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annotate Framework/Volumes/ImageBuffer3D.cpp @ 684:7719eb852dd5

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new class: VolumeImageGeometry
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 16 May 2019 16:47:46 +0200
parents dbc1d8bfc68a
children 9a474e90e832
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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) 2017-2019 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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24 #include "../Toolbox/GeometryToolbox.h"
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25
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26 #include <Core/Images/ImageProcessing.h>
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27 #include <Core/Logging.h>
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28 #include <Core/OrthancException.h>
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29
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30 #include <string.h>
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32 namespace OrthancStone
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33 {
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34 void ImageBuffer3D::GetAxialSliceAccessor(Orthanc::ImageAccessor& target,
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35 unsigned int slice,
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36 bool readOnly) const
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37 {
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38 if (slice >= depth_)
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39 {
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40 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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41 }
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43 if (readOnly)
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44 {
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45 target.AssignReadOnly(format_, width_, height_, image_.GetPitch(),
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46 image_.GetConstRow(height_ * (depth_ - 1 - slice)));
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47 }
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48 else
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49 {
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50 target.AssignWritable(format_, width_, height_, image_.GetPitch(),
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51 image_.GetRow(height_ * (depth_ - 1 - slice)));
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52 }
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53 }
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56 void ImageBuffer3D::GetCoronalSliceAccessor(Orthanc::ImageAccessor& target,
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57 unsigned int slice,
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58 bool readOnly) const
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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 if (readOnly)
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66 {
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67 target.AssignReadOnly(format_, width_, depth_, image_.GetPitch() * height_,
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68 image_.GetConstRow(slice));
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69 }
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70 else
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71 {
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72 target.AssignWritable(format_, width_, depth_, image_.GetPitch() * height_,
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73 image_.GetRow(slice));
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74 }
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75 }
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78 Orthanc::Image* ImageBuffer3D::ExtractSagittalSlice(unsigned int slice) const
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79 {
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80 if (slice >= width_)
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81 {
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82 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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83 }
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84
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85 std::auto_ptr<Orthanc::Image> result(new Orthanc::Image(format_, height_, depth_, false));
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86
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87 unsigned int bytesPerPixel = Orthanc::GetBytesPerPixel(format_);
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88
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89 for (unsigned int z = 0; z < depth_; z++)
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90 {
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91 //uint8_t* target = reinterpret_cast<uint8_t*>(result->GetRow(depth_ - 1 - z));
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92 uint8_t* target = reinterpret_cast<uint8_t*>(result->GetRow(z));
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93
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94 for (unsigned int y = 0; y < height_; y++)
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95 {
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96 const void* source = (reinterpret_cast<const uint8_t*>(image_.GetConstRow(y + z * height_)) +
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97 bytesPerPixel * slice);
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98
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99 memcpy(target, source, bytesPerPixel);
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100 target += bytesPerPixel;
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101 }
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102 }
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103
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104 return result.release();
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105 }
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107
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108 ImageBuffer3D::ImageBuffer3D(Orthanc::PixelFormat format,
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109 unsigned int width,
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110 unsigned int height,
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111 unsigned int depth,
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112 bool computeRange) :
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113 image_(format, width, height * depth, false),
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114 format_(format),
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115 width_(width),
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116 height_(height),
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117 depth_(depth),
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118 computeRange_(computeRange),
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119 hasRange_(false)
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120 {
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121 geometry_.SetSize(width, height, depth);
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122
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123 LOG(INFO) << "Created a 3D image of size " << width << "x" << height
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124 << "x" << depth << " in " << Orthanc::EnumerationToString(format)
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125 << " (" << (GetEstimatedMemorySize() / (1024ll * 1024ll)) << "MB)";
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126 }
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128
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129 void ImageBuffer3D::Clear()
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130 {
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131 memset(image_.GetBuffer(), 0, image_.GetHeight() * image_.GetPitch());
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132 }
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136
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137 ParallelSlices* ImageBuffer3D::GetGeometry(VolumeProjection projection) const
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138 {
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139 const Vector dimensions = geometry_.GetVoxelDimensions(VolumeProjection_Axial);
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140 const CoordinateSystem3D& axial = geometry_.GetAxialGeometry();
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141
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142 std::auto_ptr<ParallelSlices> result(new ParallelSlices);
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143
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144 switch (projection)
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145 {
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146 case VolumeProjection_Axial:
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147 for (unsigned int z = 0; z < depth_; z++)
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148 {
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149 Vector origin = axial.GetOrigin();
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150 origin += static_cast<double>(z) * dimensions[2] * axial.GetNormal();
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151
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152 result->AddSlice(origin,
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153 axial.GetAxisX(),
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154 axial.GetAxisY());
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155 }
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156 break;
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157
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158 case VolumeProjection_Coronal:
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159 for (unsigned int y = 0; y < height_; y++)
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160 {
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161 Vector origin = axial.GetOrigin();
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162 origin += static_cast<double>(y) * dimensions[1] * axial.GetAxisY();
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163 origin += static_cast<double>(depth_ - 1) * dimensions[2] * axial.GetNormal();
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164
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165 result->AddSlice(origin,
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166 axial.GetAxisX(),
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167 -axial.GetNormal());
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168 }
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169 break;
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170
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171 case VolumeProjection_Sagittal:
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172 for (unsigned int x = 0; x < width_; x++)
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173 {
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174 Vector origin = axial.GetOrigin();
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175 origin += static_cast<double>(x) * dimensions[0] * axial.GetAxisX();
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176 origin += static_cast<double>(depth_ - 1) * dimensions[2] * axial.GetNormal();
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177
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178 result->AddSlice(origin,
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179 axial.GetAxisY(),
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180 -axial.GetNormal());
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181 }
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182 break;
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183
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184 default:
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185 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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186 }
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187
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188 return result.release();
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189 }
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190
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191
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192 uint64_t ImageBuffer3D::GetEstimatedMemorySize() const
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193 {
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194 return image_.GetPitch() * image_.GetHeight() * Orthanc::GetBytesPerPixel(format_);
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195 }
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196
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197
119
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198 void ImageBuffer3D::ExtendImageRange(const Orthanc::ImageAccessor& slice)
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199 {
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200 if (!computeRange_ ||
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201 slice.GetWidth() == 0 ||
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202 slice.GetHeight() == 0)
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203 {
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204 return;
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205 }
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206
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207 float sliceMin, sliceMax;
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208
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209 switch (slice.GetFormat())
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210 {
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211 case Orthanc::PixelFormat_Grayscale8:
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212 case Orthanc::PixelFormat_Grayscale16:
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213 case Orthanc::PixelFormat_Grayscale32:
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214 case Orthanc::PixelFormat_SignedGrayscale16:
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215 {
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216 int64_t a, b;
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217 Orthanc::ImageProcessing::GetMinMaxIntegerValue(a, b, slice);
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218 sliceMin = static_cast<float>(a);
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219 sliceMax = static_cast<float>(b);
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220 break;
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221 }
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222
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223 case Orthanc::PixelFormat_Float32:
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224 Orthanc::ImageProcessing::GetMinMaxFloatValue(sliceMin, sliceMax, slice);
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225 break;
119
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226
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227 default:
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228 return;
119
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229 }
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230
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231 if (hasRange_)
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232 {
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233 minValue_ = std::min(minValue_, sliceMin);
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234 maxValue_ = std::max(maxValue_, sliceMax);
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235 }
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236 else
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237 {
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238 hasRange_ = true;
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239 minValue_ = sliceMin;
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240 maxValue_ = sliceMax;
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241 }
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242 }
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243
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244
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245 bool ImageBuffer3D::GetRange(float& minValue,
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246 float& maxValue) const
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247 {
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248 if (hasRange_)
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249 {
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250 minValue = minValue_;
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251 maxValue = maxValue_;
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252 return true;
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253 }
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254 else
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255 {
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256 return false;
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257 }
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258 }
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259
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260
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261 bool ImageBuffer3D::FitWindowingToRange(RenderStyle& style,
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262 const DicomFrameConverter& converter) const
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263 {
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264 if (hasRange_)
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265 {
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266 style.windowing_ = ImageWindowing_Custom;
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267 style.customWindowCenter_ = converter.Apply((minValue_ + maxValue_) / 2.0);
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268 style.customWindowWidth_ = converter.Apply(maxValue_ - minValue_);
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269
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270 if (style.customWindowWidth_ > 1)
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271 {
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272 return true;
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273 }
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274 }
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275
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276 style.windowing_ = ImageWindowing_Custom;
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277 style.customWindowCenter_ = 128.0;
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278 style.customWindowWidth_ = 256.0;
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279 return false;
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280 }
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281
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282
192
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283 ImageBuffer3D::SliceReader::SliceReader(const ImageBuffer3D& that,
0
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284 VolumeProjection projection,
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285 unsigned int slice)
0
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286 {
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287 switch (projection)
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288 {
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289 case VolumeProjection_Axial:
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290 that.GetAxialSliceAccessor(accessor_, slice, true);
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291 break;
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292
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293 case VolumeProjection_Coronal:
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294 that.GetCoronalSliceAccessor(accessor_, slice, true);
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295 break;
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296
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297 case VolumeProjection_Sagittal:
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298 sagittal_.reset(that.ExtractSagittalSlice(slice));
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299 sagittal_->GetReadOnlyAccessor(accessor_);
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300 break;
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301
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302 default:
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303 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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304 }
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305 }
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306
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307
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308 void ImageBuffer3D::SliceWriter::Flush()
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309 {
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310 if (modified_)
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311 {
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312 if (sagittal_.get() != NULL)
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313 {
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314 // TODO
318
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315 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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316 }
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317
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318 // Update the dynamic range of the underlying image, if
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319 // "computeRange_" is set to true
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320 that_.ExtendImageRange(accessor_);
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321 }
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322 }
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323
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324
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325 ImageBuffer3D::SliceWriter::SliceWriter(ImageBuffer3D& that,
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326 VolumeProjection projection,
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327 unsigned int slice) :
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328 that_(that),
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329 modified_(false)
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330 {
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331 switch (projection)
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332 {
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333 case VolumeProjection_Axial:
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334 that.GetAxialSliceAccessor(accessor_, slice, false);
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335 break;
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336
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337 case VolumeProjection_Coronal:
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338 that.GetCoronalSliceAccessor(accessor_, slice, false);
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339 break;
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340
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341 case VolumeProjection_Sagittal:
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342 sagittal_.reset(that.ExtractSagittalSlice(slice));
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343 sagittal_->GetWriteableAccessor(accessor_);
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344 break;
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345
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346 default:
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347 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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348 }
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349 }
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350
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351
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352 uint8_t ImageBuffer3D::GetVoxelGrayscale8(unsigned int x,
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353 unsigned int y,
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354 unsigned int z) const
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355 {
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356 if (format_ != Orthanc::PixelFormat_Grayscale8)
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357 {
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358 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
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359 }
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360
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361 if (x >= width_ ||
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362 y >= height_ ||
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363 z >= depth_)
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364 {
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365 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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366 }
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367
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368 const void* p = image_.GetConstRow(y + height_ * (depth_ - 1 - z));
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369 return reinterpret_cast<const uint8_t*>(p) [x];
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370 }
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371
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372
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373 uint16_t ImageBuffer3D::GetVoxelGrayscale16(unsigned int x,
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374 unsigned int y,
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375 unsigned int z) const
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376 {
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377 if (format_ != Orthanc::PixelFormat_Grayscale16)
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378 {
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379 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
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380 }
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381
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382 if (x >= width_ ||
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383 y >= height_ ||
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384 z >= depth_)
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385 {
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386 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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387 }
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388
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389 const void* p = image_.GetConstRow(y + height_ * (depth_ - 1 - z));
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390 return reinterpret_cast<const uint16_t*>(p) [x];
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391 }
0
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392 }