Mercurial > hg > orthanc-stone

annotate Framework/Loaders/DicomStructureSetLoader.cpp @ 1019:29f5f2031310

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Added a way to specificy which structures are to be initially displayed (the default being ALL structures displayed) + the loader maintains a list of structure display state, that can be modified continuously + the cache now takes the initial list of structure into account for computing the entry + added methods to change the loaded structure visibility + disabled the alternate loaders (DicomStructureSetLoader2 and friends) + disabled corresponding tests
author Benjamin Golinvaux <bgo@osimis.io>
date Fri, 27 Sep 2019 13:32:05 +0200
parents 4f28d9459e31
children 7014c2397b45
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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 "../Toolbox/GeometryToolbox.h"
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26
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27 #include <algorithm>
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28
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29 #if 0
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30 bool logbgo233 = false;
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31 bool logbgo115 = false;
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32 #endif
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33
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34 namespace OrthancStone
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35 {
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36
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37 #if 0
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38 void DumpDicomMap(std::ostream& o, const Orthanc::DicomMap& dicomMap)
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39 {
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40 using namespace std;
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41 //ios_base::fmtflags state = o.flags();
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42 //o.flags(ios::right | ios::hex);
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43 //o << "(" << setfill('0') << setw(4) << tag.GetGroup()
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44 // << "," << setw(4) << tag.GetElement() << ")";
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45 //o.flags(state);
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46 Json::Value val;
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47 dicomMap.Serialize(val);
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48 o << val;
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49 //return o;
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50 }
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51 #endif
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52
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53
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54 class DicomStructureSetLoader::AddReferencedInstance : public LoaderStateMachine::State
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55 {
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56 private:
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57 std::string instanceId_;
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58
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59 public:
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60 AddReferencedInstance(DicomStructureSetLoader& that,
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61 const std::string& instanceId) :
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62 State(that),
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63 instanceId_(instanceId)
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64 {
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65 }
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66
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67 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message)
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68 {
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69 Json::Value tags;
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70 message.ParseJsonBody(tags);
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71
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72 Orthanc::DicomMap dicom;
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73 dicom.FromDicomAsJson(tags);
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74
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75 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>();
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76
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77 loader.content_->AddReferencedSlice(dicom);
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78
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79 loader.countProcessedInstances_ ++;
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80 assert(loader.countProcessedInstances_ <= loader.countReferencedInstances_);
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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 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 (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::auto_ptr<OrthancRestApiCommand> command(new 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->SetPayload(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 OrthancRestApiCommand::SuccessMessage& message)
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160 {
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161 #if 0
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162 if (logbgo115)
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163 LOG(TRACE) << "DicomStructureSetLoader::LoadStructure::Handle() (SUCCESS)";
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164 #endif
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165 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>();
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166
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167 {
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168 OrthancPlugins::FullOrthancDataset dicom(message.GetAnswer());
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169 loader.content_.reset(new DicomStructureSet(dicom));
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170 size_t structureCount = loader.content_->GetStructuresCount();
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171 loader.structureVisibility_.resize(structureCount);
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172 for (size_t i = 0; i < structureCount; ++i)
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173 {
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174 // if nothing is specified in the ctor, this means we want everything visible
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175 if (loader.initiallyVisibleStructures_.size() == 0)
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176 {
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177 loader.structureVisibility_.at(i) = true;
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178 }
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179 else
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180 {
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181 // otherwise, we only enable visibility for those structures whose
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182 // names are mentioned in the initiallyVisibleStructures_ array
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183 const std::string& structureName = loader.content_->GetStructureName(i);
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184
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185 std::vector<std::string>::iterator foundIt =
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186 std::find(
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187 loader.initiallyVisibleStructures_.begin(),
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188 loader.initiallyVisibleStructures_.end(),
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189 structureName);
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190 std::vector<std::string>::iterator endIt = loader.initiallyVisibleStructures_.end();
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191 if (foundIt != endIt)
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192 loader.structureVisibility_.at(i) = true;
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193 else
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194 loader.structureVisibility_.at(i) = false;
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195 }
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196 }
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197 }
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198
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199 // Some (admittedly invalid) Dicom files have empty values in the
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200 // 0008,1155 tag. We try our best to cope with this.
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201 std::set<std::string> instances;
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202 std::set<std::string> nonEmptyInstances;
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203 loader.content_->GetReferencedInstances(instances);
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204 for (std::set<std::string>::const_iterator
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205 it = instances.begin(); it != instances.end(); ++it)
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206 {
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207 std::string instance = Orthanc::Toolbox::StripSpaces(*it);
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208 if(instance != "")
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209 nonEmptyInstances.insert(instance);
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210 }
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211
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212 loader.countReferencedInstances_ =
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213 static_cast<unsigned int>(nonEmptyInstances.size());
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214
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215 for (std::set<std::string>::const_iterator
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216 it = nonEmptyInstances.begin(); it != nonEmptyInstances.end(); ++it)
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217 {
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218 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand);
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219 command->SetUri("/tools/lookup");
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220 command->SetMethod(Orthanc::HttpMethod_Post);
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221 command->SetBody(*it);
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222 command->SetPayload(new LookupInstance(loader, *it));
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223 Schedule(command.release());
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224 }
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225 }
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226 };
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227
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228
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229 class DicomStructureSetLoader::Slice : public IExtractedSlice
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230 {
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231 private:
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232 const DicomStructureSet& content_;
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233 uint64_t revision_;
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234 bool isValid_;
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235 std::vector<bool> visibility_;
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236
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237 public:
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238 /**
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239 The visibility vector must either:
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240 - be empty
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241 or
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242 - contain the same number of items as the number of structures in the
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243 structure set.
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244 In the first case (empty vector), all the structures are displayed.
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245 In the second case, the visibility of each structure is defined by the
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246 content of the vector at the corresponding index.
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247 */
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248 Slice(const DicomStructureSet& content,
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249 uint64_t revision,
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250 const CoordinateSystem3D& cuttingPlane,
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251 std::vector<bool> visibility = std::vector<bool>())
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252 : content_(content)
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253 , revision_(revision)
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254 , visibility_(visibility)
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255 {
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256 ORTHANC_ASSERT((visibility_.size() == content_.GetStructuresCount())
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257 || (visibility_.size() == 0u));
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258
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259 bool opposite;
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260
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261 const Vector normal = content.GetNormal();
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262 isValid_ = (
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263 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetNormal()) ||
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264 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisX()) ||
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265 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisY()));
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266 }
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267
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268 virtual bool IsValid()
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269 {
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270 return isValid_;
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271 }
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272
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273 virtual uint64_t GetRevision()
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274 {
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275 return revision_;
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276 }
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277
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278 virtual ISceneLayer* CreateSceneLayer(const ILayerStyleConfigurator* configurator,
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279 const CoordinateSystem3D& cuttingPlane)
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280 {
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281 assert(isValid_);
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282
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283 std::auto_ptr<PolylineSceneLayer> layer(new PolylineSceneLayer);
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284 layer->SetThickness(2);
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285
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286 for (size_t i = 0; i < content_.GetStructuresCount(); i++)
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287 {
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288 if ((visibility_.size() == 0) || visibility_.at(i))
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289 {
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290 const Color& color = content_.GetStructureColor(i);
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291
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292 #ifdef USE_BOOST_UNION_FOR_POLYGONS
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293 std::vector< std::vector<Point2D> > polygons;
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294
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295 if (content_.ProjectStructure(polygons, i, cuttingPlane))
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296 {
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297 for (size_t j = 0; j < polygons.size(); j++)
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298 {
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299 PolylineSceneLayer::Chain chain;
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300 chain.resize(polygons[j].size());
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301
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302 for (size_t k = 0; k < polygons[j].size(); k++)
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303 {
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304 chain[k] = ScenePoint2D(polygons[j][k].x, polygons[j][k].y);
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305 }
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306
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307 layer->AddChain(chain, true /* closed */, color);
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308 }
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309 }
1000
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310 #else
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311 std::vector< std::pair<Point2D, Point2D> > segments;
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312
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313 if (content_.ProjectStructure(segments, i, cuttingPlane))
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314 {
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315 for (size_t j = 0; j < segments.size(); j++)
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316 {
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317 PolylineSceneLayer::Chain chain;
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318 chain.resize(2);
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319
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320 chain[0] = ScenePoint2D(segments[j].first.x, segments[j].first.y);
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321 chain[1] = ScenePoint2D(segments[j].second.x, segments[j].second.y);
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322
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323 layer->AddChain(chain, false /* NOT closed */, color);
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324 }
1000
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325 }
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326 #endif
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327 }
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328 }
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329
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330 return layer.release();
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331 }
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332 };
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333
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334
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335 DicomStructureSetLoader::DicomStructureSetLoader(IOracle& oracle,
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336 IObservable& oracleObservable) :
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337 LoaderStateMachine(oracle, oracleObservable),
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338 IObservable(oracleObservable.GetBroker()),
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339 revision_(0),
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340 countProcessedInstances_(0),
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341 countReferencedInstances_(0),
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342 structuresReady_(false)
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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 void DicomStructureSetLoader::SetStructureDisplayState(size_t structureIndex, bool display)
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348 {
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349 structureVisibility_.at(structureIndex) = display;
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350 revision_++;
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351 }
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352
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353 DicomStructureSetLoader::~DicomStructureSetLoader()
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354 {
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355 LOG(TRACE) << "DicomStructureSetLoader::~DicomStructureSetLoader()";
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356 }
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357
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358 void DicomStructureSetLoader::LoadInstance(
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359 const std::string& instanceId,
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360 const std::vector<std::string>& initiallyVisibleStructures)
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361 {
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362 Start();
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363
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364 instanceId_ = instanceId;
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365 initiallyVisibleStructures_ = initiallyVisibleStructures;
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366
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367 {
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368 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand);
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369 command->SetHttpHeader("Accept-Encoding", "gzip");
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370
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371 std::string uri = "/instances/" + instanceId + "/tags?ignore-length=3006-0050";
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372
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373 command->SetUri(uri);
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374 command->SetPayload(new LoadStructure(*this));
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375 Schedule(command.release());
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376 }
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377 }
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378
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379
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380 IVolumeSlicer::IExtractedSlice* DicomStructureSetLoader::ExtractSlice(const CoordinateSystem3D& cuttingPlane)
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381 {
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382 if (content_.get() == NULL)
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383 {
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384 // Geometry is not available yet
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385 return new IVolumeSlicer::InvalidSlice;
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386 }
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387 else
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388 {
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389 return new Slice(*content_, revision_, cuttingPlane, structureVisibility_);
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390 }
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391 }
937
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392
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393 void DicomStructureSetLoader::SetStructuresReady()
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394 {
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395 ORTHANC_ASSERT(!structuresReady_);
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diff changeset
396 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
397 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
398 }
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
399
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
400 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
401 {
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
402 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
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
815
df442f1ba0c6 reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
405 }