1 | |
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2 | /* |
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3 | * ---------------------------------------------------------------------- |
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4 | * Nanovis: Visualization of Nanoelectronics Data |
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5 | * |
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6 | * dxReader.cpp |
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7 | * This module contains openDX readers for 2D and 3D volumes. |
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8 | * |
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9 | * ====================================================================== |
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10 | * AUTHOR: Wei Qiao <qiaow@purdue.edu> |
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11 | * Michael McLennan <mmclennan@purdue.edu> |
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12 | * Purdue Rendering and Perceptualization Lab (PURPL) |
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13 | * |
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14 | * Copyright (c) 2004-2006 Purdue Research Foundation |
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15 | * |
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16 | * See the file "license.terms" for information on usage and |
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17 | * redistribution of this file, and for a DISCLAIMER OF ALL WARRANTIES. |
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18 | * ====================================================================== |
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19 | */ |
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20 | |
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21 | #include <stdio.h> |
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22 | #include <math.h> |
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23 | #include <fstream> |
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24 | #include <iostream> |
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25 | #include <sstream> |
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26 | #include <string> |
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27 | #include <sys/types.h> |
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28 | #include <unistd.h> |
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29 | |
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30 | #include "Nv.h" |
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31 | |
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32 | #include "nanovis.h" |
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33 | #include "RpField1D.h" |
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34 | #include "RpFieldRect3D.h" |
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35 | #include "RpFieldPrism3D.h" |
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36 | |
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37 | //transfer function headers |
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38 | #include "ZincBlendeVolume.h" |
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39 | #include "NvZincBlendeReconstructor.h" |
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40 | |
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41 | //#define _LOCAL_ZINC_TEST_ |
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42 | |
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43 | /* |
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44 | * Load a 3D vector field from a dx-format file |
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45 | */ |
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46 | void |
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47 | load_vector_stream(int index, std::iostream& fin) |
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48 | { |
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49 | int dummy, nx, ny, nz, nxy, npts; |
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50 | double x0, y0, z0, dx, dy, dz, ddx, ddy, ddz; |
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51 | char line[128], type[128], *start; |
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52 | |
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53 | do { |
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54 | fin.getline(line,sizeof(line)-1); |
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55 | for (start=&line[0]; *start == ' ' || *start == '\t'; start++) |
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56 | ; // skip leading blanks |
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57 | |
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58 | if (*start != '#') { // skip comment lines |
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59 | if (sscanf(start, "object %d class gridpositions counts %d %d %d", &dummy, &nx, &ny, &nz) == 4) { |
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60 | // found grid size |
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61 | } |
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62 | else if (sscanf(start, "origin %lg %lg %lg", &x0, &y0, &z0) == 3) { |
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63 | // found origin |
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64 | } |
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65 | else if (sscanf(start, "delta %lg %lg %lg", &ddx, &ddy, &ddz) == 3) { |
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66 | // found one of the delta lines |
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67 | if (ddx != 0.0) { dx = ddx; } |
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68 | else if (ddy != 0.0) { dy = ddy; } |
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69 | else if (ddz != 0.0) { dz = ddz; } |
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70 | } |
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71 | else if (sscanf(start, "object %d class array type %s shape 3 rank 1 items %d data follows", &dummy, type, &npts) == 3) { |
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72 | if (npts != nx*ny*nz) { |
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73 | std::cerr << "inconsistent data: expected " << nx*ny*nz << " points but found " << npts << " points" << std::endl; |
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74 | return; |
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75 | } |
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76 | break; |
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77 | } |
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78 | else if (sscanf(start, "object %d class array type %s rank 0 times %d data follows", &dummy, type, &npts) == 3) { |
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79 | if (npts != nx*ny*nz) { |
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80 | std::cerr << "inconsistent data: expected " << nx*ny*nz << " points but found " << npts << " points" << std::endl; |
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81 | return; |
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82 | } |
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83 | break; |
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84 | } |
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85 | } |
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86 | } while (!fin.eof()); |
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87 | |
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88 | // read data points |
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89 | if (!fin.eof()) { |
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90 | Rappture::Mesh1D xgrid(x0, x0+nx*dx, nx); |
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91 | Rappture::Mesh1D ygrid(y0, y0+ny*dy, ny); |
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92 | Rappture::Mesh1D zgrid(z0, z0+nz*dz, nz); |
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93 | Rappture::FieldRect3D xfield(xgrid, ygrid, zgrid); |
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94 | Rappture::FieldRect3D yfield(xgrid, ygrid, zgrid); |
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95 | Rappture::FieldRect3D zfield(xgrid, ygrid, zgrid); |
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96 | |
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97 | double vx, vy, vz; |
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98 | int nread = 0; |
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99 | for (int ix=0; ix < nx; ix++) { |
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100 | for (int iy=0; iy < ny; iy++) { |
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101 | for (int iz=0; iz < nz; iz++) { |
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102 | if (fin.eof() || nread > npts) { |
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103 | break; |
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104 | } |
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105 | fin.getline(line,sizeof(line)-1); |
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106 | if (sscanf(line, "%lg %lg %lg", &vx, &vy, &vz) == 3) { |
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107 | int nindex = iz*nx*ny + iy*nx + ix; |
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108 | xfield.define(nindex, vx); |
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109 | yfield.define(nindex, vy); |
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110 | zfield.define(nindex, vz); |
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111 | nread++; |
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112 | } |
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113 | } |
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114 | } |
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115 | } |
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116 | |
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117 | // make sure that we read all of the expected points |
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118 | if (nread != nx*ny*nz) { |
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119 | std::cerr << "inconsistent data: expected " << nx*ny*nz << " points but found " << nread << " points" << std::endl; |
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120 | return; |
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121 | } |
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122 | |
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123 | // figure out a good mesh spacing |
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124 | int nsample = 30; |
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125 | dx = xfield.rangeMax(Rappture::xaxis) - xfield.rangeMin(Rappture::xaxis); |
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126 | dy = xfield.rangeMax(Rappture::yaxis) - xfield.rangeMin(Rappture::yaxis); |
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127 | dz = xfield.rangeMax(Rappture::zaxis) - xfield.rangeMin(Rappture::zaxis); |
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128 | double dmin = pow((dx*dy*dz)/(nsample*nsample*nsample), 0.333); |
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129 | |
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130 | nx = (int)ceil(dx/dmin); |
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131 | ny = (int)ceil(dy/dmin); |
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132 | nz = (int)ceil(dz/dmin); |
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133 | |
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134 | #ifndef NV40 |
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135 | // must be an even power of 2 for older cards |
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136 | nx = (int)pow(2.0, ceil(log10((double)nx)/log10(2.0))); |
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137 | ny = (int)pow(2.0, ceil(log10((double)ny)/log10(2.0))); |
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138 | nz = (int)pow(2.0, ceil(log10((double)nz)/log10(2.0))); |
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139 | #endif |
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140 | |
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141 | float *data = new float[3*nx*ny*nz]; |
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142 | |
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143 | std::cout << "generating " << nx << "x" << ny << "x" << nz << " = " << nx*ny*nz << " points" << std::endl; |
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144 | |
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145 | // generate the uniformly sampled data that we need for a volume |
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146 | double vmin = 0.0; |
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147 | double vmax = 0.0; |
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148 | double nzero_min = 0.0; |
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149 | int ngen = 0; |
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150 | for (int iz=0; iz < nz; iz++) { |
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151 | double zval = z0 + iz*dmin; |
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152 | for (int iy=0; iy < ny; iy++) { |
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153 | double yval = y0 + iy*dmin; |
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154 | for (int ix=0; ix < nx; ix++) { |
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155 | double xval = x0 + ix*dmin; |
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156 | |
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157 | vx = xfield.value(xval,yval,zval); |
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158 | vy = yfield.value(xval,yval,zval); |
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159 | vz = zfield.value(xval,yval,zval); |
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160 | //vx = 1; |
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161 | //vy = 1; |
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162 | vz = 0; |
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163 | double vm = sqrt(vx*vx + vy*vy + vz*vz); |
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164 | |
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165 | if (vm < vmin) { vmin = vm; } |
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166 | if (vm > vmax) { vmax = vm; } |
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167 | if (vm != 0.0f && vm < nzero_min) |
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168 | { |
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169 | nzero_min = vm; |
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170 | } |
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171 | |
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172 | data[ngen++] = vx; |
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173 | data[ngen++] = vy; |
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174 | data[ngen++] = vz; |
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175 | } |
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176 | } |
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177 | } |
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178 | |
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179 | ngen = 0; |
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180 | for (ngen=0; ngen < npts; ngen++) { |
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181 | data[ngen] = (data[ngen]/(2.0*vmax) + 0.5); |
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182 | } |
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183 | |
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184 | NanoVis::load_volume(index, nx, ny, nz, 3, data, vmin, vmax, nzero_min); |
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185 | delete [] data; |
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186 | } else { |
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187 | std::cerr << "WARNING: data not found in stream" << std::endl; |
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188 | } |
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189 | } |
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190 | |
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191 | |
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192 | /* Load a 3D volume from a dx-format file |
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193 | */ |
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194 | Rappture::Outcome |
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195 | load_volume_stream2(int index, std::iostream& fin) { |
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196 | Rappture::Outcome result; |
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197 | |
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198 | Rappture::MeshTri2D xymesh; |
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199 | int dummy, nx, ny, nz, nxy, npts; |
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200 | double x0, y0, z0, dx, dy, dz, ddx, ddy, ddz; |
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201 | char line[128], type[128], *start; |
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202 | |
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203 | int isrect = 1; |
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204 | |
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205 | float* voldata = 0; |
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206 | do { |
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207 | fin.getline(line,sizeof(line)-1); |
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208 | for (start=&line[0]; *start == ' ' || *start == '\t'; start++) |
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209 | ; // skip leading blanks |
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210 | |
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211 | if (*start != '#') { // skip comment lines |
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212 | printf("%s\n", line); |
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213 | if (sscanf(start, "object %d class gridpositions counts %d %d %d", &dummy, &nx, &ny, &nz) == 4) { |
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214 | // found grid size |
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215 | isrect = 1; |
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216 | } |
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217 | else if (sscanf(start, "object %d class array type float rank 1 shape 3 items %d data follows", &dummy, &nxy) == 2) { |
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218 | isrect = 0; |
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219 | double xx, yy, zz; |
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220 | for (int i=0; i < nxy; i++) { |
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221 | fin.getline(line, sizeof(line)); |
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222 | fin.getline(line,sizeof(line)-1); |
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223 | if (sscanf(line, "%lg %lg %lg", &xx, &yy, &zz) == 3) { |
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224 | xymesh.addNode( Rappture::Node2D(xx,yy) ); |
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225 | } |
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226 | } |
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227 | char mesg[256]; |
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228 | sprintf(mesg,"test"); |
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229 | result.error(mesg); |
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230 | return result; |
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231 | |
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232 | char fpts[128]; |
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233 | sprintf(fpts, "/tmp/tmppts%d", getpid()); |
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234 | char fcells[128]; |
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235 | sprintf(fcells, "/tmp/tmpcells%d", getpid()); |
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236 | |
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237 | std::ofstream ftmp(fpts); |
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238 | // save corners of bounding box first, to work around meshing |
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239 | // problems in voronoi utility |
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240 | ftmp << xymesh.rangeMin(Rappture::xaxis) << " " |
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241 | << xymesh.rangeMin(Rappture::yaxis) << std::endl; |
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242 | ftmp << xymesh.rangeMax(Rappture::xaxis) << " " |
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243 | << xymesh.rangeMin(Rappture::yaxis) << std::endl; |
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244 | ftmp << xymesh.rangeMax(Rappture::xaxis) << " " |
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245 | << xymesh.rangeMax(Rappture::yaxis) << std::endl; |
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246 | ftmp << xymesh.rangeMin(Rappture::xaxis) << " " |
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247 | << xymesh.rangeMax(Rappture::yaxis) << std::endl; |
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248 | for (int i=0; i < nxy; i++) { |
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249 | ftmp << xymesh.atNode(i).x() << " " << xymesh.atNode(i).y() << std::endl; |
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250 | |
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251 | } |
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252 | ftmp.close(); |
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253 | |
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254 | char cmdstr[512]; |
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255 | sprintf(cmdstr, "voronoi -t < %s > %s", fpts, fcells); |
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256 | if (system(cmdstr) == 0) { |
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257 | int cx, cy, cz; |
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258 | std::ifstream ftri(fcells); |
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259 | while (!ftri.eof()) { |
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260 | ftri.getline(line,sizeof(line)-1); |
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261 | if (sscanf(line, "%d %d %d", &cx, &cy, &cz) == 3) { |
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262 | if (cx >= 4 && cy >= 4 && cz >= 4) { |
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263 | // skip first 4 boundary points |
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264 | xymesh.addCell(cx-4, cy-4, cz-4); |
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265 | } |
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266 | } |
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267 | } |
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268 | ftri.close(); |
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269 | } else { |
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270 | return result.error("triangularization failed"); |
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271 | } |
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272 | |
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273 | sprintf(cmdstr, "rm -f %s %s", fpts, fcells); |
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274 | system(cmdstr); |
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275 | } |
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276 | else if (sscanf(start, "object %d class regulararray count %d", &dummy, &nz) == 2) { |
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277 | // found z-grid |
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278 | } |
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279 | else if (sscanf(start, "origin %lg %lg %lg", &x0, &y0, &z0) == 3) { |
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280 | // found origin |
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281 | } |
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282 | else if (sscanf(start, "delta %lg %lg %lg", &ddx, &ddy, &ddz) == 3) { |
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283 | // found one of the delta lines |
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284 | if (ddx != 0.0) { dx = ddx; } |
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285 | else if (ddy != 0.0) { dy = ddy; } |
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286 | else if (ddz != 0.0) { dz = ddz; } |
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287 | } |
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288 | else if (sscanf(start, "object %d class array type %s rank 0 items %d data follows", &dummy, type, &npts) == 3) { |
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289 | if (isrect && (npts != nx*ny*nz)) { |
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290 | char mesg[256]; |
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291 | sprintf(mesg,"inconsistent data: expected %d points but found %d points", nx*ny*nz, npts); |
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292 | return result.error(mesg); |
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293 | } |
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294 | else if (!isrect && (npts != nxy*nz)) { |
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295 | char mesg[256]; |
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296 | sprintf(mesg,"inconsistent data: expected %d points but found %d points", nxy*nz, npts); |
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297 | return result.error(mesg); |
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298 | } |
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299 | break; |
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300 | } |
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301 | else if (sscanf(start, "object %d class array type %s rank 0 times %d data follows", &dummy, type, &npts) == 3) { |
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302 | if (npts != nx*ny*nz) { |
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303 | char mesg[256]; |
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304 | sprintf(mesg,"inconsistent data: expected %d points but found %d points", nx*ny*nz, npts); |
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305 | return result.error(mesg); |
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306 | } |
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307 | break; |
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308 | } |
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309 | } |
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310 | } while (!fin.eof()); |
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311 | |
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312 | // read data points |
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313 | if (!fin.eof()) { |
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314 | if (isrect) { |
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315 | double dval[6]; |
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316 | int nread = 0; |
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317 | int ix = 0; |
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318 | int iy = 0; |
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319 | int iz = 0; |
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320 | float* data = new float[nx * ny * nz * 4]; |
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321 | memset(data, 0, nx*ny*nz*4); |
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322 | double vmin = 1e21; |
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323 | double nzero_min = 1e21; |
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324 | double vmax = -1e21; |
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325 | |
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326 | |
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327 | while (!fin.eof() && nread < npts) { |
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328 | fin.getline(line,sizeof(line)-1); |
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329 | int n = sscanf(line, "%lg %lg %lg %lg %lg %lg", &dval[0], &dval[1], &dval[2], &dval[3], &dval[4], &dval[5]); |
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330 | |
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331 | for (int p=0; p < n; p++) { |
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332 | int nindex = (iz*nx*ny + iy*nx + ix) * 4; |
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333 | data[nindex] = dval[p]; |
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334 | |
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335 | if (dval[p] < vmin) vmin = dval[p]; |
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336 | if (dval[p] > vmax) vmax = dval[p]; |
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337 | if (dval[p] != 0.0f && dval[p] < nzero_min) |
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338 | { |
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339 | nzero_min = dval[p]; |
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340 | } |
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341 | |
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342 | nread++; |
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343 | if (++iz >= nz) { |
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344 | iz = 0; |
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345 | if (++iy >= ny) { |
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346 | iy = 0; |
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347 | ++ix; |
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348 | } |
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349 | } |
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350 | } |
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351 | } |
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352 | |
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353 | // make sure that we read all of the expected points |
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354 | if (nread != nx*ny*nz) { |
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355 | char mesg[256]; |
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356 | sprintf(mesg,"inconsistent data: expected %d points but found %d points", nx*ny*nz, nread); |
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357 | result.error(mesg); |
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358 | return result; |
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359 | } |
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360 | |
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361 | double dv = vmax - vmin; |
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362 | int count = nx*ny*nz; |
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363 | int ngen = 0; |
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364 | double v; |
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365 | printf("test2\n"); |
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366 | fflush(stdout); |
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367 | if (dv == 0.0) { dv = 1.0; } |
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368 | for (int i = 0; i < count; ++i) |
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369 | { |
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370 | v = data[ngen]; |
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371 | // scale all values [0-1], -1 => out of bounds |
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372 | v = (isnan(v)) ? -1.0 : (v - vmin)/dv; |
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373 | data[ngen] = v; |
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374 | ngen += 4; |
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375 | } |
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376 | |
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377 | // Compute the gradient of this data. BE CAREFUL: center |
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378 | // calculation on each node to avoid skew in either direction. |
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379 | ngen = 0; |
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380 | for (int iz=0; iz < nz; iz++) { |
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381 | for (int iy=0; iy < ny; iy++) { |
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382 | for (int ix=0; ix < nx; ix++) { |
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383 | // gradient in x-direction |
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384 | double valm1 = (ix == 0) ? 0.0 : data[ngen - 4]; |
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385 | double valp1 = (ix == nx-1) ? 0.0 : data[ngen + 4]; |
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386 | if (valm1 < 0 || valp1 < 0) { |
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387 | data[ngen+1] = 0.0; |
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388 | } else { |
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389 | data[ngen+1] = valp1-valm1; // assume dx=1 |
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390 | //data[ngen+1] = ((valp1-valm1) + 1) * 0.5; // assume dx=1 |
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391 | } |
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392 | |
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393 | // gradient in y-direction |
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394 | valm1 = (iy == 0) ? 0.0 : data[ngen-4*nx]; |
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395 | valp1 = (iy == ny-1) ? 0.0 : data[ngen+4*nx]; |
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396 | if (valm1 < 0 || valp1 < 0) { |
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397 | data[ngen+2] = 0.0; |
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398 | } else { |
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399 | data[ngen+2] = valp1-valm1; // assume dx=1 |
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400 | //data[ngen+2] = ((valp1-valm1) + 1) * 0.5; // assume dy=1 |
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401 | } |
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402 | |
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403 | // gradient in z-direction |
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404 | valm1 = (iz == 0) ? 0.0 : data[ngen-4*nx*ny]; |
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405 | valp1 = (iz == nz-1) ? 0.0 : data[ngen+4*nx*ny]; |
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406 | if (valm1 < 0 || valp1 < 0) { |
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407 | data[ngen+3] = 0.0; |
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408 | } else { |
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409 | data[ngen+3] = valp1-valm1; // assume dx=1 |
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410 | //data[ngen+3] = ((valp1-valm1) + 1.0) * 0.5; // assume dz=1 |
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411 | } |
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412 | |
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413 | ngen += 4; |
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414 | } |
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415 | } |
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416 | } |
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417 | |
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418 | dx = nx; |
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419 | dy = ny; |
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420 | dz = nz; |
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421 | NanoVis::load_volume(index, nx, ny, nz, 4, data, |
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422 | vmin, vmax, nzero_min); |
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423 | |
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424 | delete [] data; |
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425 | |
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426 | } else { |
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427 | Rappture::Mesh1D zgrid(z0, z0+nz*dz, nz); |
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428 | Rappture::FieldPrism3D field(xymesh, zgrid); |
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429 | |
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430 | double dval; |
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431 | int nread = 0; |
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432 | int ixy = 0; |
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433 | int iz = 0; |
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434 | while (!fin.eof() && nread < npts) { |
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435 | if (!(fin >> dval).fail()) { |
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436 | int nid = nxy*iz + ixy; |
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437 | field.define(nid, dval); |
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438 | |
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439 | nread++; |
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440 | if (++iz >= nz) { |
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441 | iz = 0; |
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442 | ixy++; |
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443 | } |
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444 | } |
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445 | } |
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446 | |
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447 | // make sure that we read all of the expected points |
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448 | if (nread != nxy*nz) { |
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449 | char mesg[256]; |
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450 | sprintf(mesg,"inconsistent data: expected %d points but found %d points", nxy*nz, nread); |
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451 | return result.error(mesg); |
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452 | } |
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453 | |
---|
454 | // figure out a good mesh spacing |
---|
455 | int nsample = 30; |
---|
456 | x0 = field.rangeMin(Rappture::xaxis); |
---|
457 | dx = field.rangeMax(Rappture::xaxis) - field.rangeMin(Rappture::xaxis); |
---|
458 | y0 = field.rangeMin(Rappture::yaxis); |
---|
459 | dy = field.rangeMax(Rappture::yaxis) - field.rangeMin(Rappture::yaxis); |
---|
460 | z0 = field.rangeMin(Rappture::zaxis); |
---|
461 | dz = field.rangeMax(Rappture::zaxis) - field.rangeMin(Rappture::zaxis); |
---|
462 | double dmin = pow((dx*dy*dz)/(nsample*nsample*nsample), 0.333); |
---|
463 | |
---|
464 | nx = (int)ceil(dx/dmin); |
---|
465 | ny = (int)ceil(dy/dmin); |
---|
466 | nz = (int)ceil(dz/dmin); |
---|
467 | #ifndef NV40 |
---|
468 | // must be an even power of 2 for older cards |
---|
469 | nx = (int)pow(2.0, ceil(log10((double)nx)/log10(2.0))); |
---|
470 | ny = (int)pow(2.0, ceil(log10((double)ny)/log10(2.0))); |
---|
471 | nz = (int)pow(2.0, ceil(log10((double)nz)/log10(2.0))); |
---|
472 | #endif |
---|
473 | float *data = new float[4*nx*ny*nz]; |
---|
474 | |
---|
475 | double vmin = field.valueMin(); |
---|
476 | double dv = field.valueMax() - field.valueMin(); |
---|
477 | if (dv == 0.0) { dv = 1.0; } |
---|
478 | |
---|
479 | // generate the uniformly sampled data that we need for a volume |
---|
480 | int ngen = 0; |
---|
481 | double nzero_min = 0.0; |
---|
482 | for (iz=0; iz < nz; iz++) { |
---|
483 | double zval = z0 + iz*dmin; |
---|
484 | for (int iy=0; iy < ny; iy++) { |
---|
485 | double yval = y0 + iy*dmin; |
---|
486 | for (int ix=0; ix < nx; ix++) { |
---|
487 | double xval = x0 + ix*dmin; |
---|
488 | double v = field.value(xval,yval,zval); |
---|
489 | |
---|
490 | if (v != 0.0f && v < nzero_min) |
---|
491 | { |
---|
492 | nzero_min = v; |
---|
493 | } |
---|
494 | // scale all values [0-1], -1 => out of bounds |
---|
495 | v = (isnan(v)) ? -1.0 : (v - vmin)/dv; |
---|
496 | data[ngen] = v; |
---|
497 | |
---|
498 | ngen += 4; |
---|
499 | } |
---|
500 | } |
---|
501 | } |
---|
502 | |
---|
503 | // Compute the gradient of this data. BE CAREFUL: center |
---|
504 | // calculation on each node to avoid skew in either direction. |
---|
505 | ngen = 0; |
---|
506 | for (int iz=0; iz < nz; iz++) { |
---|
507 | for (int iy=0; iy < ny; iy++) { |
---|
508 | for (int ix=0; ix < nx; ix++) { |
---|
509 | // gradient in x-direction |
---|
510 | double valm1 = (ix == 0) ? 0.0 : data[ngen-4]; |
---|
511 | double valp1 = (ix == nx-1) ? 0.0 : data[ngen+4]; |
---|
512 | if (valm1 < 0 || valp1 < 0) { |
---|
513 | data[ngen+1] = 0.0; |
---|
514 | } else { |
---|
515 | //data[ngen+1] = valp1-valm1; // assume dx=1 |
---|
516 | data[ngen+1] = ((valp1-valm1) + 1.0) * 0.5; // assume dz=1 |
---|
517 | } |
---|
518 | |
---|
519 | // gradient in y-direction |
---|
520 | valm1 = (iy == 0) ? 0.0 : data[ngen-4*nx]; |
---|
521 | valp1 = (iy == ny-1) ? 0.0 : data[ngen+4*nx]; |
---|
522 | if (valm1 < 0 || valp1 < 0) { |
---|
523 | data[ngen+2] = 0.0; |
---|
524 | } else { |
---|
525 | //data[ngen+2] = valp1-valm1; // assume dy=1 |
---|
526 | data[ngen+2] = ((valp1-valm1) + 1.0) * 0.5; // assume dz=1 |
---|
527 | } |
---|
528 | |
---|
529 | // gradient in z-direction |
---|
530 | valm1 = (iz == 0) ? 0.0 : data[ngen-4*nx*ny]; |
---|
531 | valp1 = (iz == nz-1) ? 0.0 : data[ngen+4*nx*ny]; |
---|
532 | if (valm1 < 0 || valp1 < 0) { |
---|
533 | data[ngen+3] = 0.0; |
---|
534 | } else { |
---|
535 | //data[ngen+3] = valp1-valm1; // assume dz=1 |
---|
536 | data[ngen+3] = ((valp1-valm1) + 1.0) * 0.5; // assume dz=1 |
---|
537 | } |
---|
538 | |
---|
539 | ngen += 4; |
---|
540 | } |
---|
541 | } |
---|
542 | } |
---|
543 | |
---|
544 | NanoVis::load_volume(index, nx, ny, nz, 4, data, |
---|
545 | field.valueMin(), field.valueMax(), nzero_min); |
---|
546 | |
---|
547 | delete [] data; |
---|
548 | } |
---|
549 | } else { |
---|
550 | return result.error("data not found in stream"); |
---|
551 | } |
---|
552 | |
---|
553 | // |
---|
554 | // Center this new volume on the origin. |
---|
555 | // |
---|
556 | float dx0 = -0.5; |
---|
557 | float dy0 = -0.5*dy/dx; |
---|
558 | float dz0 = -0.5*dz/dx; |
---|
559 | NanoVis::volume[index]->move(Vector3(dx0, dy0, dz0)); |
---|
560 | |
---|
561 | return result; |
---|
562 | } |
---|
563 | |
---|
564 | Rappture::Outcome |
---|
565 | load_volume_stream(int index, std::iostream& fin) |
---|
566 | { |
---|
567 | Rappture::Outcome result; |
---|
568 | |
---|
569 | Rappture::MeshTri2D xymesh; |
---|
570 | int dummy, nx, ny, nz, nxy, npts; |
---|
571 | double x0, y0, z0, dx, dy, dz, ddx, ddy, ddz; |
---|
572 | char line[128], type[128], *start; |
---|
573 | |
---|
574 | int isrect = 1; |
---|
575 | |
---|
576 | do { |
---|
577 | fin.getline(line,sizeof(line)-1); |
---|
578 | for (start=&line[0]; *start == ' ' || *start == '\t'; start++) |
---|
579 | ; // skip leading blanks |
---|
580 | |
---|
581 | if (*start != '#') { // skip comment lines |
---|
582 | if (sscanf(start, "object %d class gridpositions counts %d %d %d", &dummy, &nx, &ny, &nz) == 4) { |
---|
583 | // found grid size |
---|
584 | isrect = 1; |
---|
585 | } |
---|
586 | else if (sscanf(start, "object %d class array type float rank 1 shape 3 items %d data follows", &dummy, &nxy) == 2) { |
---|
587 | isrect = 0; |
---|
588 | |
---|
589 | double xx, yy, zz; |
---|
590 | for (int i=0; i < nxy; i++) { |
---|
591 | fin.getline(line,sizeof(line)-1); |
---|
592 | if (sscanf(line, "%lg %lg %lg", &xx, &yy, &zz) == 3) { |
---|
593 | xymesh.addNode( Rappture::Node2D(xx,yy) ); |
---|
594 | } |
---|
595 | } |
---|
596 | |
---|
597 | char fpts[128]; |
---|
598 | sprintf(fpts, "/tmp/tmppts%d", getpid()); |
---|
599 | char fcells[128]; |
---|
600 | sprintf(fcells, "/tmp/tmpcells%d", getpid()); |
---|
601 | |
---|
602 | std::ofstream ftmp(fpts); |
---|
603 | // save corners of bounding box first, to work around meshing |
---|
604 | // problems in voronoi utility |
---|
605 | ftmp << xymesh.rangeMin(Rappture::xaxis) << " " |
---|
606 | << xymesh.rangeMin(Rappture::yaxis) << std::endl; |
---|
607 | ftmp << xymesh.rangeMax(Rappture::xaxis) << " " |
---|
608 | << xymesh.rangeMin(Rappture::yaxis) << std::endl; |
---|
609 | ftmp << xymesh.rangeMax(Rappture::xaxis) << " " |
---|
610 | << xymesh.rangeMax(Rappture::yaxis) << std::endl; |
---|
611 | ftmp << xymesh.rangeMin(Rappture::xaxis) << " " |
---|
612 | << xymesh.rangeMax(Rappture::yaxis) << std::endl; |
---|
613 | for (int i=0; i < nxy; i++) { |
---|
614 | ftmp << xymesh.atNode(i).x() << " " << xymesh.atNode(i).y() << std::endl; |
---|
615 | |
---|
616 | } |
---|
617 | ftmp.close(); |
---|
618 | |
---|
619 | char cmdstr[512]; |
---|
620 | sprintf(cmdstr, "voronoi -t < %s > %s", fpts, fcells); |
---|
621 | if (system(cmdstr) == 0) { |
---|
622 | int cx, cy, cz; |
---|
623 | std::ifstream ftri(fcells); |
---|
624 | while (!ftri.eof()) { |
---|
625 | ftri.getline(line,sizeof(line)-1); |
---|
626 | if (sscanf(line, "%d %d %d", &cx, &cy, &cz) == 3) { |
---|
627 | if (cx >= 4 && cy >= 4 && cz >= 4) { |
---|
628 | // skip first 4 boundary points |
---|
629 | xymesh.addCell(cx-4, cy-4, cz-4); |
---|
630 | } |
---|
631 | } |
---|
632 | } |
---|
633 | ftri.close(); |
---|
634 | } else { |
---|
635 | return result.error("triangularization failed"); |
---|
636 | } |
---|
637 | |
---|
638 | sprintf(cmdstr, "rm -f %s %s", fpts, fcells); |
---|
639 | system(cmdstr); |
---|
640 | } |
---|
641 | else if (sscanf(start, "object %d class regulararray count %d", &dummy, &nz) == 2) { |
---|
642 | // found z-grid |
---|
643 | } |
---|
644 | else if (sscanf(start, "origin %lg %lg %lg", &x0, &y0, &z0) == 3) { |
---|
645 | // found origin |
---|
646 | } |
---|
647 | else if (sscanf(start, "delta %lg %lg %lg", &ddx, &ddy, &ddz) == 3) { |
---|
648 | // found one of the delta lines |
---|
649 | if (ddx != 0.0) { dx = ddx; } |
---|
650 | else if (ddy != 0.0) { dy = ddy; } |
---|
651 | else if (ddz != 0.0) { dz = ddz; } |
---|
652 | } |
---|
653 | else if (sscanf(start, "object %d class array type %s rank 0 items %d data follows", &dummy, type, &npts) == 3) { |
---|
654 | if (isrect && (npts != nx*ny*nz)) { |
---|
655 | char mesg[256]; |
---|
656 | sprintf(mesg,"inconsistent data: expected %d points but found %d points", nx*ny*nz, npts); |
---|
657 | return result.error(mesg); |
---|
658 | } |
---|
659 | else if (!isrect && (npts != nxy*nz)) { |
---|
660 | char mesg[256]; |
---|
661 | sprintf(mesg,"inconsistent data: expected %d points but found %d points", nxy*nz, npts); |
---|
662 | return result.error(mesg); |
---|
663 | } |
---|
664 | break; |
---|
665 | } |
---|
666 | else if (sscanf(start, "object %d class array type %s rank 0 times %d data follows", &dummy, type, &npts) == 3) { |
---|
667 | if (npts != nx*ny*nz) { |
---|
668 | char mesg[256]; |
---|
669 | sprintf(mesg,"inconsistent data: expected %d points but found %d points", nx*ny*nz, npts); |
---|
670 | return result.error(mesg); |
---|
671 | } |
---|
672 | break; |
---|
673 | } |
---|
674 | } |
---|
675 | } while (!fin.eof()); |
---|
676 | |
---|
677 | // read data points |
---|
678 | if (!fin.eof()) { |
---|
679 | if (isrect) { |
---|
680 | Rappture::Mesh1D xgrid(x0, x0+nx*dx, nx); |
---|
681 | Rappture::Mesh1D ygrid(y0, y0+ny*dy, ny); |
---|
682 | Rappture::Mesh1D zgrid(z0, z0+nz*dz, nz); |
---|
683 | Rappture::FieldRect3D field(xgrid, ygrid, zgrid); |
---|
684 | |
---|
685 | double dval[6]; |
---|
686 | int nread = 0; |
---|
687 | int ix = 0; |
---|
688 | int iy = 0; |
---|
689 | int iz = 0; |
---|
690 | while (!fin.eof() && nread < npts) { |
---|
691 | fin.getline(line,sizeof(line)-1); |
---|
692 | int n = sscanf(line, "%lg %lg %lg %lg %lg %lg", &dval[0], &dval[1], &dval[2], &dval[3], &dval[4], &dval[5]); |
---|
693 | |
---|
694 | for (int p=0; p < n; p++) { |
---|
695 | int nindex = iz*nx*ny + iy*nx + ix; |
---|
696 | field.define(nindex, dval[p]); |
---|
697 | nread++; |
---|
698 | if (++iz >= nz) { |
---|
699 | iz = 0; |
---|
700 | if (++iy >= ny) { |
---|
701 | iy = 0; |
---|
702 | ++ix; |
---|
703 | } |
---|
704 | } |
---|
705 | } |
---|
706 | } |
---|
707 | |
---|
708 | // make sure that we read all of the expected points |
---|
709 | if (nread != nx*ny*nz) { |
---|
710 | char mesg[256]; |
---|
711 | sprintf(mesg,"inconsistent data: expected %d points but found %d points", nx*ny*nz, nread); |
---|
712 | result.error(mesg); |
---|
713 | return result; |
---|
714 | } |
---|
715 | |
---|
716 | // figure out a good mesh spacing |
---|
717 | int nsample = 30; |
---|
718 | dx = field.rangeMax(Rappture::xaxis) - field.rangeMin(Rappture::xaxis); |
---|
719 | dy = field.rangeMax(Rappture::yaxis) - field.rangeMin(Rappture::yaxis); |
---|
720 | dz = field.rangeMax(Rappture::zaxis) - field.rangeMin(Rappture::zaxis); |
---|
721 | double dmin = pow((dx*dy*dz)/(nsample*nsample*nsample), 0.333); |
---|
722 | |
---|
723 | nx = (int)ceil(dx/dmin); |
---|
724 | ny = (int)ceil(dy/dmin); |
---|
725 | nz = (int)ceil(dz/dmin); |
---|
726 | |
---|
727 | #ifndef NV40 |
---|
728 | // must be an even power of 2 for older cards |
---|
729 | nx = (int)pow(2.0, ceil(log10((double)nx)/log10(2.0))); |
---|
730 | ny = (int)pow(2.0, ceil(log10((double)ny)/log10(2.0))); |
---|
731 | nz = (int)pow(2.0, ceil(log10((double)nz)/log10(2.0))); |
---|
732 | #endif |
---|
733 | |
---|
734 | float *data = new float[4*nx*ny*nz]; |
---|
735 | |
---|
736 | double vmin = field.valueMin(); |
---|
737 | double dv = field.valueMax() - field.valueMin(); |
---|
738 | if (dv == 0.0) { dv = 1.0; } |
---|
739 | |
---|
740 | // generate the uniformly sampled data that we need for a volume |
---|
741 | int ngen = 0; |
---|
742 | double nzero_min = 0.0; |
---|
743 | for (int iz=0; iz < nz; iz++) { |
---|
744 | double zval = z0 + iz*dmin; |
---|
745 | for (int iy=0; iy < ny; iy++) { |
---|
746 | double yval = y0 + iy*dmin; |
---|
747 | for (int ix=0; ix < nx; ix++) { |
---|
748 | double xval = x0 + ix*dmin; |
---|
749 | double v = field.value(xval,yval,zval); |
---|
750 | |
---|
751 | if (v != 0.0f && v < nzero_min) |
---|
752 | { |
---|
753 | nzero_min = v; |
---|
754 | } |
---|
755 | |
---|
756 | // scale all values [0-1], -1 => out of bounds |
---|
757 | v = (isnan(v)) ? -1.0 : (v - vmin)/dv; |
---|
758 | |
---|
759 | data[ngen] = v; |
---|
760 | ngen += 4; |
---|
761 | } |
---|
762 | } |
---|
763 | } |
---|
764 | |
---|
765 | // Compute the gradient of this data. BE CAREFUL: center |
---|
766 | // calculation on each node to avoid skew in either direction. |
---|
767 | ngen = 0; |
---|
768 | for (int iz=0; iz < nz; iz++) { |
---|
769 | for (int iy=0; iy < ny; iy++) { |
---|
770 | for (int ix=0; ix < nx; ix++) { |
---|
771 | // gradient in x-direction |
---|
772 | double valm1 = (ix == 0) ? 0.0 : data[ngen-4]; |
---|
773 | double valp1 = (ix == nx-1) ? 0.0 : data[ngen+4]; |
---|
774 | if (valm1 < 0 || valp1 < 0) { |
---|
775 | data[ngen+1] = 0.0; |
---|
776 | } else { |
---|
777 | data[ngen+1] = ((valp1-valm1) + 1) * 0.5; // assume dx=1 |
---|
778 | } |
---|
779 | |
---|
780 | // gradient in y-direction |
---|
781 | valm1 = (iy == 0) ? 0.0 : data[ngen-4*nx]; |
---|
782 | valp1 = (iy == ny-1) ? 0.0 : data[ngen+4*nx]; |
---|
783 | if (valm1 < 0 || valp1 < 0) { |
---|
784 | data[ngen+2] = 0.0; |
---|
785 | } else { |
---|
786 | //data[ngen+2] = valp1-valm1; // assume dy=1 |
---|
787 | data[ngen+2] = ((valp1-valm1) + 1) * 0.5; // assume dx=1 |
---|
788 | } |
---|
789 | |
---|
790 | // gradient in z-direction |
---|
791 | valm1 = (iz == 0) ? 0.0 : data[ngen-4*nx*ny]; |
---|
792 | valp1 = (iz == nz-1) ? 0.0 : data[ngen+4*nx*ny]; |
---|
793 | if (valm1 < 0 || valp1 < 0) { |
---|
794 | data[ngen+3] = 0.0; |
---|
795 | } else { |
---|
796 | //data[ngen+3] = valp1-valm1; // assume dz=1 |
---|
797 | data[ngen+3] = ((valp1-valm1) + 1) * 0.5; // assume dz=1 |
---|
798 | } |
---|
799 | |
---|
800 | ngen += 4; |
---|
801 | } |
---|
802 | } |
---|
803 | } |
---|
804 | |
---|
805 | NanoVis::load_volume(index, nx, ny, nz, 4, data, |
---|
806 | field.valueMin(), field.valueMax(), nzero_min); |
---|
807 | |
---|
808 | delete [] data; |
---|
809 | |
---|
810 | } else { |
---|
811 | Rappture::Mesh1D zgrid(z0, z0+nz*dz, nz); |
---|
812 | Rappture::FieldPrism3D field(xymesh, zgrid); |
---|
813 | |
---|
814 | double dval; |
---|
815 | int nread = 0; |
---|
816 | int ixy = 0; |
---|
817 | int iz = 0; |
---|
818 | while (!fin.eof() && nread < npts) { |
---|
819 | if (!(fin >> dval).fail()) { |
---|
820 | int nid = nxy*iz + ixy; |
---|
821 | field.define(nid, dval); |
---|
822 | |
---|
823 | nread++; |
---|
824 | if (++iz >= nz) { |
---|
825 | iz = 0; |
---|
826 | ixy++; |
---|
827 | } |
---|
828 | } |
---|
829 | } |
---|
830 | |
---|
831 | // make sure that we read all of the expected points |
---|
832 | if (nread != nxy*nz) { |
---|
833 | char mesg[256]; |
---|
834 | sprintf(mesg,"inconsistent data: expected %d points but found %d points", nxy*nz, nread); |
---|
835 | return result.error(mesg); |
---|
836 | } |
---|
837 | |
---|
838 | // figure out a good mesh spacing |
---|
839 | int nsample = 30; |
---|
840 | x0 = field.rangeMin(Rappture::xaxis); |
---|
841 | dx = field.rangeMax(Rappture::xaxis) - field.rangeMin(Rappture::xaxis); |
---|
842 | y0 = field.rangeMin(Rappture::yaxis); |
---|
843 | dy = field.rangeMax(Rappture::yaxis) - field.rangeMin(Rappture::yaxis); |
---|
844 | z0 = field.rangeMin(Rappture::zaxis); |
---|
845 | dz = field.rangeMax(Rappture::zaxis) - field.rangeMin(Rappture::zaxis); |
---|
846 | double dmin = pow((dx*dy*dz)/(nsample*nsample*nsample), 0.333); |
---|
847 | |
---|
848 | nx = (int)ceil(dx/dmin); |
---|
849 | ny = (int)ceil(dy/dmin); |
---|
850 | nz = (int)ceil(dz/dmin); |
---|
851 | #ifndef NV40 |
---|
852 | // must be an even power of 2 for older cards |
---|
853 | nx = (int)pow(2.0, ceil(log10((double)nx)/log10(2.0))); |
---|
854 | ny = (int)pow(2.0, ceil(log10((double)ny)/log10(2.0))); |
---|
855 | nz = (int)pow(2.0, ceil(log10((double)nz)/log10(2.0))); |
---|
856 | #endif |
---|
857 | float *data = new float[4*nx*ny*nz]; |
---|
858 | |
---|
859 | double vmin = field.valueMin(); |
---|
860 | double dv = field.valueMax() - field.valueMin(); |
---|
861 | if (dv == 0.0) { dv = 1.0; } |
---|
862 | |
---|
863 | // generate the uniformly sampled data that we need for a volume |
---|
864 | int ngen = 0; |
---|
865 | double nzero_min = 0.0; |
---|
866 | for (iz=0; iz < nz; iz++) { |
---|
867 | double zval = z0 + iz*dmin; |
---|
868 | for (int iy=0; iy < ny; iy++) { |
---|
869 | double yval = y0 + iy*dmin; |
---|
870 | for (int ix=0; ix < nx; ix++) { |
---|
871 | double xval = x0 + ix*dmin; |
---|
872 | double v = field.value(xval,yval,zval); |
---|
873 | |
---|
874 | if (v != 0.0f && v < nzero_min) |
---|
875 | { |
---|
876 | nzero_min = v; |
---|
877 | } |
---|
878 | // scale all values [0-1], -1 => out of bounds |
---|
879 | v = (isnan(v)) ? -1.0 : (v - vmin)/dv; |
---|
880 | data[ngen] = v; |
---|
881 | |
---|
882 | ngen += 4; |
---|
883 | } |
---|
884 | } |
---|
885 | } |
---|
886 | |
---|
887 | // Compute the gradient of this data. BE CAREFUL: center |
---|
888 | // calculation on each node to avoid skew in either direction. |
---|
889 | ngen = 0; |
---|
890 | for (int iz=0; iz < nz; iz++) { |
---|
891 | for (int iy=0; iy < ny; iy++) { |
---|
892 | for (int ix=0; ix < nx; ix++) { |
---|
893 | // gradient in x-direction |
---|
894 | double valm1 = (ix == 0) ? 0.0 : data[ngen-1]; |
---|
895 | double valp1 = (ix == nx-1) ? 0.0 : data[ngen+1]; |
---|
896 | if (valm1 < 0 || valp1 < 0) { |
---|
897 | data[ngen+1] = 0.0; |
---|
898 | } else { |
---|
899 | //data[ngen+1] = valp1-valm1; // assume dx=1 |
---|
900 | data[ngen+1] = ((valp1-valm1) + 1) * 0.5; // assume dx=1 |
---|
901 | } |
---|
902 | |
---|
903 | // gradient in y-direction |
---|
904 | valm1 = (iy == 0) ? 0.0 : data[ngen-4*nx]; |
---|
905 | valp1 = (iy == ny-1) ? 0.0 : data[ngen+4*nx]; |
---|
906 | if (valm1 < 0 || valp1 < 0) { |
---|
907 | data[ngen+2] = 0.0; |
---|
908 | } else { |
---|
909 | //data[ngen+2] = valp1-valm1; // assume dy=1 |
---|
910 | data[ngen+2] = ((valp1-valm1) + 1) * 0.5; // assume dy=1 |
---|
911 | } |
---|
912 | |
---|
913 | // gradient in z-direction |
---|
914 | valm1 = (iz == 0) ? 0.0 : data[ngen-4*nx*ny]; |
---|
915 | valp1 = (iz == nz-1) ? 0.0 : data[ngen+4*nx*ny]; |
---|
916 | if (valm1 < 0 || valp1 < 0) { |
---|
917 | data[ngen+3] = 0.0; |
---|
918 | } else { |
---|
919 | //data[ngen+3] = valp1-valm1; // assume dz=1 |
---|
920 | data[ngen+3] = ((valp1-valm1) + 1) * 0.5; // assume dz=1 |
---|
921 | } |
---|
922 | |
---|
923 | ngen += 4; |
---|
924 | } |
---|
925 | } |
---|
926 | } |
---|
927 | |
---|
928 | NanoVis::load_volume(index, nx, ny, nz, 4, data, |
---|
929 | field.valueMin(), field.valueMax(), nzero_min); |
---|
930 | |
---|
931 | delete [] data; |
---|
932 | } |
---|
933 | } else { |
---|
934 | return result.error("data not found in stream"); |
---|
935 | } |
---|
936 | |
---|
937 | // |
---|
938 | // Center this new volume on the origin. |
---|
939 | // |
---|
940 | float dx0 = -0.5; |
---|
941 | float dy0 = -0.5*dy/dx; |
---|
942 | float dz0 = -0.5*dz/dx; |
---|
943 | NanoVis::volume[index]->move(Vector3(dx0, dy0, dz0)); |
---|
944 | |
---|
945 | return result; |
---|
946 | } |
---|