Mercurial > hg > orthanc-stone

annotate Framework/Loaders/DicomStructureSetLoader.cpp @ 1128:8e3763d1736a broker

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removing CustomOracleCommand
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 05 Nov 2019 22:39:25 +0100
parents e713f1a99861
children
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1 /**
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2 * Stone of Orthanc
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2019 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU Affero General Public License
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9 * as published by the Free Software Foundation, either version 3 of
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10 * the License, or (at your option) any later version.
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11 *
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12 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * Affero General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU Affero General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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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 #if 0
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33 bool logbgo233 = false;
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34 bool logbgo115 = false;
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35 #endif
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36
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37 namespace OrthancStone
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38 {
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39
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40 #if 0
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41 void DumpDicomMap(std::ostream& o, const Orthanc::DicomMap& dicomMap)
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42 {
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43 using namespace std;
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44 //ios_base::fmtflags state = o.flags();
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45 //o.flags(ios::right | ios::hex);
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46 //o << "(" << setfill('0') << setw(4) << tag.GetGroup()
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47 // << "," << setw(4) << tag.GetElement() << ")";
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48 //o.flags(state);
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49 Json::Value val;
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50 dicomMap.Serialize(val);
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51 o << val;
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52 //return o;
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53 }
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54 #endif
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55
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56
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57 class DicomStructureSetLoader::AddReferencedInstance : public LoaderStateMachine::State
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58 {
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59 private:
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60 std::string instanceId_;
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61
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62 public:
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63 AddReferencedInstance(DicomStructureSetLoader& that,
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64 const std::string& instanceId) :
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65 State(that),
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66 instanceId_(instanceId)
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67 {
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68 }
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69
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70 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message)
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71 {
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72 Json::Value tags;
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73 message.ParseJsonBody(tags);
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74
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75 Orthanc::DicomMap dicom;
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76 dicom.FromDicomAsJson(tags);
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77
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78 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>();
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79
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80 loader.content_->AddReferencedSlice(dicom);
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81
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82 loader.countProcessedInstances_ ++;
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83 assert(loader.countProcessedInstances_ <= loader.countReferencedInstances_);
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84
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85 if (loader.countProcessedInstances_ == loader.countReferencedInstances_)
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86 {
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87 // All the referenced instances have been loaded, finalize the RT-STRUCT
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88 loader.content_->CheckReferencedSlices();
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89 loader.revision_++;
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90 loader.SetStructuresReady();
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91 }
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92 }
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93 };
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94
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95
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96 // State that converts a "SOP Instance UID" to an Orthanc identifier
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97 class DicomStructureSetLoader::LookupInstance : public LoaderStateMachine::State
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98 {
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99 private:
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100 std::string sopInstanceUid_;
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101
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102 public:
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103 LookupInstance(DicomStructureSetLoader& that,
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104 const std::string& sopInstanceUid) :
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105 State(that),
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106 sopInstanceUid_(sopInstanceUid)
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107 {
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108 }
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109
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110 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message)
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111 {
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112 #if 0
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113 LOG(TRACE) << "DicomStructureSetLoader::LookupInstance::Handle() (SUCCESS)";
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114 #endif
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115 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>();
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116
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117 Json::Value lookup;
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118 message.ParseJsonBody(lookup);
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119
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120 if (lookup.type() != Json::arrayValue ||
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121 lookup.size() != 1 ||
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122 !lookup[0].isMember("Type") ||
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123 !lookup[0].isMember("Path") ||
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124 lookup[0]["Type"].type() != Json::stringValue ||
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125 lookup[0]["ID"].type() != Json::stringValue ||
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126 lookup[0]["Type"].asString() != "Instance")
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127 {
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128 std::stringstream msg;
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129 msg << "Unknown resource! message.GetAnswer() = " << message.GetAnswer() << " message.GetAnswerHeaders() = ";
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130 for (OrthancRestApiCommand::HttpHeaders::const_iterator it = message.GetAnswerHeaders().begin();
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131 it != message.GetAnswerHeaders().end(); ++it)
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132 {
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133 msg << "\nkey: \"" << it->first << "\" value: \"" << it->second << "\"\n";
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134 }
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135 const std::string msgStr = msg.str();
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136 LOG(ERROR) << msgStr;
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137 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
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138 }
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139
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140 const std::string instanceId = lookup[0]["ID"].asString();
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141
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142 {
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143 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand);
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144 command->SetHttpHeader("Accept-Encoding", "gzip");
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145 std::string uri = "/instances/" + instanceId + "/tags";
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146 command->SetUri(uri);
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147 command->AcquirePayload(new AddReferencedInstance(loader, instanceId));
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148 Schedule(command.release());
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149 }
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150 }
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151 };
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152
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153
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154 class DicomStructureSetLoader::LoadStructure : public LoaderStateMachine::State
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155 {
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156 public:
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157 LoadStructure(DicomStructureSetLoader& that) :
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158 State(that)
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159 {
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160 }
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161
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162 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message)
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163 {
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164 #if 0
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165 if (logbgo115)
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166 LOG(TRACE) << "DicomStructureSetLoader::LoadStructure::Handle() (SUCCESS)";
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167 #endif
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168 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>();
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169
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170 {
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171 OrthancPlugins::FullOrthancDataset dicom(message.GetAnswer());
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172 loader.content_.reset(new DicomStructureSet(dicom));
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173 size_t structureCount = loader.content_->GetStructuresCount();
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174 loader.structureVisibility_.resize(structureCount);
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175 bool everythingVisible = false;
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176 if ((loader.initiallyVisibleStructures_.size() == 1)
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177 && (loader.initiallyVisibleStructures_[0].size() == 1)
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178 && (loader.initiallyVisibleStructures_[0][0] == '*'))
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179 {
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180 everythingVisible = true;
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181 }
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182
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183 for (size_t i = 0; i < structureCount; ++i)
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184 {
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185 // if a single "*" string is supplied, this means we want everything
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186 // to be visible...
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187 if(everythingVisible)
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188 {
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189 loader.structureVisibility_.at(i) = true;
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190 }
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191 else
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192 {
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193 // otherwise, we only enable visibility for those structures whose
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194 // names are mentioned in the initiallyVisibleStructures_ array
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195 const std::string& structureName = loader.content_->GetStructureName(i);
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196
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197 std::vector<std::string>::iterator foundIt =
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198 std::find(
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199 loader.initiallyVisibleStructures_.begin(),
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200 loader.initiallyVisibleStructures_.end(),
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201 structureName);
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202 std::vector<std::string>::iterator endIt = loader.initiallyVisibleStructures_.end();
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203 if (foundIt != endIt)
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204 loader.structureVisibility_.at(i) = true;
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205 else
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206 loader.structureVisibility_.at(i) = false;
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207 }
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208 }
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209 }
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210
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211 // Some (admittedly invalid) Dicom files have empty values in the
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212 // 0008,1155 tag. We try our best to cope with this.
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213 std::set<std::string> instances;
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214 std::set<std::string> nonEmptyInstances;
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215 loader.content_->GetReferencedInstances(instances);
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216 for (std::set<std::string>::const_iterator
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217 it = instances.begin(); it != instances.end(); ++it)
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218 {
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219 std::string instance = Orthanc::Toolbox::StripSpaces(*it);
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220 if(instance != "")
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221 nonEmptyInstances.insert(instance);
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222 }
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223
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224 loader.countReferencedInstances_ =
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225 static_cast<unsigned int>(nonEmptyInstances.size());
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226
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227 for (std::set<std::string>::const_iterator
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228 it = nonEmptyInstances.begin(); it != nonEmptyInstances.end(); ++it)
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229 {
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230 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand);
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231 command->SetUri("/tools/lookup");
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232 command->SetMethod(Orthanc::HttpMethod_Post);
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233 command->SetBody(*it);
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234 command->AcquirePayload(new LookupInstance(loader, *it));
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235 Schedule(command.release());
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236 }
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237 }
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238 };
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239
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240
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241 class DicomStructureSetLoader::Slice : public IExtractedSlice
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242 {
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243 private:
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244 const DicomStructureSet& content_;
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245 uint64_t revision_;
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246 bool isValid_;
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247 std::vector<bool> visibility_;
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248
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249 public:
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250 /**
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251 The visibility vector must either:
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252 - be empty
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253 or
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254 - contain the same number of items as the number of structures in the
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255 structure set.
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256 In the first case (empty vector), all the structures are displayed.
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257 In the second case, the visibility of each structure is defined by the
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258 content of the vector at the corresponding index.
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259 */
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260 Slice(const DicomStructureSet& content,
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261 uint64_t revision,
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262 const CoordinateSystem3D& cuttingPlane,
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263 std::vector<bool> visibility = std::vector<bool>())
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264 : content_(content)
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265 , revision_(revision)
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266 , visibility_(visibility)
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267 {
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268 ORTHANC_ASSERT((visibility_.size() == content_.GetStructuresCount())
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269 || (visibility_.size() == 0u));
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270
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271 bool opposite;
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272
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273 const Vector normal = content.GetNormal();
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274 isValid_ = (
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275 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetNormal()) ||
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276 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisX()) ||
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277 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisY()));
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278 }
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279
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280 virtual bool IsValid()
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281 {
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282 return isValid_;
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283 }
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284
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285 virtual uint64_t GetRevision()
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286 {
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287 return revision_;
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288 }
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289
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290 virtual ISceneLayer* CreateSceneLayer(const ILayerStyleConfigurator* configurator,
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291 const CoordinateSystem3D& cuttingPlane)
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292 {
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293 assert(isValid_);
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294
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295 std::auto_ptr<PolylineSceneLayer> layer(new PolylineSceneLayer);
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296 layer->SetThickness(2);
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297
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298 for (size_t i = 0; i < content_.GetStructuresCount(); i++)
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299 {
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300 if ((visibility_.size() == 0) || visibility_.at(i))
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301 {
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302 const Color& color = content_.GetStructureColor(i);
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303
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304 #ifdef USE_BOOST_UNION_FOR_POLYGONS
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305 std::vector< std::vector<Point2D> > polygons;
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306
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307 if (content_.ProjectStructure(polygons, i, cuttingPlane))
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308 {
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309 for (size_t j = 0; j < polygons.size(); j++)
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310 {
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311 PolylineSceneLayer::Chain chain;
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312 chain.resize(polygons[j].size());
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313
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314 for (size_t k = 0; k < polygons[j].size(); k++)
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315 {
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316 chain[k] = ScenePoint2D(polygons[j][k].x, polygons[j][k].y);
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317 }
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318
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319 layer->AddChain(chain, true /* closed */, color);
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320 }
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321 }
1000
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322 #else
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323 std::vector< std::pair<Point2D, Point2D> > segments;
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324
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325 if (content_.ProjectStructure(segments, i, cuttingPlane))
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326 {
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327 for (size_t j = 0; j < segments.size(); j++)
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328 {
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329 PolylineSceneLayer::Chain chain;
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330 chain.resize(2);
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331
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332 chain[0] = ScenePoint2D(segments[j].first.x, segments[j].first.y);
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333 chain[1] = ScenePoint2D(segments[j].second.x, segments[j].second.y);
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334
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335 layer->AddChain(chain, false /* NOT closed */, color);
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336 }
1000
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337 }
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338 #endif
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339 }
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340 }
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341
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342 return layer.release();
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343 }
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344 };
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345
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346
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347 DicomStructureSetLoader::DicomStructureSetLoader(IOracle& oracle,
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348 IObservable& oracleObservable) :
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349 LoaderStateMachine(oracle, oracleObservable),
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350 revision_(0),
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351 countProcessedInstances_(0),
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352 countReferencedInstances_(0),
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353 structuresReady_(false)
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354 {
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355 }
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356
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357
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358 void DicomStructureSetLoader::SetStructureDisplayState(size_t structureIndex, bool display)
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359 {
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360 structureVisibility_.at(structureIndex) = display;
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361 revision_++;
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362 }
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363
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364 DicomStructureSetLoader::~DicomStructureSetLoader()
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365 {
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366 LOG(TRACE) << "DicomStructureSetLoader::~DicomStructureSetLoader()";
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367 }
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368
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369 void DicomStructureSetLoader::LoadInstance(
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370 const std::string& instanceId,
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371 const std::vector<std::string>& initiallyVisibleStructures)
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372 {
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373 Start();
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374
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375 instanceId_ = instanceId;
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376 initiallyVisibleStructures_ = initiallyVisibleStructures;
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377
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378 {
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379 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand);
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380 command->SetHttpHeader("Accept-Encoding", "gzip");
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381
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382 std::string uri = "/instances/" + instanceId + "/tags?ignore-length=3006-0050";
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diff changeset
383
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diff changeset
384 command->SetUri(uri);
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diff changeset
385 command->AcquirePayload(new LoadStructure(*this));
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386 Schedule(command.release());
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387 }
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388 }
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389
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390
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391 IVolumeSlicer::IExtractedSlice* DicomStructureSetLoader::ExtractSlice(const CoordinateSystem3D& cuttingPlane)
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392 {
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393 if (content_.get() == NULL)
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394 {
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395 // Geometry is not available yet
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396 return new IVolumeSlicer::InvalidSlice;
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397 }
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398 else
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399 {
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400 return new Slice(*content_, revision_, cuttingPlane, structureVisibility_);
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401 }
df442f1ba0c6 reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
402 }
937
86ac61a040c9 Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
Benjamin Golinvaux <bgo@osimis.io>
parents: 935
diff changeset
403
86ac61a040c9 Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
Benjamin Golinvaux <bgo@osimis.io>
parents: 935
diff changeset
404 void DicomStructureSetLoader::SetStructuresReady()
86ac61a040c9 Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
Benjamin Golinvaux <bgo@osimis.io>
parents: 935
diff changeset
405 {
86ac61a040c9 Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
Benjamin Golinvaux <bgo@osimis.io>
parents: 935
diff changeset
406 ORTHANC_ASSERT(!structuresReady_);
86ac61a040c9 Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
Benjamin Golinvaux <bgo@osimis.io>
parents: 935
diff changeset
407 structuresReady_ = true;
86ac61a040c9 Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
Benjamin Golinvaux <bgo@osimis.io>
parents: 935
diff changeset
408 BroadcastMessage(DicomStructureSetLoader::StructuresReady(*this));
86ac61a040c9 Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
Benjamin Golinvaux <bgo@osimis.io>
parents: 935
diff changeset
409 }
86ac61a040c9 Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
Benjamin Golinvaux <bgo@osimis.io>
parents: 935
diff changeset
410
86ac61a040c9 Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
Benjamin Golinvaux <bgo@osimis.io>
parents: 935
diff changeset
411 bool DicomStructureSetLoader::AreStructuresReady() const
86ac61a040c9 Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
Benjamin Golinvaux <bgo@osimis.io>
parents: 935
diff changeset
412 {
86ac61a040c9 Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
Benjamin Golinvaux <bgo@osimis.io>
parents: 935
diff changeset
413 return structuresReady_;
86ac61a040c9 Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
Benjamin Golinvaux <bgo@osimis.io>
parents: 935
diff changeset
414 }
86ac61a040c9 Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
Benjamin Golinvaux <bgo@osimis.io>
parents: 935
diff changeset
415
815
df442f1ba0c6 reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
416 }