1 | #include <stdio.h> |
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2 | #include <string.h> |
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3 | #include <stdlib.h> |
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4 | #include "NvZincBlendeReconstructor.h" |
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5 | #include "ZincBlendeVolume.h" |
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6 | |
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7 | |
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8 | //#define _LOADER_DEBUG_ |
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9 | |
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10 | NvZincBlendeReconstructor* NvZincBlendeReconstructor::_instance = NULL; |
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11 | |
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12 | NvZincBlendeReconstructor::NvZincBlendeReconstructor() |
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13 | { |
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14 | } |
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15 | |
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16 | NvZincBlendeReconstructor::~NvZincBlendeReconstructor() |
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17 | { |
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18 | } |
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19 | |
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20 | NvZincBlendeReconstructor* NvZincBlendeReconstructor::getInstance() |
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21 | { |
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22 | if (_instance == NULL) |
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23 | { |
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24 | return (_instance = new NvZincBlendeReconstructor()); |
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25 | } |
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26 | |
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27 | return _instance; |
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28 | } |
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29 | |
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30 | ZincBlendeVolume* NvZincBlendeReconstructor::loadFromFile(const char* fileName) |
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31 | { |
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32 | Vector3 origin, delta; |
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33 | |
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34 | std::ifstream stream; |
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35 | stream.open(fileName, std::ios::binary); |
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36 | |
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37 | ZincBlendeVolume* volume = loadFromStream(stream); |
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38 | |
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39 | stream.close(); |
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40 | |
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41 | return volume; |
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42 | } |
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43 | |
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44 | ZincBlendeVolume* NvZincBlendeReconstructor::loadFromStream(std::istream& stream) |
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45 | { |
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46 | ZincBlendeVolume* volume = 0; |
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47 | Vector3 origin, delta; |
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48 | int width = 0, height = 0, depth = 0; |
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49 | void* data = NULL; |
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50 | int version = 1; |
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51 | |
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52 | char str[5][20]; |
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53 | do { |
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54 | getLine(stream); |
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55 | if (buff[0] == '#') |
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56 | { |
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57 | continue; |
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58 | } |
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59 | else if (strstr((const char*) buff, "object") != 0) |
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60 | { |
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61 | #ifdef _LOADER_DEBUG_ |
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62 | printf("VERSION 1\n"); |
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63 | fflush(stdout); |
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64 | #endif |
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65 | version = 1; |
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66 | break; |
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67 | } |
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68 | else if (strstr(buff, "record format") != 0) |
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69 | { |
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70 | #ifdef _LOADER_DEBUG_ |
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71 | printf("VERSION 2\n"); |
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72 | fflush(stdout); |
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73 | #endif |
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74 | version = 2; |
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75 | break; |
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76 | } |
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77 | } while(1); |
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78 | |
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79 | |
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80 | if (version == 1) { |
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81 | float dummy; |
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82 | |
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83 | 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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84 | getLine(stream); |
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85 | sscanf(buff, "%s%f%f%f", str[0], &(origin.x), &(origin.y), &(origin.z)); |
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86 | getLine(stream); |
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87 | sscanf(buff, "%s%f%f%f", str[0], &(delta.x), &dummy, &dummy); |
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88 | getLine(stream); |
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89 | sscanf(buff, "%s%f%f%f", str[0], &dummy, &(delta.y), &dummy); |
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90 | getLine(stream); |
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91 | sscanf(buff, "%s%f%f%f", str[0], &dummy, &dummy, &(delta.z)); |
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92 | do { |
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93 | getLine(stream); |
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94 | } while(strcmp(buff, "<\\HDR>") != 0); |
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95 | |
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96 | width = width / 4; |
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97 | height = height / 4; |
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98 | depth = depth / 4; |
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99 | //data = new double[width * height * depth * 8 * 4]; |
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100 | data = malloc(width * height * depth * 8 * 4 * sizeof(double)); |
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101 | // 8 atom per cell, 4 double (x, y, z, and probability) per atom |
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102 | try { |
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103 | stream.read((char*) data, width * height * depth * 8 * 4 * sizeof(double)); |
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104 | } |
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105 | catch (...) |
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106 | { |
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107 | printf("ERROR\n"); |
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108 | } |
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109 | |
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110 | volume = buildUp(origin, delta, width, height, depth, data); |
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111 | |
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112 | free(data); |
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113 | } |
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114 | else if (version == 2) |
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115 | { |
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116 | const char* pt; |
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117 | int datacount; |
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118 | double emptyvalue; |
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119 | do { |
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120 | getLine(stream); |
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121 | if ((pt = strstr(buff, "delta")) != 0) |
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122 | { |
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123 | sscanf(pt, "%s%f%f%f", str[0], &(delta.x), &(delta.y), &(delta.z)); |
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124 | #ifdef _LOADER_DEBUG_ |
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125 | printf("delta : %f %f %f\n", delta.x, delta.y, delta.z); |
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126 | fflush(stdout); |
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127 | #endif |
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128 | } |
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129 | else if ((pt = strstr(buff, "datacount")) != 0) |
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130 | { |
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131 | sscanf(pt, "%s%d", str[0], &datacount); |
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132 | #ifdef _LOADER_DEBUG_ |
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133 | printf("datacount = %d\n", datacount); |
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134 | fflush(stdout); |
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135 | #endif |
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136 | } |
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137 | else if ((pt = strstr(buff, "datatype")) != 0) |
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138 | { |
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139 | sscanf(pt, "%s%s", str[0], str[1]); |
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140 | if (strcmp(str[1], "double64")) |
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141 | { |
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142 | } |
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143 | } |
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144 | else if ((pt = strstr(buff, "count")) != 0) |
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145 | { |
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146 | sscanf(pt, "%s%d%d%d", str[0], &width, &height, &depth); |
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147 | #ifdef _LOADER_DEBUG_ |
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148 | printf("width height depth %d %d %d\n", width, height, depth); |
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149 | fflush(stdout); |
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150 | #endif |
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151 | } |
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152 | else if ((pt = strstr(buff, "emptymark")) != 0) |
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153 | { |
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154 | sscanf(pt, "%s%lf", str[0], &emptyvalue); |
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155 | #ifdef _LOADER_DEBUG_ |
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156 | printf("empryvalue %lf\n", emptyvalue); |
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157 | fflush(stdout); |
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158 | #endif |
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159 | } |
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160 | else if ((pt = strstr(buff, "emprymark")) != 0) |
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161 | { |
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162 | sscanf(pt, "%s%lf", str[0], &emptyvalue); |
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163 | #ifdef _LOADER_DEBUG_ |
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164 | printf("emptyvalue %lf\n", emptyvalue); |
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165 | #endif |
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166 | } |
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167 | } while(strcmp(buff, "<\\HDR>") != 0 && strcmp(buff, "</HDR>") != 0); |
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168 | |
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169 | data = malloc(width * height * depth * 8 * 4 * sizeof(double)); |
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170 | memset(data, 0, width * height * depth * 8 * 4 * sizeof(double)); |
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171 | stream.read((char*) data, width * height * depth * 8 * 4 * sizeof(double)); |
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172 | |
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173 | volume = buildUp(origin, delta, width, height, depth, datacount, emptyvalue, data); |
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174 | free(data); |
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175 | } |
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176 | return volume; |
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177 | } |
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178 | |
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179 | struct _NvAtomInfo { |
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180 | double indexX, indexY, indexZ; |
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181 | double atom; |
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182 | |
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183 | int getIndex(int width, int height) const |
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184 | { |
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185 | // NOTE |
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186 | // Zinc blende data has different axises from OpenGL |
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187 | // + z -> +x (OpenGL) |
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188 | // + x -> +y (OpenGL) |
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189 | // + y -> +z (OpenGL), But in 3D texture coordinate is the opposite direction of z |
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190 | // The reasone why index is multiplied by 4 is that one unit cell has half of eight atoms |
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191 | // ,i.e. four atoms are mapped into RGBA component of one texel |
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192 | //return ((int) (indexZ - 1)+ (int) (indexX - 1) * width + (int) (indexY - 1) * width * height) * 4; |
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193 | return ((int) (indexX - 1)+ (int) (indexY - 1) * width + (int) (indexZ - 1) * width * height) * 4; |
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194 | } |
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195 | }; |
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196 | |
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197 | |
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198 | template<class T> |
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199 | inline T _NvMax2(T a, T b) { return ((a >= b)? a : b); } |
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200 | |
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201 | template<class T> |
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202 | inline T _NvMin2(T a, T b) { return ((a >= b)? a : b); } |
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203 | |
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204 | template<class T> |
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205 | inline T _NvMax3(T a, T b, T c) { return ((a >= b)? ((a >= c) ? a : c) : ((b >= c)? b : c)); } |
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206 | |
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207 | template<class T> |
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208 | inline T _NvMin3(T a, T b, T c) { return ((a <= b)? ((a <= c) ? a : c) : ((b <= c)? b : c)); } |
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209 | |
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210 | template<class T> |
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211 | inline T _NvMax9(T* a, T curMax) { 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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212 | |
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213 | template<class T> |
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214 | inline T _NvMin9(T* a, T curMax) { 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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215 | |
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216 | template<class T> |
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217 | inline T _NvMax4(T* a) { return _NvMax2(_NvMax2(a[0], a[1]), _NvMax2(a[2], a[3])); } |
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218 | |
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219 | template<class T> |
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220 | inline T _NvMin4(T* a) { return _NvMin2(_NvMin2(a[0], a[1]), _NvMin2(a[2], a[3])); } |
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221 | |
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222 | |
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223 | ZincBlendeVolume* |
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224 | NvZincBlendeReconstructor::buildUp(const Vector3& origin, const Vector3& delta, |
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225 | int width, int height, int depth, void* data) |
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226 | { |
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227 | ZincBlendeVolume* zincBlendeVolume = NULL; |
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228 | |
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229 | float *fourAnionVolume, *fourCationVolume; |
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230 | int cellCount = width * height * depth; |
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231 | fourAnionVolume = new float[cellCount * sizeof(float) * 4]; |
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232 | fourCationVolume = new float[cellCount * sizeof(float) * 4]; |
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233 | |
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234 | _NvAtomInfo* srcPtr = (_NvAtomInfo*) data; |
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235 | |
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236 | float vmin, vmax, nzero_min; |
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237 | float* component4A, *component4B; |
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238 | int index; |
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239 | |
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240 | nzero_min = 0.0f; /* Suppress compiler warning. */ |
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241 | vmin = vmax = srcPtr->atom; |
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242 | |
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243 | int i; |
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244 | for (i = 0; i < cellCount; ++i) |
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245 | { |
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246 | index = srcPtr->getIndex(width, height); |
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247 | |
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248 | #ifdef _LOADER_DEBUG_ |
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249 | printf("index %d\n", index); |
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250 | fflush(stdout); |
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251 | #endif |
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252 | |
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253 | component4A = fourAnionVolume + index; |
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254 | component4B = fourCationVolume + index; |
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255 | |
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256 | component4A[0] = (float) srcPtr->atom; srcPtr++; |
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257 | component4A[1] = (float) srcPtr->atom; srcPtr++; |
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258 | component4A[2] = (float) srcPtr->atom; srcPtr++; |
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259 | component4A[3] = (float) srcPtr->atom; srcPtr++; |
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260 | |
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261 | component4B[0] = (float) srcPtr->atom; srcPtr++; |
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262 | component4B[1] = (float) srcPtr->atom; srcPtr++; |
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263 | component4B[2] = (float) srcPtr->atom; srcPtr++; |
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264 | component4B[3] = (float) srcPtr->atom; srcPtr++; |
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265 | |
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266 | vmax = _NvMax3(_NvMax4(component4A), _NvMax4(component4B), vmax); |
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267 | vmin = _NvMin3(_NvMin4(component4A), _NvMin4(component4B), vmin); |
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268 | |
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269 | if (vmin != 0.0 && vmin < nzero_min) |
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270 | { |
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271 | nzero_min = vmin; |
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272 | } |
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273 | } |
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274 | |
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275 | double dv = vmax - vmin; |
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276 | if (vmax != 0.0f) |
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277 | { |
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278 | for (i=0; i < cellCount; ++i) |
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279 | { |
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280 | fourAnionVolume[i] = (fourAnionVolume[i] - vmin)/ dv; |
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281 | fourCationVolume[i] = (fourCationVolume[i] - vmin) / dv; |
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282 | } |
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283 | } |
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284 | |
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285 | Vector3 cellSize; |
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286 | cellSize.x = 0.25 / width; |
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287 | cellSize.y = 0.25 / height; |
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288 | cellSize.z = 0.25 / depth; |
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289 | |
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290 | zincBlendeVolume = new ZincBlendeVolume(origin.x, origin.y, origin.z, |
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291 | width, height, depth, 1, 4, |
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292 | fourAnionVolume, fourCationVolume, |
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293 | vmin, vmax, nzero_min, cellSize); |
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294 | |
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295 | return zincBlendeVolume; |
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296 | } |
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297 | |
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298 | ZincBlendeVolume* NvZincBlendeReconstructor::buildUp(const Vector3& origin, const Vector3& delta, int width, int height, int depth, int datacount, double emptyvalue, void* data) |
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299 | { |
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300 | ZincBlendeVolume* zincBlendeVolume = NULL; |
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301 | float *fourAnionVolume, *fourCationVolume; |
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302 | int size = width * height * depth * 4; |
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303 | fourAnionVolume = new float[size]; |
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304 | fourCationVolume = new float[size]; |
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305 | |
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306 | memset(fourAnionVolume, 0, size * sizeof(float)); |
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307 | memset(fourCationVolume, 0, size * sizeof(float)); |
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308 | |
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309 | _NvAtomInfo* srcPtr = (_NvAtomInfo*) data; |
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310 | |
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311 | float* component4A, *component4B; |
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312 | float vmin, vmax, nzero_min; |
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313 | int index; |
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314 | nzero_min = 1e23f; |
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315 | vmin = vmax = srcPtr->atom; |
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316 | int i; |
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317 | for (i = 0; i < datacount; ++i) |
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318 | { |
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319 | |
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320 | index = srcPtr->getIndex(width, height); |
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321 | |
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322 | #ifdef _LOADER_DEBUG_ |
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323 | printf("[%d] index %d (width:%lf height:%lf depth:%lf)\n", i, index, srcPtr->indexX, srcPtr->indexY, srcPtr->indexZ); |
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324 | fflush(stdout); |
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325 | #endif |
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326 | |
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327 | if (index < 0) { |
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328 | #ifdef _LOADER_DEBUG_ |
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329 | printf("There is an invalid data\n"); |
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330 | fflush(stdout); |
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331 | #endif |
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332 | srcPtr +=8; |
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333 | continue; |
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334 | } |
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335 | |
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336 | component4A = fourAnionVolume + index; |
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337 | component4B = fourCationVolume + index; |
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338 | |
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339 | component4A[0] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
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340 | component4A[1] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
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341 | component4A[2] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
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342 | component4A[3] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
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343 | |
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344 | component4B[0] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
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345 | component4B[1] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
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346 | component4B[2] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
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347 | component4B[3] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
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348 | |
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349 | vmax = _NvMax3(_NvMax4(component4A), _NvMax4(component4B), vmax); |
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350 | vmin = _NvMin3(_NvMin4(component4A), _NvMin4(component4B), vmin); |
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351 | |
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352 | if (vmin != 0.0 && vmin < nzero_min) |
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353 | { |
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354 | nzero_min = vmin; |
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355 | } |
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356 | |
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357 | } |
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358 | |
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359 | double dv = vmax - vmin; |
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360 | if (vmax != 0.0f) |
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361 | { |
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362 | for (i=0; i < datacount; ++i) |
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363 | { |
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364 | fourAnionVolume[i] = (fourAnionVolume[i] - vmin)/ dv; |
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365 | fourCationVolume[i] = (fourCationVolume[i] - vmin) / dv; |
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366 | } |
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367 | } |
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368 | |
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369 | Vector3 cellSize; |
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370 | cellSize.x = 0.25 / width; |
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371 | cellSize.y = 0.25 / height; |
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372 | cellSize.z = 0.25 / depth; |
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373 | |
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374 | zincBlendeVolume = new ZincBlendeVolume(origin.x, origin.y, origin.z, |
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375 | width, height, depth, 1, 4, |
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376 | fourAnionVolume, fourCationVolume, |
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377 | vmin, vmax, nzero_min, cellSize); |
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378 | |
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379 | return zincBlendeVolume; |
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380 | } |
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381 | |
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382 | void NvZincBlendeReconstructor::getLine(std::istream& sin) |
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383 | { |
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384 | char ch; |
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385 | int index = 0; |
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386 | do { |
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387 | sin.get(ch); |
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388 | if (ch == '\n') break; |
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389 | buff[index++] = ch; |
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390 | if (ch == '>') |
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391 | { |
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392 | if (buff[1] == '\\') |
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393 | break; |
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394 | } |
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395 | } while (!sin.eof()); |
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396 | |
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397 | buff[index] = '\0'; |
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398 | |
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399 | #ifdef _LOADER_DEBUG_ |
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400 | printf("%s", buff); |
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401 | fflush(stdout); |
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402 | #endif |
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403 | } |
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404 | |
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405 | ZincBlendeVolume* NvZincBlendeReconstructor::loadFromMemory(void* dataBlock) |
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406 | { |
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407 | ZincBlendeVolume* volume = 0; |
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408 | Vector3 origin, delta; |
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409 | int width = 0, height = 0, depth = 0; |
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410 | void* data = NULL; |
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411 | int version = 1; |
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412 | |
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413 | unsigned char* stream = (unsigned char*)dataBlock; |
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414 | char str[5][20]; |
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415 | do { |
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416 | getLine(stream); |
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417 | if (buff[0] == '#') |
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418 | { |
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419 | continue; |
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420 | } |
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421 | else if (strstr((const char*) buff, "object") != 0) |
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422 | { |
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423 | printf("VERSION 1\n"); |
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424 | fflush(stdout); |
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425 | version = 1; |
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426 | break; |
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427 | } |
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428 | else if (strstr(buff, "record format") != 0) |
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429 | { |
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430 | printf("VERSION 2\n"); |
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431 | fflush(stdout); |
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432 | version = 2; |
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433 | break; |
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434 | } |
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435 | } while(1); |
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436 | |
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437 | |
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438 | if (version == 1) |
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439 | { |
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440 | float dummy; |
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441 | |
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442 | 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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443 | getLine(stream); |
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444 | sscanf(buff, "%s%f%f%f", str[0], &(origin.x), &(origin.y), &(origin.z)); |
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445 | getLine(stream); |
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446 | sscanf(buff, "%s%f%f%f", str[0], &(delta.x), &dummy, &dummy); |
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447 | getLine(stream); |
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448 | sscanf(buff, "%s%f%f%f", str[0], &dummy, &(delta.y), &dummy); |
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449 | getLine(stream); |
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450 | sscanf(buff, "%s%f%f%f", str[0], &dummy, &dummy, &(delta.z)); |
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451 | do { |
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452 | getLine(stream); |
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453 | } while(strcmp(buff, "<\\HDR>") != 0); |
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454 | |
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455 | width = width / 4; |
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456 | height = height / 4; |
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457 | depth = depth / 4; |
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458 | data = malloc(width * height * depth * 8 * 4 * sizeof(double)); |
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459 | // 8 atom per cell, 4 double (x, y, z, and probability) per atom |
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460 | try { |
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461 | memcpy(data, stream, width * height * depth * 8 * 4 * sizeof(double)); |
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462 | } |
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463 | catch (...) |
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464 | { |
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465 | printf("ERROR\n"); |
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466 | } |
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467 | |
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468 | volume = buildUp(origin, delta, width, height, depth, data); |
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469 | |
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470 | free(data); |
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471 | } |
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472 | else if (version == 2) |
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473 | { |
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474 | const char* pt; |
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475 | int datacount = -1; |
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476 | double emptyvalue; |
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477 | do { |
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478 | getLine(stream); |
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479 | if ((pt = strstr(buff, "delta")) != 0) |
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480 | { |
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481 | sscanf(pt, "%s%f%f%f", str[0], &(delta.x), &(delta.y), &(delta.z)); |
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482 | #ifdef _LOADER_DEBUG_ |
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483 | printf("delta : %f %f %f\n", delta.x, delta.y, delta.z); |
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484 | fflush(stdout); |
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485 | #endif |
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486 | } |
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487 | else if ((pt = strstr(buff, "datacount")) != 0) |
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488 | { |
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489 | sscanf(pt, "%s%d", str[0], &datacount); |
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490 | printf("datacount = %d\n", datacount); |
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491 | fflush(stdout); |
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492 | } |
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493 | else if ((pt = strstr(buff, "datatype")) != 0) |
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494 | { |
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495 | sscanf(pt, "%s%s", str[0], str[1]); |
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496 | if (strcmp(str[1], "double64")) |
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497 | { |
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498 | } |
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499 | } |
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500 | else if ((pt = strstr(buff, "count")) != 0) |
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501 | { |
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502 | sscanf(pt, "%s%d%d%d", str[0], &width, &height, &depth); |
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503 | #ifdef _LOADER_DEBUG_ |
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504 | printf("width height depth %d %d %d\n", width, height, depth); |
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505 | fflush(stdout); |
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506 | #endif |
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507 | } |
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508 | else if ((pt = strstr(buff, "emptymark")) != 0) |
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509 | { |
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510 | sscanf(pt, "%s%lf", str[0], &emptyvalue); |
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511 | #ifdef _LOADER_DEBUG_ |
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512 | printf("empryvalue %lf\n", emptyvalue); |
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513 | fflush(stdout); |
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514 | #endif |
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515 | } |
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516 | else if ((pt = strstr(buff, "emprymark")) != 0) |
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517 | { |
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518 | sscanf(pt, "%s%lf", str[0], &emptyvalue); |
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519 | #ifdef _LOADER_DEBUG_ |
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520 | printf("emptyvalue %lf\n", emptyvalue); |
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521 | #endif |
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522 | } |
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523 | } while(strcmp(buff, "<\\HDR>") != 0 && strcmp(buff, "</HDR>") != 0); |
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524 | |
---|
525 | if (datacount == -1) datacount = width * height * depth; |
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526 | |
---|
527 | data = malloc(datacount * 8 * 4 * sizeof(double)); |
---|
528 | memset(data, 0, datacount * 8 * 4 * sizeof(double)); |
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529 | memcpy(data, stream, datacount * 8 * 4 * sizeof(double)); |
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530 | |
---|
531 | volume = buildUp(origin, delta, width, height, depth, datacount, emptyvalue, data); |
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532 | |
---|
533 | free(data); |
---|
534 | } |
---|
535 | return volume; |
---|
536 | } |
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537 | |
---|
538 | void NvZincBlendeReconstructor::getLine(unsigned char*& stream) |
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539 | { |
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540 | char ch; |
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541 | int index = 0; |
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542 | do { |
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543 | ch = stream[0]; |
---|
544 | ++stream; |
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545 | if (ch == '\n') break; |
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546 | buff[index++] = ch; |
---|
547 | if (ch == '>') |
---|
548 | { |
---|
549 | if (buff[1] == '\\') |
---|
550 | break; |
---|
551 | } |
---|
552 | } while (1); |
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553 | |
---|
554 | buff[index] = '\0'; |
---|
555 | |
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556 | #ifdef _LOADER_DEBUG_ |
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557 | printf("%s", buff); |
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558 | fflush(stdout); |
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559 | #endif |
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560 | } |
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