n{self._best_values}')
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diff changeset
2179 self._out_of_bounds = None
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diff changeset
2180 self._max_nfev = None
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diff changeset
2181 self._redchi = None
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diff changeset
2182 self._success = None
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diff changeset
2183 self._best_fit = None
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diff changeset
2184 self._best_errors = None
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parents: 65
diff changeset
2185 assert(self._best_values is not None)
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diff changeset
2186 assert(self._best_values.shape[0] == num_best_parameters)
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parents: 65
diff changeset
2187 assert(self._best_values.shape[1:] == self._map_shape)
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diff changeset
2188 if self._transpose is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2189 self._best_values = np.transpose(self._best_values,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2190 [0]+[i+1 for i in self._transpose])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2191 self._best_values = [np.reshape(self._best_values[i], self._map_dim)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2192 for i in range(num_best_parameters)]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2193 if self._norm is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2194 for i, name in enumerate(self._best_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2195 if self._parameter_norms.get(name, False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2196 self._best_values[i] /= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2197 #RV print('\nAfter flatten and normalize:')
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diff changeset
2198 #RV print(f'self._best_values:\n{self._best_values}')
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diff changeset
2199
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diff changeset
2200 # Normalize the initial parameters (and best values for a refit)
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diff changeset
2201 # print('\nIn FitMap before normalize:')
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diff changeset
2202 # self._parameters.pretty_print()
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diff changeset
2203 # print(f'\nparameter_norms:\n{self._parameter_norms}\n')
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diff changeset
2204 self._normalize()
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diff changeset
2205 # print('\nIn FitMap after normalize:')
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diff changeset
2206 # self._parameters.pretty_print()
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diff changeset
2207 # print(f'\nparameter_norms:\n{self._parameter_norms}\n')
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diff changeset
2208
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2209 # Prevent initial values from sitting at boundaries
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diff changeset
2210 self._parameter_bounds = {name:{'min': par.min, 'max': par.max}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2211 for name, par in self._parameters.items() if par.vary}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2212 for name, par in self._parameters.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2213 if par.vary:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2214 par.set(value=self._reset_par_at_boundary(par, par.value))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2215 # print('\nAfter checking boundaries:')
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diff changeset
2216 # self._parameters.pretty_print()
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diff changeset
2217
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2218 # Set parameter bounds to unbound (only use bounds when fit fails)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2219 if self._try_no_bounds:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2220 for name in self._parameter_bounds.keys():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2221 self._parameters[name].set(min=-np.inf, max=np.inf)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2222
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2223 # Allocate memory to store fit results
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2224 if self._mask is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2225 x_size = self._x.size
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2226 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2227 x_size = self._x[~self._mask].size
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2228 if num_proc == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2229 self._out_of_bounds_flat = np.zeros(self._map_dim, dtype=bool)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2230 self._max_nfev_flat = np.zeros(self._map_dim, dtype=bool)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2231 self._redchi_flat = np.zeros(self._map_dim, dtype=np.float64)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2232 self._success_flat = np.zeros(self._map_dim, dtype=bool)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2233 self._best_fit_flat = np.zeros((self._map_dim, x_size),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2234 dtype=self._ymap_norm.dtype)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2235 self._best_errors_flat = [np.zeros(self._map_dim, dtype=np.float64)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2236 for _ in range(num_best_parameters+num_new_parameters)]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2237 if self._result is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2238 self._best_values_flat = [np.zeros(self._map_dim, dtype=np.float64)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2239 for _ in range(num_best_parameters)]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2240 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2241 self._best_values_flat = self._best_values
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2242 self._best_values_flat += [np.zeros(self._map_dim, dtype=np.float64)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2243 for _ in range(num_new_parameters)]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2244 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2245 self._memfolder = './joblib_memmap'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2246 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2247 mkdir(self._memfolder)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2248 except FileExistsError:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2249 pass
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2250 filename_memmap = path.join(self._memfolder, 'out_of_bounds_memmap')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2251 self._out_of_bounds_flat = np.memmap(filename_memmap, dtype=bool,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2252 shape=(self._map_dim), mode='w+')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2253 filename_memmap = path.join(self._memfolder, 'max_nfev_memmap')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2254 self._max_nfev_flat = np.memmap(filename_memmap, dtype=bool,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2255 shape=(self._map_dim), mode='w+')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2256 filename_memmap = path.join(self._memfolder, 'redchi_memmap')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2257 self._redchi_flat = np.memmap(filename_memmap, dtype=np.float64,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2258 shape=(self._map_dim), mode='w+')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2259 filename_memmap = path.join(self._memfolder, 'success_memmap')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2260 self._success_flat = np.memmap(filename_memmap, dtype=bool,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2261 shape=(self._map_dim), mode='w+')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2262 filename_memmap = path.join(self._memfolder, 'best_fit_memmap')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2263 self._best_fit_flat = np.memmap(filename_memmap, dtype=self._ymap_norm.dtype,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2264 shape=(self._map_dim, x_size), mode='w+')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2265 self._best_errors_flat = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2266 for i in range(num_best_parameters+num_new_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2267 filename_memmap = path.join(self._memfolder, f'best_errors_memmap_{i}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2268 self._best_errors_flat.append(np.memmap(filename_memmap, dtype=np.float64,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2269 shape=self._map_dim, mode='w+'))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2270 self._best_values_flat = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2271 for i in range(num_best_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2272 filename_memmap = path.join(self._memfolder, f'best_values_memmap_{i}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2273 self._best_values_flat.append(np.memmap(filename_memmap, dtype=np.float64,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2274 shape=self._map_dim, mode='w+'))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2275 if self._result is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2276 self._best_values_flat[i][:] = self._best_values[i][:]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2277 for i in range(num_new_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2278 filename_memmap = path.join(self._memfolder,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2279 f'best_values_memmap_{i+num_best_parameters}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2280 self._best_values_flat.append(np.memmap(filename_memmap, dtype=np.float64,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2281 shape=self._map_dim, mode='w+'))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2282
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2283 # Update the best parameter list
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2284 if num_new_parameters:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2285 self._best_parameters += self._new_parameters
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2286
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2287 # Perform the first fit to get model component info and initial parameters
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2288 current_best_values = {}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2289 # print(f'0 before:\n{current_best_values}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2290 # t1 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2291 self._result = self._fit(0, current_best_values, return_result=True, **kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2292 # t2 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2293 # print(f'0 after:\n{current_best_values}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2294 # print('\nAfter the first fit:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2295 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2296 # print(self._result.fit_report(show_correl=False))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2297
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2298 # Remove all irrelevant content from self._result
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2299 for attr in ('_abort', 'aborted', 'aic', 'best_fit', 'best_values', 'bic', 'calc_covar',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2300 'call_kws', 'chisqr', 'ci_out', 'col_deriv', 'covar', 'data', 'errorbars',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2301 'flatchain', 'ier', 'init_vals', 'init_fit', 'iter_cb', 'jacfcn', 'kws',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2302 'last_internal_values', 'lmdif_message', 'message', 'method', 'nan_policy',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2303 'ndata', 'nfev', 'nfree', 'params', 'redchi', 'reduce_fcn', 'residual', 'result',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2304 'scale_covar', 'show_candidates', 'calc_covar', 'success', 'userargs', 'userfcn',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2305 'userkws', 'values', 'var_names', 'weights', 'user_options'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2306 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2307 delattr(self._result, attr)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2308 except AttributeError:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2309 # logging.warning(f'Unknown attribute {attr} in fit.FtMap._cleanup_result')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2310 pass
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2311
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2312 # t3 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2313 if num_proc == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2314 # Perform the remaining fits serially
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diff changeset
2315 for n in range(1, self._map_dim):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2316 # print(f'{n} before:\n{current_best_values}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2317 self._fit(n, current_best_values, **kwargs)
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diff changeset
2318 # print(f'{n} after:\n{current_best_values}')
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diff changeset
2319 else:
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diff changeset
2320 # Perform the remaining fits in parallel
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diff changeset
2321 num_fit = self._map_dim-1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2322 # print(f'num_fit = {num_fit}')
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diff changeset
2323 if num_proc > num_fit:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2324 logging.warning(f'The requested number of processors ({num_proc}) exceeds the '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2325 f'number of fits, num_proc reduced to ({num_fit})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2326 num_proc = num_fit
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2327 num_fit_per_proc = 1
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diff changeset
2328 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2329 num_fit_per_proc = round((num_fit)/num_proc)
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diff changeset
2330 if num_proc*num_fit_per_proc < num_fit:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2331 num_fit_per_proc +=1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2332 # print(f'num_fit_per_proc = {num_fit_per_proc}')
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diff changeset
2333 num_fit_batch = min(num_fit_per_proc, 40)
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diff changeset
2334 # print(f'num_fit_batch = {num_fit_batch}')
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diff changeset
2335 with Parallel(n_jobs=num_proc) as parallel:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2336 parallel(delayed(self._fit_parallel)(current_best_values, num_fit_batch,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2337 n_start, **kwargs) for n_start in range(1, self._map_dim, num_fit_batch))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2338 # t4 = time()
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diff changeset
2339
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2340 # Renormalize the initial parameters for external use
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2341 if self._norm is not None and self._normalized:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2342 init_values = {}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2343 for name, value in self._result.init_values.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2344 if name not in self._parameter_norms or self._parameters[name].expr is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2345 init_values[name] = value
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2346 elif self._parameter_norms[name]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2347 init_values[name] = value*self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2348 self._result.init_values = init_values
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2349 for name, par in self._result.init_params.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2350 if par.expr is None and self._parameter_norms.get(name, False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2351 _min = par.min
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2352 _max = par.max
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diff changeset
2353 value = par.value*self._norm[1]
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diff changeset
2354 if not np.isinf(_min) and abs(_min) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2355 _min *= self._norm[1]
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diff changeset
2356 if not np.isinf(_max) and abs(_max) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2357 _max *= self._norm[1]
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diff changeset
2358 par.set(value=value, min=_min, max=_max)
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diff changeset
2359 par.init_value = par.value
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diff changeset
2360
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diff changeset
2361 # Remap the best results
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2362 # t5 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2363 self._out_of_bounds = np.copy(np.reshape(self._out_of_bounds_flat, self._map_shape))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2364 self._max_nfev = np.copy(np.reshape(self._max_nfev_flat, self._map_shape))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2365 self._redchi = np.copy(np.reshape(self._redchi_flat, self._map_shape))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2366 self._success = np.copy(np.reshape(self._success_flat, self._map_shape))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2367 self._best_fit = np.copy(np.reshape(self._best_fit_flat,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2368 list(self._map_shape)+[x_size]))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2369 self._best_values = np.asarray([np.reshape(par, list(self._map_shape))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2370 for par in self._best_values_flat])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2371 self._best_errors = np.asarray([np.reshape(par, list(self._map_shape))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2372 for par in self._best_errors_flat])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2373 if self._inv_transpose is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2374 self._out_of_bounds = np.transpose(self._out_of_bounds, self._inv_transpose)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2375 self._max_nfev = np.transpose(self._max_nfev, self._inv_transpose)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2376 self._redchi = np.transpose(self._redchi, self._inv_transpose)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2377 self._success = np.transpose(self._success, self._inv_transpose)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2378 self._best_fit = np.transpose(self._best_fit,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2379 list(self._inv_transpose)+[len(self._inv_transpose)])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2380 self._best_values = np.transpose(self._best_values,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2381 [0]+[i+1 for i in self._inv_transpose])
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diff changeset
2382 self._best_errors = np.transpose(self._best_errors,
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diff changeset
2383 [0]+[i+1 for i in self._inv_transpose])
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diff changeset
2384 del self._out_of_bounds_flat
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diff changeset
2385 del self._max_nfev_flat
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2386 del self._redchi_flat
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2387 del self._success_flat
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2388 del self._best_fit_flat
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2389 del self._best_values_flat
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2390 del self._best_errors_flat
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2391 # t6 = time()
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diff changeset
2392
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diff changeset
2393 # Restore parameter bounds and renormalize the parameters
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2394 for name, par in self._parameter_bounds.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2395 self._parameters[name].set(min=par['min'], max=par['max'])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2396 self._normalized = False
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diff changeset
2397 if self._norm is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2398 for name, norm in self._parameter_norms.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2399 par = self._parameters[name]
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diff changeset
2400 if par.expr is None and norm:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2401 value = par.value*self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2402 _min = par.min
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2403 _max = par.max
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2404 if not np.isinf(_min) and abs(_min) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2405 _min *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2406 if not np.isinf(_max) and abs(_max) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2407 _max *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2408 par.set(value=value, min=_min, max=_max)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2409 # t7 = time()
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diff changeset
2410 # print(f'total run time in fit: {t7-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2411 # print(f'run time first fit: {t2-t1:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2412 # print(f'run time remaining fits: {t4-t3:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2413 # print(f'run time remapping results: {t6-t5:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2414
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2415 # print('\n\nAt end fit:')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2416 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2417 # print(f'self._best_values:\n{self._best_values}\n\n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2418
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2419 # Free the shared memory
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2420 self.freemem()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2421
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2422 def _fit_parallel(self, current_best_values, num, n_start, **kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2423 num = min(num, self._map_dim-n_start)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2424 for n in range(num):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2425 # print(f'{n_start+n} before:\n{current_best_values}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2426 self._fit(n_start+n, current_best_values, **kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2427 # print(f'{n_start+n} after:\n{current_best_values}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2428
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2429 def _fit(self, n, current_best_values, return_result=False, **kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2430 #RV print(f'\n\nstart FitMap._fit {n}\n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2431 #RV print(f'current_best_values = {current_best_values}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2432 #RV print(f'self._best_parameters = {self._best_parameters}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2433 #RV print(f'self._new_parameters = {self._new_parameters}\n\n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2434 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2435 # Set parameters to current best values, but prevent them from sitting at boundaries
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2436 if self._new_parameters is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2437 # Initial fit
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2438 for name, value in current_best_values.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2439 par = self._parameters[name]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2440 par.set(value=self._reset_par_at_boundary(par, value))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2441 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2442 # Refit
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2443 for i, name in enumerate(self._best_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2444 par = self._parameters[name]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2445 if name in self._new_parameters:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2446 if name in current_best_values:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2447 par.set(value=self._reset_par_at_boundary(par, current_best_values[name]))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2448 elif par.expr is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2449 par.set(value=self._best_values[i][n])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2450 #RV print(f'\nbefore fit {n}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2451 #RV self._parameters.pretty_print()
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parents: 65
diff changeset
2452 if self._mask is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2453 result = self._model.fit(self._ymap_norm[n], self._parameters, x=self._x, **kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2454 else:
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parents: 65
diff changeset
2455 result = self._model.fit(self._ymap_norm[n][~self._mask], self._parameters,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2456 x=self._x[~self._mask], **kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2457 # print(f'\nafter fit {n}')
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parents: 65
diff changeset
2458 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2459 # print(result.fit_report(show_correl=False))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2460 out_of_bounds = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2461 for name, par in self._parameter_bounds.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2462 value = result.params[name].value
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2463 if not np.isinf(par['min']) and value < par['min']:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2464 out_of_bounds = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2465 break
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2466 if not np.isinf(par['max']) and value > par['max']:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2467 out_of_bounds = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2468 break
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2469 self._out_of_bounds_flat[n] = out_of_bounds
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2470 if self._try_no_bounds and out_of_bounds:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2471 # Rerun fit with parameter bounds in place
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2472 for name, par in self._parameter_bounds.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2473 self._parameters[name].set(min=par['min'], max=par['max'])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2474 # Set parameters to current best values, but prevent them from sitting at boundaries
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2475 if self._new_parameters is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2476 # Initial fit
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2477 for name, value in current_best_values.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2478 par = self._parameters[name]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2479 par.set(value=self._reset_par_at_boundary(par, value))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2480 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2481 # Refit
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2482 for i, name in enumerate(self._best_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2483 par = self._parameters[name]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2484 if name in self._new_parameters:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2485 if name in current_best_values:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2486 par.set(value=self._reset_par_at_boundary(par,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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diff changeset
2487 current_best_values[name]))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2488 elif par.expr is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2489 par.set(value=self._best_values[i][n])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2490 # print('\nbefore fit')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2491 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2492 # print(result.fit_report(show_correl=False))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2493 if self._mask is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2494 result = self._model.fit(self._ymap_norm[n], self._parameters, x=self._x, **kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2495 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2496 result = self._model.fit(self._ymap_norm[n][~self._mask], self._parameters,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2497 x=self._x[~self._mask], **kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2498 # print(f'\nafter fit {n}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2499 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2500 # print(result.fit_report(show_correl=False))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2501 out_of_bounds = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2502 for name, par in self._parameter_bounds.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2503 value = result.params[name].value
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2504 if not np.isinf(par['min']) and value < par['min']:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2505 out_of_bounds = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2506 break
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2507 if not np.isinf(par['max']) and value > par['max']:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2508 out_of_bounds = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2509 break
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2510 # print(f'{n} redchi < redchi_cutoff = {result.redchi < self._redchi_cutoff} success = {result.success} out_of_bounds = {out_of_bounds}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2511 # Reset parameters back to unbound
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2512 for name in self._parameter_bounds.keys():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2513 self._parameters[name].set(min=-np.inf, max=np.inf)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2514 assert(not out_of_bounds)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2515 if result.redchi >= self._redchi_cutoff:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2516 result.success = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2517 if result.nfev == result.max_nfev:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2518 # print(f'Maximum number of function evaluations reached for n = {n}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2519 # logging.warning(f'Maximum number of function evaluations reached for n = {n}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2520 if result.redchi < self._redchi_cutoff:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2521 result.success = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2522 self._max_nfev_flat[n] = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2523 if result.success:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2524 assert(all(True for par in current_best_values if par in result.params.values()))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2525 for par in result.params.values():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2526 if par.vary:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2527 current_best_values[par.name] = par.value
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2528 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2529 logging.warning(f'Fit for n = {n} failed: {result.lmdif_message}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2530 # Renormalize the data and results
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2531 self._renormalize(n, result)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2532 if self._print_report:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2533 print(result.fit_report(show_correl=False))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2534 if self._plot:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2535 dims = np.unravel_index(n, self._map_shape)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2536 if self._inv_transpose is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2537 dims= tuple(dims[self._inv_transpose[i]] for i in range(len(dims)))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2538 super().plot(result=result, y=np.asarray(self._ymap[dims]), plot_comp_legends=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2539 skip_init=self._skip_init, title=str(dims))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2540 #RV print(f'\n\nend FitMap._fit {n}\n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2541 #RV print(f'current_best_values = {current_best_values}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2542 # self._parameters.pretty_print()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2543 # print(result.fit_report(show_correl=False))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2544 #RV print(f'\nself._best_values_flat:\n{self._best_values_flat}\n\n')
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parents: 65
diff changeset
2545 if return_result:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2546 return(result)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2547
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2548 def _renormalize(self, n, result):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2549 self._redchi_flat[n] = np.float64(result.redchi)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2550 self._success_flat[n] = result.success
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2551 if self._norm is None or not self._normalized:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2552 self._best_fit_flat[n] = result.best_fit
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2553 for i, name in enumerate(self._best_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2554 self._best_values_flat[i][n] = np.float64(result.params[name].value)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2555 self._best_errors_flat[i][n] = np.float64(result.params[name].stderr)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2556 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2557 pars = set(self._parameter_norms) & set(self._best_parameters)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2558 for name, par in result.params.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2559 if name in pars and self._parameter_norms[name]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2560 if par.stderr is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2561 par.stderr *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2562 if par.expr is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
2563 par.value *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2564 if self._print_report:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2565 if par.init_value is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2566 par.init_value *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2567 if not np.isinf(par.min) and abs(par.min) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2568 par.min *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2569 if not np.isinf(par.max) and abs(par.max) != float_min:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2570 par.max *= self._norm[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2571 self._best_fit_flat[n] = result.best_fit*self._norm[1]+self._norm[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2572 for i, name in enumerate(self._best_parameters):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2573 self._best_values_flat[i][n] = np.float64(result.params[name].value)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 65
diff changeset
2574 self._best_errors_flat[i][n] = np.float64(result.params[name].stderr)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2575 if self._plot:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2576 if not self._skip_init:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2577 result.init_fit = result.init_fit*self._norm[1]+self._norm[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 65
diff changeset
2578 result.best_fit = np.copy(self._best_fit_flat[n])