1 | /** |
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2 | This software was developed by the University of Tennessee as part of the |
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3 | Distributed Data Analysis of Neutron Scattering Experiments (DANSE) |
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4 | project funded by the US National Science Foundation. |
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5 | |
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6 | If you use DANSE applications to do scientific research that leads to |
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7 | publication, we ask that you acknowledge the use of the software with the |
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8 | following sentence: |
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9 | |
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10 | "This work benefited from DANSE software developed under NSF award DMR-0520547." |
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11 | |
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12 | copyright 2008, University of Tennessee |
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13 | */ |
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14 | |
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15 | /** CGaussian |
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16 | * |
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17 | * C extension |
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18 | * |
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19 | * WARNING: THIS FILE WAS GENERATED BY WRAPPERGENERATOR.PY |
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20 | * DO NOT MODIFY THIS FILE, MODIFY gaussian.h |
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21 | * AND RE-RUN THE GENERATOR SCRIPT |
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22 | * |
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23 | */ |
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24 | #define NO_IMPORT_ARRAY |
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25 | #define PY_ARRAY_UNIQUE_SYMBOL PyArray_API_sans |
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26 | |
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27 | extern "C" { |
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28 | #include <Python.h> |
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29 | #include <arrayobject.h> |
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30 | #include "structmember.h" |
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31 | #include <stdio.h> |
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32 | #include <stdlib.h> |
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33 | #include <math.h> |
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34 | #include <time.h> |
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35 | #include "gaussian.h" |
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36 | } |
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37 | |
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38 | #include "models.hh" |
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39 | #include "dispersion_visitor.hh" |
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40 | |
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41 | /// Error object for raised exceptions |
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42 | static PyObject * CGaussianError = NULL; |
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43 | |
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44 | |
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45 | // Class definition |
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46 | typedef struct { |
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47 | PyObject_HEAD |
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48 | /// Parameters |
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49 | PyObject * params; |
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50 | /// Dispersion parameters |
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51 | PyObject * dispersion; |
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52 | /// Underlying model object |
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53 | Gaussian * model; |
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54 | /// Log for unit testing |
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55 | PyObject * log; |
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56 | } CGaussian; |
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57 | |
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58 | |
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59 | static void |
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60 | CGaussian_dealloc(CGaussian* self) |
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61 | { |
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62 | self->ob_type->tp_free((PyObject*)self); |
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63 | |
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64 | |
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65 | } |
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66 | |
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67 | static PyObject * |
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68 | CGaussian_new(PyTypeObject *type, PyObject *args, PyObject *kwds) |
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69 | { |
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70 | CGaussian *self; |
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71 | |
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72 | self = (CGaussian *)type->tp_alloc(type, 0); |
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73 | |
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74 | return (PyObject *)self; |
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75 | } |
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76 | |
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77 | static int |
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78 | CGaussian_init(CGaussian *self, PyObject *args, PyObject *kwds) |
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79 | { |
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80 | if (self != NULL) { |
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81 | |
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82 | // Create parameters |
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83 | self->params = PyDict_New(); |
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84 | self->dispersion = PyDict_New(); |
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85 | self->model = new Gaussian(); |
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86 | |
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87 | // Initialize parameter dictionary |
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88 | PyDict_SetItemString(self->params,"scale",Py_BuildValue("d",1.000000)); |
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89 | PyDict_SetItemString(self->params,"sigma",Py_BuildValue("d",1.000000)); |
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90 | PyDict_SetItemString(self->params,"center",Py_BuildValue("d",0.000000)); |
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91 | // Initialize dispersion / averaging parameter dict |
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92 | DispersionVisitor* visitor = new DispersionVisitor(); |
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93 | PyObject * disp_dict; |
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94 | |
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95 | |
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96 | |
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97 | // Create empty log |
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98 | self->log = PyDict_New(); |
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99 | |
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100 | |
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101 | |
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102 | } |
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103 | return 0; |
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104 | } |
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105 | |
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106 | static PyMemberDef CGaussian_members[] = { |
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107 | {"params", T_OBJECT, offsetof(CGaussian, params), 0, |
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108 | "Parameters"}, |
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109 | {"dispersion", T_OBJECT, offsetof(CGaussian, dispersion), 0, |
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110 | "Dispersion parameters"}, |
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111 | {"log", T_OBJECT, offsetof(CGaussian, log), 0, |
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112 | "Log"}, |
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113 | {NULL} /* Sentinel */ |
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114 | }; |
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115 | |
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116 | /** Read double from PyObject |
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117 | @param p PyObject |
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118 | @return double |
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119 | */ |
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120 | double CGaussian_readDouble(PyObject *p) { |
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121 | if (PyFloat_Check(p)==1) { |
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122 | return (double)(((PyFloatObject *)(p))->ob_fval); |
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123 | } else if (PyInt_Check(p)==1) { |
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124 | return (double)(((PyIntObject *)(p))->ob_ival); |
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125 | } else if (PyLong_Check(p)==1) { |
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126 | return (double)PyLong_AsLong(p); |
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127 | } else { |
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128 | return 0.0; |
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129 | } |
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130 | } |
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131 | /** |
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132 | * Function to call to evaluate model |
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133 | * @param args: input numpy array q[] |
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134 | * @return: numpy array object |
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135 | */ |
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136 | |
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137 | static PyObject *evaluateOneDim(Gaussian* model, PyArrayObject *q){ |
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138 | PyArrayObject *result; |
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139 | |
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140 | // Check validity of array q , q must be of dimension 1, an array of double |
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141 | if (q->nd != 1 || q->descr->type_num != PyArray_DOUBLE) |
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142 | { |
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143 | //const char * message= "Invalid array: q->nd=%d,type_num=%d\n",q->nd,q->descr->type_num; |
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144 | //PyErr_SetString(PyExc_ValueError , message); |
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145 | return NULL; |
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146 | } |
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147 | result = (PyArrayObject *)PyArray_FromDims(q->nd, (int *)(q->dimensions), |
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148 | PyArray_DOUBLE); |
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149 | if (result == NULL) { |
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150 | const char * message= "Could not create result "; |
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151 | PyErr_SetString(PyExc_RuntimeError , message); |
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152 | return NULL; |
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153 | } |
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154 | for (int i = 0; i < q->dimensions[0]; i++){ |
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155 | double q_value = *(double *)(q->data + i*q->strides[0]); |
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156 | double *result_value = (double *)(result->data + i*result->strides[0]); |
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157 | *result_value =(*model)(q_value); |
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158 | } |
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159 | return PyArray_Return(result); |
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160 | } |
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161 | |
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162 | /** |
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163 | * Function to call to evaluate model |
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164 | * @param args: input numpy array [x[],y[]] |
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165 | * @return: numpy array object |
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166 | */ |
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167 | static PyObject * evaluateTwoDimXY( Gaussian* model, |
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168 | PyArrayObject *x, PyArrayObject *y) |
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169 | { |
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170 | PyArrayObject *result; |
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171 | int i,j, x_len, y_len, dims[2]; |
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172 | //check validity of input vectors |
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173 | if (x->nd != 2 || x->descr->type_num != PyArray_DOUBLE |
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174 | || y->nd != 2 || y->descr->type_num != PyArray_DOUBLE |
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175 | || y->dimensions[1] != x->dimensions[0]){ |
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176 | const char * message= "evaluateTwoDimXY expect 2 numpy arrays"; |
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177 | PyErr_SetString(PyExc_ValueError , message); |
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178 | return NULL; |
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179 | } |
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180 | |
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181 | if (PyArray_Check(x) && PyArray_Check(y)) { |
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182 | |
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183 | x_len = dims[1]= x->dimensions[1]; |
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184 | y_len = dims[0]= y->dimensions[0]; |
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185 | |
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186 | // Make a new double matrix of same dims |
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187 | result=(PyArrayObject *) PyArray_FromDims(2,dims,NPY_DOUBLE); |
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188 | if (result == NULL){ |
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189 | const char * message= "Could not create result "; |
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190 | PyErr_SetString(PyExc_RuntimeError , message); |
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191 | return NULL; |
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192 | } |
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193 | |
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194 | /* Do the calculation. */ |
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195 | for ( j=0; j< y_len; j++) { |
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196 | for ( i=0; i< x_len; i++) { |
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197 | double x_value = *(double *)(x->data + i*x->strides[1]); |
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198 | double y_value = *(double *)(y->data + j*y->strides[0]); |
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199 | double *result_value = (double *)(result->data + |
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200 | i*result->strides[1] + j*result->strides[0]); |
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201 | *result_value = (*model)(x_value, y_value); |
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202 | } |
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203 | } |
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204 | return PyArray_Return(result); |
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205 | |
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206 | }else{ |
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207 | PyErr_SetString(CGaussianError, |
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208 | "CGaussian.evaluateTwoDimXY couldn't run."); |
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209 | return NULL; |
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210 | } |
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211 | } |
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212 | /** |
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213 | * evalDistribution function evaluate a model function with input vector |
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214 | * @param args: input q as vector or [qx, qy] where qx, qy are vectors |
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215 | * |
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216 | */ |
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217 | static PyObject * evalDistribution(CGaussian *self, PyObject *args){ |
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218 | PyObject *qx, *qy; |
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219 | PyArrayObject * pars; |
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220 | int npars ,mpars; |
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221 | |
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222 | // Get parameters |
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223 | |
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224 | // Reader parameter dictionary |
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225 | self->model->scale = PyFloat_AsDouble( PyDict_GetItemString(self->params, "scale") ); |
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226 | self->model->sigma = PyFloat_AsDouble( PyDict_GetItemString(self->params, "sigma") ); |
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227 | self->model->center = PyFloat_AsDouble( PyDict_GetItemString(self->params, "center") ); |
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228 | // Read in dispersion parameters |
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229 | PyObject* disp_dict; |
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230 | DispersionVisitor* visitor = new DispersionVisitor(); |
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231 | |
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232 | |
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233 | // Get input and determine whether we have to supply a 1D or 2D return value. |
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234 | if ( !PyArg_ParseTuple(args,"O",&pars) ) { |
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235 | PyErr_SetString(CGaussianError, |
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236 | "CGaussian.evalDistribution expects a q value."); |
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237 | return NULL; |
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238 | } |
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239 | // Check params |
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240 | |
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241 | if(PyArray_Check(pars)==1) { |
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242 | |
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243 | // Length of list should 1 or 2 |
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244 | npars = pars->nd; |
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245 | if(npars==1) { |
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246 | // input is a numpy array |
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247 | if (PyArray_Check(pars)) { |
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248 | return evaluateOneDim(self->model, (PyArrayObject*)pars); |
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249 | } |
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250 | }else{ |
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251 | PyErr_SetString(CGaussianError, |
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252 | "CGaussian.evalDistribution expect numpy array of one dimension."); |
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253 | return NULL; |
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254 | } |
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255 | }else if( PyList_Check(pars)==1) { |
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256 | // Length of list should be 2 for I(qx,qy) |
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257 | mpars = PyList_GET_SIZE(pars); |
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258 | if(mpars!=2) { |
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259 | PyErr_SetString(CGaussianError, |
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260 | "CGaussian.evalDistribution expects a list of dimension 2."); |
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261 | return NULL; |
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262 | } |
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263 | qx = PyList_GET_ITEM(pars,0); |
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264 | qy = PyList_GET_ITEM(pars,1); |
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265 | if (PyArray_Check(qx) && PyArray_Check(qy)) { |
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266 | return evaluateTwoDimXY(self->model, (PyArrayObject*)qx, |
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267 | (PyArrayObject*)qy); |
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268 | }else{ |
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269 | PyErr_SetString(CGaussianError, |
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270 | "CGaussian.evalDistribution expect 2 numpy arrays in list."); |
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271 | return NULL; |
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272 | } |
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273 | } |
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274 | PyErr_SetString(CGaussianError, |
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275 | "CGaussian.evalDistribution couln't be run."); |
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276 | return NULL; |
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277 | |
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278 | } |
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279 | |
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280 | /** |
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281 | * Function to call to evaluate model |
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282 | * @param args: input q or [q,phi] |
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283 | * @return: function value |
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284 | */ |
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285 | static PyObject * run(CGaussian *self, PyObject *args) { |
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286 | double q_value, phi_value; |
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287 | PyObject* pars; |
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288 | int npars; |
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289 | |
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290 | // Get parameters |
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291 | |
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292 | // Reader parameter dictionary |
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293 | self->model->scale = PyFloat_AsDouble( PyDict_GetItemString(self->params, "scale") ); |
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294 | self->model->sigma = PyFloat_AsDouble( PyDict_GetItemString(self->params, "sigma") ); |
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295 | self->model->center = PyFloat_AsDouble( PyDict_GetItemString(self->params, "center") ); |
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296 | // Read in dispersion parameters |
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297 | PyObject* disp_dict; |
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298 | DispersionVisitor* visitor = new DispersionVisitor(); |
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299 | |
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300 | |
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301 | // Get input and determine whether we have to supply a 1D or 2D return value. |
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302 | if ( !PyArg_ParseTuple(args,"O",&pars) ) { |
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303 | PyErr_SetString(CGaussianError, |
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304 | "CGaussian.run expects a q value."); |
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305 | return NULL; |
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306 | } |
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307 | |
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308 | // Check params |
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309 | if( PyList_Check(pars)==1) { |
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310 | |
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311 | // Length of list should be 2 for I(q,phi) |
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312 | npars = PyList_GET_SIZE(pars); |
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313 | if(npars!=2) { |
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314 | PyErr_SetString(CGaussianError, |
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315 | "CGaussian.run expects a double or a list of dimension 2."); |
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316 | return NULL; |
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317 | } |
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318 | // We have a vector q, get the q and phi values at which |
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319 | // to evaluate I(q,phi) |
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320 | q_value = CGaussian_readDouble(PyList_GET_ITEM(pars,0)); |
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321 | phi_value = CGaussian_readDouble(PyList_GET_ITEM(pars,1)); |
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322 | // Skip zero |
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323 | if (q_value==0) { |
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324 | return Py_BuildValue("d",0.0); |
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325 | } |
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326 | return Py_BuildValue("d",(*(self->model)).evaluate_rphi(q_value,phi_value)); |
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327 | |
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328 | } else { |
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329 | |
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330 | // We have a scalar q, we will evaluate I(q) |
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331 | q_value = CGaussian_readDouble(pars); |
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332 | |
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333 | return Py_BuildValue("d",(*(self->model))(q_value)); |
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334 | } |
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335 | } |
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336 | |
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337 | /** |
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338 | * Function to call to evaluate model in cartesian coordinates |
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339 | * @param args: input q or [qx, qy]] |
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340 | * @return: function value |
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341 | */ |
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342 | static PyObject * runXY(CGaussian *self, PyObject *args) { |
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343 | double qx_value, qy_value; |
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344 | PyObject* pars; |
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345 | int npars; |
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346 | |
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347 | // Get parameters |
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348 | |
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349 | // Reader parameter dictionary |
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350 | self->model->scale = PyFloat_AsDouble( PyDict_GetItemString(self->params, "scale") ); |
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351 | self->model->sigma = PyFloat_AsDouble( PyDict_GetItemString(self->params, "sigma") ); |
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352 | self->model->center = PyFloat_AsDouble( PyDict_GetItemString(self->params, "center") ); |
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353 | // Read in dispersion parameters |
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354 | PyObject* disp_dict; |
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355 | DispersionVisitor* visitor = new DispersionVisitor(); |
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356 | |
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357 | |
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358 | // Get input and determine whether we have to supply a 1D or 2D return value. |
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359 | if ( !PyArg_ParseTuple(args,"O",&pars) ) { |
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360 | PyErr_SetString(CGaussianError, |
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361 | "CGaussian.run expects a q value."); |
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362 | return NULL; |
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363 | } |
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364 | |
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365 | // Check params |
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366 | if( PyList_Check(pars)==1) { |
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367 | |
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368 | // Length of list should be 2 for I(qx, qy)) |
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369 | npars = PyList_GET_SIZE(pars); |
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370 | if(npars!=2) { |
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371 | PyErr_SetString(CGaussianError, |
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372 | "CGaussian.run expects a double or a list of dimension 2."); |
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373 | return NULL; |
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374 | } |
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375 | // We have a vector q, get the qx and qy values at which |
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376 | // to evaluate I(qx,qy) |
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377 | qx_value = CGaussian_readDouble(PyList_GET_ITEM(pars,0)); |
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378 | qy_value = CGaussian_readDouble(PyList_GET_ITEM(pars,1)); |
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379 | return Py_BuildValue("d",(*(self->model))(qx_value,qy_value)); |
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380 | |
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381 | } else { |
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382 | |
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383 | // We have a scalar q, we will evaluate I(q) |
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384 | qx_value = CGaussian_readDouble(pars); |
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385 | |
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386 | return Py_BuildValue("d",(*(self->model))(qx_value)); |
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387 | } |
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388 | } |
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389 | |
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390 | static PyObject * reset(CGaussian *self, PyObject *args) { |
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391 | |
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392 | |
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393 | return Py_BuildValue("d",0.0); |
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394 | } |
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395 | |
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396 | static PyObject * set_dispersion(CGaussian *self, PyObject *args) { |
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397 | PyObject * disp; |
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398 | const char * par_name; |
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399 | |
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400 | if ( !PyArg_ParseTuple(args,"sO", &par_name, &disp) ) { |
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401 | PyErr_SetString(CGaussianError, |
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402 | "CGaussian.set_dispersion expects a DispersionModel object."); |
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403 | return NULL; |
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404 | } |
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405 | void *temp = PyCObject_AsVoidPtr(disp); |
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406 | DispersionModel * dispersion = static_cast<DispersionModel *>(temp); |
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407 | |
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408 | |
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409 | // Ugliness necessary to go from python to C |
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410 | // TODO: refactor this |
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411 | { |
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412 | PyErr_SetString(CGaussianError, |
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413 | "CGaussian.set_dispersion expects a valid parameter name."); |
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414 | return NULL; |
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415 | } |
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416 | |
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417 | DispersionVisitor* visitor = new DispersionVisitor(); |
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418 | PyObject * disp_dict = PyDict_New(); |
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419 | dispersion->accept_as_source(visitor, dispersion, disp_dict); |
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420 | PyDict_SetItemString(self->dispersion, par_name, disp_dict); |
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421 | return Py_BuildValue("i",1); |
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422 | } |
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423 | |
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424 | |
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425 | static PyMethodDef CGaussian_methods[] = { |
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426 | {"run", (PyCFunction)run , METH_VARARGS, |
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427 | "Evaluate the model at a given Q or Q, phi"}, |
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428 | {"runXY", (PyCFunction)runXY , METH_VARARGS, |
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429 | "Evaluate the model at a given Q or Qx, Qy"}, |
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430 | |
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431 | {"evalDistribution", (PyCFunction)evalDistribution , METH_VARARGS, |
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432 | "Evaluate the model at a given Q or Qx, Qy vector "}, |
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433 | {"reset", (PyCFunction)reset , METH_VARARGS, |
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434 | "Reset pair correlation"}, |
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435 | {"set_dispersion", (PyCFunction)set_dispersion , METH_VARARGS, |
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436 | "Set the dispersion model for a given parameter"}, |
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437 | {NULL} |
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438 | }; |
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439 | |
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440 | static PyTypeObject CGaussianType = { |
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441 | PyObject_HEAD_INIT(NULL) |
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442 | 0, /*ob_size*/ |
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443 | "CGaussian", /*tp_name*/ |
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444 | sizeof(CGaussian), /*tp_basicsize*/ |
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445 | 0, /*tp_itemsize*/ |
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446 | (destructor)CGaussian_dealloc, /*tp_dealloc*/ |
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447 | 0, /*tp_print*/ |
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448 | 0, /*tp_getattr*/ |
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449 | 0, /*tp_setattr*/ |
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450 | 0, /*tp_compare*/ |
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451 | 0, /*tp_repr*/ |
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452 | 0, /*tp_as_number*/ |
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453 | 0, /*tp_as_sequence*/ |
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454 | 0, /*tp_as_mapping*/ |
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455 | 0, /*tp_hash */ |
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456 | 0, /*tp_call*/ |
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457 | 0, /*tp_str*/ |
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458 | 0, /*tp_getattro*/ |
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459 | 0, /*tp_setattro*/ |
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460 | 0, /*tp_as_buffer*/ |
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461 | Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/ |
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462 | "CGaussian objects", /* tp_doc */ |
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463 | 0, /* tp_traverse */ |
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464 | 0, /* tp_clear */ |
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465 | 0, /* tp_richcompare */ |
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466 | 0, /* tp_weaklistoffset */ |
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467 | 0, /* tp_iter */ |
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468 | 0, /* tp_iternext */ |
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469 | CGaussian_methods, /* tp_methods */ |
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470 | CGaussian_members, /* tp_members */ |
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471 | 0, /* tp_getset */ |
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472 | 0, /* tp_base */ |
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473 | 0, /* tp_dict */ |
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474 | 0, /* tp_descr_get */ |
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475 | 0, /* tp_descr_set */ |
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476 | 0, /* tp_dictoffset */ |
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477 | (initproc)CGaussian_init, /* tp_init */ |
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478 | 0, /* tp_alloc */ |
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479 | CGaussian_new, /* tp_new */ |
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480 | }; |
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481 | |
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482 | |
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483 | //static PyMethodDef module_methods[] = { |
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484 | // {NULL} |
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485 | //}; |
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486 | |
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487 | /** |
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488 | * Function used to add the model class to a module |
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489 | * @param module: module to add the class to |
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490 | */ |
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491 | void addCGaussian(PyObject *module) { |
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492 | PyObject *d; |
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493 | |
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494 | if (PyType_Ready(&CGaussianType) < 0) |
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495 | return; |
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496 | |
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497 | Py_INCREF(&CGaussianType); |
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498 | PyModule_AddObject(module, "CGaussian", (PyObject *)&CGaussianType); |
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499 | |
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500 | d = PyModule_GetDict(module); |
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501 | CGaussianError = PyErr_NewException("CGaussian.error", NULL, NULL); |
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502 | PyDict_SetItemString(d, "CGaussianError", CGaussianError); |
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503 | } |
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504 | |
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