1 | /* -*- mode: c++; c-basic-offset: 4; indent-tabs-mode: nil -*- */ |
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2 | /* |
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3 | * Copyright (c) 2004-2013 HUBzero Foundation, LLC |
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4 | * |
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5 | * Authors: |
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6 | * Insoo Woo <iwoo@purdue.edu> |
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7 | */ |
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8 | #include <cstdio> |
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9 | #include <cstring> |
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10 | #include <cstdlib> |
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11 | #include <fstream> |
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12 | |
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13 | #include <vrmath/Vector3f.h> |
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14 | |
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15 | #include "ZincBlendeReconstructor.h" |
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16 | #include "ZincBlendeVolume.h" |
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17 | #include "Trace.h" |
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18 | |
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19 | using namespace nv; |
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20 | using namespace vrmath; |
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21 | |
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22 | ZincBlendeReconstructor *ZincBlendeReconstructor::_instance = NULL; |
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23 | |
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24 | ZincBlendeReconstructor::ZincBlendeReconstructor() |
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25 | { |
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26 | } |
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27 | |
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28 | ZincBlendeReconstructor::~ZincBlendeReconstructor() |
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29 | { |
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30 | } |
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31 | |
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32 | ZincBlendeReconstructor *ZincBlendeReconstructor::getInstance() |
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33 | { |
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34 | if (_instance == NULL) { |
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35 | return (_instance = new ZincBlendeReconstructor()); |
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36 | } |
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37 | |
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38 | return _instance; |
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39 | } |
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40 | |
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41 | ZincBlendeVolume *ZincBlendeReconstructor::loadFromFile(const char *fileName) |
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42 | { |
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43 | std::ifstream stream; |
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44 | stream.open(fileName, std::ios::binary); |
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45 | |
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46 | ZincBlendeVolume *volume = loadFromStream(stream); |
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47 | |
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48 | stream.close(); |
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49 | |
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50 | return volume; |
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51 | } |
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52 | |
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53 | ZincBlendeVolume *ZincBlendeReconstructor::loadFromStream(std::istream& stream) |
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54 | { |
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55 | ZincBlendeVolume *volume = NULL; |
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56 | Vector3f origin, delta; |
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57 | int width = 0, height = 0, depth = 0; |
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58 | void *data = NULL; |
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59 | int version = 1; |
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60 | |
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61 | char str[5][20]; |
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62 | do { |
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63 | getLine(stream); |
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64 | if (_buff[0] == '#') { |
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65 | continue; |
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66 | } else if (strstr((const char*) _buff, "object") != 0) { |
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67 | TRACE("VERSION 1"); |
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68 | version = 1; |
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69 | break; |
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70 | } else if (strstr(_buff, "record format") != 0) { |
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71 | TRACE("VERSION 2"); |
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72 | version = 2; |
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73 | break; |
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74 | } |
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75 | } while (1); |
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76 | |
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77 | if (version == 1) { |
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78 | float dummy; |
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79 | |
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80 | sscanf(_buff, "%s%s%s%s%s%d%d%d", str[0], str[1], str[2], str[3], str[4], &width, &height, &depth); |
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81 | getLine(stream); |
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82 | sscanf(_buff, "%s%f%f%f", str[0], &(origin.x), &(origin.y), &(origin.z)); |
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83 | getLine(stream); |
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84 | sscanf(_buff, "%s%f%f%f", str[0], &(delta.x), &dummy, &dummy); |
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85 | getLine(stream); |
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86 | sscanf(_buff, "%s%f%f%f", str[0], &dummy, &(delta.y), &dummy); |
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87 | getLine(stream); |
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88 | sscanf(_buff, "%s%f%f%f", str[0], &dummy, &dummy, &(delta.z)); |
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89 | do { |
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90 | getLine(stream); |
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91 | } while (strcmp(_buff, "<\\HDR>") != 0); |
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92 | |
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93 | width = width / 4; |
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94 | height = height / 4; |
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95 | depth = depth / 4; |
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96 | //data = new double[width * height * depth * 8 * 4]; |
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97 | data = malloc(width * height * depth * 8 * 4 * sizeof(double)); |
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98 | // 8 atom per cell, 4 double (x, y, z, and probability) per atom |
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99 | try { |
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100 | stream.read((char *)data, width * height * depth * 8 * 4 * sizeof(double)); |
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101 | } catch (...) { |
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102 | ERROR("Caught exception trying to read stream"); |
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103 | } |
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104 | |
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105 | volume = buildUp(origin, delta, width, height, depth, data); |
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106 | |
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107 | free(data); |
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108 | } else if (version == 2) { |
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109 | const char *pt; |
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110 | int datacount; |
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111 | double emptyvalue; |
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112 | do { |
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113 | getLine(stream); |
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114 | if ((pt = strstr(_buff, "delta")) != 0) { |
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115 | sscanf(pt, "%s%f%f%f", str[0], &(delta.x), &(delta.y), &(delta.z)); |
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116 | #ifdef _LOADER_DEBUG_ |
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117 | TRACE("delta : %f %f %f", delta.x, delta.y, delta.z); |
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118 | #endif |
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119 | } else if ((pt = strstr(_buff, "datacount")) != 0) { |
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120 | sscanf(pt, "%s%d", str[0], &datacount); |
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121 | #ifdef _LOADER_DEBUG_ |
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122 | TRACE("datacount = %d", datacount); |
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123 | #endif |
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124 | } else if ((pt = strstr(_buff, "datatype")) != 0) { |
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125 | sscanf(pt, "%s%s", str[0], str[1]); |
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126 | if (strcmp(str[1], "double64")) { |
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127 | } |
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128 | } else if ((pt = strstr(_buff, "count")) != 0) { |
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129 | sscanf(pt, "%s%d%d%d", str[0], &width, &height, &depth); |
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130 | #ifdef _LOADER_DEBUG_ |
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131 | TRACE("width height depth %d %d %d", width, height, depth); |
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132 | #endif |
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133 | } else if ((pt = strstr(_buff, "emptymark")) != 0) { |
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134 | sscanf(pt, "%s%lf", str[0], &emptyvalue); |
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135 | #ifdef _LOADER_DEBUG_ |
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136 | TRACE("emptyvalue %lf", emptyvalue); |
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137 | #endif |
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138 | } |
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139 | } while (strcmp(_buff, "<\\HDR>") != 0 && strcmp(_buff, "</HDR>") != 0); |
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140 | |
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141 | data = malloc(width * height * depth * 8 * 4 * sizeof(double)); |
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142 | memset(data, 0, width * height * depth * 8 * 4 * sizeof(double)); |
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143 | stream.read((char *) data, width * height * depth * 8 * 4 * sizeof(double)); |
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144 | |
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145 | volume = buildUp(origin, delta, width, height, depth, datacount, emptyvalue, data); |
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146 | free(data); |
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147 | } |
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148 | return volume; |
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149 | } |
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150 | |
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151 | struct _NvAtomInfo { |
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152 | double indexX, indexY, indexZ; |
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153 | double atom; |
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154 | |
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155 | int getIndex(int width, int height) const |
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156 | { |
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157 | // NOTE |
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158 | // Zinc blende data has different axes from OpenGL |
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159 | // + z -> +x (OpenGL) |
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160 | // + x -> +y (OpenGL) |
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161 | // + y -> +z (OpenGL), But in 3D texture coordinate is the opposite direction of z |
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162 | // The reason why index is multiplied by 4 is that one unit cell has half of eight atoms, |
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163 | // i.e. four atoms are mapped into RGBA component of one texel |
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164 | //return ((int) (indexZ - 1)+ (int) (indexX - 1) * width + (int) (indexY - 1) * width * height) * 4; |
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165 | return ((int)(indexX - 1) + (int)(indexY - 1) * width + (int)(indexZ - 1) * width * height) * 4; |
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166 | } |
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167 | }; |
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168 | |
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169 | template<class T> |
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170 | inline T _NvMax2(T a, T b) |
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171 | { return ((a >= b)? a : b); } |
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172 | |
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173 | template<class T> |
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174 | inline T _NvMin2(T a, T b) |
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175 | { return ((a >= b)? a : b); } |
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176 | |
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177 | template<class T> |
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178 | inline T _NvMax3(T a, T b, T c) |
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179 | { return ((a >= b)? ((a >= c) ? a : c) : ((b >= c)? b : c)); } |
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180 | |
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181 | template<class T> |
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182 | inline T _NvMin3(T a, T b, T c) |
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183 | { return ((a <= b)? ((a <= c) ? a : c) : ((b <= c)? b : c)); } |
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184 | |
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185 | template<class T> |
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186 | inline T _NvMax9(T* a, T curMax) |
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187 | { return _NvMax3(_NvMax3(a[0], a[1], a[2]), _NvMax3(a[3], a[4], a[5]), _NvMax3(a[6], a[7], curMax)); } |
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188 | |
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189 | template<class T> |
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190 | inline T _NvMin9(T* a, T curMax) |
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191 | { return _NvMin3(_NvMax3(a[0], a[1], a[2]), _NvMin3(a[3], a[4], a[5]), _NvMin3(a[6], a[7], curMax)); } |
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192 | |
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193 | template<class T> |
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194 | inline T _NvMax4(T* a) |
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195 | { return _NvMax2(_NvMax2(a[0], a[1]), _NvMax2(a[2], a[3])); } |
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196 | |
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197 | template<class T> |
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198 | inline T _NvMin4(T* a) |
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199 | { return _NvMin2(_NvMin2(a[0], a[1]), _NvMin2(a[2], a[3])); } |
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200 | |
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201 | ZincBlendeVolume * |
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202 | ZincBlendeReconstructor::buildUp(const Vector3f& origin, const Vector3f& delta, |
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203 | int width, int height, int depth, void *data) |
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204 | { |
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205 | ZincBlendeVolume *zincBlendeVolume = NULL; |
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206 | |
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207 | float *fourAnionVolume, *fourCationVolume; |
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208 | int cellCount = width * height * depth; |
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209 | fourAnionVolume = new float[cellCount * sizeof(float) * 4]; |
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210 | fourCationVolume = new float[cellCount * sizeof(float) * 4]; |
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211 | |
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212 | _NvAtomInfo *srcPtr = (_NvAtomInfo *)data; |
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213 | |
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214 | float vmin, vmax, nzero_min; |
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215 | float *component4A, *component4B; |
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216 | int index; |
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217 | |
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218 | nzero_min = 0.0f; /* Suppress compiler warning. */ |
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219 | vmin = vmax = srcPtr->atom; |
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220 | |
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221 | for (int i = 0; i < cellCount; ++i) { |
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222 | index = srcPtr->getIndex(width, height); |
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223 | |
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224 | #ifdef _LOADER_DEBUG_ |
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225 | TRACE("index %d", index); |
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226 | #endif |
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227 | |
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228 | component4A = fourAnionVolume + index; |
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229 | component4B = fourCationVolume + index; |
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230 | |
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231 | component4A[0] = (float)srcPtr->atom; srcPtr++; |
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232 | component4A[1] = (float)srcPtr->atom; srcPtr++; |
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233 | component4A[2] = (float)srcPtr->atom; srcPtr++; |
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234 | component4A[3] = (float)srcPtr->atom; srcPtr++; |
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235 | |
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236 | component4B[0] = (float)srcPtr->atom; srcPtr++; |
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237 | component4B[1] = (float)srcPtr->atom; srcPtr++; |
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238 | component4B[2] = (float)srcPtr->atom; srcPtr++; |
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239 | component4B[3] = (float)srcPtr->atom; srcPtr++; |
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240 | |
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241 | vmax = _NvMax3(_NvMax4(component4A), _NvMax4(component4B), vmax); |
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242 | vmin = _NvMin3(_NvMin4(component4A), _NvMin4(component4B), vmin); |
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243 | |
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244 | if (vmin != 0.0 && vmin < nzero_min) { |
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245 | nzero_min = vmin; |
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246 | } |
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247 | } |
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248 | |
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249 | double dv = vmax - vmin; |
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250 | if (vmax != 0.0f) { |
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251 | for (int i = 0; i < cellCount; ++i) { |
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252 | fourAnionVolume[i] = (fourAnionVolume[i] - vmin)/ dv; |
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253 | fourCationVolume[i] = (fourCationVolume[i] - vmin) / dv; |
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254 | } |
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255 | } |
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256 | |
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257 | Vector3f cellSize; |
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258 | cellSize.x = 0.25 / width; |
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259 | cellSize.y = 0.25 / height; |
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260 | cellSize.z = 0.25 / depth; |
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261 | |
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262 | zincBlendeVolume = new ZincBlendeVolume(origin.x, origin.y, origin.z, |
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263 | width, height, depth, 4, |
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264 | fourAnionVolume, fourCationVolume, |
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265 | vmin, vmax, nzero_min, cellSize); |
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266 | |
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267 | return zincBlendeVolume; |
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268 | } |
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269 | |
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270 | ZincBlendeVolume * |
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271 | ZincBlendeReconstructor::buildUp(const Vector3f& origin, const Vector3f& delta, |
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272 | int width, int height, int depth, |
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273 | int datacount, double emptyvalue, void* data) |
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274 | { |
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275 | ZincBlendeVolume *zincBlendeVolume = NULL; |
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276 | float *fourAnionVolume, *fourCationVolume; |
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277 | int size = width * height * depth * 4; |
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278 | fourAnionVolume = new float[size]; |
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279 | fourCationVolume = new float[size]; |
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280 | |
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281 | memset(fourAnionVolume, 0, size * sizeof(float)); |
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282 | memset(fourCationVolume, 0, size * sizeof(float)); |
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283 | |
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284 | _NvAtomInfo *srcPtr = (_NvAtomInfo *) data; |
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285 | |
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286 | float *component4A, *component4B; |
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287 | float vmin, vmax, nzero_min; |
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288 | int index; |
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289 | nzero_min = 1e23f; |
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290 | vmin = vmax = srcPtr->atom; |
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291 | for (int i = 0; i < datacount; ++i) { |
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292 | index = srcPtr->getIndex(width, height); |
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293 | |
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294 | #ifdef _LOADER_DEBUG_ |
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295 | TRACE("[%d] index %d (width:%lf height:%lf depth:%lf)", i, index, srcPtr->indexX, srcPtr->indexY, srcPtr->indexZ); |
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296 | #endif |
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297 | |
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298 | if (index < 0) { |
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299 | #ifdef _LOADER_DEBUG_ |
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300 | TRACE("There is an invalid data"); |
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301 | #endif |
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302 | srcPtr +=8; |
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303 | continue; |
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304 | } |
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305 | |
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306 | component4A = fourAnionVolume + index; |
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307 | component4B = fourCationVolume + index; |
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308 | |
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309 | component4A[0] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
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310 | component4A[1] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
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311 | component4A[2] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
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312 | component4A[3] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
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313 | |
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314 | component4B[0] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
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315 | component4B[1] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
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316 | component4B[2] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
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317 | component4B[3] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
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318 | |
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319 | vmax = _NvMax3(_NvMax4(component4A), _NvMax4(component4B), vmax); |
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320 | vmin = _NvMin3(_NvMin4(component4A), _NvMin4(component4B), vmin); |
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321 | |
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322 | if (vmin != 0.0 && vmin < nzero_min) { |
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323 | nzero_min = vmin; |
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324 | } |
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325 | } |
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326 | |
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327 | double dv = vmax - vmin; |
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328 | if (vmax != 0.0f) { |
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329 | for (int i = 0; i < datacount; ++i) { |
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330 | fourAnionVolume[i] = (fourAnionVolume[i] - vmin)/ dv; |
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331 | fourCationVolume[i] = (fourCationVolume[i] - vmin) / dv; |
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332 | } |
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333 | } |
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334 | |
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335 | Vector3f cellSize; |
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336 | cellSize.x = 0.25 / width; |
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337 | cellSize.y = 0.25 / height; |
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338 | cellSize.z = 0.25 / depth; |
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339 | |
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340 | zincBlendeVolume = new ZincBlendeVolume(origin.x, origin.y, origin.z, |
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341 | width, height, depth, 4, |
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342 | fourAnionVolume, fourCationVolume, |
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343 | vmin, vmax, nzero_min, cellSize); |
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344 | |
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345 | return zincBlendeVolume; |
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346 | } |
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347 | |
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348 | void ZincBlendeReconstructor::getLine(std::istream& sin) |
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349 | { |
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350 | char ch; |
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351 | int index = 0; |
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352 | do { |
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353 | sin.get(ch); |
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354 | if (ch == '\n') break; |
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355 | _buff[index++] = ch; |
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356 | if (ch == '>') { |
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357 | if (_buff[1] == '\\') |
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358 | break; |
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359 | } |
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360 | } while (!sin.eof()); |
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361 | |
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362 | _buff[index] = '\0'; |
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363 | |
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364 | #ifdef _LOADER_DEBUG_ |
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365 | TRACE("%s", _buff); |
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366 | #endif |
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367 | } |
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368 | |
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369 | ZincBlendeVolume * |
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370 | ZincBlendeReconstructor::loadFromMemory(const void *dataBlock) |
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371 | { |
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372 | ZincBlendeVolume *volume = NULL; |
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373 | Vector3f origin, delta; |
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374 | int width = 0, height = 0, depth = 0; |
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375 | void *data = NULL; |
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376 | int version = 1; |
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377 | |
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378 | const unsigned char *stream = (const unsigned char *)dataBlock; |
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379 | char str[5][20]; |
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380 | do { |
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381 | getLine(stream); |
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382 | if (_buff[0] == '#') { |
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383 | continue; |
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384 | } else if (strstr((const char *)_buff, "object") != 0) { |
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385 | TRACE("VERSION 1"); |
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386 | version = 1; |
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387 | break; |
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388 | } else if (strstr(_buff, "record format") != 0) { |
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389 | TRACE("VERSION 2"); |
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390 | version = 2; |
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391 | break; |
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392 | } |
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393 | } while (1); |
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394 | |
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395 | if (version == 1) { |
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396 | float dummy; |
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397 | |
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398 | sscanf(_buff, "%s%s%s%s%s%d%d%d", str[0], str[1], str[2], str[3], str[4],&width, &height, &depth); |
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399 | getLine(stream); |
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400 | sscanf(_buff, "%s%f%f%f", str[0], &(origin.x), &(origin.y), &(origin.z)); |
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401 | getLine(stream); |
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402 | sscanf(_buff, "%s%f%f%f", str[0], &(delta.x), &dummy, &dummy); |
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403 | getLine(stream); |
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404 | sscanf(_buff, "%s%f%f%f", str[0], &dummy, &(delta.y), &dummy); |
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405 | getLine(stream); |
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406 | sscanf(_buff, "%s%f%f%f", str[0], &dummy, &dummy, &(delta.z)); |
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407 | do { |
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408 | getLine(stream); |
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409 | } while (strcmp(_buff, "<\\HDR>") != 0); |
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410 | |
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411 | width = width / 4; |
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412 | height = height / 4; |
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413 | depth = depth / 4; |
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414 | data = malloc(width * height * depth * 8 * 4 * sizeof(double)); |
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415 | // 8 atom per cell, 4 double (x, y, z, and probability) per atom |
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416 | memcpy(data, stream, width * height * depth * 8 * 4 * sizeof(double)); |
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417 | |
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418 | volume = buildUp(origin, delta, width, height, depth, data); |
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419 | |
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420 | free(data); |
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421 | } else if (version == 2) { |
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422 | const char *pt; |
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423 | int datacount = -1; |
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424 | double emptyvalue; |
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425 | do { |
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426 | getLine(stream); |
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427 | if ((pt = strstr(_buff, "delta")) != 0) { |
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428 | sscanf(pt, "%s%f%f%f", str[0], &(delta.x), &(delta.y), &(delta.z)); |
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429 | #ifdef _LOADER_DEBUG_ |
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430 | TRACE("delta : %f %f %f", delta.x, delta.y, delta.z); |
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431 | #endif |
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432 | } else if ((pt = strstr(_buff, "datacount")) != 0) { |
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433 | sscanf(pt, "%s%d", str[0], &datacount); |
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434 | TRACE("datacount = %d", datacount); |
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435 | } else if ((pt = strstr(_buff, "datatype")) != 0) { |
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436 | sscanf(pt, "%s%s", str[0], str[1]); |
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437 | if (strcmp(str[1], "double64")) { |
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438 | } |
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439 | } else if ((pt = strstr(_buff, "count")) != 0) { |
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440 | sscanf(pt, "%s%d%d%d", str[0], &width, &height, &depth); |
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441 | #ifdef _LOADER_DEBUG_ |
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442 | TRACE("width height depth %d %d %d", width, height, depth); |
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443 | #endif |
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444 | } else if ((pt = strstr(_buff, "emptymark")) != 0) { |
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445 | sscanf(pt, "%s%lf", str[0], &emptyvalue); |
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446 | #ifdef _LOADER_DEBUG_ |
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447 | TRACE("emptyvalue %lf", emptyvalue); |
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448 | #endif |
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449 | } |
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450 | } while (strcmp(_buff, "<\\HDR>") != 0 && strcmp(_buff, "</HDR>") != 0); |
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451 | |
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452 | if (datacount == -1) datacount = width * height * depth; |
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453 | |
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454 | data = malloc(datacount * 8 * 4 * sizeof(double)); |
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455 | memset(data, 0, datacount * 8 * 4 * sizeof(double)); |
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456 | memcpy(data, stream, datacount * 8 * 4 * sizeof(double)); |
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457 | |
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458 | volume = buildUp(origin, delta, width, height, depth, datacount, emptyvalue, data); |
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459 | |
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460 | free(data); |
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461 | } |
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462 | return volume; |
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463 | } |
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464 | |
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465 | void ZincBlendeReconstructor::getLine(const unsigned char*& stream) |
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466 | { |
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467 | char ch; |
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468 | int index = 0; |
---|
469 | do { |
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470 | ch = stream[0]; |
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471 | ++stream; |
---|
472 | if (ch == '\n') break; |
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473 | _buff[index++] = ch; |
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474 | if (ch == '>') { |
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475 | if (_buff[1] == '\\') |
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476 | break; |
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477 | } |
---|
478 | } while (1); |
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479 | |
---|
480 | _buff[index] = '\0'; |
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481 | |
---|
482 | #ifdef _LOADER_DEBUG_ |
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483 | TRACE("%s", _buff); |
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484 | #endif |
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485 | } |
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