1 | /* -*- mode: c++; c-basic-offset: 4; indent-tabs-mode: nil -*- */ |
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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) 2004-2013 HUBzero Foundation, LLC |
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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 | #include <stdio.h> |
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21 | #include <math.h> |
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22 | #include <sys/types.h> |
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23 | #include <unistd.h> |
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24 | #include <float.h> |
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25 | |
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26 | #include <fstream> |
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27 | #include <iostream> |
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28 | #include <sstream> |
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29 | #include <string> |
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30 | |
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31 | #include <RpOutcome.h> |
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32 | #include <RpField1D.h> |
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33 | #include <RpFieldRect3D.h> |
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34 | #include <RpFieldPrism3D.h> |
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35 | |
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36 | // common file/data reader functions |
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37 | #include "ReaderCommon.h" |
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38 | |
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39 | #include "config.h" |
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40 | #include "nanovis.h" |
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41 | #include "Unirect.h" |
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42 | #include "Volume.h" |
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43 | #include "ZincBlendeVolume.h" |
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44 | #include "NvZincBlendeReconstructor.h" |
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45 | |
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46 | /** |
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47 | * \brief Load a 3D volume from a dx-format file |
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48 | * |
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49 | * In DX format: |
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50 | * rank 0 means scalars, |
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51 | * rank 1 means vectors, |
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52 | * rank 2 means matrices, |
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53 | * rank 3 means tensors |
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54 | * |
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55 | * For rank 1, shape is a single number equal to the number of dimensions. |
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56 | * e.g. rank 1 shape 3 means a 3-component vector field |
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57 | */ |
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58 | Volume * |
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59 | load_dx_volume_stream(Rappture::Outcome& result, const char *tag, |
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60 | std::iostream& fin) |
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61 | { |
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62 | TRACE("Enter tag:%s", tag); |
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63 | |
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64 | Rappture::MeshTri2D xymesh; |
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65 | int dummy, nx, ny, nz, nxy, npts; |
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66 | // origin |
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67 | double x0, y0, z0; |
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68 | // deltas (cell dimensions) |
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69 | double dx, dy, dz; |
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70 | // length of volume edges |
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71 | double lx, ly, lz; |
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72 | // temps for delta values |
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73 | double ddx, ddy, ddz; |
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74 | char line[128], type[128], *start; |
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75 | |
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76 | int isrect = 1; |
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77 | |
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78 | dx = dy = dz = 0.0; |
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79 | x0 = y0 = z0 = 0.0; // May not have an origin line. |
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80 | nx = ny = nz = npts = nxy = 0; |
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81 | while (!fin.eof()) { |
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82 | fin.getline(line, sizeof(line) - 1); |
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83 | if (fin.fail()) { |
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84 | result.error("error in data stream"); |
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85 | return NULL; |
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86 | } |
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87 | for (start = line; *start == ' ' || *start == '\t'; start++) |
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88 | ; // skip leading blanks |
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89 | |
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90 | if (*start != '#') { // skip comment lines |
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91 | if (sscanf(start, "object %d class gridpositions counts %d %d %d", |
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92 | &dummy, &nx, &ny, &nz) == 4) { |
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93 | // found grid size |
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94 | isrect = 1; |
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95 | } else if (sscanf(start, "object %d class array type float rank 1 shape 3 items %d data follows", |
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96 | &dummy, &nxy) == 2) { |
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97 | isrect = 0; |
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98 | |
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99 | double xx, yy, zz; |
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100 | for (int i = 0; i < nxy; i++) { |
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101 | fin.getline(line,sizeof(line)-1); |
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102 | if (sscanf(line, "%lg %lg %lg", &xx, &yy, &zz) == 3) { |
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103 | xymesh.addNode(Rappture::Node2D(xx, yy)); |
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104 | } |
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105 | } |
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106 | |
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107 | char fpts[128]; |
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108 | sprintf(fpts, "/tmp/tmppts%d", getpid()); |
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109 | char fcells[128]; |
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110 | sprintf(fcells, "/tmp/tmpcells%d", getpid()); |
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111 | |
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112 | std::ofstream ftmp(fpts); |
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113 | // save corners of bounding box first, to work around meshing |
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114 | // problems in voronoi utility |
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115 | int numBoundaryPoints = 4; |
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116 | |
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117 | // Bump out the bounds by an epsilon to avoid problem when |
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118 | // corner points are already nodes |
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119 | double XEPS = (xymesh.rangeMax(Rappture::xaxis) - |
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120 | xymesh.rangeMin(Rappture::xaxis)) / 10.0f; |
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121 | |
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122 | double YEPS = (xymesh.rangeMax(Rappture::yaxis) - |
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123 | xymesh.rangeMin(Rappture::yaxis)) / 10.0f; |
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124 | |
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125 | ftmp << xymesh.rangeMin(Rappture::xaxis) - XEPS << " " |
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126 | << xymesh.rangeMin(Rappture::yaxis) - YEPS << std::endl; |
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127 | ftmp << xymesh.rangeMax(Rappture::xaxis) + XEPS << " " |
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128 | << xymesh.rangeMin(Rappture::yaxis) - YEPS << std::endl; |
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129 | ftmp << xymesh.rangeMax(Rappture::xaxis) + XEPS << " " |
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130 | << xymesh.rangeMax(Rappture::yaxis) + YEPS << std::endl; |
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131 | ftmp << xymesh.rangeMin(Rappture::xaxis) - XEPS << " " |
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132 | << xymesh.rangeMax(Rappture::yaxis) + YEPS << std::endl; |
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133 | |
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134 | for (int i = 0; i < nxy; i++) { |
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135 | ftmp << xymesh.atNode(i).x() << " " << xymesh.atNode(i).y() << std::endl; |
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136 | } |
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137 | ftmp.close(); |
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138 | |
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139 | char cmdstr[512]; |
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140 | sprintf(cmdstr, "voronoi -t < %s > %s", fpts, fcells); |
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141 | if (system(cmdstr) == 0) { |
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142 | int cx, cy, cz; |
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143 | std::ifstream ftri(fcells); |
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144 | while (!ftri.eof()) { |
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145 | ftri.getline(line,sizeof(line)-1); |
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146 | if (sscanf(line, "%d %d %d", &cx, &cy, &cz) == 3) { |
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147 | if (cx >= numBoundaryPoints && |
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148 | cy >= numBoundaryPoints && |
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149 | cz >= numBoundaryPoints) { |
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150 | // skip boundary points we added |
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151 | xymesh.addCell(cx - numBoundaryPoints, |
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152 | cy - numBoundaryPoints, |
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153 | cz - numBoundaryPoints); |
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154 | } |
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155 | } |
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156 | } |
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157 | ftri.close(); |
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158 | } else { |
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159 | result.error("triangularization failed"); |
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160 | return NULL; |
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161 | } |
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162 | unlink(fpts); |
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163 | unlink(fcells); |
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164 | } else if (sscanf(start, "object %d class regulararray count %d", &dummy, &nz) == 2) { |
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165 | // found z-grid |
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166 | } else if (sscanf(start, "origin %lg %lg %lg", &x0, &y0, &z0) == 3) { |
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167 | // found origin |
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168 | } else if (sscanf(start, "delta %lg %lg %lg", &ddx, &ddy, &ddz) == 3) { |
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169 | // found one of the delta lines |
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170 | int count = 0; |
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171 | if (ddx != 0.0) { |
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172 | dx = ddx; |
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173 | count++; |
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174 | } |
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175 | if (ddy != 0.0) { |
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176 | dy = ddy; |
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177 | count++; |
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178 | } |
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179 | if (ddz != 0.0) { |
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180 | dz = ddz; |
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181 | count++; |
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182 | } |
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183 | if (count > 1) { |
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184 | result.addError("don't know how to handle multiple non-zero" |
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185 | " delta values"); |
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186 | return NULL; |
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187 | } |
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188 | } else if (sscanf(start, "object %d class array type %s rank 0 items %d data follows", |
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189 | &dummy, type, &npts) == 3) { |
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190 | if (isrect && (npts != nx*ny*nz)) { |
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191 | result.addError("inconsistent data: expected %d points" |
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192 | " but found %d points", nx*ny*nz, npts); |
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193 | return NULL; |
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194 | } else if (!isrect && (npts != nxy*nz)) { |
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195 | result.addError("inconsistent data: expected %d points" |
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196 | " but found %d points", nxy*nz, npts); |
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197 | return NULL; |
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198 | } |
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199 | break; |
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200 | } else if (sscanf(start, "object %d class array type %s rank 0 times %d data follows", |
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201 | &dummy, type, &npts) == 3) { |
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202 | if (npts != nx*ny*nz) { |
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203 | result.addError("inconsistent data: expected %d points" |
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204 | " but found %d points", nx*ny*nz, npts); |
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205 | return NULL; |
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206 | } |
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207 | break; |
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208 | } |
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209 | } |
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210 | } |
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211 | |
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212 | TRACE("found nx=%d ny=%d nxy=%d nz=%d\ndx=%f dy=%f dz=%f\nx0=%f y0=%f z0=%f", |
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213 | nx, ny, nxy, nz, dx, dy, dz, x0, y0, z0); |
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214 | |
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215 | lx = (nx - 1) * dx; |
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216 | ly = (ny - 1) * dy; |
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217 | lz = (nz - 1) * dz; |
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218 | |
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219 | // read data points |
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220 | if (fin.eof()) { |
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221 | result.error("data not found in stream"); |
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222 | return NULL; |
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223 | } |
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224 | Volume *volume = NULL; |
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225 | float *data = NULL; |
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226 | double vmin = DBL_MAX; |
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227 | double nzero_min = DBL_MAX; |
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228 | double vmax = -DBL_MAX; |
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229 | if (isrect) { |
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230 | #ifdef DOWNSAMPLE_DATA |
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231 | Rappture::Mesh1D xgrid(x0, x0 + lx, nx); |
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232 | Rappture::Mesh1D ygrid(y0, y0 + ly, ny); |
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233 | Rappture::Mesh1D zgrid(z0, z0 + lz, nz); |
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234 | Rappture::FieldRect3D field(xgrid, ygrid, zgrid); |
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235 | #else // !DOWNSAMPLE_DATA |
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236 | data = new float[nx * ny * nz * 4]; |
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237 | memset(data, 0, nx*ny*nz*4); |
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238 | #endif // DOWNSAMPLE_DATA |
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239 | double dval[6]; |
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240 | int nread = 0; |
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241 | int ix = 0; |
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242 | int iy = 0; |
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243 | int iz = 0; |
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244 | |
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245 | while (!fin.eof() && nread < npts) { |
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246 | fin.getline(line,sizeof(line)-1); |
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247 | if (fin.fail()) { |
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248 | result.addError("error reading data points"); |
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249 | return NULL; |
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250 | } |
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251 | int n = sscanf(line, "%lg %lg %lg %lg %lg %lg", |
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252 | &dval[0], &dval[1], &dval[2], &dval[3], &dval[4], &dval[5]); |
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253 | for (int p = 0; p < n; p++) { |
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254 | #ifdef notdef |
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255 | if (isnan(dval[p])) { |
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256 | TRACE("Found NAN in input at %d,%d,%d", ix, iy, iz); |
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257 | } |
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258 | #endif |
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259 | #ifdef DOWNSAMPLE_DATA |
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260 | int nindex = iz*nx*ny + iy*nx + ix; |
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261 | field.define(nindex, dval[p]); |
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262 | #else // !DOWNSAMPLE_DATA |
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263 | int nindex = (iz*nx*ny + iy*nx + ix) * 4; |
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264 | data[nindex] = dval[p]; |
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265 | |
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266 | if (dval[p] < vmin) { |
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267 | vmin = dval[p]; |
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268 | } else if (dval[p] > vmax) { |
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269 | vmax = dval[p]; |
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270 | } |
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271 | if (dval[p] != 0.0 && dval[p] < nzero_min) { |
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272 | nzero_min = dval[p]; |
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273 | } |
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274 | #endif // DOWNSAMPLE_DATA |
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275 | nread++; |
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276 | if (++iz >= nz) { |
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277 | iz = 0; |
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278 | if (++iy >= ny) { |
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279 | iy = 0; |
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280 | ++ix; |
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281 | } |
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282 | } |
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283 | } |
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284 | } |
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285 | |
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286 | // make sure that we read all of the expected points |
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287 | if (nread != npts) { |
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288 | result.addError("inconsistent data: expected %d points" |
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289 | " but found %d points", npts, nread); |
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290 | return NULL; |
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291 | } |
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292 | |
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293 | #ifndef DOWNSAMPLE_DATA |
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294 | |
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295 | // scale all values [0-1], -1 => out of bounds |
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296 | normalizeScalar(data, npts, 4, vmin, vmax); |
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297 | computeSimpleGradient(data, nx, ny, nz, |
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298 | dx, dy, dz); |
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299 | #else // DOWNSAMPLE_DATA |
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300 | // figure out a good mesh spacing |
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301 | int nsample = 64; |
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302 | double dmin = pow((lx*ly*lz)/((nsample-1)*(nsample-1)*(nsample-1)), 0.333); |
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303 | |
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304 | nx = (int)ceil(lx/dmin) + 1; |
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305 | ny = (int)ceil(ly/dmin) + 1; |
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306 | nz = (int)ceil(lz/dmin) + 1; |
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307 | |
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308 | #ifndef HAVE_NPOT_TEXTURES |
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309 | // must be an even power of 2 for older cards |
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310 | nx = (int)pow(2.0, ceil(log10((double)nx)/log10(2.0))); |
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311 | ny = (int)pow(2.0, ceil(log10((double)ny)/log10(2.0))); |
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312 | nz = (int)pow(2.0, ceil(log10((double)nz)/log10(2.0))); |
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313 | #endif |
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314 | |
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315 | dx = lx /(double)(nx - 1); |
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316 | dy = ly /(double)(ny - 1); |
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317 | dz = lz /(double)(nz - 1); |
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318 | |
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319 | vmin = field.valueMin(); |
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320 | vmax = field.valueMax(); |
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321 | nzero_min = DBL_MAX; |
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322 | double dv = vmax - vmin; |
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323 | if (dv == 0.0) { |
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324 | dv = 1.0; |
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325 | } |
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326 | |
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327 | int ngen = 0; |
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328 | #ifdef FILTER_GRADIENTS |
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329 | // Sobel filter expects a single float at |
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330 | // each node |
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331 | const int step = 1; |
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332 | float *cdata = new float[nx*ny*nz * step]; |
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333 | #else // !FILTER_GRADIENTS |
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334 | // Leave 3 floats of space for gradients |
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335 | // to be filled in by computeSimpleGradient() |
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336 | const int step = 4; |
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337 | data = new float[nx*ny*nz * step]; |
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338 | #endif // FILTER_GRADIENTS |
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339 | |
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340 | for (int iz = 0; iz < nz; iz++) { |
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341 | double zval = z0 + iz*dz; |
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342 | for (int iy = 0; iy < ny; iy++) { |
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343 | double yval = y0 + iy*dy; |
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344 | for (int ix = 0; ix < nx; ix++) { |
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345 | double xval = x0 + ix*dx; |
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346 | double v = field.value(xval, yval, zval); |
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347 | #ifdef notdef |
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348 | if (isnan(v)) { |
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349 | TRACE("NAN at %d,%d,%d: (%g, %g, %g)", ix, iy, iz, xval, yval, zval); |
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350 | } |
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351 | #endif |
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352 | if (v != 0.0 && v < nzero_min) { |
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353 | nzero_min = v; |
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354 | } |
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355 | #ifdef FILTER_GRADIENTS |
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356 | // NOT normalized, may have NaNs (FIXME: how does gradient filter handle NaN?) |
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357 | cdata[ngen] = v; |
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358 | #else // !FILTER_GRADIENTS |
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359 | // scale all values [0-1], -1 => out of bounds |
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360 | v = (isnan(v)) ? -1.0 : (v - vmin)/dv; |
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361 | data[ngen] = v; |
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362 | #endif // FILTER_GRADIENTS |
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363 | ngen += step; |
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364 | } |
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365 | } |
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366 | } |
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367 | #ifdef FILTER_GRADIENTS |
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368 | // computeGradient returns a new array with gradients |
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369 | // filled in, so data is now 4 floats per node |
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370 | data = computeGradient(cdata, nx, ny, nz, |
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371 | dx, dy, dz, |
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372 | vmin, vmax); |
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373 | delete [] cdata; |
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374 | #else // !FILTER_GRADIENTS |
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375 | computeSimpleGradient(data, nx, ny, nz, |
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376 | dx, dy, dz); |
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377 | #endif // FILTER_GRADIENTS |
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378 | |
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379 | #endif // DOWNSAMPLE_DATA |
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380 | } else { |
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381 | Rappture::Mesh1D zgrid(z0, z0 + (nz-1)*dz, nz); |
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382 | Rappture::FieldPrism3D field(xymesh, zgrid); |
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383 | |
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384 | double dval; |
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385 | int nread = 0; |
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386 | int ixy = 0; |
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387 | int iz = 0; |
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388 | while (!fin.eof() && nread < npts) { |
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389 | fin >> dval; |
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390 | if (fin.fail()) { |
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391 | result.addError("after %d of %d points: can't read number", |
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392 | nread, npts); |
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393 | return NULL; |
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394 | } else { |
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395 | int nid = nxy*iz + ixy; |
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396 | field.define(nid, dval); |
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397 | |
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398 | nread++; |
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399 | if (++iz >= nz) { |
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400 | iz = 0; |
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401 | ixy++; |
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402 | } |
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403 | } |
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404 | } |
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405 | |
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406 | // make sure that we read all of the expected points |
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407 | if (nread != npts) { |
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408 | result.addError("inconsistent data: expected %d points" |
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409 | " but found %d points", npts, nread); |
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410 | return NULL; |
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411 | } |
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412 | |
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413 | x0 = field.rangeMin(Rappture::xaxis); |
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414 | lx = field.rangeMax(Rappture::xaxis) - field.rangeMin(Rappture::xaxis); |
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415 | y0 = field.rangeMin(Rappture::yaxis); |
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416 | ly = field.rangeMax(Rappture::yaxis) - field.rangeMin(Rappture::yaxis); |
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417 | z0 = field.rangeMin(Rappture::zaxis); |
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418 | lz = field.rangeMax(Rappture::zaxis) - field.rangeMin(Rappture::zaxis); |
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419 | |
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420 | // figure out a good mesh spacing |
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421 | int nsample = 64; |
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422 | double dmin = pow((lx*ly*lz)/((nsample-1)*(nsample-1)*(nsample-1)), 0.333); |
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423 | |
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424 | nx = (int)ceil(lx/dmin) + 1; |
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425 | ny = (int)ceil(ly/dmin) + 1; |
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426 | nz = (int)ceil(lz/dmin) + 1; |
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427 | #ifndef HAVE_NPOT_TEXTURES |
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428 | // must be an even power of 2 for older cards |
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429 | nx = (int)pow(2.0, ceil(log10((double)nx)/log10(2.0))); |
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430 | ny = (int)pow(2.0, ceil(log10((double)ny)/log10(2.0))); |
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431 | nz = (int)pow(2.0, ceil(log10((double)nz)/log10(2.0))); |
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432 | #endif |
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433 | |
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434 | dx = lx /(double)(nx - 1); |
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435 | dy = ly /(double)(ny - 1); |
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436 | dz = lz /(double)(nz - 1); |
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437 | |
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438 | vmin = field.valueMin(); |
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439 | vmax = field.valueMax(); |
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440 | nzero_min = DBL_MAX; |
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441 | double dv = vmax - vmin; |
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442 | if (dv == 0.0) { |
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443 | dv = 1.0; |
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444 | } |
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445 | |
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446 | data = new float[4*nx*ny*nz]; |
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447 | // generate the uniformly sampled data that we need for a volume |
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448 | int ngen = 0; |
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449 | for (int iz = 0; iz < nz; iz++) { |
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450 | double zval = z0 + iz*dz; |
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451 | for (int iy = 0; iy < ny; iy++) { |
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452 | double yval = y0 + iy*dy; |
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453 | for (int ix = 0; ix < nx; ix++) { |
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454 | double xval = x0 + ix*dx; |
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455 | double v = field.value(xval, yval, zval); |
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456 | |
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457 | if (v != 0.0 && v < nzero_min) { |
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458 | nzero_min = v; |
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459 | } |
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460 | // scale all values [0-1], -1 => out of bounds |
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461 | v = (isnan(v)) ? -1.0 : (v - vmin)/dv; |
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462 | data[ngen] = v; |
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463 | |
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464 | ngen += 4; |
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465 | } |
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466 | } |
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467 | } |
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468 | |
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469 | computeSimpleGradient(data, nx, ny, nz, |
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470 | dx, dy, dz); |
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471 | } |
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472 | |
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473 | TRACE("nx = %i ny = %i nz = %i", nx, ny, nz); |
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474 | TRACE("x0 = %lg y0 = %lg z0 = %lg", x0, y0, z0); |
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475 | TRACE("lx = %lg ly = %lg lz = %lg", lx, ly, lz); |
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476 | TRACE("dx = %lg dy = %lg dz = %lg", dx, dy, dz); |
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477 | TRACE("dataMin = %lg dataMax = %lg nzero_min = %lg", |
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478 | vmin, vmax, nzero_min); |
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479 | |
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480 | volume = NanoVis::loadVolume(tag, nx, ny, nz, 4, data, |
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481 | vmin, vmax, nzero_min); |
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482 | volume->xAxis.setRange(x0, x0 + lx); |
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483 | volume->yAxis.setRange(y0, y0 + ly); |
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484 | volume->zAxis.setRange(z0, z0 + lz); |
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485 | volume->updatePending = true; |
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486 | |
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487 | delete [] data; |
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488 | |
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489 | // |
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490 | // Center this new volume on the origin. |
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491 | // |
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492 | float dx0 = -0.5; |
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493 | float dy0 = -0.5*ly/lx; |
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494 | float dz0 = -0.5*lz/lx; |
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495 | if (volume) { |
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496 | volume->location(vrmath::Vector3f(dx0, dy0, dz0)); |
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497 | TRACE("Set volume location to %g %g %g", dx0, dy0, dz0); |
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498 | } |
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499 | return volume; |
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500 | } |
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