Mercurial > hg > orthanc-stone

annotate Framework/Loaders/DicomStructureSetLoader.cpp @ 1385:ffe9beb7c5d3

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Added LoadInstanceFullVisibility for default-visible RTSTRUCT
author Benjamin Golinvaux <bgo@osimis.io>
date Mon, 27 Apr 2020 16:47:46 +0200
parents f4a06ad1580b
children d959bc8f6c1b
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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) 2017-2020 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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20
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21
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22 #include "DicomStructureSetLoader.h"
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23
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24 #include "../Scene2D/PolylineSceneLayer.h"
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25 #include "../StoneException.h"
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26 #include "../Toolbox/GeometryToolbox.h"
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27
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28 #include <Core/Toolbox.h>
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29
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30 #include <algorithm>
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31
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32 namespace OrthancStone
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33 {
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34
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35 #if 0
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36 void DumpDicomMap(std::ostream& o, const Orthanc::DicomMap& dicomMap)
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37 {
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38 using namespace std;
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39 //ios_base::fmtflags state = o.flags();
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40 //o.flags(ios::right | ios::hex);
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41 //o << "(" << setfill('0') << setw(4) << tag.GetGroup()
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42 // << "," << setw(4) << tag.GetElement() << ")";
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43 //o.flags(state);
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44 Json::Value val;
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45 dicomMap.Serialize(val);
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46 o << val;
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47 //return o;
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48 }
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49 #endif
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50
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51
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52 class DicomStructureSetLoader::AddReferencedInstance : public LoaderStateMachine::State
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53 {
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54 private:
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55 std::string instanceId_;
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56
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57 public:
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58 AddReferencedInstance(DicomStructureSetLoader& that,
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59 const std::string& instanceId) :
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60 State(that),
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61 instanceId_(instanceId)
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62 {
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63 }
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64
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65 virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message)
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66 {
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67 Json::Value tags;
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68 message.ParseJsonBody(tags);
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69
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70 Orthanc::DicomMap dicom;
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71 dicom.FromDicomAsJson(tags);
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72
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73 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>();
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74
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75 loader.content_->AddReferencedSlice(dicom);
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76 loader.countProcessedInstances_ ++;
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77 assert(loader.countProcessedInstances_ <= loader.countReferencedInstances_);
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78
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79 loader.revision_++;
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80 loader.SetStructuresUpdated();
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81
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82 if (loader.countProcessedInstances_ == loader.countReferencedInstances_)
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83 {
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84 // All the referenced instances have been loaded, finalize the RT-STRUCT
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85 loader.content_->CheckReferencedSlices();
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86 loader.revision_++;
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87 loader.SetStructuresReady();
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88 }
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89 }
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90 };
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91
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92
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93 // State that converts a "SOP Instance UID" to an Orthanc identifier
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94 class DicomStructureSetLoader::LookupInstance : public LoaderStateMachine::State
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95 {
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96 private:
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97 std::string sopInstanceUid_;
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98
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99 public:
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100 LookupInstance(DicomStructureSetLoader& that,
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101 const std::string& sopInstanceUid) :
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102 State(that),
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103 sopInstanceUid_(sopInstanceUid)
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104 {
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105 }
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106
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107 virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message)
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108 {
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109 #if 0
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110 LOG(TRACE) << "DicomStructureSetLoader::LookupInstance::Handle() (SUCCESS)";
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111 #endif
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112 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>();
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113
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114 Json::Value lookup;
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115 message.ParseJsonBody(lookup);
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116
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117 if (lookup.type() != Json::arrayValue ||
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118 lookup.size() != 1 ||
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119 !lookup[0].isMember("Type") ||
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120 !lookup[0].isMember("Path") ||
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121 lookup[0]["Type"].type() != Json::stringValue ||
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122 lookup[0]["ID"].type() != Json::stringValue ||
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123 lookup[0]["Type"].asString() != "Instance")
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124 {
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125 std::stringstream msg;
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126 msg << "Unknown resource! message.GetAnswer() = " << message.GetAnswer() << " message.GetAnswerHeaders() = ";
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127 for (OrthancStone::OrthancRestApiCommand::HttpHeaders::const_iterator it = message.GetAnswerHeaders().begin();
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128 it != message.GetAnswerHeaders().end(); ++it)
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129 {
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130 msg << "\nkey: \"" << it->first << "\" value: \"" << it->second << "\"\n";
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131 }
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132 const std::string msgStr = msg.str();
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133 LOG(ERROR) << msgStr;
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134 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
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135 }
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136
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137 const std::string instanceId = lookup[0]["ID"].asString();
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138
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139 {
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140 std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand);
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141 command->SetHttpHeader("Accept-Encoding", "gzip");
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142 std::string uri = "/instances/" + instanceId + "/tags";
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143 command->SetUri(uri);
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144 command->AcquirePayload(new AddReferencedInstance(loader, instanceId));
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145 Schedule(command.release());
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146 }
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147 }
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148 };
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149
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150
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151 class DicomStructureSetLoader::LoadStructure : public LoaderStateMachine::State
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152 {
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153 public:
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154 LoadStructure(DicomStructureSetLoader& that) :
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155 State(that)
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156 {
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157 }
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158
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159 virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message)
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160 {
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161 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>();
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162
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163 {
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164 OrthancPlugins::FullOrthancDataset dicom(message.GetAnswer());
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165 loader.content_.reset(new OrthancStone::DicomStructureSet(dicom));
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166 size_t structureCount = loader.content_->GetStructuresCount();
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167 loader.structureVisibility_.resize(structureCount);
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168 bool everythingVisible = false;
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169 if ((loader.initiallyVisibleStructures_.size() == 1)
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170 && (loader.initiallyVisibleStructures_[0].size() == 1)
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171 && (loader.initiallyVisibleStructures_[0][0] == '*'))
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172 {
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173 everythingVisible = true;
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174 }
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175
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176 for (size_t i = 0; i < structureCount; ++i)
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177 {
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178 // if a single "*" string is supplied, this means we want everything
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179 // to be visible...
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180 if(everythingVisible)
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181 {
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182 loader.structureVisibility_.at(i) = true;
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183 }
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184 else
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185 {
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186 // otherwise, we only enable visibility for those structures whose
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187 // names are mentioned in the initiallyVisibleStructures_ array
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188 const std::string& structureName = loader.content_->GetStructureName(i);
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189
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190 std::vector<std::string>::iterator foundIt =
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191 std::find(
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192 loader.initiallyVisibleStructures_.begin(),
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193 loader.initiallyVisibleStructures_.end(),
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194 structureName);
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195 std::vector<std::string>::iterator endIt = loader.initiallyVisibleStructures_.end();
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196 if (foundIt != endIt)
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197 loader.structureVisibility_.at(i) = true;
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198 else
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199 loader.structureVisibility_.at(i) = false;
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200 }
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201 }
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202 }
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203
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204 // Some (admittedly invalid) Dicom files have empty values in the
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205 // 0008,1155 tag. We try our best to cope with this.
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206 std::set<std::string> instances;
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207 std::set<std::string> nonEmptyInstances;
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208 loader.content_->GetReferencedInstances(instances);
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209 for (std::set<std::string>::const_iterator
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210 it = instances.begin(); it != instances.end(); ++it)
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211 {
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212 std::string instance = Orthanc::Toolbox::StripSpaces(*it);
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213 if(instance != "")
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214 nonEmptyInstances.insert(instance);
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215 }
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216
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217 loader.countReferencedInstances_ =
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218 static_cast<unsigned int>(nonEmptyInstances.size());
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219
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220 for (std::set<std::string>::const_iterator
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221 it = nonEmptyInstances.begin(); it != nonEmptyInstances.end(); ++it)
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222 {
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223 std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand);
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224 command->SetUri("/tools/lookup");
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225 command->SetMethod(Orthanc::HttpMethod_Post);
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226 command->SetBody(*it);
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227 command->AcquirePayload(new LookupInstance(loader, *it));
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228 Schedule(command.release());
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229 }
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230 }
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231 };
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232
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233
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234 class DicomStructureSetLoader::Slice : public IExtractedSlice
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235 {
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236 private:
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237 const OrthancStone::DicomStructureSet& content_;
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238 uint64_t revision_;
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239 bool isValid_;
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240 std::vector<bool> visibility_;
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241
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242 public:
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243 /**
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244 The visibility vector must either:
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245 - be empty
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246 or
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247 - contain the same number of items as the number of structures in the
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248 structure set.
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249 In the first case (empty vector), all the structures are displayed.
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250 In the second case, the visibility of each structure is defined by the
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251 content of the vector at the corresponding index.
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252 */
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253 Slice(const OrthancStone::DicomStructureSet& content,
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254 uint64_t revision,
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255 const OrthancStone::CoordinateSystem3D& cuttingPlane,
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256 std::vector<bool> visibility = std::vector<bool>())
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257 : content_(content)
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258 , revision_(revision)
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259 , visibility_(visibility)
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260 {
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261 ORTHANC_ASSERT((visibility_.size() == content_.GetStructuresCount())
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262 || (visibility_.size() == 0u));
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263
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264 bool opposite;
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265
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266 const OrthancStone::Vector normal = content.GetNormal();
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267 isValid_ = (
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268 OrthancStone::GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetNormal()) ||
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269 OrthancStone::GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisX()) ||
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270 OrthancStone::GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisY()));
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271 }
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272
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273 virtual bool IsValid()
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274 {
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275 return isValid_;
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276 }
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277
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278 virtual uint64_t GetRevision()
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279 {
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280 return revision_;
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281 }
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282
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283 virtual OrthancStone::ISceneLayer* CreateSceneLayer(
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284 const OrthancStone::ILayerStyleConfigurator* configurator,
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285 const OrthancStone::CoordinateSystem3D& cuttingPlane)
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286 {
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287 assert(isValid_);
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288
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289 std::unique_ptr<OrthancStone::PolylineSceneLayer> layer(new OrthancStone::PolylineSceneLayer);
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290 layer->SetThickness(2);
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291
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292 for (size_t i = 0; i < content_.GetStructuresCount(); i++)
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293 {
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294 if ((visibility_.size() == 0) || visibility_.at(i))
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295 {
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296 const OrthancStone::Color& color = content_.GetStructureColor(i);
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297
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298 #ifdef USE_BOOST_UNION_FOR_POLYGONS
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299 std::vector< std::vector<OrthancStone::Point2D> > polygons;
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300
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301 if (content_.ProjectStructure(polygons, i, cuttingPlane))
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302 {
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303 for (size_t j = 0; j < polygons.size(); j++)
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304 {
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305 PolylineSceneLayer::Chain chain;
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306 chain.resize(polygons[j].size());
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307
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308 for (size_t k = 0; k < polygons[j].size(); k++)
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309 {
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310 chain[k] = ScenePoint2D(polygons[j][k].x, polygons[j][k].y);
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311 }
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312
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313 layer->AddChain(chain, true /* closed */, color);
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314 }
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315 }
1000
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316 #else
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317 std::vector< std::pair<OrthancStone::Point2D, OrthancStone::Point2D> > segments;
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318
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319 if (content_.ProjectStructure(segments, i, cuttingPlane))
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320 {
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321 for (size_t j = 0; j < segments.size(); j++)
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322 {
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323 OrthancStone::PolylineSceneLayer::Chain chain;
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324 chain.resize(2);
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325
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326 chain[0] = OrthancStone::ScenePoint2D(segments[j].first.x, segments[j].first.y);
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327 chain[1] = OrthancStone::ScenePoint2D(segments[j].second.x, segments[j].second.y);
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328
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329 layer->AddChain(chain, false /* NOT closed */, color);
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330 }
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331 }
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332 #endif
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333 }
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334 }
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335
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336 return layer.release();
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337 }
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338 };
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339
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340
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341 DicomStructureSetLoader::DicomStructureSetLoader(
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342 OrthancStone::ILoadersContext& loadersContext)
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343 : LoaderStateMachine(loadersContext)
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344 , loadersContext_(loadersContext)
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345 , revision_(0)
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346 , countProcessedInstances_(0)
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347 , countReferencedInstances_(0)
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348 , structuresReady_(false)
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349 {
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350 }
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351
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352
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diff changeset
353 boost::shared_ptr<OrthancStone::DicomStructureSetLoader> DicomStructureSetLoader::Create(OrthancStone::ILoadersContext& loadersContext)
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354 {
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355 boost::shared_ptr<DicomStructureSetLoader> obj(
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356 new DicomStructureSetLoader(
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357 loadersContext));
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358 obj->LoaderStateMachine::PostConstructor();
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359 return obj;
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360
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361 }
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362
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363 void DicomStructureSetLoader::SetStructureDisplayState(size_t structureIndex, bool display)
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364 {
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365 structureVisibility_.at(structureIndex) = display;
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366 revision_++;
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367 }
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368
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369 DicomStructureSetLoader::~DicomStructureSetLoader()
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370 {
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371 LOG(TRACE) << "DicomStructureSetLoader::~DicomStructureSetLoader()";
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372 }
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373
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374 void DicomStructureSetLoader::LoadInstance(
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375 const std::string& instanceId,
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376 const std::vector<std::string>& initiallyVisibleStructures)
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377 {
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378 Start();
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379
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380 instanceId_ = instanceId;
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381 initiallyVisibleStructures_ = initiallyVisibleStructures;
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382
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383 {
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384 std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand);
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385 command->SetHttpHeader("Accept-Encoding", "gzip");
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386
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387 std::string uri = "/instances/" + instanceId + "/tags?ignore-length=3006-0050";
981
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diff changeset
388
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diff changeset
389 command->SetUri(uri);
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390 command->AcquirePayload(new LoadStructure(*this));
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391 Schedule(command.release());
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392 }
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393 }
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394
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395 void DicomStructureSetLoader::LoadInstanceFullVisibility(const std::string& instanceId)
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396 {
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397 std::vector<std::string> initiallyVisibleStructures;
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398 initiallyVisibleStructures.push_back("*"); // wildcard to make all structure sets visible
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399 LoadInstance(instanceId, initiallyVisibleStructures);
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400 }
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401
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402 OrthancStone::IVolumeSlicer::IExtractedSlice* DicomStructureSetLoader::ExtractSlice(const OrthancStone::CoordinateSystem3D& cuttingPlane)
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403 {
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404 if (content_.get() == NULL)
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405 {
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406 // Geometry is not available yet
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407 return new OrthancStone::IVolumeSlicer::InvalidSlice;
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408 }
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409 else
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410 {
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411 return new Slice(*content_, revision_, cuttingPlane, structureVisibility_);
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412 }
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413 }
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414
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415 void DicomStructureSetLoader::SetStructuresUpdated()
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416 {
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417 BroadcastMessage(DicomStructureSetLoader::StructuresUpdated(*this));
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418 }
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419
937
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420 void DicomStructureSetLoader::SetStructuresReady()
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421 {
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422 ORTHANC_ASSERT(!structuresReady_);
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423 structuresReady_ = true;
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424 BroadcastMessage(DicomStructureSetLoader::StructuresReady(*this));
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425 }
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426
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427 bool DicomStructureSetLoader::AreStructuresReady() const
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428 {
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429 return structuresReady_;
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430 }
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431
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432 }