1 | """ |
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2 | SAS model constructor. |
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3 | |
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4 | Small angle scattering models are defined by a set of kernel functions: |
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5 | |
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6 | *Iq(q, p1, p2, ...)* returns the scattering at q for a form with |
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7 | particular dimensions averaged over all orientations. |
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8 | |
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9 | *Iqxy(qx, qy, p1, p2, ...)* returns the scattering at qx,qy for a form |
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10 | with particular dimensions for a single orientation. |
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11 | |
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12 | *Imagnetic(qx, qy, result[], p1, p2, ...)* returns the scattering for the |
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13 | polarized neutron spin states (up-up, up-down, down-up, down-down) for |
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14 | a form with particular dimensions for a single orientation. |
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15 | |
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16 | *form_volume(p1, p2, ...)* returns the volume of the form with particular |
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17 | dimension. |
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18 | |
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19 | *ER(p1, p2, ...)* returns the effective radius of the form with |
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20 | particular dimensions. |
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21 | |
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22 | *VR(p1, p2, ...)* returns the volume ratio for core-shell style forms. |
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23 | |
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24 | These functions are defined in a kernel module .py script and an associated |
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25 | set of .c files. The model constructor will use them to create models with |
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26 | polydispersity across volume and orientation parameters, and provide |
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27 | scale and background parameters for each model. |
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28 | |
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29 | *Iq*, *Iqxy*, *Imagnetic* and *form_volume* should be stylized C-99 |
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30 | functions written for OpenCL. All functions need prototype declarations |
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31 | even if the are defined before they are used. OpenCL does not support |
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32 | *#include* preprocessor directives, so instead the list of includes needs |
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33 | to be given as part of the metadata in the kernel module definition. |
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34 | The included files should be listed using a path relative to the kernel |
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35 | module, or if using "lib/file.c" if it is one of the standard includes |
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36 | provided with the sasmodels source. The includes need to be listed in |
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37 | order so that functions are defined before they are used. |
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38 | |
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39 | Floating point values should be declared as *double*. For single precision |
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40 | calculations, *double* will be replaced by *float*. The single precision |
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41 | conversion will also tag floating point constants with "f" to make them |
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42 | single precision constants. When using integral values in floating point |
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43 | expressions, they should be expressed as floating point values by including |
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44 | a decimal point. This includes 0., 1. and 2. |
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45 | |
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46 | OpenCL has a *sincos* function which can improve performance when both |
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47 | the *sin* and *cos* values are needed for a particular argument. Since |
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48 | this function does not exist in C99, all use of *sincos* should be |
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49 | replaced by the macro *SINCOS(value,sn,cn)* where *sn* and *cn* are |
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50 | previously declared *double* variables. When compiled for systems without |
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51 | OpenCL, *SINCOS* will be replaced by *sin* and *cos* calls. If *value* is |
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52 | an expression, it will appear twice in this case; whether or not it will be |
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53 | evaluated twice depends on the quality of the compiler. |
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54 | |
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55 | If the input parameters are invalid, the scattering calculator should |
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56 | return a negative number. Particularly with polydispersity, there are |
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57 | some sets of shape parameters which lead to nonsensical forms, such |
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58 | as a capped cylinder where the cap radius is smaller than the |
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59 | cylinder radius. The polydispersity calculation will ignore these points, |
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60 | effectively chopping the parameter weight distributions at the boundary |
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61 | of the infeasible region. The resulting scattering will be set to |
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62 | background. This will work correctly even when polydispersity is off. |
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63 | |
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64 | *ER* and *VR* are python functions which operate on parameter vectors. |
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65 | The constructor code will generate the necessary vectors for computing |
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66 | them with the desired polydispersity. |
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67 | |
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68 | The available kernel parameters are defined as a list, with each parameter |
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69 | defined as a sublist with the following elements: |
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70 | |
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71 | *name* is the name that will be used in the call to the kernel |
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72 | function and the name that will be displayed to the user. Names |
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73 | should be lower case, with words separated by underscore. If |
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74 | acronyms are used, the whole acronym should be upper case. |
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75 | |
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76 | *units* should be one of *degrees* for angles, *Ang* for lengths, |
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77 | *1e-6/Ang^2* for SLDs. |
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78 | |
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79 | *default value* will be the initial value for the model when it |
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80 | is selected, or when an initial value is not otherwise specified. |
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81 | |
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82 | [*lb*, *ub*] are the hard limits on the parameter value, used to limit |
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83 | the polydispersity density function. In the fit, the parameter limits |
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84 | given to the fit are the limits on the central value of the parameter. |
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85 | If there is polydispersity, it will evaluate parameter values outside |
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86 | the fit limits, but not outside the hard limits specified in the model. |
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87 | If there are no limits, use +/-inf imported from numpy. |
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88 | |
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89 | *type* indicates how the parameter will be used. "volume" parameters |
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90 | will be used in all functions. "orientation" parameters will be used |
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91 | in *Iqxy* and *Imagnetic*. "magnetic* parameters will be used in |
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92 | *Imagnetic* only. If *type* is the empty string, the parameter will |
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93 | be used in all of *Iq*, *Iqxy* and *Imagnetic*. |
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94 | |
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95 | *description* is a short description of the parameter. This will |
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96 | be displayed in the parameter table and used as a tool tip for the |
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97 | parameter value in the user interface. |
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98 | |
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99 | The kernel module must set variables defining the kernel meta data: |
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100 | |
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101 | *name* is the model name |
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102 | |
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103 | *title* is a short description of the model, suitable for a tool tip, |
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104 | or a one line model summary in a table of models. |
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105 | |
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106 | *description* is an extended description of the model to be displayed |
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107 | while the model parameters are being edited. |
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108 | |
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109 | *parameters* is the list of parameters. Parameters in the kernel |
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110 | functions must appear in the same order as they appear in the |
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111 | parameters list. Two additional parameters, *scale* and *background* |
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112 | are added to the beginning of the parameter list. They will show up |
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113 | in the documentation as model parameters, but they are never sent to |
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114 | the kernel functions. |
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115 | |
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116 | *source* is the list of C-99 source files that must be joined to |
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117 | create the OpenCL kernel functions. The files defining the functions |
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118 | need to be listed before the files which use the functions. |
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119 | |
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120 | *ER* is a python function defining the effective radius. If it is |
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121 | not present, the effective radius is 0. |
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122 | |
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123 | *VR* is a python function defining the volume ratio. If it is not |
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124 | present, the volume ratio is 1. |
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125 | |
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126 | *form_volume*, *Iq*, *Iqxy*, *Imagnetic* are strings containing the |
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127 | C source code for the body of the volume, Iq, and Iqxy functions |
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128 | respectively. These can also be defined in the last source file. |
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129 | |
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130 | An *info* dictionary is constructed from the kernel meta data and |
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131 | returned to the caller. It includes the additional fields |
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132 | |
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133 | |
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134 | The model evaluator, function call sequence consists of q inputs and the return vector, |
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135 | followed by the loop value/weight vector, followed by the values for |
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136 | the non-polydisperse parameters, followed by the lengths of the |
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137 | polydispersity loops. To construct the call for 1D models, the |
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138 | categories *fixed-1d* and *pd-1d* list the names of the parameters |
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139 | of the non-polydisperse and the polydisperse parameters respectively. |
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140 | Similarly, *fixed-2d* and *pd-2d* provide parameter names for 2D models. |
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141 | The *pd-rel* category is a set of those parameters which give |
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142 | polydispersitiy as a portion of the value (so a 10% length dispersity |
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143 | would use a polydispersity value of 0.1) rather than absolute |
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144 | dispersity such as an angle plus or minus 15 degrees. |
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145 | |
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146 | The *volume* category lists the volume parameters in order for calls |
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147 | to volume within the kernel (used for volume normalization) and for |
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148 | calls to ER and VR for effective radius and volume ratio respectively. |
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149 | |
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150 | The *orientation* and *magnetic* categories list the orientation and |
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151 | magnetic parameters. These are used by the sasview interface. The |
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152 | blank category is for parameters such as scale which don't have any |
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153 | other marking. |
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154 | |
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155 | The doc string at the start of the kernel module will be used to |
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156 | construct the model documentation web pages. Embedded figures should |
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157 | appear in the subdirectory "img" beside the model definition, and tagged |
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158 | with the kernel module name to avoid collision with other models. Some |
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159 | file systems are case-sensitive, so only use lower case characters for |
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160 | file names and extensions. |
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161 | |
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162 | |
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163 | The function :func:`make` loads the metadata from the module and returns |
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164 | the kernel source. The function :func:`doc` extracts the doc string |
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165 | and adds the parameter table to the top. The function :func:`sources` |
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166 | returns a list of files required by the model. |
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167 | """ |
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168 | |
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169 | # TODO: identify model files which have changed since loading and reload them. |
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170 | |
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171 | __all__ = ["make, doc", "sources", "use_single"] |
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172 | |
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173 | import sys |
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174 | import os |
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175 | import os.path |
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176 | import re |
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177 | |
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178 | import numpy as np |
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179 | |
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180 | F64 = np.dtype('float64') |
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181 | F32 = np.dtype('float32') |
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182 | |
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183 | # Scale and background, which are parameters common to every form factor |
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184 | COMMON_PARAMETERS = [ |
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185 | [ "scale", "", 1, [0, np.inf], "", "Source intensity" ], |
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186 | [ "background", "1/cm", 0, [0, np.inf], "", "Source background" ], |
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187 | ] |
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188 | |
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189 | |
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190 | # Conversion from units defined in the parameter table for each model |
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191 | # to units displayed in the sphinx documentation. |
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192 | RST_UNITS = { |
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193 | "Ang": "|Ang|", |
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194 | "1/Ang^2": "|Ang^-2|", |
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195 | "1e-6/Ang^2": "|1e-6Ang^-2|", |
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196 | "degrees": "degree", |
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197 | "1/cm": "|cm^-1|", |
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198 | "": "None", |
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199 | } |
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200 | |
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201 | # Headers for the parameters tables in th sphinx documentation |
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202 | PARTABLE_HEADERS = [ |
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203 | "Parameter", |
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204 | "Description", |
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205 | "Units", |
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206 | "Default value", |
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207 | ] |
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208 | |
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209 | # Minimum width for a default value (this is shorter than the column header |
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210 | # width, so will be ignored). |
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211 | PARTABLE_VALUE_WIDTH = 10 |
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212 | |
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213 | # Header included before every kernel. |
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214 | # This makes sure that the appropriate math constants are defined, and does |
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215 | # whatever is required to make the kernel compile as pure C rather than |
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216 | # as an OpenCL kernel. |
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217 | KERNEL_HEADER = """\ |
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218 | // GENERATED CODE --- DO NOT EDIT --- |
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219 | // Code is produced by sasmodels.gen from sasmodels/models/MODEL.c |
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220 | |
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221 | #ifdef __OPENCL_VERSION__ |
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222 | # define USE_OPENCL |
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223 | #endif |
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224 | |
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225 | // If opencl is not available, then we are compiling a C function |
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226 | // Note: if using a C++ compiler, then define kernel as extern "C" |
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227 | #ifndef USE_OPENCL |
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228 | # ifdef __cplusplus |
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229 | #include <cmath> |
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230 | #if defined(_MSC_VER) |
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231 | #define kernel extern "C" __declspec( dllexport ) |
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232 | #else |
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233 | #define kernel extern "C" |
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234 | #endif |
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235 | using namespace std; |
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236 | inline void SINCOS(double angle, double &svar, double &cvar) |
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237 | { svar=sin(angle); cvar=cos(angle); } |
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238 | # else |
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239 | #include <math.h> |
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240 | #if defined(_MSC_VER) |
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241 | #define kernel __declspec( dllexport ) |
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242 | #else |
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243 | #define kernel |
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244 | #endif |
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245 | #define SINCOS(angle,svar,cvar) do {svar=sin(angle);cvar=cos(angle);} while (0) |
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246 | # endif |
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247 | # define global |
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248 | # define local |
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249 | # define constant const |
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250 | # define powr(a,b) pow(a,b) |
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251 | #else |
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252 | # ifdef USE_SINCOS |
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253 | # define SINCOS(angle,svar,cvar) svar=sincos(angle,&cvar) |
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254 | # else |
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255 | # define SINCOS(angle,svar,cvar) do {svar=sin(angle);cvar=cos(angle);} while (0) |
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256 | # endif |
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257 | #endif |
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258 | |
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259 | // Standard mathematical constants: |
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260 | // M_E, M_LOG2E, M_LOG10E, M_LN2, M_LN10, M_PI, M_PI_2=pi/2, M_PI_4=pi/4, |
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261 | // M_1_PI=1/pi, M_2_PI=2/pi, M_2_SQRTPI=2/sqrt(pi), SQRT2, SQRT1_2=sqrt(1/2) |
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262 | // OpenCL defines M_constant_F for float constants, and nothing if double |
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263 | // is not enabled on the card, which is why these constants may be missing |
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264 | #ifndef M_PI |
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265 | # define M_PI 3.141592653589793 |
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266 | #endif |
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267 | #ifndef M_PI_2 |
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268 | # define M_PI_2 1.570796326794897 |
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269 | #endif |
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270 | #ifndef M_PI_4 |
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271 | # define M_PI_4 0.7853981633974483 |
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272 | #endif |
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273 | |
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274 | // Non-standard pi/180, used for converting between degrees and radians |
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275 | #ifndef M_PI_180 |
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276 | # define M_PI_180 0.017453292519943295 |
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277 | #endif |
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278 | """ |
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279 | |
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280 | |
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281 | # The I(q) kernel and the I(qx, qy) kernel have one and two q parameters |
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282 | # respectively, so the template builder will need to do extra work to |
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283 | # declare, initialize and pass the q parameters. |
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284 | KERNEL_1D = { |
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285 | 'fn': "Iq", |
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286 | 'q_par_decl': "global const double *q,", |
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287 | 'qinit': "const double qi = q[i];", |
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288 | 'qcall': "qi", |
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289 | 'qwork': ["q"], |
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290 | } |
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291 | |
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292 | KERNEL_2D = { |
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293 | 'fn': "Iqxy", |
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294 | 'q_par_decl': "global const double *qx,\n global const double *qy,", |
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295 | 'qinit': "const double qxi = qx[i];\n const double qyi = qy[i];", |
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296 | 'qcall': "qxi, qyi", |
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297 | 'qwork': ["qx", "qy"], |
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298 | } |
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299 | |
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300 | # Generic kernel template for the polydispersity loop. |
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301 | # This defines the opencl kernel that is available to the host. The same |
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302 | # structure is used for Iq and Iqxy kernels, so extra flexibility is needed |
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303 | # for q parameters. The polydispersity loop is built elsewhere and |
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304 | # substituted into this template. |
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305 | KERNEL_TEMPLATE = """\ |
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306 | kernel void %(name)s( |
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307 | %(q_par_decl)s |
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308 | global double *result, |
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309 | #ifdef USE_OPENCL |
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310 | global double *loops_g, |
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311 | #else |
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312 | const int Nq, |
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313 | #endif |
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314 | local double *loops, |
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315 | const double cutoff, |
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316 | %(par_decl)s |
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317 | ) |
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318 | { |
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319 | #ifdef USE_OPENCL |
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320 | // copy loops info to local memory |
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321 | event_t e = async_work_group_copy(loops, loops_g, (%(pd_length)s)*2, 0); |
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322 | wait_group_events(1, &e); |
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323 | |
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324 | int i = get_global_id(0); |
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325 | int Nq = get_global_size(0); |
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326 | #endif |
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327 | |
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328 | #ifdef USE_OPENCL |
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329 | if (i < Nq) |
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330 | #else |
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331 | #pragma omp parallel for |
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332 | for (int i=0; i < Nq; i++) |
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333 | #endif |
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334 | { |
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335 | %(qinit)s |
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336 | double ret=0.0, norm=0.0; |
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337 | double vol=0.0, norm_vol=0.0; |
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338 | %(loops)s |
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339 | if (vol*norm_vol != 0.0) { |
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340 | ret *= norm_vol/vol; |
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341 | } |
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342 | result[i] = scale*ret/norm+background; |
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343 | } |
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344 | } |
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345 | """ |
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346 | |
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347 | # Polydispersity loop level. |
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348 | # This pulls the parameter value and weight from the looping vector in order |
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349 | # in preperation for a nested loop. |
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350 | LOOP_OPEN="""\ |
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351 | for (int %(name)s_i=0; %(name)s_i < N%(name)s; %(name)s_i++) { |
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352 | const double %(name)s = loops[2*(%(name)s_i%(offset)s)]; |
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353 | const double %(name)s_w = loops[2*(%(name)s_i%(offset)s)+1];\ |
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354 | """ |
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355 | |
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356 | # Polydispersity loop body. |
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357 | # This computes the weight, and if it is sufficient, calls the scattering |
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358 | # function and adds it to the total. If there is a volume normalization, |
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359 | # it will also be added here. |
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360 | LOOP_BODY="""\ |
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361 | const double weight = %(weight_product)s; |
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362 | if (weight > cutoff) { |
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363 | const double I = %(fn)s(%(qcall)s, %(pcall)s); |
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364 | if (I>=0.0) { // scattering cannot be negative |
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365 | ret += weight*I%(sasview_spherical)s; |
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366 | norm += weight; |
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367 | %(volume_norm)s |
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368 | } |
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369 | //else { printf("exclude qx,qy,I:%%g,%%g,%%g\\n",%(qcall)s,I); } |
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370 | } |
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371 | //else { printf("exclude weight:%%g\\n",weight); }\ |
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372 | """ |
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373 | |
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374 | # Use this when integrating over orientation |
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375 | SPHERICAL_CORRECTION="""\ |
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376 | // Correction factor for spherical integration p(theta) I(q) sin(theta) dtheta |
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377 | double spherical_correction = (Ntheta>1 ? fabs(sin(M_PI_180*theta)) : 1.0);\ |
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378 | """ |
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379 | # Use this to reproduce sasview behaviour |
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380 | SASVIEW_SPHERICAL_CORRECTION="""\ |
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381 | // Correction factor for spherical integration p(theta) I(q) sin(theta) dtheta |
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382 | double spherical_correction = (Ntheta>1 ? fabs(cos(M_PI_180*theta))*M_PI_2 : 1.0);\ |
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383 | """ |
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384 | |
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385 | # Volume normalization. |
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386 | # If there are "volume" polydispersity parameters, then these will be used |
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387 | # to call the form_volume function from the user supplied kernel, and accumulate |
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388 | # a normalized weight. |
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389 | VOLUME_NORM="""const double vol_weight = %(weight)s; |
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390 | vol += vol_weight*form_volume(%(pars)s); |
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391 | norm_vol += vol_weight;\ |
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392 | """ |
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393 | |
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394 | # functions defined as strings in the .py module |
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395 | WORK_FUNCTION="""\ |
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396 | double %(name)s(%(pars)s); |
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397 | double %(name)s(%(pars)s) |
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398 | { |
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399 | %(body)s |
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400 | }\ |
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401 | """ |
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402 | |
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403 | # Documentation header for the module, giving the model name, its short |
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404 | # description and its parameter table. The remainder of the doc comes |
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405 | # from the module docstring. |
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406 | DOC_HEADER=""".. _%(name)s: |
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407 | |
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408 | %(label)s |
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409 | ======================================================= |
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410 | |
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411 | %(title)s |
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412 | |
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413 | %(parameters)s |
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414 | |
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415 | The returned value is scaled to units of |cm^-1|. |
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416 | |
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417 | %(docs)s |
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418 | """ |
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419 | |
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420 | def indent(s, depth): |
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421 | """ |
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422 | Indent a string of text with *depth* additional spaces on each line. |
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423 | """ |
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424 | spaces = " "*depth |
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425 | sep = "\n"+spaces |
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426 | return spaces + sep.join(s.split("\n")) |
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427 | |
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428 | |
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429 | def kernel_name(info, is_2D): |
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430 | """ |
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431 | Name of the exported kernel symbol. |
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432 | """ |
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433 | return info['name'] + "_" + ("Iqxy" if is_2D else "Iq") |
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434 | |
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435 | |
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436 | def use_single(source): |
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437 | """ |
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438 | Convert code from double precision to single precision. |
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439 | """ |
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440 | source = re.sub(r'(^|[^a-zA-Z0-9_])double($|[^a-zA-Z0-9_])', |
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441 | r'\1float\2', source) |
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442 | source = re.sub(r'[^a-zA-Z_](\d*[.]\d+|\d+[.]\d*)([eE][+-]?\d+)?', |
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443 | r'\g<0>f', source) |
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444 | return source |
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445 | |
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446 | |
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447 | def make_kernel(info, is_2D): |
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448 | """ |
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449 | Build a kernel call from metadata supplied by the user. |
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450 | |
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451 | *info* is the json object defined in the kernel file. |
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452 | |
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453 | *form* is either "Iq" or "Iqxy". |
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454 | |
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455 | This does not create a complete OpenCL kernel source, only the top |
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456 | level kernel call with polydispersity and a call to the appropriate |
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457 | Iq or Iqxy function. |
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458 | """ |
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459 | |
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460 | # If we are building the Iqxy kernel, we need to propagate qx,qy |
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461 | # parameters, otherwise we can |
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462 | dim = "2d" if is_2D else "1d" |
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463 | fixed_pars = info['partype']['fixed-'+dim] |
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464 | pd_pars = info['partype']['pd-'+dim] |
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465 | vol_pars = info['partype']['volume'] |
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466 | q_pars = KERNEL_2D if is_2D else KERNEL_1D |
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467 | fn = q_pars['fn'] |
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468 | |
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469 | # Build polydispersity loops |
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470 | depth = 4 |
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471 | offset = "" |
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472 | loop_head = [] |
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473 | loop_end = [] |
---|
474 | for name in pd_pars: |
---|
475 | subst = { 'name': name, 'offset': offset } |
---|
476 | loop_head.append(indent(LOOP_OPEN%subst, depth)) |
---|
477 | loop_end.insert(0, (" "*depth) + "}") |
---|
478 | offset += '+N'+name |
---|
479 | depth += 2 |
---|
480 | |
---|
481 | # The volume parameters in the inner loop are used to call the volume() |
---|
482 | # function in the kernel, with the parameters defined in vol_pars and the |
---|
483 | # weight product defined in weight. If there are no volume parameters, |
---|
484 | # then there will be no volume normalization. |
---|
485 | if vol_pars: |
---|
486 | subst = { |
---|
487 | 'weight': "*".join(p+"_w" for p in vol_pars), |
---|
488 | 'pars': ", ".join(vol_pars), |
---|
489 | } |
---|
490 | volume_norm = VOLUME_NORM%subst |
---|
491 | else: |
---|
492 | volume_norm = "" |
---|
493 | |
---|
494 | # Define the inner loop function call |
---|
495 | # The parameters to the f(q,p1,p2...) call should occur in the same |
---|
496 | # order as given in the parameter info structure. This may be different |
---|
497 | # from the parameter order in the call to the kernel since the kernel |
---|
498 | # call places all fixed parameters before all polydisperse parameters. |
---|
499 | fq_pars = [p[0] for p in info['parameters'][len(COMMON_PARAMETERS):] |
---|
500 | if p[0] in set(fixed_pars+pd_pars)] |
---|
501 | if False and "theta" in pd_pars: |
---|
502 | spherical_correction = [indent(SPHERICAL_CORRECTION, depth)] |
---|
503 | weights = [p+"_w" for p in pd_pars]+['spherical_correction'] |
---|
504 | sasview_spherical = "" |
---|
505 | elif True and "theta" in pd_pars: |
---|
506 | spherical_correction = [indent(SASVIEW_SPHERICAL_CORRECTION,depth)] |
---|
507 | weights = [p+"_w" for p in pd_pars] |
---|
508 | sasview_spherical = "*spherical_correction" |
---|
509 | else: |
---|
510 | spherical_correction = [] |
---|
511 | weights = [p+"_w" for p in pd_pars] |
---|
512 | sasview_spherical = "" |
---|
513 | subst = { |
---|
514 | 'weight_product': "*".join(weights), |
---|
515 | 'volume_norm': volume_norm, |
---|
516 | 'fn': fn, |
---|
517 | 'qcall': q_pars['qcall'], |
---|
518 | 'pcall': ", ".join(fq_pars), # skip scale and background |
---|
519 | 'sasview_spherical': sasview_spherical, |
---|
520 | } |
---|
521 | loop_body = [indent(LOOP_BODY%subst, depth)] |
---|
522 | loops = "\n".join(loop_head+spherical_correction+loop_body+loop_end) |
---|
523 | |
---|
524 | # declarations for non-pd followed by pd pars |
---|
525 | # e.g., |
---|
526 | # const double sld, |
---|
527 | # const int Nradius |
---|
528 | fixed_par_decl = ",\n ".join("const double %s"%p for p in fixed_pars) |
---|
529 | pd_par_decl = ",\n ".join("const int N%s"%p for p in pd_pars) |
---|
530 | if fixed_par_decl and pd_par_decl: |
---|
531 | par_decl = ",\n ".join((fixed_par_decl, pd_par_decl)) |
---|
532 | elif fixed_par_decl: |
---|
533 | par_decl = fixed_par_decl |
---|
534 | else: |
---|
535 | par_decl = pd_par_decl |
---|
536 | |
---|
537 | # Finally, put the pieces together in the kernel. |
---|
538 | subst = { |
---|
539 | # kernel name is, e.g., cylinder_Iq |
---|
540 | 'name': kernel_name(info, is_2D), |
---|
541 | # to declare, e.g., global double q[], |
---|
542 | 'q_par_decl': q_pars['q_par_decl'], |
---|
543 | # to declare, e.g., double sld, int Nradius, int Nlength |
---|
544 | 'par_decl': par_decl, |
---|
545 | # to copy global to local pd pars we need, e.g., Nradius+Nlength |
---|
546 | 'pd_length': "+".join('N'+p for p in pd_pars), |
---|
547 | # the q initializers, e.g., double qi = q[i]; |
---|
548 | 'qinit': q_pars['qinit'], |
---|
549 | # the actual polydispersity loop |
---|
550 | 'loops': loops, |
---|
551 | } |
---|
552 | kernel = KERNEL_TEMPLATE%subst |
---|
553 | |
---|
554 | # If the working function is defined in the kernel metadata as a |
---|
555 | # string, translate the string to an actual function definition |
---|
556 | # and put it before the kernel. |
---|
557 | if info[fn]: |
---|
558 | subst = { |
---|
559 | 'name': fn, |
---|
560 | 'pars': ", ".join("double "+p for p in q_pars['qwork']+fq_pars), |
---|
561 | 'body': info[fn], |
---|
562 | } |
---|
563 | kernel = "\n".join((WORK_FUNCTION%subst, kernel)) |
---|
564 | return kernel |
---|
565 | |
---|
566 | def make_partable(pars): |
---|
567 | """ |
---|
568 | Generate the parameter table to include in the sphinx documentation. |
---|
569 | """ |
---|
570 | pars = COMMON_PARAMETERS + pars |
---|
571 | column_widths = [ |
---|
572 | max(len(p[0]) for p in pars), |
---|
573 | max(len(p[-1]) for p in pars), |
---|
574 | max(len(RST_UNITS[p[1]]) for p in pars), |
---|
575 | PARTABLE_VALUE_WIDTH, |
---|
576 | ] |
---|
577 | column_widths = [max(w, len(h)) |
---|
578 | for w,h in zip(column_widths, PARTABLE_HEADERS)] |
---|
579 | |
---|
580 | sep = " ".join("="*w for w in column_widths) |
---|
581 | lines = [ |
---|
582 | sep, |
---|
583 | " ".join("%-*s"%(w,h) for w,h in zip(column_widths, PARTABLE_HEADERS)), |
---|
584 | sep, |
---|
585 | ] |
---|
586 | for p in pars: |
---|
587 | lines.append(" ".join([ |
---|
588 | "%-*s"%(column_widths[0],p[0]), |
---|
589 | "%-*s"%(column_widths[1],p[-1]), |
---|
590 | "%-*s"%(column_widths[2],RST_UNITS[p[1]]), |
---|
591 | "%*g"%(column_widths[3],p[2]), |
---|
592 | ])) |
---|
593 | lines.append(sep) |
---|
594 | return "\n".join(lines) |
---|
595 | |
---|
596 | def _search(search_path, filename): |
---|
597 | """ |
---|
598 | Find *filename* in *search_path*. |
---|
599 | |
---|
600 | Raises ValueError if file does not exist. |
---|
601 | """ |
---|
602 | for path in search_path: |
---|
603 | target = os.path.join(path, filename) |
---|
604 | if os.path.exists(target): |
---|
605 | return target |
---|
606 | raise ValueError("%r not found in %s"%(filename, search_path)) |
---|
607 | |
---|
608 | def sources(info): |
---|
609 | """ |
---|
610 | Return a list of the sources file paths for the module. |
---|
611 | """ |
---|
612 | from os.path import abspath, dirname, join as joinpath |
---|
613 | search_path = [ dirname(info['filename']), |
---|
614 | abspath(joinpath(dirname(__file__),'models')) ] |
---|
615 | return [_search(search_path, f) for f in info['source']] |
---|
616 | |
---|
617 | def make_model(info): |
---|
618 | """ |
---|
619 | Generate the code for the kernel defined by info, using source files |
---|
620 | found in the given search path. |
---|
621 | """ |
---|
622 | source = [open(f).read() for f in sources(info)] |
---|
623 | # If the form volume is defined as a string, then wrap it in a |
---|
624 | # function definition and place it after the external sources but |
---|
625 | # before the kernel functions. If the kernel functions are strings, |
---|
626 | # they will be translated in the make_kernel call. |
---|
627 | if info['form_volume']: |
---|
628 | subst = { |
---|
629 | 'name': "form_volume", |
---|
630 | 'pars': ", ".join("double "+p for p in info['partype']['volume']), |
---|
631 | 'body': info['form_volume'], |
---|
632 | } |
---|
633 | source.append(WORK_FUNCTION%subst) |
---|
634 | kernel_Iq = make_kernel(info, is_2D=False) |
---|
635 | kernel_Iqxy = make_kernel(info, is_2D=True) |
---|
636 | kernel = "\n\n".join([KERNEL_HEADER]+source+[kernel_Iq, kernel_Iqxy]) |
---|
637 | return kernel |
---|
638 | |
---|
639 | def categorize_parameters(pars): |
---|
640 | """ |
---|
641 | Build parameter categories out of the the parameter definitions. |
---|
642 | |
---|
643 | Returns a dictionary of categories. |
---|
644 | """ |
---|
645 | partype = { |
---|
646 | 'volume': [], 'orientation': [], 'magnetic': [], '': [], |
---|
647 | 'fixed-1d': [], 'fixed-2d': [], 'pd-1d': [], 'pd-2d': [], |
---|
648 | 'pd-rel': set(), |
---|
649 | } |
---|
650 | |
---|
651 | for p in pars: |
---|
652 | name,ptype = p[0],p[4] |
---|
653 | if ptype == 'volume': |
---|
654 | partype['pd-1d'].append(name) |
---|
655 | partype['pd-2d'].append(name) |
---|
656 | partype['pd-rel'].add(name) |
---|
657 | elif ptype == 'magnetic': |
---|
658 | partype['fixed-2d'].append(name) |
---|
659 | elif ptype == 'orientation': |
---|
660 | partype['pd-2d'].append(name) |
---|
661 | elif ptype == '': |
---|
662 | partype['fixed-1d'].append(name) |
---|
663 | partype['fixed-2d'].append(name) |
---|
664 | else: |
---|
665 | raise ValueError("unknown parameter type %r"%ptype) |
---|
666 | partype[ptype].append(name) |
---|
667 | |
---|
668 | return partype |
---|
669 | |
---|
670 | def make(kernel_module): |
---|
671 | """ |
---|
672 | Build an OpenCL/ctypes function from the definition in *kernel_module*. |
---|
673 | |
---|
674 | The module can be loaded with a normal python import statement if you |
---|
675 | know which module you need, or with __import__('sasmodels.model.'+name) |
---|
676 | if the name is in a string. |
---|
677 | """ |
---|
678 | # TODO: allow Iq and Iqxy to be defined in python |
---|
679 | from os.path import abspath |
---|
680 | #print kernelfile |
---|
681 | info = dict( |
---|
682 | filename = abspath(kernel_module.__file__), |
---|
683 | name = kernel_module.name, |
---|
684 | title = kernel_module.title, |
---|
685 | description = kernel_module.description, |
---|
686 | parameters = COMMON_PARAMETERS + kernel_module.parameters, |
---|
687 | source = getattr(kernel_module, 'source', []), |
---|
688 | ) |
---|
689 | # Fill in attributes which default to None |
---|
690 | info.update((k,getattr(kernel_module, k, None)) |
---|
691 | for k in ('ER', 'VR', 'form_volume', 'Iq', 'Iqxy')) |
---|
692 | # Fill in the derived attributes |
---|
693 | info['limits'] = dict((p[0],p[3]) for p in info['parameters']) |
---|
694 | info['partype'] = categorize_parameters(info['parameters']) |
---|
695 | |
---|
696 | source = make_model(info) |
---|
697 | |
---|
698 | return source, info |
---|
699 | |
---|
700 | def doc(kernel_module): |
---|
701 | """ |
---|
702 | Return the documentation for the model. |
---|
703 | """ |
---|
704 | subst = dict(name=kernel_module.name.replace('_','-'), |
---|
705 | label=" ".join(kernel_module.name.split('_')).capitalize(), |
---|
706 | title=kernel_module.title, |
---|
707 | parameters=make_partable(kernel_module.parameters), |
---|
708 | docs=kernel_module.__doc__) |
---|
709 | return DOC_HEADER%subst |
---|
710 | |
---|
711 | |
---|
712 | |
---|
713 | def demo_time(): |
---|
714 | import datetime |
---|
715 | tic = datetime.datetime.now() |
---|
716 | toc = lambda: (datetime.datetime.now()-tic).total_seconds() |
---|
717 | path = os.path.dirname("__file__") |
---|
718 | doc, c = make_model(os.path.join(path, "models", "cylinder.c")) |
---|
719 | print "time:",toc() |
---|
720 | |
---|
721 | def demo(): |
---|
722 | from os.path import join as joinpath, dirname |
---|
723 | c, info, doc = make_model(joinpath(dirname(__file__), "models", "cylinder.c")) |
---|
724 | #print doc |
---|
725 | #print c |
---|
726 | |
---|
727 | if __name__ == "__main__": |
---|
728 | demo() |
---|