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annotate Framework/Volumes/ImageBuffer3D.cpp @ 316:ce48c3b3b0e9

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fix for new ImageAccessor API
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 08 Oct 2018 12:45:27 +0200
parents 5412adf19980
children 557c8ff1db5c 88c79f1537de
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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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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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30 namespace OrthancStone
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31 {
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32 void ImageBuffer3D::GetAxialSliceAccessor(Orthanc::ImageAccessor& target,
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33 unsigned int slice,
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34 bool readOnly) const
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35 {
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36 if (slice >= depth_)
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37 {
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38 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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39 }
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41 if (readOnly)
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42 {
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43 target.AssignReadOnly(format_, width_, height_, image_.GetPitch(),
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44 image_.GetConstRow(height_ * (depth_ - 1 - slice)));
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45 }
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46 else
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47 {
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48 target.AssignWritable(format_, width_, height_, image_.GetPitch(),
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49 image_.GetRow(height_ * (depth_ - 1 - slice)));
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50 }
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51 }
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54 void ImageBuffer3D::GetCoronalSliceAccessor(Orthanc::ImageAccessor& target,
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55 unsigned int slice,
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56 bool readOnly) const
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57 {
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58 if (slice >= height_)
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59 {
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60 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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61 }
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63 if (readOnly)
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64 {
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65 target.AssignReadOnly(format_, width_, depth_, image_.GetPitch() * height_,
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66 image_.GetConstRow(slice));
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67 }
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68 else
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69 {
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70 target.AssignWritable(format_, width_, depth_, image_.GetPitch() * height_,
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71 image_.GetRow(slice));
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72 }
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73 }
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76 Orthanc::Image* ImageBuffer3D::ExtractSagittalSlice(unsigned int slice) const
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77 {
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78 if (slice >= width_)
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79 {
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80 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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81 }
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82
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83 std::auto_ptr<Orthanc::Image> result(new Orthanc::Image(format_, height_, depth_, false));
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84
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85 unsigned int bytesPerPixel = Orthanc::GetBytesPerPixel(format_);
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86
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87 for (unsigned int z = 0; z < depth_; z++)
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88 {
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89 //uint8_t* target = reinterpret_cast<uint8_t*>(result->GetRow(depth_ - 1 - z));
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90 uint8_t* target = reinterpret_cast<uint8_t*>(result->GetRow(z));
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91
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92 for (unsigned int y = 0; y < height_; y++)
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93 {
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94 const void* source = (reinterpret_cast<const uint8_t*>(image_.GetConstRow(y + z * height_)) +
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95 bytesPerPixel * slice);
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96
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97 memcpy(target, source, bytesPerPixel);
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98 target += bytesPerPixel;
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99 }
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100 }
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101
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102 return result.release();
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103 }
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105
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106 ImageBuffer3D::ImageBuffer3D(Orthanc::PixelFormat format,
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107 unsigned int width,
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108 unsigned int height,
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109 unsigned int depth,
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110 bool computeRange) :
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111 image_(format, width, height * depth, false),
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112 format_(format),
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113 width_(width),
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114 height_(height),
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115 depth_(depth),
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116 computeRange_(computeRange),
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117 hasRange_(false)
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118 {
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119 LinearAlgebra::AssignVector(voxelDimensions_, 1, 1, 1);
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120
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121 LOG(INFO) << "Created an image of "
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122 << (GetEstimatedMemorySize() / (1024ll * 1024ll)) << "MB";
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123 }
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125
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126 void ImageBuffer3D::Clear()
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127 {
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128 memset(image_.GetBuffer(), 0, image_.GetHeight() * image_.GetPitch());
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129 }
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131
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132 void ImageBuffer3D::SetAxialGeometry(const CoordinateSystem3D& geometry)
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133 {
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134 axialGeometry_ = geometry;
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135 }
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137
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138 void ImageBuffer3D::SetVoxelDimensions(double x,
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139 double y,
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140 double z)
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141 {
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142 if (x <= 0 ||
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143 y <= 0 ||
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144 z <= 0)
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145 {
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146 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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147 }
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149 {
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150 LinearAlgebra::AssignVector(voxelDimensions_, x, y, z);
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151 }
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152 }
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153
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154
139
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155 Vector ImageBuffer3D::GetVoxelDimensions(VolumeProjection projection) const
0
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156 {
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157 Vector result;
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158 switch (projection)
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159 {
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160 case VolumeProjection_Axial:
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161 result = voxelDimensions_;
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162 break;
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163
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164 case VolumeProjection_Coronal:
158
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165 LinearAlgebra::AssignVector(result, voxelDimensions_[0], voxelDimensions_[2], voxelDimensions_[1]);
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166 break;
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167
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168 case VolumeProjection_Sagittal:
158
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169 LinearAlgebra::AssignVector(result, voxelDimensions_[1], voxelDimensions_[2], voxelDimensions_[0]);
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170 break;
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171
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172 default:
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173 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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174 }
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175
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176 return result;
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177 }
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178
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179
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180 void ImageBuffer3D::GetSliceSize(unsigned int& width,
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181 unsigned int& height,
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182 VolumeProjection projection)
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183 {
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184 switch (projection)
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185 {
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186 case VolumeProjection_Axial:
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187 width = width_;
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188 height = height_;
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189 break;
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190
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191 case VolumeProjection_Coronal:
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192 width = width_;
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193 height = depth_;
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194 break;
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195
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196 case VolumeProjection_Sagittal:
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197 width = height_;
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198 height = depth_;
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199 break;
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200
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201 default:
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202 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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203 }
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204 }
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205
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206
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207 ParallelSlices* ImageBuffer3D::GetGeometry(VolumeProjection projection) const
0
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208 {
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209 std::auto_ptr<ParallelSlices> result(new ParallelSlices);
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210
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211 switch (projection)
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212 {
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213 case VolumeProjection_Axial:
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214 for (unsigned int z = 0; z < depth_; z++)
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215 {
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216 Vector origin = axialGeometry_.GetOrigin();
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217 origin += static_cast<double>(z) * voxelDimensions_[2] * axialGeometry_.GetNormal();
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218
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219 result->AddSlice(origin,
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220 axialGeometry_.GetAxisX(),
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221 axialGeometry_.GetAxisY());
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222 }
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223 break;
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224
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225 case VolumeProjection_Coronal:
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226 for (unsigned int y = 0; y < height_; y++)
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227 {
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228 Vector origin = axialGeometry_.GetOrigin();
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229 origin += static_cast<double>(y) * voxelDimensions_[1] * axialGeometry_.GetAxisY();
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230 origin += static_cast<double>(depth_ - 1) * voxelDimensions_[2] * axialGeometry_.GetNormal();
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231
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232 result->AddSlice(origin,
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233 axialGeometry_.GetAxisX(),
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234 -axialGeometry_.GetNormal());
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235 }
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236 break;
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237
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238 case VolumeProjection_Sagittal:
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239 for (unsigned int x = 0; x < width_; x++)
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240 {
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241 Vector origin = axialGeometry_.GetOrigin();
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242 origin += static_cast<double>(x) * voxelDimensions_[0] * axialGeometry_.GetAxisX();
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243 origin += static_cast<double>(depth_ - 1) * voxelDimensions_[2] * axialGeometry_.GetNormal();
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244
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245 result->AddSlice(origin,
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246 axialGeometry_.GetAxisY(),
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247 -axialGeometry_.GetNormal());
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248 }
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249 break;
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250
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251 default:
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252 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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253 }
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254
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255 return result.release();
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256 }
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257
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258
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259 uint64_t ImageBuffer3D::GetEstimatedMemorySize() const
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260 {
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261 return image_.GetPitch() * image_.GetHeight() * Orthanc::GetBytesPerPixel(format_);
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262 }
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263
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264
119
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265 void ImageBuffer3D::ExtendImageRange(const Orthanc::ImageAccessor& slice)
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266 {
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267 if (!computeRange_ ||
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268 slice.GetWidth() == 0 ||
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269 slice.GetHeight() == 0)
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270 {
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271 return;
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272 }
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273
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274 float sliceMin, sliceMax;
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275
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276 switch (slice.GetFormat())
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277 {
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278 case Orthanc::PixelFormat_Grayscale8:
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279 case Orthanc::PixelFormat_Grayscale16:
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280 case Orthanc::PixelFormat_Grayscale32:
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281 case Orthanc::PixelFormat_SignedGrayscale16:
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282 {
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283 int64_t a, b;
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284 Orthanc::ImageProcessing::GetMinMaxIntegerValue(a, b, slice);
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285 sliceMin = static_cast<float>(a);
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286 sliceMax = static_cast<float>(b);
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287 break;
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288 }
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289
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290 case Orthanc::PixelFormat_Float32:
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291 Orthanc::ImageProcessing::GetMinMaxFloatValue(sliceMin, sliceMax, slice);
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292 break;
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293
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294 default:
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295 return;
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296 }
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297
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298 if (hasRange_)
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299 {
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300 minValue_ = std::min(minValue_, sliceMin);
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301 maxValue_ = std::max(maxValue_, sliceMax);
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302 }
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303 else
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304 {
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305 hasRange_ = true;
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306 minValue_ = sliceMin;
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307 maxValue_ = sliceMax;
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308 }
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309 }
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diff changeset
310
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311
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312 bool ImageBuffer3D::GetRange(float& minValue,
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313 float& maxValue) const
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314 {
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315 if (hasRange_)
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316 {
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317 minValue = minValue_;
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318 maxValue = maxValue_;
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319 return true;
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320 }
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321 else
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322 {
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323 return false;
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324 }
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325 }
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326
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327
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328 bool ImageBuffer3D::FitWindowingToRange(RenderStyle& style,
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329 const DicomFrameConverter& converter) const
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330 {
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331 if (hasRange_)
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332 {
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333 style.windowing_ = ImageWindowing_Custom;
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334 style.customWindowCenter_ = converter.Apply((minValue_ + maxValue_) / 2.0);
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335 style.customWindowWidth_ = converter.Apply(maxValue_ - minValue_);
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diff changeset
336
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337 if (style.customWindowWidth_ > 1)
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338 {
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339 return true;
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340 }
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341 }
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diff changeset
342
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343 style.windowing_ = ImageWindowing_Custom;
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344 style.customWindowCenter_ = 128.0;
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345 style.customWindowWidth_ = 256.0;
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346 return false;
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347 }
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348
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349
192
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350 ImageBuffer3D::SliceReader::SliceReader(const ImageBuffer3D& that,
0
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351 VolumeProjection projection,
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352 unsigned int slice)
0
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353 {
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354 switch (projection)
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355 {
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356 case VolumeProjection_Axial:
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357 that.GetAxialSliceAccessor(accessor_, slice, true);
0
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358 break;
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359
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360 case VolumeProjection_Coronal:
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361 that.GetCoronalSliceAccessor(accessor_, slice, true);
0
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362 break;
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363
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364 case VolumeProjection_Sagittal:
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365 sagittal_.reset(that.ExtractSagittalSlice(slice));
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366 sagittal_->GetReadOnlyAccessor(accessor_);
0
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367 break;
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368
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369 default:
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370 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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371 }
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372 }
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373
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374
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375 void ImageBuffer3D::SliceWriter::Flush()
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376 {
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diff changeset
377 if (modified_)
0
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378 {
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diff changeset
379 if (sagittal_.get() != NULL)
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380 {
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381 // TODO
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382 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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diff changeset
383 }
119
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diff changeset
384
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385 // Update the dynamic range of the underlying image, if
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386 // "computeRange_" is set to true
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387 that_.ExtendImageRange(accessor_);
0
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388 }
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parents:
diff changeset
389 }
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parents:
diff changeset
390
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diff changeset
391
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392 ImageBuffer3D::SliceWriter::SliceWriter(ImageBuffer3D& that,
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393 VolumeProjection projection,
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394 unsigned int slice) :
119
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diff changeset
395 that_(that),
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diff changeset
396 modified_(false)
0
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diff changeset
397 {
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398 switch (projection)
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399 {
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400 case VolumeProjection_Axial:
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diff changeset
401 that.GetAxialSliceAccessor(accessor_, slice, false);
0
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402 break;
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parents:
diff changeset
403
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parents:
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404 case VolumeProjection_Coronal:
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diff changeset
405 that.GetCoronalSliceAccessor(accessor_, slice, false);
0
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406 break;
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parents:
diff changeset
407
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diff changeset
408 case VolumeProjection_Sagittal:
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409 sagittal_.reset(that.ExtractSagittalSlice(slice));
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diff changeset
410 sagittal_->GetWriteableAccessor(accessor_);
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411 break;
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parents:
diff changeset
412
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parents:
diff changeset
413 default:
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diff changeset
414 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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parents:
diff changeset
415 }
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diff changeset
416 }
139
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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parents: 135
diff changeset
417
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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diff changeset
418
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diff changeset
419 uint8_t ImageBuffer3D::GetVoxelGrayscale8(unsigned int x,
141
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diff changeset
420 unsigned int y,
88bca952cb17 ImageBuffer3D::GetPixelGrayscale8
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diff changeset
421 unsigned int z) const
88bca952cb17 ImageBuffer3D::GetPixelGrayscale8
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422 {
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423 if (format_ != Orthanc::PixelFormat_Grayscale8)
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diff changeset
424 {
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diff changeset
425 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
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diff changeset
426 }
88bca952cb17 ImageBuffer3D::GetPixelGrayscale8
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parents: 139
diff changeset
427
88bca952cb17 ImageBuffer3D::GetPixelGrayscale8
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parents: 139
diff changeset
428 if (x >= width_ ||
88bca952cb17 ImageBuffer3D::GetPixelGrayscale8
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parents: 139
diff changeset
429 y >= height_ ||
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parents: 139
diff changeset
430 z >= depth_)
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diff changeset
431 {
88bca952cb17 ImageBuffer3D::GetPixelGrayscale8
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parents: 139
diff changeset
432 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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parents: 139
diff changeset
433 }
88bca952cb17 ImageBuffer3D::GetPixelGrayscale8
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parents: 139
diff changeset
434
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diff changeset
435 const void* p = image_.GetConstRow(y + height_ * (depth_ - 1 - z));
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diff changeset
436 return reinterpret_cast<const uint8_t*>(p) [x];
88bca952cb17 ImageBuffer3D::GetPixelGrayscale8
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parents: 139
diff changeset
437 }
88bca952cb17 ImageBuffer3D::GetPixelGrayscale8
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parents: 139
diff changeset
438
88bca952cb17 ImageBuffer3D::GetPixelGrayscale8
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parents: 139
diff changeset
439
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parents: 141
diff changeset
440 uint16_t ImageBuffer3D::GetVoxelGrayscale16(unsigned int x,
139
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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parents: 135
diff changeset
441 unsigned int y,
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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diff changeset
442 unsigned int z) const
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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parents: 135
diff changeset
443 {
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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diff changeset
444 if (format_ != Orthanc::PixelFormat_Grayscale16)
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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parents: 135
diff changeset
445 {
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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parents: 135
diff changeset
446 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
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parents: 135
diff changeset
447 }
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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parents: 135
diff changeset
448
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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parents: 135
diff changeset
449 if (x >= width_ ||
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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parents: 135
diff changeset
450 y >= height_ ||
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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parents: 135
diff changeset
451 z >= depth_)
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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parents: 135
diff changeset
452 {
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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parents: 135
diff changeset
453 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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parents: 135
diff changeset
454 }
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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parents: 135
diff changeset
455
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
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parents: 135
diff changeset
456 const void* p = image_.GetConstRow(y + height_ * (depth_ - 1 - z));
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457 return reinterpret_cast<const uint16_t*>(p) [x];
22628d37ef5c ImageBuffer3D::GetPixelGrayscale16
Sebastien Jodogne <s.jodogne@gmail.com>
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458 }
187
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
Sebastien Jodogne <s.jodogne@gmail.com>
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459
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 158
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460
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 158
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461 Vector ImageBuffer3D::GetCoordinates(float x,
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
Sebastien Jodogne <s.jodogne@gmail.com>
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462 float y,
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 158
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463 float z) const
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
Sebastien Jodogne <s.jodogne@gmail.com>
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464 {
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 158
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465 Vector ps = GetVoxelDimensions(OrthancStone::VolumeProjection_Axial);
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
Sebastien Jodogne <s.jodogne@gmail.com>
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466
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 158
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467 const CoordinateSystem3D& axial = GetAxialGeometry();
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
Sebastien Jodogne <s.jodogne@gmail.com>
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468
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 158
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469 Vector origin = (axial.MapSliceToWorldCoordinates(-0.5 * ps[0], -0.5 * ps[1]) -
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
Sebastien Jodogne <s.jodogne@gmail.com>
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470 0.5 * ps[2] * axial.GetNormal());
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 158
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471
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
Sebastien Jodogne <s.jodogne@gmail.com>
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472 return (origin +
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 158
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473 axial.GetAxisX() * ps[0] * x * static_cast<double>(GetWidth()) +
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
Sebastien Jodogne <s.jodogne@gmail.com>
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474 axial.GetAxisY() * ps[1] * y * static_cast<double>(GetHeight()) +
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 158
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475 axial.GetNormal() * ps[2] * z * static_cast<double>(GetDepth()));
a12ca0f4aaaa ImageBuffer3D::GetCoordinates
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parents: 158
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476 }
0
351ab0da0150 initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
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477 }