[2798] | 1 | /* -*- mode: c++; c-basic-offset: 4; indent-tabs-mode: nil -*- */ |
---|
[3502] | 2 | /* |
---|
| 3 | * Copyright (c) 2004-2013 HUBzero Foundation, LLC |
---|
[3611] | 4 | * |
---|
| 5 | * Authors: |
---|
| 6 | * Insoo Woo <iwoo@purdue.edu> |
---|
[3502] | 7 | */ |
---|
[4894] | 8 | #include <cstdio> |
---|
| 9 | #include <cstring> |
---|
| 10 | #include <cstdlib> |
---|
| 11 | #include <fstream> |
---|
[2844] | 12 | |
---|
[3492] | 13 | #include <vrmath/Vector3f.h> |
---|
| 14 | |
---|
[3611] | 15 | #include "ZincBlendeReconstructor.h" |
---|
[601] | 16 | #include "ZincBlendeVolume.h" |
---|
[3492] | 17 | #include "Trace.h" |
---|
[601] | 18 | |
---|
[3611] | 19 | using namespace nv; |
---|
[3492] | 20 | using namespace vrmath; |
---|
| 21 | |
---|
[3611] | 22 | ZincBlendeReconstructor *ZincBlendeReconstructor::_instance = NULL; |
---|
[806] | 23 | |
---|
[3611] | 24 | ZincBlendeReconstructor::ZincBlendeReconstructor() |
---|
[601] | 25 | { |
---|
| 26 | } |
---|
| 27 | |
---|
[3611] | 28 | ZincBlendeReconstructor::~ZincBlendeReconstructor() |
---|
[601] | 29 | { |
---|
| 30 | } |
---|
| 31 | |
---|
[3611] | 32 | ZincBlendeReconstructor *ZincBlendeReconstructor::getInstance() |
---|
[601] | 33 | { |
---|
[2822] | 34 | if (_instance == NULL) { |
---|
[3611] | 35 | return (_instance = new ZincBlendeReconstructor()); |
---|
[601] | 36 | } |
---|
| 37 | |
---|
| 38 | return _instance; |
---|
| 39 | } |
---|
| 40 | |
---|
[3611] | 41 | ZincBlendeVolume *ZincBlendeReconstructor::loadFromFile(const char *fileName) |
---|
[601] | 42 | { |
---|
[800] | 43 | std::ifstream stream; |
---|
| 44 | stream.open(fileName, std::ios::binary); |
---|
[617] | 45 | |
---|
[2822] | 46 | ZincBlendeVolume *volume = loadFromStream(stream); |
---|
[617] | 47 | |
---|
| 48 | stream.close(); |
---|
| 49 | |
---|
| 50 | return volume; |
---|
| 51 | } |
---|
| 52 | |
---|
[3611] | 53 | ZincBlendeVolume *ZincBlendeReconstructor::loadFromStream(std::istream& stream) |
---|
[617] | 54 | { |
---|
[2822] | 55 | ZincBlendeVolume *volume = NULL; |
---|
[3492] | 56 | Vector3f origin, delta; |
---|
[617] | 57 | int width = 0, height = 0, depth = 0; |
---|
[2822] | 58 | void *data = NULL; |
---|
[800] | 59 | int version = 1; |
---|
[617] | 60 | |
---|
| 61 | char str[5][20]; |
---|
| 62 | do { |
---|
| 63 | getLine(stream); |
---|
[4063] | 64 | if (_buff[0] == '#') { |
---|
[800] | 65 | continue; |
---|
[4063] | 66 | } else if (strstr((const char*) _buff, "object") != 0) { |
---|
[3452] | 67 | TRACE("VERSION 1"); |
---|
[2822] | 68 | version = 1; |
---|
| 69 | break; |
---|
[4063] | 70 | } else if (strstr(_buff, "record format") != 0) { |
---|
[3452] | 71 | TRACE("VERSION 2"); |
---|
[2822] | 72 | version = 2; |
---|
| 73 | break; |
---|
[800] | 74 | } |
---|
[2822] | 75 | } while (1); |
---|
[617] | 76 | |
---|
[953] | 77 | if (version == 1) { |
---|
| 78 | float dummy; |
---|
| 79 | |
---|
[4063] | 80 | sscanf(_buff, "%s%s%s%s%s%d%d%d", str[0], str[1], str[2], str[3], str[4], &width, &height, &depth); |
---|
[800] | 81 | getLine(stream); |
---|
[4063] | 82 | sscanf(_buff, "%s%f%f%f", str[0], &(origin.x), &(origin.y), &(origin.z)); |
---|
[800] | 83 | getLine(stream); |
---|
[4063] | 84 | sscanf(_buff, "%s%f%f%f", str[0], &(delta.x), &dummy, &dummy); |
---|
[800] | 85 | getLine(stream); |
---|
[4063] | 86 | sscanf(_buff, "%s%f%f%f", str[0], &dummy, &(delta.y), &dummy); |
---|
[800] | 87 | getLine(stream); |
---|
[4063] | 88 | sscanf(_buff, "%s%f%f%f", str[0], &dummy, &dummy, &(delta.z)); |
---|
[800] | 89 | do { |
---|
| 90 | getLine(stream); |
---|
[4063] | 91 | } while (strcmp(_buff, "<\\HDR>") != 0); |
---|
[617] | 92 | |
---|
[800] | 93 | width = width / 4; |
---|
| 94 | height = height / 4; |
---|
| 95 | depth = depth / 4; |
---|
| 96 | //data = new double[width * height * depth * 8 * 4]; |
---|
| 97 | data = malloc(width * height * depth * 8 * 4 * sizeof(double)); |
---|
[2822] | 98 | // 8 atom per cell, 4 double (x, y, z, and probability) per atom |
---|
[800] | 99 | try { |
---|
[2822] | 100 | stream.read((char *)data, width * height * depth * 8 * 4 * sizeof(double)); |
---|
| 101 | } catch (...) { |
---|
[3452] | 102 | ERROR("Caught exception trying to read stream"); |
---|
[800] | 103 | } |
---|
[617] | 104 | |
---|
[800] | 105 | volume = buildUp(origin, delta, width, height, depth, data); |
---|
[617] | 106 | |
---|
[800] | 107 | free(data); |
---|
[2822] | 108 | } else if (version == 2) { |
---|
| 109 | const char *pt; |
---|
[800] | 110 | int datacount; |
---|
| 111 | double emptyvalue; |
---|
| 112 | do { |
---|
| 113 | getLine(stream); |
---|
[4063] | 114 | if ((pt = strstr(_buff, "delta")) != 0) { |
---|
[800] | 115 | sscanf(pt, "%s%f%f%f", str[0], &(delta.x), &(delta.y), &(delta.z)); |
---|
[806] | 116 | #ifdef _LOADER_DEBUG_ |
---|
[3452] | 117 | TRACE("delta : %f %f %f", delta.x, delta.y, delta.z); |
---|
[806] | 118 | #endif |
---|
[4063] | 119 | } else if ((pt = strstr(_buff, "datacount")) != 0) { |
---|
[800] | 120 | sscanf(pt, "%s%d", str[0], &datacount); |
---|
[806] | 121 | #ifdef _LOADER_DEBUG_ |
---|
[3452] | 122 | TRACE("datacount = %d", datacount); |
---|
[806] | 123 | #endif |
---|
[4063] | 124 | } else if ((pt = strstr(_buff, "datatype")) != 0) { |
---|
[800] | 125 | sscanf(pt, "%s%s", str[0], str[1]); |
---|
[2822] | 126 | if (strcmp(str[1], "double64")) { |
---|
[800] | 127 | } |
---|
[4063] | 128 | } else if ((pt = strstr(_buff, "count")) != 0) { |
---|
[800] | 129 | sscanf(pt, "%s%d%d%d", str[0], &width, &height, &depth); |
---|
[806] | 130 | #ifdef _LOADER_DEBUG_ |
---|
[3452] | 131 | TRACE("width height depth %d %d %d", width, height, depth); |
---|
[806] | 132 | #endif |
---|
[4063] | 133 | } else if ((pt = strstr(_buff, "emptymark")) != 0) { |
---|
[800] | 134 | sscanf(pt, "%s%lf", str[0], &emptyvalue); |
---|
[806] | 135 | #ifdef _LOADER_DEBUG_ |
---|
[3452] | 136 | TRACE("emptyvalue %lf", emptyvalue); |
---|
[806] | 137 | #endif |
---|
[4063] | 138 | } else if ((pt = strstr(_buff, "emprymark")) != 0) { |
---|
[800] | 139 | sscanf(pt, "%s%lf", str[0], &emptyvalue); |
---|
[806] | 140 | #ifdef _LOADER_DEBUG_ |
---|
[3452] | 141 | TRACE("emptyvalue %lf", emptyvalue); |
---|
[806] | 142 | #endif |
---|
[800] | 143 | } |
---|
[4063] | 144 | } while (strcmp(_buff, "<\\HDR>") != 0 && strcmp(_buff, "</HDR>") != 0); |
---|
[800] | 145 | |
---|
| 146 | data = malloc(width * height * depth * 8 * 4 * sizeof(double)); |
---|
[804] | 147 | memset(data, 0, width * height * depth * 8 * 4 * sizeof(double)); |
---|
[2822] | 148 | stream.read((char *) data, width * height * depth * 8 * 4 * sizeof(double)); |
---|
[800] | 149 | |
---|
| 150 | volume = buildUp(origin, delta, width, height, depth, datacount, emptyvalue, data); |
---|
| 151 | free(data); |
---|
[617] | 152 | } |
---|
[800] | 153 | return volume; |
---|
[601] | 154 | } |
---|
| 155 | |
---|
[617] | 156 | struct _NvAtomInfo { |
---|
| 157 | double indexX, indexY, indexZ; |
---|
| 158 | double atom; |
---|
[601] | 159 | |
---|
| 160 | int getIndex(int width, int height) const |
---|
| 161 | { |
---|
| 162 | // NOTE |
---|
[2844] | 163 | // Zinc blende data has different axes from OpenGL |
---|
[601] | 164 | // + z -> +x (OpenGL) |
---|
| 165 | // + x -> +y (OpenGL) |
---|
| 166 | // + y -> +z (OpenGL), But in 3D texture coordinate is the opposite direction of z |
---|
[2844] | 167 | // The reason why index is multiplied by 4 is that one unit cell has half of eight atoms, |
---|
| 168 | // i.e. four atoms are mapped into RGBA component of one texel |
---|
[777] | 169 | //return ((int) (indexZ - 1)+ (int) (indexX - 1) * width + (int) (indexY - 1) * width * height) * 4; |
---|
[2822] | 170 | return ((int)(indexX - 1) + (int)(indexY - 1) * width + (int)(indexZ - 1) * width * height) * 4; |
---|
[601] | 171 | } |
---|
| 172 | }; |
---|
| 173 | |
---|
| 174 | template<class T> |
---|
[2822] | 175 | inline T _NvMax2(T a, T b) |
---|
| 176 | { return ((a >= b)? a : b); } |
---|
[601] | 177 | |
---|
| 178 | template<class T> |
---|
[2822] | 179 | inline T _NvMin2(T a, T b) |
---|
| 180 | { return ((a >= b)? a : b); } |
---|
[601] | 181 | |
---|
| 182 | template<class T> |
---|
[2822] | 183 | inline T _NvMax3(T a, T b, T c) |
---|
| 184 | { return ((a >= b)? ((a >= c) ? a : c) : ((b >= c)? b : c)); } |
---|
[601] | 185 | |
---|
| 186 | template<class T> |
---|
[2822] | 187 | inline T _NvMin3(T a, T b, T c) |
---|
| 188 | { return ((a <= b)? ((a <= c) ? a : c) : ((b <= c)? b : c)); } |
---|
[601] | 189 | |
---|
| 190 | template<class T> |
---|
[2822] | 191 | inline T _NvMax9(T* a, T curMax) |
---|
| 192 | { return _NvMax3(_NvMax3(a[0], a[1], a[2]), _NvMax3(a[3], a[4], a[5]), _NvMax3(a[6], a[7], curMax)); } |
---|
[601] | 193 | |
---|
| 194 | template<class T> |
---|
[2822] | 195 | inline T _NvMin9(T* a, T curMax) |
---|
| 196 | { return _NvMin3(_NvMax3(a[0], a[1], a[2]), _NvMin3(a[3], a[4], a[5]), _NvMin3(a[6], a[7], curMax)); } |
---|
[601] | 197 | |
---|
[617] | 198 | template<class T> |
---|
[2822] | 199 | inline T _NvMax4(T* a) |
---|
| 200 | { return _NvMax2(_NvMax2(a[0], a[1]), _NvMax2(a[2], a[3])); } |
---|
[617] | 201 | |
---|
| 202 | template<class T> |
---|
[2822] | 203 | inline T _NvMin4(T* a) |
---|
| 204 | { return _NvMin2(_NvMin2(a[0], a[1]), _NvMin2(a[2], a[3])); } |
---|
[617] | 205 | |
---|
[2822] | 206 | ZincBlendeVolume * |
---|
[3611] | 207 | ZincBlendeReconstructor::buildUp(const Vector3f& origin, const Vector3f& delta, |
---|
[2844] | 208 | int width, int height, int depth, void *data) |
---|
[601] | 209 | { |
---|
[2822] | 210 | ZincBlendeVolume *zincBlendeVolume = NULL; |
---|
[601] | 211 | |
---|
[617] | 212 | float *fourAnionVolume, *fourCationVolume; |
---|
[601] | 213 | int cellCount = width * height * depth; |
---|
[617] | 214 | fourAnionVolume = new float[cellCount * sizeof(float) * 4]; |
---|
| 215 | fourCationVolume = new float[cellCount * sizeof(float) * 4]; |
---|
[601] | 216 | |
---|
[2822] | 217 | _NvAtomInfo *srcPtr = (_NvAtomInfo *)data; |
---|
[601] | 218 | |
---|
[777] | 219 | float vmin, vmax, nzero_min; |
---|
[2822] | 220 | float *component4A, *component4B; |
---|
[601] | 221 | int index; |
---|
| 222 | |
---|
[953] | 223 | nzero_min = 0.0f; /* Suppress compiler warning. */ |
---|
[617] | 224 | vmin = vmax = srcPtr->atom; |
---|
| 225 | |
---|
[2822] | 226 | for (int i = 0; i < cellCount; ++i) { |
---|
[601] | 227 | index = srcPtr->getIndex(width, height); |
---|
[804] | 228 | |
---|
[806] | 229 | #ifdef _LOADER_DEBUG_ |
---|
[3452] | 230 | TRACE("index %d", index); |
---|
[806] | 231 | #endif |
---|
[804] | 232 | |
---|
[617] | 233 | component4A = fourAnionVolume + index; |
---|
| 234 | component4B = fourCationVolume + index; |
---|
[601] | 235 | |
---|
[2822] | 236 | component4A[0] = (float)srcPtr->atom; srcPtr++; |
---|
| 237 | component4A[1] = (float)srcPtr->atom; srcPtr++; |
---|
| 238 | component4A[2] = (float)srcPtr->atom; srcPtr++; |
---|
| 239 | component4A[3] = (float)srcPtr->atom; srcPtr++; |
---|
[617] | 240 | |
---|
[2822] | 241 | component4B[0] = (float)srcPtr->atom; srcPtr++; |
---|
| 242 | component4B[1] = (float)srcPtr->atom; srcPtr++; |
---|
| 243 | component4B[2] = (float)srcPtr->atom; srcPtr++; |
---|
| 244 | component4B[3] = (float)srcPtr->atom; srcPtr++; |
---|
[601] | 245 | |
---|
[617] | 246 | vmax = _NvMax3(_NvMax4(component4A), _NvMax4(component4B), vmax); |
---|
| 247 | vmin = _NvMin3(_NvMin4(component4A), _NvMin4(component4B), vmin); |
---|
[777] | 248 | |
---|
[2822] | 249 | if (vmin != 0.0 && vmin < nzero_min) { |
---|
| 250 | nzero_min = vmin; |
---|
[777] | 251 | } |
---|
[617] | 252 | } |
---|
[601] | 253 | |
---|
[617] | 254 | double dv = vmax - vmin; |
---|
[2822] | 255 | if (vmax != 0.0f) { |
---|
| 256 | for (int i = 0; i < cellCount; ++i) { |
---|
[617] | 257 | fourAnionVolume[i] = (fourAnionVolume[i] - vmin)/ dv; |
---|
| 258 | fourCationVolume[i] = (fourCationVolume[i] - vmin) / dv; |
---|
| 259 | } |
---|
| 260 | } |
---|
[601] | 261 | |
---|
[3492] | 262 | Vector3f cellSize; |
---|
[617] | 263 | cellSize.x = 0.25 / width; |
---|
| 264 | cellSize.y = 0.25 / height; |
---|
| 265 | cellSize.z = 0.25 / depth; |
---|
[601] | 266 | |
---|
[3630] | 267 | zincBlendeVolume = new ZincBlendeVolume(width, height, depth, 4, |
---|
[617] | 268 | fourAnionVolume, fourCationVolume, |
---|
[777] | 269 | vmin, vmax, nzero_min, cellSize); |
---|
[601] | 270 | |
---|
[3630] | 271 | zincBlendeVolume->xAxis.setRange(origin.x, origin.x + delta.x * (width-1)); |
---|
| 272 | zincBlendeVolume->yAxis.setRange(origin.y, origin.y + delta.y * (height-1)); |
---|
| 273 | zincBlendeVolume->zAxis.setRange(origin.z, origin.z + delta.z * (depth-1)); |
---|
| 274 | |
---|
[601] | 275 | return zincBlendeVolume; |
---|
| 276 | } |
---|
| 277 | |
---|
[2822] | 278 | ZincBlendeVolume * |
---|
[3611] | 279 | ZincBlendeReconstructor::buildUp(const Vector3f& origin, const Vector3f& delta, |
---|
[2822] | 280 | int width, int height, int depth, |
---|
| 281 | int datacount, double emptyvalue, void* data) |
---|
[800] | 282 | { |
---|
[2822] | 283 | ZincBlendeVolume *zincBlendeVolume = NULL; |
---|
[800] | 284 | float *fourAnionVolume, *fourCationVolume; |
---|
| 285 | int size = width * height * depth * 4; |
---|
| 286 | fourAnionVolume = new float[size]; |
---|
| 287 | fourCationVolume = new float[size]; |
---|
| 288 | |
---|
| 289 | memset(fourAnionVolume, 0, size * sizeof(float)); |
---|
| 290 | memset(fourCationVolume, 0, size * sizeof(float)); |
---|
| 291 | |
---|
[2822] | 292 | _NvAtomInfo *srcPtr = (_NvAtomInfo *) data; |
---|
[800] | 293 | |
---|
[2822] | 294 | float *component4A, *component4B; |
---|
[800] | 295 | float vmin, vmax, nzero_min; |
---|
| 296 | int index; |
---|
| 297 | nzero_min = 1e23f; |
---|
| 298 | vmin = vmax = srcPtr->atom; |
---|
[2822] | 299 | for (int i = 0; i < datacount; ++i) { |
---|
[800] | 300 | index = srcPtr->getIndex(width, height); |
---|
[806] | 301 | |
---|
| 302 | #ifdef _LOADER_DEBUG_ |
---|
[3452] | 303 | TRACE("[%d] index %d (width:%lf height:%lf depth:%lf)", i, index, srcPtr->indexX, srcPtr->indexY, srcPtr->indexZ); |
---|
[806] | 304 | #endif |
---|
[804] | 305 | |
---|
| 306 | if (index < 0) { |
---|
[806] | 307 | #ifdef _LOADER_DEBUG_ |
---|
[3452] | 308 | TRACE("There is an invalid data"); |
---|
[806] | 309 | #endif |
---|
[804] | 310 | srcPtr +=8; |
---|
| 311 | continue; |
---|
| 312 | } |
---|
| 313 | |
---|
[800] | 314 | component4A = fourAnionVolume + index; |
---|
| 315 | component4B = fourCationVolume + index; |
---|
| 316 | |
---|
| 317 | component4A[0] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
---|
| 318 | component4A[1] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
---|
| 319 | component4A[2] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
---|
| 320 | component4A[3] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
---|
| 321 | |
---|
| 322 | component4B[0] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
---|
| 323 | component4B[1] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
---|
| 324 | component4B[2] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
---|
| 325 | component4B[3] = (srcPtr->atom != emptyvalue)? (float) srcPtr->atom : 0.0f; srcPtr++; |
---|
| 326 | |
---|
| 327 | vmax = _NvMax3(_NvMax4(component4A), _NvMax4(component4B), vmax); |
---|
| 328 | vmin = _NvMin3(_NvMin4(component4A), _NvMin4(component4B), vmin); |
---|
| 329 | |
---|
[2822] | 330 | if (vmin != 0.0 && vmin < nzero_min) { |
---|
[800] | 331 | nzero_min = vmin; |
---|
| 332 | } |
---|
| 333 | } |
---|
| 334 | |
---|
| 335 | double dv = vmax - vmin; |
---|
[2822] | 336 | if (vmax != 0.0f) { |
---|
| 337 | for (int i = 0; i < datacount; ++i) { |
---|
[800] | 338 | fourAnionVolume[i] = (fourAnionVolume[i] - vmin)/ dv; |
---|
| 339 | fourCationVolume[i] = (fourCationVolume[i] - vmin) / dv; |
---|
| 340 | } |
---|
| 341 | } |
---|
| 342 | |
---|
[3492] | 343 | Vector3f cellSize; |
---|
[800] | 344 | cellSize.x = 0.25 / width; |
---|
| 345 | cellSize.y = 0.25 / height; |
---|
| 346 | cellSize.z = 0.25 / depth; |
---|
| 347 | |
---|
[3630] | 348 | zincBlendeVolume = new ZincBlendeVolume(width, height, depth, 4, |
---|
[800] | 349 | fourAnionVolume, fourCationVolume, |
---|
| 350 | vmin, vmax, nzero_min, cellSize); |
---|
| 351 | |
---|
[3630] | 352 | zincBlendeVolume->xAxis.setRange(origin.x, origin.x + delta.x * (width-1)); |
---|
| 353 | zincBlendeVolume->yAxis.setRange(origin.y, origin.y + delta.y * (height-1)); |
---|
| 354 | zincBlendeVolume->zAxis.setRange(origin.z, origin.z + delta.z * (depth-1)); |
---|
| 355 | |
---|
[800] | 356 | return zincBlendeVolume; |
---|
| 357 | } |
---|
| 358 | |
---|
[3611] | 359 | void ZincBlendeReconstructor::getLine(std::istream& sin) |
---|
[617] | 360 | { |
---|
| 361 | char ch; |
---|
| 362 | int index = 0; |
---|
| 363 | do { |
---|
| 364 | sin.get(ch); |
---|
| 365 | if (ch == '\n') break; |
---|
[4063] | 366 | _buff[index++] = ch; |
---|
[2822] | 367 | if (ch == '>') { |
---|
[4063] | 368 | if (_buff[1] == '\\') |
---|
[617] | 369 | break; |
---|
| 370 | } |
---|
| 371 | } while (!sin.eof()); |
---|
| 372 | |
---|
[4063] | 373 | _buff[index] = '\0'; |
---|
[804] | 374 | |
---|
[806] | 375 | #ifdef _LOADER_DEBUG_ |
---|
[4063] | 376 | TRACE("%s", _buff); |
---|
[806] | 377 | #endif |
---|
[617] | 378 | } |
---|
| 379 | |
---|
[2822] | 380 | ZincBlendeVolume * |
---|
[4063] | 381 | ZincBlendeReconstructor::loadFromMemory(const void *dataBlock) |
---|
[804] | 382 | { |
---|
[2822] | 383 | ZincBlendeVolume *volume = NULL; |
---|
[3492] | 384 | Vector3f origin, delta; |
---|
[804] | 385 | int width = 0, height = 0, depth = 0; |
---|
[2822] | 386 | void *data = NULL; |
---|
[804] | 387 | int version = 1; |
---|
| 388 | |
---|
[4063] | 389 | const unsigned char *stream = (const unsigned char *)dataBlock; |
---|
[804] | 390 | char str[5][20]; |
---|
| 391 | do { |
---|
| 392 | getLine(stream); |
---|
[4063] | 393 | if (_buff[0] == '#') { |
---|
[804] | 394 | continue; |
---|
[4063] | 395 | } else if (strstr((const char *)_buff, "object") != 0) { |
---|
[3452] | 396 | TRACE("VERSION 1"); |
---|
[2822] | 397 | version = 1; |
---|
| 398 | break; |
---|
[4063] | 399 | } else if (strstr(_buff, "record format") != 0) { |
---|
[3452] | 400 | TRACE("VERSION 2"); |
---|
[2822] | 401 | version = 2; |
---|
| 402 | break; |
---|
[804] | 403 | } |
---|
[2822] | 404 | } while (1); |
---|
[804] | 405 | |
---|
[2822] | 406 | if (version == 1) { |
---|
[953] | 407 | float dummy; |
---|
| 408 | |
---|
[4063] | 409 | sscanf(_buff, "%s%s%s%s%s%d%d%d", str[0], str[1], str[2], str[3], str[4],&width, &height, &depth); |
---|
[804] | 410 | getLine(stream); |
---|
[4063] | 411 | sscanf(_buff, "%s%f%f%f", str[0], &(origin.x), &(origin.y), &(origin.z)); |
---|
[804] | 412 | getLine(stream); |
---|
[4063] | 413 | sscanf(_buff, "%s%f%f%f", str[0], &(delta.x), &dummy, &dummy); |
---|
[804] | 414 | getLine(stream); |
---|
[4063] | 415 | sscanf(_buff, "%s%f%f%f", str[0], &dummy, &(delta.y), &dummy); |
---|
[804] | 416 | getLine(stream); |
---|
[4063] | 417 | sscanf(_buff, "%s%f%f%f", str[0], &dummy, &dummy, &(delta.z)); |
---|
[804] | 418 | do { |
---|
| 419 | getLine(stream); |
---|
[4063] | 420 | } while (strcmp(_buff, "<\\HDR>") != 0); |
---|
[804] | 421 | |
---|
| 422 | width = width / 4; |
---|
| 423 | height = height / 4; |
---|
| 424 | depth = depth / 4; |
---|
| 425 | data = malloc(width * height * depth * 8 * 4 * sizeof(double)); |
---|
[2822] | 426 | // 8 atom per cell, 4 double (x, y, z, and probability) per atom |
---|
| 427 | memcpy(data, stream, width * height * depth * 8 * 4 * sizeof(double)); |
---|
[804] | 428 | |
---|
| 429 | volume = buildUp(origin, delta, width, height, depth, data); |
---|
| 430 | |
---|
| 431 | free(data); |
---|
[2822] | 432 | } else if (version == 2) { |
---|
| 433 | const char *pt; |
---|
[804] | 434 | int datacount = -1; |
---|
| 435 | double emptyvalue; |
---|
| 436 | do { |
---|
| 437 | getLine(stream); |
---|
[4063] | 438 | if ((pt = strstr(_buff, "delta")) != 0) { |
---|
[804] | 439 | sscanf(pt, "%s%f%f%f", str[0], &(delta.x), &(delta.y), &(delta.z)); |
---|
[806] | 440 | #ifdef _LOADER_DEBUG_ |
---|
[3452] | 441 | TRACE("delta : %f %f %f", delta.x, delta.y, delta.z); |
---|
[806] | 442 | #endif |
---|
[4063] | 443 | } else if ((pt = strstr(_buff, "datacount")) != 0) { |
---|
[804] | 444 | sscanf(pt, "%s%d", str[0], &datacount); |
---|
[3452] | 445 | TRACE("datacount = %d", datacount); |
---|
[4063] | 446 | } else if ((pt = strstr(_buff, "datatype")) != 0) { |
---|
[804] | 447 | sscanf(pt, "%s%s", str[0], str[1]); |
---|
[2822] | 448 | if (strcmp(str[1], "double64")) { |
---|
[804] | 449 | } |
---|
[4063] | 450 | } else if ((pt = strstr(_buff, "count")) != 0) { |
---|
[804] | 451 | sscanf(pt, "%s%d%d%d", str[0], &width, &height, &depth); |
---|
[806] | 452 | #ifdef _LOADER_DEBUG_ |
---|
[3452] | 453 | TRACE("width height depth %d %d %d", width, height, depth); |
---|
[806] | 454 | #endif |
---|
[4063] | 455 | } else if ((pt = strstr(_buff, "emptymark")) != 0) { |
---|
[804] | 456 | sscanf(pt, "%s%lf", str[0], &emptyvalue); |
---|
[806] | 457 | #ifdef _LOADER_DEBUG_ |
---|
[3452] | 458 | TRACE("emptyvalue %lf", emptyvalue); |
---|
[806] | 459 | #endif |
---|
[4063] | 460 | } else if ((pt = strstr(_buff, "emprymark")) != 0) { |
---|
[804] | 461 | sscanf(pt, "%s%lf", str[0], &emptyvalue); |
---|
[806] | 462 | #ifdef _LOADER_DEBUG_ |
---|
[3452] | 463 | TRACE("emptyvalue %lf", emptyvalue); |
---|
[806] | 464 | #endif |
---|
[804] | 465 | } |
---|
[4063] | 466 | } while (strcmp(_buff, "<\\HDR>") != 0 && strcmp(_buff, "</HDR>") != 0); |
---|
[804] | 467 | |
---|
| 468 | if (datacount == -1) datacount = width * height * depth; |
---|
| 469 | |
---|
| 470 | data = malloc(datacount * 8 * 4 * sizeof(double)); |
---|
| 471 | memset(data, 0, datacount * 8 * 4 * sizeof(double)); |
---|
| 472 | memcpy(data, stream, datacount * 8 * 4 * sizeof(double)); |
---|
| 473 | |
---|
| 474 | volume = buildUp(origin, delta, width, height, depth, datacount, emptyvalue, data); |
---|
| 475 | |
---|
| 476 | free(data); |
---|
| 477 | } |
---|
| 478 | return volume; |
---|
| 479 | } |
---|
| 480 | |
---|
[4063] | 481 | void ZincBlendeReconstructor::getLine(const unsigned char*& stream) |
---|
[804] | 482 | { |
---|
| 483 | char ch; |
---|
| 484 | int index = 0; |
---|
| 485 | do { |
---|
| 486 | ch = stream[0]; |
---|
| 487 | ++stream; |
---|
| 488 | if (ch == '\n') break; |
---|
[4063] | 489 | _buff[index++] = ch; |
---|
[2822] | 490 | if (ch == '>') { |
---|
[4063] | 491 | if (_buff[1] == '\\') |
---|
[804] | 492 | break; |
---|
| 493 | } |
---|
| 494 | } while (1); |
---|
| 495 | |
---|
[4063] | 496 | _buff[index] = '\0'; |
---|
[804] | 497 | |
---|
[806] | 498 | #ifdef _LOADER_DEBUG_ |
---|
[4063] | 499 | TRACE("%s", _buff); |
---|
[806] | 500 | #endif |
---|
[804] | 501 | } |
---|