1 | |
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2 | import numpy as np |
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3 | |
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4 | # TODO: turn ModelInfo into a proper class |
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5 | ModelInfo = dict |
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6 | |
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7 | COMMON_PARAMETERS = [ |
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8 | ["scale", "", 1, [0, np.inf], "", "Source intensity"], |
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9 | ["background", "1/cm", 1e-3, [0, np.inf], "", "Source background"], |
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10 | ] |
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11 | assert (len(COMMON_PARAMETERS) == 2 |
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12 | and COMMON_PARAMETERS[0][0]=="scale" |
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13 | and COMMON_PARAMETERS[1][0]=="background"), "don't change common parameters" |
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14 | # assumptions about common parameters exist throughout the code, such as: |
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15 | # (1) kernel functions Iq, Iqxy, form_volume, ... don't see them |
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16 | # (2) kernel drivers assume scale is par[0] and background is par[1] |
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17 | # (3) mixture models drop the background on components and replace the scale |
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18 | # with a scale that varies from [-inf, inf] |
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19 | # (4) product models drop the background and reassign scale |
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20 | # and maybe other places. |
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21 | # Note that scale and background cannot be coordinated parameters whose value |
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22 | # depends on the some polydisperse parameter with the current implementation |
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23 | |
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24 | def make_parameter_table(pars): |
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25 | processed = [] |
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26 | for p in pars: |
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27 | if not isinstance(p, list) or len(p) != 6: |
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28 | raise ValueError("Parameter should be [name, units, default, limits, type, desc], but got %r" |
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29 | %str(p)) |
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30 | processed.append(parse_parameter(*p)) |
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31 | partable = ParameterTable(processed) |
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32 | return partable |
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33 | |
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34 | def parse_parameter(name, units='', default=None, |
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35 | limits=(-np.inf, np.inf), type='', description=''): |
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36 | # Parameter is a user facing class. Do robust type checking. |
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37 | if not isstr(name): |
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38 | raise ValueError("expected string for parameter name %r"%name) |
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39 | if not isstr(units): |
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40 | raise ValueError("expected units to be a string for %s"%name) |
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41 | # if limits is a list of strings, then this is a choice list |
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42 | # field, and limits are 1 to length of string list |
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43 | if isinstance(limits, list) and all(isstr(k) for k in limits): |
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44 | choices = limits |
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45 | limits = [1, len(choices)] |
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46 | else: |
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47 | choices = None |
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48 | # TODO: maybe allow limits of None for (-inf, inf) |
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49 | try: |
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50 | low, high = limits |
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51 | if not isinstance(low, (int, float)): |
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52 | raise TypeError("low is not numeric") |
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53 | if not isinstance(high, (int, float)): |
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54 | raise TypeError("high is not numeric") |
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55 | if low >= high: |
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56 | raise ValueError("require low < high") |
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57 | except: |
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58 | raise ValueError("invalid limits %s for %s"%(limits, name)) |
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59 | |
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60 | if not isinstance(default, (int, float)): |
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61 | raise ValueError("expected default %r to be a number for %s" |
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62 | % (default, name)) |
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63 | if default < low or default > high: |
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64 | raise ValueError("default value %r not in range for %s" |
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65 | % (default, name)) |
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66 | |
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67 | if type not in ("volume", "orientation", "sld", "magnetic", ""): |
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68 | raise ValueError("unexpected type %r for %s" % (type, name)) |
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69 | |
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70 | if not isstr(description): |
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71 | raise ValueError("expected description to be a string") |
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72 | |
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73 | |
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74 | # Parameter id for name[n] does not include [n] |
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75 | if "[" in name: |
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76 | if not name.endswith(']'): |
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77 | raise ValueError("Expected name[len] for vector parameter %s"%name) |
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78 | pid, ref = name[:-1].split('[', 1) |
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79 | ref = ref.strip() |
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80 | else: |
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81 | pid, ref = name, None |
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82 | |
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83 | |
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84 | # automatically identify sld types |
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85 | if type=='' and (pid.startswith('sld') or pid.endswith('sld')): |
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86 | type = 'sld' |
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87 | |
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88 | # Check if using a vector definition, name[k], as the parameter name |
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89 | if ref: |
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90 | if ref == '': |
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91 | raise ValueError("Need to specify vector length for %s"%name) |
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92 | try: |
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93 | length = int(ref) |
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94 | control = None |
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95 | except: |
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96 | length = None |
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97 | control = ref |
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98 | else: |
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99 | length = 1 |
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100 | control = None |
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101 | |
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102 | # Build the parameter |
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103 | parameter = Parameter(name=name, units=units, default=default, |
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104 | limits=limits, type=type, description=description) |
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105 | |
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106 | # TODO: need better control over whether a parameter is polydisperse |
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107 | parameter.polydisperse = type in ('orientation', 'volume') |
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108 | parameter.relative_pd = type in ('volume') |
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109 | parameter.choices = choices |
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110 | parameter.length = length |
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111 | parameter.length_control = control |
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112 | |
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113 | return parameter |
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114 | |
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115 | class Parameter(object): |
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116 | """ |
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117 | The available kernel parameters are defined as a list, with each parameter |
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118 | defined as a sublist with the following elements: |
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119 | |
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120 | *name* is the name that will be used in the call to the kernel |
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121 | function and the name that will be displayed to the user. Names |
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122 | should be lower case, with words separated by underscore. If |
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123 | acronyms are used, the whole acronym should be upper case. |
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124 | |
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125 | *units* should be one of *degrees* for angles, *Ang* for lengths, |
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126 | *1e-6/Ang^2* for SLDs. |
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127 | |
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128 | *default value* will be the initial value for the model when it |
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129 | is selected, or when an initial value is not otherwise specified. |
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130 | |
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131 | *limits = [lb, ub]* are the hard limits on the parameter value, used to |
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132 | limit the polydispersity density function. In the fit, the parameter limits |
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133 | given to the fit are the limits on the central value of the parameter. |
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134 | If there is polydispersity, it will evaluate parameter values outside |
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135 | the fit limits, but not outside the hard limits specified in the model. |
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136 | If there are no limits, use +/-inf imported from numpy. |
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137 | |
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138 | *type* indicates how the parameter will be used. "volume" parameters |
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139 | will be used in all functions. "orientation" parameters will be used |
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140 | in *Iqxy* and *Imagnetic*. "magnetic* parameters will be used in |
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141 | *Imagnetic* only. If *type* is the empty string, the parameter will |
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142 | be used in all of *Iq*, *Iqxy* and *Imagnetic*. "sld" parameters |
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143 | can automatically be promoted to magnetic parameters, each of which |
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144 | will have a magnitude and a direction, which may be different from |
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145 | other sld parameters. |
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146 | |
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147 | *description* is a short description of the parameter. This will |
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148 | be displayed in the parameter table and used as a tool tip for the |
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149 | parameter value in the user interface. |
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150 | |
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151 | Additional values can be set after the parameter is created: |
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152 | |
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153 | *length* is the length of the field if it is a vector field |
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154 | *length_control* is the parameter which sets the vector length |
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155 | *polydisperse* is true if the parameter accepts a polydispersity |
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156 | *relative_pd* is true if that polydispersity is relative |
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157 | |
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158 | In the usual process these values are set by :func:`make_parameter_table` |
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159 | and :func:`parse_parameter` therein. |
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160 | """ |
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161 | def __init__(self, name, units='', default=None, limits=(-np.inf, np.inf), |
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162 | type='', description=''): |
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163 | self.id = name.split('[')[0].strip() |
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164 | self.name = name |
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165 | self.default = default |
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166 | self.limits = limits |
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167 | self.type = type |
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168 | self.description = description |
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169 | self.choices = None |
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170 | |
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171 | # Length and length_control will be filled in by |
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172 | # set_vector_length_from_reference(partable) once the complete |
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173 | # parameter table is available. |
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174 | self.length = 1 |
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175 | self.length_control = None |
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176 | |
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177 | # TODO: need better control over whether a parameter is polydisperse |
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178 | self.polydisperse = False |
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179 | self.relative_pd = False |
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180 | |
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181 | def as_definition(self): |
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182 | """ |
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183 | Declare space for the variable in a parameter structure. |
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184 | |
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185 | For example, the parameter thickness with length 3 will |
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186 | return "double thickness[3];", with no spaces before and |
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187 | no new line character afterward. |
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188 | """ |
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189 | if self.length == 1: |
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190 | return "double %s;"%self.id |
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191 | else: |
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192 | return "double %s[%d];"%(self.id, self.length) |
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193 | |
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194 | def as_function_argument(self): |
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195 | """ |
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196 | Declare the variable as a function argument. |
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197 | |
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198 | For example, the parameter thickness with length 3 will |
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199 | return "double *thickness", with no spaces before and |
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200 | no comma afterward. |
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201 | """ |
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202 | if self.length == 1: |
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203 | return "double %s"%self.id |
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204 | else: |
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205 | return "double *%s"%self.id |
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206 | |
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207 | def as_call_reference(self, prefix=""): |
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208 | # Note: if the parameter is a struct type, then we will need to use |
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209 | # &prefix+id. For scalars and vectors we can just use prefix+id. |
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210 | return prefix + self.id |
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211 | |
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212 | def __str__(self): |
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213 | return "<%s>"%self.name |
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214 | |
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215 | def __repr__(self): |
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216 | return "P<%s>"%self.name |
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217 | |
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218 | class ParameterTable(object): |
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219 | # scale and background are implicit parameters |
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220 | COMMON = [Parameter(*p) for p in COMMON_PARAMETERS] |
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221 | |
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222 | def __init__(self, parameters): |
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223 | self.parameters = self.COMMON + parameters |
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224 | self._name_table= dict((p.name, p) for p in parameters) |
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225 | self._categorize_parameters() |
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226 | |
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227 | self._set_vector_lengths() |
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228 | self._set_defaults() |
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229 | |
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230 | def _set_vector_lengths(self): |
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231 | # Sort out the length of the vector parameters such as thickness[n] |
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232 | for p in self.parameters: |
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233 | if p.length_control: |
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234 | ref = self._name_table[p.length_control] |
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235 | low, high = ref.limits |
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236 | if int(low) != low or int(high) != high or low<0 or high>20: |
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237 | raise ValueError("expected limits on %s to be within [0, 20]"%ref.name) |
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238 | p.length = high |
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239 | |
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240 | def _set_defaults(self): |
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241 | # Construct default values, including vector defaults |
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242 | defaults = {} |
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243 | for p in self.parameters: |
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244 | if p.length == 1: |
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245 | defaults[p.id] = p.default |
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246 | else: |
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247 | for k in range(p.length): |
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248 | defaults["%s[%d]"%(p.id, k)] = p.default |
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249 | self.defaults = defaults |
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250 | |
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251 | def __getitem__(self, k): |
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252 | if isinstance(k, (int, slice)): |
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253 | return self.parameters[k] |
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254 | else: |
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255 | return self._name_table[k] |
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256 | |
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257 | def __contains__(self, key): |
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258 | return key in self._name_table |
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259 | |
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260 | def __iter__(self): |
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261 | return iter(self.parameters) |
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262 | |
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263 | def kernel_pars(self, ptype=None): |
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264 | """ |
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265 | Return the parameters to the user kernel which match the given type. |
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266 | |
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267 | Types include '1d' for Iq kernels, '2d' for Iqxy kernels and |
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268 | 'volume' for form_volume kernels. |
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269 | """ |
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270 | # Assumes background and scale are the first two parameters |
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271 | if ptype is None: |
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272 | return self.parameters[2:] |
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273 | else: |
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274 | return [p for p in self.parameters[2:] if p in self.type[ptype]] |
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275 | |
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276 | def _categorize_parameters(self): |
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277 | """ |
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278 | Build parameter categories out of the the parameter definitions. |
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279 | |
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280 | Returns a dictionary of categories. |
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281 | |
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282 | Note: these categories are subject to change, depending on the needs of |
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283 | the UI and the needs of the kernel calling function. |
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284 | |
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285 | The categories are as follows: |
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286 | |
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287 | * *volume* list of volume parameter names |
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288 | * *orientation* list of orientation parameters |
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289 | * *magnetic* list of magnetic parameters |
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290 | * *sld* list of parameters that have no type info |
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291 | * *other* list of parameters that have no type info |
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292 | |
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293 | Each parameter is in one and only one category. |
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294 | """ |
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295 | pars = self.parameters |
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296 | |
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297 | par_type = { |
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298 | 'volume': [], 'orientation': [], 'magnetic': [], 'sld': [], 'other': [], |
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299 | } |
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300 | for p in self.parameters: |
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301 | par_type[p.type if p.type else 'other'].append(p) |
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302 | par_type['1d'] = [p for p in pars if p.type not in ('orientation', 'magnetic')] |
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303 | par_type['2d'] = [p for p in pars if p.type != 'magnetic'] |
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304 | par_type['pd'] = [p for p in pars if p.polydisperse] |
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305 | par_type['pd_relative'] = [p for p in pars if p.relative_pd] |
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306 | self.type = par_type |
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307 | |
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308 | # find index of theta (or whatever variable is used for spherical |
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309 | # normalization during polydispersity... |
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310 | if 'theta' in par_type['2d']: |
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311 | # TODO: may be an off-by 2 bug due to background and scale |
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312 | # TODO: is theta always the polar coordinate? |
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313 | self.theta_par = [k for k,p in enumerate(pars) if p.name=='theta'][0] |
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314 | else: |
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315 | self.theta_par = -1 |
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316 | |
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317 | @property |
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318 | def num_pd(self): |
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319 | """ |
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320 | Number of distributional parameters in the model (polydispersity in |
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321 | shape dimensions and orientational distributions). |
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322 | """ |
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323 | return sum(p.length for p in self.type['pd']) |
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324 | |
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325 | @property |
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326 | def has_2d(self): |
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327 | return self.type['orientation'] or self.type['magnetic'] |
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328 | |
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329 | |
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330 | def isstr(x): |
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331 | # TODO: 2-3 compatible tests for str, including unicode strings |
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332 | return isinstance(x, str) |
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333 | |
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