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0
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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 *
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6 * This program is free software: you can redistribute it and/or
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7 * modify it under the terms of the GNU General Public License as
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8 * published by the Free Software Foundation, either version 3 of the
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9 * License, or (at your option) any later version.
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10 *
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11 * In addition, as a special exception, the copyright holders of this
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12 * program give permission to link the code of its release with the
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13 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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14 * that use the same license as the "OpenSSL" library), and distribute
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15 * the linked executables. You must obey the GNU General Public License
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16 * in all respects for all of the code used other than "OpenSSL". If you
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17 * modify file(s) with this exception, you may extend this exception to
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18 * your version of the file(s), but you are not obligated to do so. If
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19 * you do not wish to do so, delete this exception statement from your
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20 * version. If you delete this exception statement from all source files
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21 * in the program, then also delete it here.
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22 *
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23 * This program is distributed in the hope that it will be useful, but
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24 * WITHOUT ANY WARRANTY; without even the implied warranty of
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25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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26 * General Public License for more details.
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27 *
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28 * You should have received a copy of the GNU General Public License
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29 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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30 **/
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31
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32
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33 #include "DicomStructureSet.h"
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34
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16
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35 #include "../../Resources/Orthanc/Core/Logging.h"
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36 #include "../../Resources/Orthanc/Core/OrthancException.h"
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0
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37 #include "../Messaging/MessagingToolbox.h"
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38
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39 #include <stdio.h>
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40 #include <boost/lexical_cast.hpp>
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41
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42 namespace OrthancStone
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43 {
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44 static const Json::Value& GetSequence(const Json::Value& instance,
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45 uint16_t group,
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46 uint16_t element)
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47 {
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48 char buf[16];
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49 sprintf(buf, "%04x,%04x", group, element);
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50
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51 if (instance.type() != Json::objectValue ||
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52 !instance.isMember(buf) ||
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53 instance[buf].type() != Json::objectValue ||
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54 !instance[buf].isMember("Type") ||
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55 !instance[buf].isMember("Value") ||
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56 instance[buf]["Type"].type() != Json::stringValue ||
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57 instance[buf]["Value"].type() != Json::arrayValue ||
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58 instance[buf]["Type"].asString() != "Sequence")
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59 {
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60 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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61 }
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62
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63 return instance[buf]["Value"];
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64 }
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65
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66
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67 static uint8_t ConvertColor(double v)
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68 {
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69 if (v < 0)
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70 {
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71 return 0;
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72 }
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73 else if (v >= 255)
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74 {
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75 return 255;
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76 }
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77 else
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78 {
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79 return static_cast<uint8_t>(v);
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80 }
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81 }
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82
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83
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84 SliceGeometry DicomStructureSet::ExtractSliceGeometry(double& sliceThickness,
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85 IOrthancConnection& orthanc,
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86 const Json::Value& contour)
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87 {
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88 const Json::Value& sequence = GetSequence(contour, 0x3006, 0x0016);
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89
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90 if (sequence.size() != 1)
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91 {
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92 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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93 }
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94
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95 DicomDataset contourImageSequence(sequence[0]);
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96 std::string parentUid = contourImageSequence.GetStringValue(std::make_pair(0x0008, 0x1155));
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97
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98 std::string post;
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99 orthanc.RestApiPost(post, "/tools/lookup", parentUid);
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100
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101 Json::Value tmp;
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102 MessagingToolbox::ParseJson(tmp, post);
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103
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104 if (tmp.type() != Json::arrayValue ||
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105 tmp.size() != 1 ||
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106 !tmp[0].isMember("Type") ||
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107 !tmp[0].isMember("Path") ||
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108 tmp[0]["Type"].type() != Json::stringValue ||
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109 tmp[0]["ID"].type() != Json::stringValue ||
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110 tmp[0]["Type"].asString() != "Instance")
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111 {
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112 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
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113 }
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114
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115 Json::Value parentInstance;
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116 MessagingToolbox::RestApiGet(parentInstance, orthanc, "/instances/" + tmp[0]["ID"].asString());
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117
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118 if (parentInstance.type() != Json::objectValue ||
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119 !parentInstance.isMember("ParentSeries") ||
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120 parentInstance["ParentSeries"].type() != Json::stringValue)
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121 {
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122 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol);
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123 }
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124
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125 std::string parentSeriesId = parentInstance["ParentSeries"].asString();
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126 bool isFirst = parentSeriesId_.empty();
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127
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128 if (isFirst)
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129 {
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130 parentSeriesId_ = parentSeriesId;
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131 }
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132 else if (parentSeriesId_ != parentSeriesId)
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133 {
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134 LOG(ERROR) << "This RT-STRUCT refers to several different series";
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135 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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136 }
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137
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138 Json::Value parentTags;
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139 MessagingToolbox::RestApiGet(parentTags, orthanc, "/instances/" + tmp[0]["ID"].asString() + "/tags?simplify");
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140
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141 if (parentTags.type() != Json::objectValue ||
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142 !parentTags.isMember("ImageOrientationPatient") ||
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143 !parentTags.isMember("ImagePositionPatient") ||
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144 parentTags["ImageOrientationPatient"].type() != Json::stringValue ||
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145 parentTags["ImagePositionPatient"].type() != Json::stringValue)
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146 {
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147 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol);
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148 }
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149
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150 SliceGeometry slice(parentTags["ImagePositionPatient"].asString(),
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151 parentTags["ImageOrientationPatient"].asString());
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152
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153 sliceThickness = 1; // 1 mm by default
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154
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155 if (parentTags.isMember("SliceThickness") &&
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156 parentTags["SliceThickness"].type() == Json::stringValue)
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157 {
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158 Vector tmp;
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159 GeometryToolbox::ParseVector(tmp, parentTags["SliceThickness"].asString());
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160 if (tmp.size() > 0)
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161 {
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162 sliceThickness = tmp[0];
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163 }
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164 }
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165
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166 if (isFirst)
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167 {
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168 normal_ = slice.GetNormal();
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169 }
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170 else if (!GeometryToolbox::IsParallel(normal_, slice.GetNormal()))
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171 {
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172 LOG(ERROR) << "Incompatible orientation of slices in this RT-STRUCT";
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173 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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174 }
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175
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176 return slice;
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177 }
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178
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179
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180 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const
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181 {
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182 if (index >= structures_.size())
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183 {
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184 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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185 }
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186
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187 return structures_[index];
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188 }
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189
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190
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191 bool DicomStructureSet::IsPolygonOnSlice(const Polygon& polygon,
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192 const SliceGeometry& geometry) const
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193 {
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194 double d = boost::numeric::ublas::inner_prod(geometry.GetOrigin(), normal_);
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195
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196 return (GeometryToolbox::IsNear(d, polygon.projectionAlongNormal_, polygon.sliceThickness_ / 2.0) &&
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197 !polygon.points_.empty());
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198 }
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199
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200
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201 DicomStructureSet::DicomStructureSet(IOrthancConnection& orthanc,
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202 const std::string& instanceId)
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203 {
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204 Json::Value instance;
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205 MessagingToolbox::RestApiGet(instance, orthanc, "/instances/" + instanceId + "/tags");
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206
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207 Json::Value rtRoiObservationSequence = GetSequence(instance, 0x3006, 0x0080);
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208 Json::Value roiContourSequence = GetSequence(instance, 0x3006, 0x0039);
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209 Json::Value structureSetRoiSequence = GetSequence(instance, 0x3006, 0x0020);
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210
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211 Json::Value::ArrayIndex count = rtRoiObservationSequence.size();
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212 if (count != roiContourSequence.size() ||
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213 count != structureSetRoiSequence.size())
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214 {
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215 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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216 }
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217
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218 structures_.resize(count);
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219 for (Json::Value::ArrayIndex i = 0; i < count; i++)
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220 {
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221 DicomDataset observation(rtRoiObservationSequence[i]);
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222 DicomDataset roi(structureSetRoiSequence[i]);
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223 DicomDataset content(roiContourSequence[i]);
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224
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225 structures_[i].interpretation_ = observation.GetStringValue(std::make_pair(0x3006, 0x00a4), "No interpretation");
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226 structures_[i].name_ = roi.GetStringValue(std::make_pair(0x3006, 0x0026), "No name");
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227 structures_[i].red_ = 255;
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228 structures_[i].green_ = 0;
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229 structures_[i].blue_ = 0;
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230
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231 DicomDataset::Tag tag(0x3006, 0x002a);
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232
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233 Vector color;
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234 if (content.HasTag(tag))
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235 {
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236 content.GetVectorValue(color, tag);
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237 if (color.size() == 3)
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238 {
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239 structures_[i].red_ = ConvertColor(color[0]);
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240 structures_[i].green_ = ConvertColor(color[1]);
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241 structures_[i].blue_ = ConvertColor(color[2]);
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242 }
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243 }
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244
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245 const Json::Value& slices = GetSequence(roiContourSequence[i], 0x3006, 0x0040);
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246
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247 LOG(WARNING) << "New RT structure: \"" << structures_[i].name_
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248 << "\" with interpretation \"" << structures_[i].interpretation_
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249 << "\" containing " << slices.size() << " slices (color: "
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250 << static_cast<int>(structures_[i].red_) << ","
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251 << static_cast<int>(structures_[i].green_) << ","
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252 << static_cast<int>(structures_[i].blue_) << ")";
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253
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254 for (Json::Value::ArrayIndex j = 0; j < slices.size(); j++)
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255 {
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256 DicomDataset slice(slices[j]);
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257
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258 unsigned int npoints = slice.GetUnsignedIntegerValue(std::make_pair(0x3006, 0x0046));
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259 LOG(INFO) << "Parsing slice containing " << npoints << " vertices";
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260
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261 if (slice.GetStringValue(std::make_pair(0x3006, 0x0042)) != "CLOSED_PLANAR")
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262 {
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263 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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264 }
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265
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266 std::string slicesData;
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267 orthanc.RestApiGet(slicesData, "/instances/" + instanceId + "/content/3006-0039/" +
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268 boost::lexical_cast<std::string>(i) + "/3006-0040/" +
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269 boost::lexical_cast<std::string>(j) + "/3006-0050");
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270
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271 Vector points;
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272 if (!GeometryToolbox::ParseVector(points, slicesData) ||
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273 points.size() != 3 * npoints)
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274 {
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275 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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276 }
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277
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278 Polygon polygon;
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279 SliceGeometry geometry = ExtractSliceGeometry(polygon.sliceThickness_, orthanc, slices[j]);
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280 polygon.projectionAlongNormal_ = geometry.ProjectAlongNormal(geometry.GetOrigin());
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281
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282 for (size_t k = 0; k < npoints; k++)
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283 {
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284 Vector v(3);
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285 v[0] = points[3 * k];
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286 v[1] = points[3 * k + 1];
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287 v[2] = points[3 * k + 2];
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288
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289 if (!GeometryToolbox::IsNear(geometry.ProjectAlongNormal(v),
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290 polygon.projectionAlongNormal_,
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291 polygon.sliceThickness_ / 2.0 /* in mm */))
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292 {
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293 LOG(ERROR) << "This RT-STRUCT contains a point that is off the slice of its instance";
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294 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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295 }
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296
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297 polygon.points_.push_back(v);
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298 }
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299
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300 structures_[i].polygons_.push_back(polygon);
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301 }
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302 }
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303
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304 if (parentSeriesId_.empty() ||
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305 normal_.size() != 3)
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306 {
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307 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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308 }
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309 }
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310
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311
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312 Vector DicomStructureSet::GetStructureCenter(size_t index) const
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313 {
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314 const Structure& structure = GetStructure(index);
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315
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316 Vector center;
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317 GeometryToolbox::AssignVector(center, 0, 0, 0);
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318 if (structure.polygons_.empty())
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319 {
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320 return center;
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321 }
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322
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323 double n = static_cast<double>(structure.polygons_.size());
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324
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325 for (Polygons::const_iterator polygon = structure.polygons_.begin();
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326 polygon != structure.polygons_.end(); ++polygon)
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327 {
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328 if (!polygon->points_.empty())
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329 {
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330 center += polygon->points_.front() / n;
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331 }
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332 }
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333
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334 return center;
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335 }
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336
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337
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338 const std::string& DicomStructureSet::GetStructureName(size_t index) const
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339 {
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340 return GetStructure(index).name_;
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341 }
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342
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343
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344 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const
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345 {
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346 return GetStructure(index).interpretation_;
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347 }
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348
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349
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350 void DicomStructureSet::GetStructureColor(uint8_t& red,
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351 uint8_t& green,
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352 uint8_t& blue,
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353 size_t index) const
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354 {
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355 const Structure& s = GetStructure(index);
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356 red = s.red_;
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357 green = s.green_;
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358 blue = s.blue_;
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359 }
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360
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361
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362 void DicomStructureSet::Render(CairoContext& context,
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363 const SliceGeometry& slice) const
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364 {
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365 cairo_t* cr = context.GetObject();
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366
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367 for (Structures::const_iterator structure = structures_.begin();
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368 structure != structures_.end(); ++structure)
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369 {
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370 for (Polygons::const_iterator polygon = structure->polygons_.begin();
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371 polygon != structure->polygons_.end(); ++polygon)
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372 {
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373 if (IsPolygonOnSlice(*polygon, slice))
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374 {
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375 context.SetSourceColor(structure->red_, structure->green_, structure->blue_);
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376
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377 Points::const_iterator p = polygon->points_.begin();
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378
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379 double x, y;
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380 slice.ProjectPoint(x, y, *p);
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381 cairo_move_to(cr, x, y);
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382 ++p;
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383
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384 while (p != polygon->points_.end())
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385 {
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386 slice.ProjectPoint(x, y, *p);
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387 cairo_line_to(cr, x, y);
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388 ++p;
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389 }
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390
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391 slice.ProjectPoint(x, y, *polygon->points_.begin());
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392 cairo_line_to(cr, x, y);
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393 }
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394 }
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395 }
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396
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397 cairo_stroke(cr);
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398 }
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399 }
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