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102
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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 Osimis, 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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20
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21
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22 #pragma once
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23
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24 #include "Layers/FrameRenderer.h"
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25 #include "Layers/LayerSourceBase.h"
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26 #include "Layers/SliceOutlineRenderer.h"
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27 #include "Toolbox/DownloadStack.h"
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28 #include "Toolbox/OrthancSlicesLoader.h"
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29 #include "Volumes/ImageBuffer3D.h"
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30 #include "Volumes/SlicedVolumeBase.h"
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31
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32 #include "../Resources/Orthanc/Core/Logging.h"
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33 #include "../Resources/Orthanc/Core/Images/ImageProcessing.h"
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34
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35 #include <boost/math/special_functions/round.hpp>
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36
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37
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38 namespace OrthancStone
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39 {
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40 class OrthancVolumeImage :
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41 public SlicedVolumeBase,
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42 private OrthancSlicesLoader::ICallback
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43 {
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44 private:
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45 OrthancSlicesLoader loader_;
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46 std::auto_ptr<ImageBuffer3D> image_;
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47 std::auto_ptr<DownloadStack> downloadStack_;
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48
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49
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50 void ScheduleSliceDownload()
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51 {
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52 assert(downloadStack_.get() != NULL);
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53
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54 unsigned int slice;
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55 if (downloadStack_->Pop(slice))
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56 {
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57 loader_.ScheduleLoadSliceImage(slice, SliceImageQuality_Jpeg90);
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58 }
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59 }
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60
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61
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62 static bool IsCompatible(const Slice& a,
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63 const Slice& b)
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64 {
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65 if (!GeometryToolbox::IsParallel(a.GetGeometry().GetNormal(),
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66 b.GetGeometry().GetNormal()))
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67 {
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68 LOG(ERROR) << "Some slice in the volume image is not parallel to the others";
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69 return false;
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70 }
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71
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72 if (a.GetConverter().GetExpectedPixelFormat() != b.GetConverter().GetExpectedPixelFormat())
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73 {
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74 LOG(ERROR) << "The pixel format changes across the slices of the volume image";
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75 return false;
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76 }
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77
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78 if (a.GetWidth() != b.GetWidth() ||
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79 a.GetHeight() != b.GetHeight())
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80 {
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81 LOG(ERROR) << "The width/height of the slices change across the volume image";
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82 return false;
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83 }
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84
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85 if (!GeometryToolbox::IsNear(a.GetPixelSpacingX(), b.GetPixelSpacingX()) ||
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86 !GeometryToolbox::IsNear(a.GetPixelSpacingY(), b.GetPixelSpacingY()))
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87 {
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88 LOG(ERROR) << "The pixel spacing of the slices change across the volume image";
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89 return false;
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90 }
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91
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92 return true;
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93 }
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94
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95
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96 static double GetDistance(const Slice& a,
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97 const Slice& b)
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98 {
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99 return fabs(a.GetGeometry().ProjectAlongNormal(a.GetGeometry().GetOrigin()) -
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100 a.GetGeometry().ProjectAlongNormal(b.GetGeometry().GetOrigin()));
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101 }
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102
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103
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104 virtual void NotifyGeometryReady(const OrthancSlicesLoader& loader)
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105 {
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106 if (loader.GetSliceCount() == 0)
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107 {
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108 LOG(ERROR) << "Empty volume image";
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109 SlicedVolumeBase::NotifyGeometryError();
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110 return;
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111 }
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112
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113 for (size_t i = 1; i < loader.GetSliceCount(); i++)
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114 {
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115 if (!IsCompatible(loader.GetSlice(0), loader.GetSlice(i)))
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116 {
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117 SlicedVolumeBase::NotifyGeometryError();
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118 return;
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119 }
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120 }
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121
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122 double spacingZ;
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123
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124 if (loader.GetSliceCount() > 1)
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125 {
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126 spacingZ = GetDistance(loader.GetSlice(0), loader.GetSlice(1));
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127 }
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128 else
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129 {
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130 // This is a volume with one single slice: Choose a dummy
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131 // z-dimension for voxels
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132 spacingZ = 1;
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133 }
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134
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135 for (size_t i = 1; i < loader.GetSliceCount(); i++)
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136 {
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137 if (!GeometryToolbox::IsNear(spacingZ, GetDistance(loader.GetSlice(i - 1), loader.GetSlice(i)),
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138 0.001 /* this is expressed in mm */))
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139 {
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140 LOG(ERROR) << "The distance between successive slices is not constant in a volume image";
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141 SlicedVolumeBase::NotifyGeometryError();
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142 return;
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143 }
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144 }
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145
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146 unsigned int width = loader.GetSlice(0).GetWidth();
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147 unsigned int height = loader.GetSlice(0).GetHeight();
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148 Orthanc::PixelFormat format = loader.GetSlice(0).GetConverter().GetExpectedPixelFormat();
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149 LOG(INFO) << "Creating a volume image of size " << width << "x" << height
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150 << "x" << loader.GetSliceCount() << " in " << Orthanc::EnumerationToString(format);
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151
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152 image_.reset(new ImageBuffer3D(format, width, height, loader.GetSliceCount()));
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153 image_->SetAxialGeometry(loader.GetSlice(0).GetGeometry());
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154 image_->SetVoxelDimensions(loader.GetSlice(0).GetPixelSpacingX(),
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155 loader.GetSlice(0).GetPixelSpacingY(), spacingZ);
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156 image_->Clear();
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157
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158 downloadStack_.reset(new DownloadStack(loader.GetSliceCount()));
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159
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160 for (unsigned int i = 0; i < 4; i++) // Limit to 4 simultaneous downloads
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161 {
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162 ScheduleSliceDownload();
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163 }
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164
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165 // TODO Check the DicomFrameConverter are constant
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166
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167 SlicedVolumeBase::NotifyGeometryReady();
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168 }
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169
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170 virtual void NotifyGeometryError(const OrthancSlicesLoader& loader)
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171 {
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172 LOG(ERROR) << "Unable to download a volume image";
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173 SlicedVolumeBase::NotifyGeometryError();
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174 }
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175
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176 virtual void NotifySliceImageReady(const OrthancSlicesLoader& loader,
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177 unsigned int sliceIndex,
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178 const Slice& slice,
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179 std::auto_ptr<Orthanc::ImageAccessor>& image,
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180 SliceImageQuality quality)
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181 {
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182 {
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183 ImageBuffer3D::SliceWriter writer(*image_, VolumeProjection_Axial, sliceIndex);
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184 Orthanc::ImageProcessing::Copy(writer.GetAccessor(), *image);
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185 }
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186
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187 SlicedVolumeBase::NotifySliceChange(sliceIndex, slice);
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188
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189 ScheduleSliceDownload();
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190 }
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191
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192 virtual void NotifySliceImageError(const OrthancSlicesLoader& loader,
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193 unsigned int sliceIndex,
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194 const Slice& slice,
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195 SliceImageQuality quality)
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196 {
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197 LOG(ERROR) << "Cannot download slice " << sliceIndex << " in a volume image";
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198 ScheduleSliceDownload();
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199 }
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200
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201 public:
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202 OrthancVolumeImage(IWebService& orthanc) :
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203 loader_(*this, orthanc)
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204 {
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205 }
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206
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207 void ScheduleLoadSeries(const std::string& seriesId)
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208 {
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209 loader_.ScheduleLoadSeries(seriesId);
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210 }
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211
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212 void ScheduleLoadInstance(const std::string& instanceId,
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213 unsigned int frame)
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214 {
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215 loader_.ScheduleLoadInstance(instanceId, frame);
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216 }
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217
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218 virtual size_t GetSliceCount() const
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219 {
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220 return loader_.GetSliceCount();
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221 }
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222
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223 virtual const Slice& GetSlice(size_t index) const
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224 {
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225 return loader_.GetSlice(index);
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226 }
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227
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228 ImageBuffer3D& GetImage() const
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229 {
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230 if (image_.get() == NULL)
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231 {
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232 // The geometry is not ready yet
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233 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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234 }
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235 else
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236 {
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237 return *image_;
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238 }
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239 }
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240 };
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241
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242
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243 class VolumeImageGeometry
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244 {
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245 private:
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246 unsigned int width_;
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247 unsigned int height_;
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248 size_t depth_;
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249 double pixelSpacingX_;
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250 double pixelSpacingY_;
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251 double sliceThickness_;
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252 SliceGeometry reference_;
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253 DicomFrameConverter converter_;
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254
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255 double ComputeAxialThickness(const OrthancVolumeImage& volume) const
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256 {
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257 double thickness;
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258
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259 size_t n = volume.GetSliceCount();
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260 if (n > 1)
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261 {
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262 const Slice& a = volume.GetSlice(0);
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263 const Slice& b = volume.GetSlice(n - 1);
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264 thickness = ((reference_.ProjectAlongNormal(b.GetGeometry().GetOrigin()) -
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265 reference_.ProjectAlongNormal(a.GetGeometry().GetOrigin())) /
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266 (static_cast<double>(n) - 1.0));
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267 }
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268 else
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269 {
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270 thickness = volume.GetSlice(0).GetThickness();
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271 }
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272
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273 if (thickness <= 0)
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274 {
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275 // The slices should have been sorted with increasing Z
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276 // (along the normal) by the OrthancSlicesLoader
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277 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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278 }
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279 else
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280 {
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281 return thickness;
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282 }
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283 }
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284
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285 void SetupAxial(const OrthancVolumeImage& volume)
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286 {
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287 const Slice& axial = volume.GetSlice(0);
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288
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289 width_ = axial.GetWidth();
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290 height_ = axial.GetHeight();
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291 depth_ = volume.GetSliceCount();
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292
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293 pixelSpacingX_ = axial.GetPixelSpacingX();
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294 pixelSpacingY_ = axial.GetPixelSpacingY();
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295 sliceThickness_ = ComputeAxialThickness(volume);
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296
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297 reference_ = axial.GetGeometry();
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298 }
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299
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300 void SetupCoronal(const OrthancVolumeImage& volume)
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301 {
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302 const Slice& axial = volume.GetSlice(0);
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303 double axialThickness = ComputeAxialThickness(volume);
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304
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305 width_ = axial.GetWidth();
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306 height_ = volume.GetSliceCount();
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307 depth_ = axial.GetHeight();
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308
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309 pixelSpacingX_ = axial.GetPixelSpacingX();
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310 pixelSpacingY_ = axialThickness;
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311 sliceThickness_ = axial.GetPixelSpacingY();
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312
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313 Vector origin = axial.GetGeometry().GetOrigin();
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314 origin += (static_cast<double>(volume.GetSliceCount() - 1) *
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315 axialThickness * axial.GetGeometry().GetNormal());
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316
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317 reference_ = SliceGeometry(origin,
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318 axial.GetGeometry().GetAxisX(),
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319 -axial.GetGeometry().GetNormal());
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320 }
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321
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322 void SetupSagittal(const OrthancVolumeImage& volume)
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323 {
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324 const Slice& axial = volume.GetSlice(0);
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325 double axialThickness = ComputeAxialThickness(volume);
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326
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327 width_ = axial.GetHeight();
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328 height_ = volume.GetSliceCount();
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329 depth_ = axial.GetWidth();
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330
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331 pixelSpacingX_ = axial.GetPixelSpacingY();
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332 pixelSpacingY_ = axialThickness;
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333 sliceThickness_ = axial.GetPixelSpacingX();
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334
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335 Vector origin = axial.GetGeometry().GetOrigin();
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336 origin += (static_cast<double>(volume.GetSliceCount() - 1) *
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337 axialThickness * axial.GetGeometry().GetNormal());
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338
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339 reference_ = SliceGeometry(origin,
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340 axial.GetGeometry().GetAxisY(),
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341 axial.GetGeometry().GetNormal());
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342 }
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343
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344 public:
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345 VolumeImageGeometry(const OrthancVolumeImage& volume,
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346 VolumeProjection projection)
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347 {
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348 if (volume.GetSliceCount() == 0)
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349 {
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350 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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351 }
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352
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353 converter_ = volume.GetSlice(0).GetConverter();
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354
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355 switch (projection)
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356 {
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357 case VolumeProjection_Axial:
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358 SetupAxial(volume);
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359 break;
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360
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361 case VolumeProjection_Coronal:
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362 SetupCoronal(volume);
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363 break;
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364
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365 case VolumeProjection_Sagittal:
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366 SetupSagittal(volume);
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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 size_t GetSliceCount() const
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375 {
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376 return depth_;
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377 }
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378
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379 const Vector& GetNormal() const
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380 {
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381 return reference_.GetNormal();
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382 }
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383
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384 bool LookupSlice(size_t& index,
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385 const SliceGeometry& slice) const
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386 {
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387 bool opposite;
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388 if (!GeometryToolbox::IsParallelOrOpposite(opposite,
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389 reference_.GetNormal(),
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390 slice.GetNormal()))
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391 {
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392 return false;
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393 }
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394
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395 double z = (reference_.ProjectAlongNormal(slice.GetOrigin()) -
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396 reference_.ProjectAlongNormal(reference_.GetOrigin())) / sliceThickness_;
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397
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398 int s = static_cast<int>(boost::math::iround(z));
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399
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400 if (s < 0 ||
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401 s >= static_cast<int>(depth_))
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402 {
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403 return false;
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404 }
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405 else
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406 {
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407 index = static_cast<size_t>(s);
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408 return true;
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409 }
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410 }
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411
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412 Slice GetSlice(size_t slice) const
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413 {
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414 if (slice < 0 ||
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415 slice >= depth_)
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416 {
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417 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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418 }
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419 else
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420 {
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421 SliceGeometry origin(reference_.GetOrigin() +
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422 static_cast<double>(slice) * sliceThickness_ * reference_.GetNormal(),
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423 reference_.GetAxisX(),
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424 reference_.GetAxisY());
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425
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426 return Slice(origin, pixelSpacingX_, pixelSpacingY_, sliceThickness_,
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427 width_, height_, converter_);
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428 }
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429 }
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430 };
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431
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432
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433
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434 class VolumeImageSource :
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435 public LayerSourceBase,
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436 private ISlicedVolume::IObserver
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437 {
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438 private:
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439 OrthancVolumeImage& volume_;
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440 std::auto_ptr<VolumeImageGeometry> axialGeometry_;
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441 std::auto_ptr<VolumeImageGeometry> coronalGeometry_;
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442 std::auto_ptr<VolumeImageGeometry> sagittalGeometry_;
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443
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444
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445 bool IsGeometryReady() const
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446 {
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447 return axialGeometry_.get() != NULL;
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448 }
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449
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450
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451 virtual void NotifyGeometryReady(const ISlicedVolume& volume)
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452 {
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453 // These 3 values are only used to speed up the ILayerSource
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454 axialGeometry_.reset(new VolumeImageGeometry(volume_, VolumeProjection_Axial));
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455 coronalGeometry_.reset(new VolumeImageGeometry(volume_, VolumeProjection_Coronal));
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456 sagittalGeometry_.reset(new VolumeImageGeometry(volume_, VolumeProjection_Sagittal));
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457
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458 LayerSourceBase::NotifyGeometryReady();
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459 }
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460
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461 virtual void NotifyGeometryError(const ISlicedVolume& volume)
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462 {
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463 LayerSourceBase::NotifyGeometryError();
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464 }
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465
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466 virtual void NotifyContentChange(const ISlicedVolume& volume)
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467 {
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468 LayerSourceBase::NotifyContentChange();
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469 }
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470
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471 virtual void NotifySliceChange(const ISlicedVolume& volume,
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472 const size_t& sliceIndex,
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473 const Slice& slice)
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474 {
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475 //LayerSourceBase::NotifySliceChange(slice);
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476
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477 // TODO Improve this?
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478 LayerSourceBase::NotifyContentChange();
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479 }
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480
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481
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482 const VolumeImageGeometry& GetProjectionGeometry(VolumeProjection projection)
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483 {
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484 if (!IsGeometryReady())
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485 {
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486 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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487 }
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488
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489 switch (projection)
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490 {
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491 case VolumeProjection_Axial:
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492 return *axialGeometry_;
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493
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494 case VolumeProjection_Sagittal:
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495 return *sagittalGeometry_;
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496
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497 case VolumeProjection_Coronal:
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498 return *coronalGeometry_;
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499
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500 default:
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501 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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502 }
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503 }
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504
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505
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506 bool DetectProjection(VolumeProjection& projection,
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507 const SliceGeometry& viewportSlice)
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508 {
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509 bool isOpposite; // Ignored
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510
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511 if (GeometryToolbox::IsParallelOrOpposite(isOpposite,
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512 viewportSlice.GetNormal(),
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513 axialGeometry_->GetNormal()))
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514 {
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515 projection = VolumeProjection_Axial;
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516 return true;
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517 }
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|
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518 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite,
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|
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519 viewportSlice.GetNormal(),
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|
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520 sagittalGeometry_->GetNormal()))
|
|
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521 {
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|
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522 projection = VolumeProjection_Sagittal;
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523 return true;
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|
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524 }
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|
525 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite,
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|
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526 viewportSlice.GetNormal(),
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|
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527 coronalGeometry_->GetNormal()))
|
|
|
528 {
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|
|
529 projection = VolumeProjection_Coronal;
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|
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530 return true;
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531 }
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532 else
|
|
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533 {
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|
|
534 return false;
|
|
|
535 }
|
|
|
536 }
|
|
|
537
|
|
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538
|
|
|
539 public:
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|
|
540 VolumeImageSource(OrthancVolumeImage& volume) :
|
|
|
541 volume_(volume)
|
|
|
542 {
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|
|
543 volume_.Register(*this);
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|
|
544 }
|
|
|
545
|
|
|
546 virtual bool GetExtent(std::vector<Vector>& points,
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|
|
547 const SliceGeometry& viewportSlice)
|
|
|
548 {
|
|
|
549 VolumeProjection projection;
|
|
|
550
|
|
|
551 if (!IsGeometryReady() ||
|
|
|
552 !DetectProjection(projection, viewportSlice))
|
|
|
553 {
|
|
|
554 return false;
|
|
|
555 }
|
|
|
556 else
|
|
|
557 {
|
|
|
558 // As the slices of the volumic image are arranged in a box,
|
|
|
559 // we only consider one single reference slice (the one with index 0).
|
|
|
560 GetProjectionGeometry(projection).GetSlice(0).GetExtent(points);
|
|
|
561
|
|
|
562 return true;
|
|
|
563 }
|
|
|
564 }
|
|
|
565
|
|
|
566
|
|
|
567 virtual void ScheduleLayerCreation(const SliceGeometry& viewportSlice)
|
|
|
568 {
|
|
|
569 VolumeProjection projection;
|
|
|
570
|
|
|
571 if (IsGeometryReady() &&
|
|
|
572 DetectProjection(projection, viewportSlice))
|
|
|
573 {
|
|
|
574 const VolumeImageGeometry& geometry = GetProjectionGeometry(projection);
|
|
|
575
|
|
|
576 size_t closest;
|
|
|
577
|
|
|
578 if (geometry.LookupSlice(closest, viewportSlice))
|
|
|
579 {
|
|
|
580 bool isFullQuality = true; // TODO
|
|
|
581
|
|
|
582 std::auto_ptr<Orthanc::Image> frame;
|
|
|
583
|
|
|
584 {
|
|
|
585 ImageBuffer3D::SliceReader reader(volume_.GetImage(), projection, closest);
|
|
|
586
|
|
|
587 // TODO Transfer ownership if non-axial, to avoid memcpy
|
|
|
588 frame.reset(Orthanc::Image::Clone(reader.GetAccessor()));
|
|
|
589 }
|
|
|
590
|
|
|
591 Slice slice = geometry.GetSlice(closest);
|
|
|
592 LayerSourceBase::NotifyLayerReady(
|
|
|
593 FrameRenderer::CreateRenderer(frame.release(), slice, isFullQuality),
|
|
|
594 //new SliceOutlineRenderer(slice),
|
|
|
595 slice, false);
|
|
|
596 return;
|
|
|
597 }
|
|
|
598 }
|
|
|
599
|
|
|
600 // Error
|
|
|
601 Slice slice;
|
|
|
602 LayerSourceBase::NotifyLayerReady(NULL, slice, true);
|
|
|
603 }
|
|
|
604 };
|
|
|
605 }
|
