Mercurial > repos > kls286 > chap_test_20230328

annotate build/lib/CHAP/models/edd.py @ 0:cbbe42422d56 draft

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author kls286
date Tue, 28 Mar 2023 15:07:30 +0000
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1 from msnctools.general import create_mask
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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2 from msnctools.material import Material
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3 from msnctools.scanparsers import SMBMCAScanParser as ScanParser
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4 import numpy as np
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5 from pathlib import PosixPath
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6 from pydantic import (BaseModel,
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7 confloat,
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8 conint,
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9 conlist,
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10 constr,
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11 FilePath,
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12 validator)
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13 from scipy.interpolate import interp1d
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14 from typing import Optional
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16
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17 class MCACeriaCalibrationConfig(BaseModel):
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18 '''Class representing metadata required to perform a Ceria calibration for an
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19 MCA detector.
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20
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21 :ivar spec_file: Path to the SPEC file containing the CeO2 scan
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22 :ivar scan_number: Number of the CeO2 scan in `spec_file`
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23 :ivar scan_step_index: Index of the scan step to use for calibration,
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24 optional. If not specified, the calibration routine will be performed on
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25 the average of all MCA spectra for the scan.
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26
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27 :ivar flux_file: csv file containing station beam energy in eV (column 0)
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28 and flux (column 1)
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29
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30 :ivar detector_name: name of the MCA to calibrate
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31 :ivar num_bins: number of channels on the MCA to calibrate
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32 :ivar max_energy_kev: maximum channel energy of the MCA in keV
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33
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34 :ivar hexrd_h5_material_file: path to a HEXRD materials.h5 file containing an
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35 entry for the material properties.
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36 :ivar hexrd_h5_material_name: Name of the material entry in
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37 `hexrd_h5_material_file`, defaults to `'CeO2'`.
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38 :ivar lattice_parameter_angstrom: lattice spacing in angstrom to use for
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39 the cubic CeO2 crystal, defaults to `5.41153`.
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40
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41 :ivar tth_max: detector rotation about hutch x axis, defaults to `90`.
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42 :ivar hkl_tth_tol: minimum resolvable difference in 2&theta between two
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43 unique HKL peaks, defaults to `0.15`.
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44
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45 :ivar fit_include_bin_ranges: list of MCA channel index ranges whose data
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46 will be included in the calibration routine
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47 :ivar fit_hkls: list of unique HKL indices to fit peaks for in the
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48 calibration routine
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49
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50 :ivar tth_initial_guess: initial guess for 2&theta
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51 :ivar slope_initial_guess: initial guess for detector channel energy
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52 correction linear slope, defaults to `1.0`.
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53 :ivar intercept_initial_guess: initial guess for detector channel energy
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54 correction y-intercept, defaults to `0.0`.
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55
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56 :ivar tth_calibrated: calibrated value for 2&theta, defaults to None
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57 :ivar slope_calibrated: calibrated value for detector channel energy
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58 correction linear slope, defaults to `None`
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59 :ivar intercept_calibrated: calibrated value for detector channel energy
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60 correction y-intercept, defaluts to None
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61
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62 :ivar max_iter: maximum number of iterations of the calibration routine,
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63 defaults to `10`.
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64 :ivar tune_tth_tol: stop iteratively tuning 2&theta when an iteration
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65 produces a change in the tuned value of 2&theta that is smaller than this
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66 value, defaults to `1e-8`.
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67 '''
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68
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69 spec_file: FilePath
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70 scan_number: conint(gt=0)
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71 scan_step_index: Optional[conint(ge=0)]
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72
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73 flux_file: FilePath
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74
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75 detector_name: constr(strip_whitespace=True, min_length=1)
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76 num_bins: conint(gt=0)
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77 max_energy_kev: confloat(gt=0)
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78
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79 hexrd_h5_material_file: FilePath
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80 hexrd_h5_material_name: constr(strip_whitespace=True, min_length=1) = 'CeO2'
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81 lattice_parameter_angstrom: confloat(gt=0) = 5.41153
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82
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83 tth_max: confloat(gt=0, allow_inf_nan=False) = 90.0
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84 hkl_tth_tol: confloat(gt=0, allow_inf_nan=False) = 0.15
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85
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86 fit_include_bin_ranges: conlist(min_items=1,
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87 item_type=conlist(item_type=conint(ge=0),
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88 min_items=2,
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89 max_items=2))
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90 fit_hkls: conlist(item_type=conint(ge=0), min_items=1)
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91
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92 tth_initial_guess: confloat(gt=0, le=tth_max, allow_inf_nan=False)
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93 slope_initial_guess: float = 1.0
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94 intercept_initial_guess: float = 0.0
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95 tth_calibrated: Optional[confloat(gt=0, allow_inf_nan=False)]
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96 slope_calibrated: Optional[confloat(allow_inf_nan=False)]
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97 intercept_calibrated: Optional[confloat(allow_inf_nan=False)]
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98
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99 max_iter: conint(gt=0) = 10
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100 tune_tth_tol: confloat(ge=0) = 1e-8
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101
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102 @validator('fit_include_bin_ranges', each_item=True)
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103 def validate_include_bin_range(cls, value, values):
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104 '''Ensure no bin ranges are outside the boundary of the detector'''
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105
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106 num_bins = values.get('num_bins')
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107 value[1] = min(value[1], num_bins)
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108 return(value)
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109
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110 def mca_data(self):
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111 '''Get the 1D array of MCA data to use for calibration.
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112
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113 :return: MCA data
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114 :rtype: np.ndarray
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115 '''
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116
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117 scanparser = ScanParser(self.spec_file, self.scan_number)
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118 if self.scan_step_index is None:
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119 data = scanparser.get_all_detector_data(self.detector_name)
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120 if scanparser.spec_scan_npts > 1:
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121 data = np.average(data, axis=1)
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122 else:
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123 data = data[0]
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124 else:
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125 data = scanparser.get_detector_data(self.detector_name, self.scan_step_index)
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126
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127 return(np.array(data))
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128
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129 def mca_mask(self):
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130 '''Get a boolean mask array to use on MCA data before fitting.
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131
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132 :return: boolean mask array
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133 :rtype: numpy.ndarray
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134 '''
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135
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136 mask = None
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137 bin_indices = np.arange(self.num_bins)
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138 for bin_range in self.fit_include_bin_ranges:
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139 mask = create_mask(bin_indices,
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140 bounds=bin_range,
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141 exclude_bounds=False,
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142 current_mask=mask)
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143
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144 return(mask)
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145
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146 def flux_correction_interpolation_function(self):
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147 '''Get an interpolation function to correct MCA data for relative energy
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148 flux of the incident beam.
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149
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150 :return: energy flux correction interpolation function
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151 :rtype: scipy.interpolate._polyint._Interpolator1D
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152 '''
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153
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154 flux = np.loadtxt(self.flux_file)
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155 energies = flux[:,0]/1.e3
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156 relative_intensities = flux[:,1]/np.max(flux[:,1])
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157 interpolation_function = interp1d(energies, relative_intensities)
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158 return(interpolation_function)
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159
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160 def material(self):
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161 '''Get CeO2 as a `msnctools.materials.Material` object.
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162
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163 :return: CeO2 material
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164 :rtype: msnctools.material.Material
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165 '''
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166
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167 material = Material(material_name=self.hexrd_h5_material_name,
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168 material_file=self.hexrd_h5_material_file,
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169 lattice_parameters_angstroms=self.lattice_parameter_angstrom)
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170 # The following kwargs will be needed if we allow the material to be
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171 # built using xrayutilities (for now, we only allow hexrd to make the
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172 # material):
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173 # sgnum=225,
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174 # atoms=['Ce4p', 'O2mdot'],
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175 # pos=[(0.,0.,0.), (0.25,0.75,0.75)],
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176 # enrgy=50000.) # Why do we need to specify an energy to get HKLs when using xrayutilities?
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177 return(material)
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178
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179 def unique_ds(self):
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180 '''Get a list of unique HKLs and their lattice spacings
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181
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182 :return: unique HKLs and their lattice spacings in angstroms
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183 :rtype: np.ndarray, np.ndarray
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184 '''
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185
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186 unique_hkls, unique_ds = self.material().get_unique_ds(tth_tol=self.hkl_tth_tol, tth_max=self.tth_max)
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187
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188 return(unique_hkls, unique_ds)
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189
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190 def fit_ds(self):
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191 '''Get a list of HKLs and their lattice spacings that will be fit in the
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192 calibration routine
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193
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194 :return: HKLs to fit and their lattice spacings in angstroms
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195 :rtype: np.ndarray, np.ndarray
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196 '''
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197
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198 unique_hkls, unique_ds = self.unique_ds()
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199
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200 fit_hkls = np.array([unique_hkls[i] for i in self.fit_hkls])
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201 fit_ds = np.array([unique_ds[i] for i in self.fit_hkls])
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202
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203 return(fit_hkls, fit_ds)
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204
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205 def dict(self):
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206 '''Return a representation of this configuration in a dictionary that is
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207 suitable for dumping to a YAML file (one that converts all instances of
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208 fields with type `PosixPath` to `str`).
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209
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210 :return: dictionary representation of the configuration.
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211 :rtype: dict
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212 '''
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213
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214 d = super().dict()
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215 for k,v in d.items():
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216 if isinstance(v, PosixPath):
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217 d[k] = str(v)
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218 return(d)