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annotate Framework/Volumes/ImageBuffer3D.cpp @ 161:197a5ddaf68c wasm

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FiniteProjectiveCamera
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 14 Feb 2018 11:29:26 +0100
parents a053ca7fa5c6
children a12ca0f4aaaa
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1 /**
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2 * Stone of Orthanc
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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e2fe9352f240 upgrade to year 2018
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5 * Copyright (C) 2017-2018 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU Affero General Public License
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9 * as published by the Free Software Foundation, either version 3 of
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10 * the License, or (at your option) any later version.
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11 *
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12 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * Affero General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU Affero General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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22 #include "ImageBuffer3D.h"
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23
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24 #include <Core/Images/ImageProcessing.h>
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25 #include <Core/Logging.h>
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26 #include <Core/OrthancException.h>
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27
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28 #include <string.h>
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29
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30 namespace OrthancStone
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31 {
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32 Orthanc::ImageAccessor ImageBuffer3D::GetAxialSliceAccessor(unsigned int slice,
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33 bool readOnly)
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34 {
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35 if (slice >= depth_)
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36 {
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37 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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38 }
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40 Orthanc::ImageAccessor accessor;
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42 if (readOnly)
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43 {
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44 accessor.AssignReadOnly(format_, width_, height_, image_.GetPitch(),
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45 image_.GetConstRow(height_ * (depth_ - 1 - slice)));
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46 }
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47 else
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48 {
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49 accessor.AssignWritable(format_, width_, height_, image_.GetPitch(),
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50 image_.GetRow(height_ * (depth_ - 1 - slice)));
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51 }
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53 return accessor;
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54 }
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57 Orthanc::ImageAccessor ImageBuffer3D::GetCoronalSliceAccessor(unsigned int slice,
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58 bool readOnly)
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59 {
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60 if (slice >= height_)
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61 {
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62 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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63 }
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65 Orthanc::ImageAccessor accessor;
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66
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67 if (readOnly)
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68 {
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69 accessor.AssignReadOnly(format_, width_, depth_, image_.GetPitch() * height_,
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70 image_.GetConstRow(slice));
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71 }
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72 else
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73 {
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74 accessor.AssignWritable(format_, width_, depth_, image_.GetPitch() * height_,
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75 image_.GetRow(slice));
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76 }
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78 return accessor;
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79 }
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82 Orthanc::Image* ImageBuffer3D::ExtractSagittalSlice(unsigned int slice) const
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83 {
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84 if (slice >= width_)
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85 {
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86 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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87 }
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88
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89 std::auto_ptr<Orthanc::Image> result(new Orthanc::Image(format_, height_, depth_, false));
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91 unsigned int bytesPerPixel = Orthanc::GetBytesPerPixel(format_);
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92
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93 for (unsigned int z = 0; z < depth_; z++)
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94 {
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95 //uint8_t* target = reinterpret_cast<uint8_t*>(result->GetRow(depth_ - 1 - z));
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96 uint8_t* target = reinterpret_cast<uint8_t*>(result->GetRow(z));
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97
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98 for (unsigned int y = 0; y < height_; y++)
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99 {
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100 const void* source = (reinterpret_cast<const uint8_t*>(image_.GetConstRow(y + z * height_)) +
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101 bytesPerPixel * slice);
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102
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103 memcpy(target, source, bytesPerPixel);
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104 target += bytesPerPixel;
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105 }
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106 }
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107
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108 return result.release();
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109 }
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112 ImageBuffer3D::ImageBuffer3D(Orthanc::PixelFormat format,
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113 unsigned int width,
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114 unsigned int height,
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115 unsigned int depth,
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116 bool computeRange) :
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117 image_(format, width, height * depth, false),
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118 format_(format),
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119 width_(width),
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120 height_(height),
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121 depth_(depth),
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122 computeRange_(computeRange),
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123 hasRange_(false)
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124 {
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125 LinearAlgebra::AssignVector(voxelDimensions_, 1, 1, 1);
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126
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127 LOG(INFO) << "Created an image of "
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128 << (GetEstimatedMemorySize() / (1024ll * 1024ll)) << "MB";
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129 }
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131
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132 void ImageBuffer3D::Clear()
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133 {
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134 memset(image_.GetBuffer(), 0, image_.GetHeight() * image_.GetPitch());
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135 }
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138 void ImageBuffer3D::SetAxialGeometry(const CoordinateSystem3D& geometry)
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139 {
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140 axialGeometry_ = geometry;
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141 }
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144 void ImageBuffer3D::SetVoxelDimensions(double x,
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145 double y,
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146 double z)
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147 {
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148 if (x <= 0 ||
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149 y <= 0 ||
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150 z <= 0)
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151 {
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152 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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153 }
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155 {
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156 LinearAlgebra::AssignVector(voxelDimensions_, x, y, z);
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157 }
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158 }
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159
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160
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161 Vector ImageBuffer3D::GetVoxelDimensions(VolumeProjection projection) const
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162 {
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163 Vector result;
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164 switch (projection)
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165 {
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166 case VolumeProjection_Axial:
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167 result = voxelDimensions_;
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168 break;
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169
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170 case VolumeProjection_Coronal:
158
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171 LinearAlgebra::AssignVector(result, voxelDimensions_[0], voxelDimensions_[2], voxelDimensions_[1]);
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172 break;
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173
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174 case VolumeProjection_Sagittal:
158
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175 LinearAlgebra::AssignVector(result, voxelDimensions_[1], voxelDimensions_[2], voxelDimensions_[0]);
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176 break;
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177
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178 default:
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179 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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180 }
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181
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182 return result;
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183 }
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184
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185
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186 void ImageBuffer3D::GetSliceSize(unsigned int& width,
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187 unsigned int& height,
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188 VolumeProjection projection)
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189 {
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190 switch (projection)
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191 {
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192 case VolumeProjection_Axial:
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193 width = width_;
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194 height = height_;
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195 break;
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196
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197 case VolumeProjection_Coronal:
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198 width = width_;
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199 height = depth_;
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200 break;
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201
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202 case VolumeProjection_Sagittal:
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203 width = height_;
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204 height = depth_;
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205 break;
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206
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207 default:
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208 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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209 }
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210 }
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211
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212
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213 ParallelSlices* ImageBuffer3D::GetGeometry(VolumeProjection projection) const
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214 {
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215 std::auto_ptr<ParallelSlices> result(new ParallelSlices);
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216
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217 switch (projection)
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218 {
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219 case VolumeProjection_Axial:
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220 for (unsigned int z = 0; z < depth_; z++)
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221 {
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222 Vector origin = axialGeometry_.GetOrigin();
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223 origin += static_cast<double>(z) * voxelDimensions_[2] * axialGeometry_.GetNormal();
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224
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225 result->AddSlice(origin,
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226 axialGeometry_.GetAxisX(),
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227 axialGeometry_.GetAxisY());
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228 }
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229 break;
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230
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231 case VolumeProjection_Coronal:
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232 for (unsigned int y = 0; y < height_; y++)
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233 {
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234 Vector origin = axialGeometry_.GetOrigin();
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235 origin += static_cast<double>(y) * voxelDimensions_[1] * axialGeometry_.GetAxisY();
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236 origin += static_cast<double>(depth_ - 1) * voxelDimensions_[2] * axialGeometry_.GetNormal();
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237
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238 result->AddSlice(origin,
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239 axialGeometry_.GetAxisX(),
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240 -axialGeometry_.GetNormal());
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241 }
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242 break;
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243
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244 case VolumeProjection_Sagittal:
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245 for (unsigned int x = 0; x < width_; x++)
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246 {
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247 Vector origin = axialGeometry_.GetOrigin();
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248 origin += static_cast<double>(x) * voxelDimensions_[0] * axialGeometry_.GetAxisX();
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249 origin += static_cast<double>(depth_ - 1) * voxelDimensions_[2] * axialGeometry_.GetNormal();
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250
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251 result->AddSlice(origin,
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252 axialGeometry_.GetAxisY(),
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253 -axialGeometry_.GetNormal());
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254 }
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255 break;
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256
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257 default:
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258 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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259 }
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260
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261 return result.release();
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262 }
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263
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264
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265 uint64_t ImageBuffer3D::GetEstimatedMemorySize() const
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266 {
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267 return image_.GetPitch() * image_.GetHeight() * Orthanc::GetBytesPerPixel(format_);
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268 }
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269
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270
119
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271 void ImageBuffer3D::ExtendImageRange(const Orthanc::ImageAccessor& slice)
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272 {
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273 if (!computeRange_ ||
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274 slice.GetWidth() == 0 ||
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275 slice.GetHeight() == 0)
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276 {
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277 return;
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278 }
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279
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280 float sliceMin, sliceMax;
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281
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282 switch (slice.GetFormat())
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283 {
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284 case Orthanc::PixelFormat_Grayscale8:
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285 case Orthanc::PixelFormat_Grayscale16:
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286 case Orthanc::PixelFormat_Grayscale32:
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287 case Orthanc::PixelFormat_SignedGrayscale16:
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288 {
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289 int64_t a, b;
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290 Orthanc::ImageProcessing::GetMinMaxIntegerValue(a, b, slice);
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291 sliceMin = static_cast<float>(a);
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292 sliceMax = static_cast<float>(b);
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293 break;
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294 }
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295
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296 case Orthanc::PixelFormat_Float32:
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297 Orthanc::ImageProcessing::GetMinMaxFloatValue(sliceMin, sliceMax, slice);
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298 break;
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299
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300 default:
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301 return;
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302 }
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303
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304 if (hasRange_)
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305 {
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306 minValue_ = std::min(minValue_, sliceMin);
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307 maxValue_ = std::max(maxValue_, sliceMax);
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308 }
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309 else
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310 {
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311 hasRange_ = true;
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312 minValue_ = sliceMin;
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313 maxValue_ = sliceMax;
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314 }
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315 }
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316
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317
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318 bool ImageBuffer3D::GetRange(float& minValue,
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319 float& maxValue) const
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320 {
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321 if (hasRange_)
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322 {
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323 minValue = minValue_;
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324 maxValue = maxValue_;
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325 return true;
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326 }
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327 else
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328 {
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329 return false;
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330 }
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331 }
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332
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333
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334 bool ImageBuffer3D::FitWindowingToRange(RenderStyle& style,
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335 const DicomFrameConverter& converter) const
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336 {
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337 if (hasRange_)
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338 {
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339 style.windowing_ = ImageWindowing_Custom;
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340 style.customWindowCenter_ = converter.Apply((minValue_ + maxValue_) / 2.0);
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341 style.customWindowWidth_ = converter.Apply(maxValue_ - minValue_);
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342
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343 if (style.customWindowWidth_ > 1)
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344 {
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345 return true;
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346 }
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347 }
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348
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349 style.windowing_ = ImageWindowing_Custom;
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350 style.customWindowCenter_ = 128.0;
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351 style.customWindowWidth_ = 256.0;
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352 return false;
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353 }
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354
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355
0
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356 ImageBuffer3D::SliceReader::SliceReader(ImageBuffer3D& that,
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357 VolumeProjection projection,
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358 unsigned int slice)
0
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359 {
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360 switch (projection)
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361 {
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362 case VolumeProjection_Axial:
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363 accessor_ = that.GetAxialSliceAccessor(slice, true);
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364 break;
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365
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366 case VolumeProjection_Coronal:
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367 accessor_ = that.GetCoronalSliceAccessor(slice, true);
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368 break;
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369
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370 case VolumeProjection_Sagittal:
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371 sagittal_.reset(that.ExtractSagittalSlice(slice));
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372 accessor_ = *sagittal_;
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373 break;
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374
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375 default:
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376 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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377 }
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378 }
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379
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380
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381 void ImageBuffer3D::SliceWriter::Flush()
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382 {
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383 if (modified_)
0
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384 {
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385 if (sagittal_.get() != NULL)
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386 {
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387 // TODO
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388 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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389 }
119
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390
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391 // Update the dynamic range of the underlying image, if
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392 // "computeRange_" is set to true
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393 that_.ExtendImageRange(accessor_);
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394 }
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diff changeset
395 }
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diff changeset
396
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397
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398 ImageBuffer3D::SliceWriter::SliceWriter(ImageBuffer3D& that,
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399 VolumeProjection projection,
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400 unsigned int slice) :
119
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diff changeset
401 that_(that),
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402 modified_(false)
0
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403 {
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diff changeset
404 switch (projection)
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405 {
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406 case VolumeProjection_Axial:
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407 accessor_ = that.GetAxialSliceAccessor(slice, false);
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408 break;
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409
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410 case VolumeProjection_Coronal:
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411 accessor_ = that.GetCoronalSliceAccessor(slice, false);
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412 break;
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413
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414 case VolumeProjection_Sagittal:
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415 sagittal_.reset(that.ExtractSagittalSlice(slice));
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416 accessor_ = *sagittal_;
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417 break;
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418
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419 default:
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420 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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421 }
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422 }
139
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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423
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424
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425 uint8_t ImageBuffer3D::GetVoxelGrayscale8(unsigned int x,
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426 unsigned int y,
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427 unsigned int z) const
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428 {
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429 if (format_ != Orthanc::PixelFormat_Grayscale8)
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430 {
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diff changeset
431 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
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diff changeset
432 }
88bca952cb17 ImageBuffer3D::GetPixelGrayscale8
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diff changeset
433
88bca952cb17 ImageBuffer3D::GetPixelGrayscale8
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diff changeset
434 if (x >= width_ ||
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435 y >= height_ ||
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diff changeset
436 z >= depth_)
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437 {
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diff changeset
438 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
88bca952cb17 ImageBuffer3D::GetPixelGrayscale8
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diff changeset
439 }
88bca952cb17 ImageBuffer3D::GetPixelGrayscale8
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diff changeset
440
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diff changeset
441 const void* p = image_.GetConstRow(y + height_ * (depth_ - 1 - z));
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diff changeset
442 return reinterpret_cast<const uint8_t*>(p) [x];
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diff changeset
443 }
88bca952cb17 ImageBuffer3D::GetPixelGrayscale8
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parents: 139
diff changeset
444
88bca952cb17 ImageBuffer3D::GetPixelGrayscale8
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diff changeset
445
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diff changeset
446 uint16_t ImageBuffer3D::GetVoxelGrayscale16(unsigned int x,
139
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diff changeset
447 unsigned int y,
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diff changeset
448 unsigned int z) const
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diff changeset
449 {
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diff changeset
450 if (format_ != Orthanc::PixelFormat_Grayscale16)
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diff changeset
451 {
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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diff changeset
452 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
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diff changeset
453 }
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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parents: 135
diff changeset
454
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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parents: 135
diff changeset
455 if (x >= width_ ||
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diff changeset
456 y >= height_ ||
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diff changeset
457 z >= depth_)
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parents: 135
diff changeset
458 {
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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parents: 135
diff changeset
459 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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parents: 135
diff changeset
460 }
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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diff changeset
461
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diff changeset
462 const void* p = image_.GetConstRow(y + height_ * (depth_ - 1 - z));
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 135
diff changeset
463 return reinterpret_cast<const uint16_t*>(p) [x];
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 135
diff changeset
464 }
0
351ab0da0150 initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
465 }