Mercurial > hg > orthanc-stone

annotate Framework/Loaders/OrthancMultiframeVolumeLoader.cpp @ 1455:30deba7bc8e2

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simplifying include_directories
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 11 Jun 2020 20:54:01 +0200
parents f4a06ad1580b
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) 2017-2020 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 "OrthancMultiframeVolumeLoader.h"
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23
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24 #include <Endianness.h>
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25 #include <Toolbox.h>
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27 namespace OrthancStone
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28 {
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29 class OrthancMultiframeVolumeLoader::LoadRTDoseGeometry : public LoaderStateMachine::State
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30 {
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31 private:
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32 std::unique_ptr<Orthanc::DicomMap> dicom_;
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33
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34 public:
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35 LoadRTDoseGeometry(OrthancMultiframeVolumeLoader& that,
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36 Orthanc::DicomMap* dicom) :
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37 State(that),
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38 dicom_(dicom)
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39 {
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40 if (dicom == NULL)
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41 {
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42 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer);
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43 }
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44
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45 }
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46
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47 virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message)
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48 {
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49 // Complete the DICOM tags with just-received "Grid Frame Offset Vector"
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50 std::string s = Orthanc::Toolbox::StripSpaces(message.GetAnswer());
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51 dicom_->SetValue(Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR, s, false);
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52
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53 GetLoader<OrthancMultiframeVolumeLoader>().SetGeometry(*dicom_);
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54 }
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55 };
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56
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57
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58 static std::string GetSopClassUid(const Orthanc::DicomMap& dicom)
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59 {
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60 std::string s;
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61 if (!dicom.LookupStringValue(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false))
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62 {
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63 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
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64 "DICOM file without SOP class UID");
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65 }
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66 else
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67 {
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68 return s;
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69 }
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70 }
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71
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72
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73 class OrthancMultiframeVolumeLoader::LoadGeometry : public State
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74 {
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75 public:
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76 LoadGeometry(OrthancMultiframeVolumeLoader& that) :
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77 State(that)
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78 {
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79 }
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80
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81 virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message)
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82 {
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83 OrthancMultiframeVolumeLoader& loader = GetLoader<OrthancMultiframeVolumeLoader>();
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84
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85 Json::Value body;
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86 message.ParseJsonBody(body);
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87
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88 if (body.type() != Json::objectValue)
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89 {
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90 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol);
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91 }
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92
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93 std::unique_ptr<Orthanc::DicomMap> dicom(new Orthanc::DicomMap);
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94 dicom->FromDicomAsJson(body);
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95
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96 if (OrthancStone::StringToSopClassUid(GetSopClassUid(*dicom)) == OrthancStone::SopClassUid_RTDose)
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97 {
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98 // Download the "Grid Frame Offset Vector" DICOM tag, that is
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99 // mandatory for RT-DOSE, but is too long to be returned by default
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100
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101 std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand);
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102 command->SetUri("/instances/" + loader.GetInstanceId() + "/content/" +
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103 Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR.Format());
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104 command->AcquirePayload(new LoadRTDoseGeometry(loader, dicom.release()));
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105
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106 Schedule(command.release());
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107 }
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108 else
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109 {
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110 loader.SetGeometry(*dicom);
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111 }
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112 }
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113 };
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114
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115 class OrthancMultiframeVolumeLoader::LoadTransferSyntax : public State
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116 {
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117 public:
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118 LoadTransferSyntax(OrthancMultiframeVolumeLoader& that) :
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119 State(that)
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120 {
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121 }
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122
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123 virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message)
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124 {
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125 GetLoader<OrthancMultiframeVolumeLoader>().SetTransferSyntax(message.GetAnswer());
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126 }
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127 };
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128
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129 class OrthancMultiframeVolumeLoader::LoadUncompressedPixelData : public State
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130 {
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131 public:
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132 LoadUncompressedPixelData(OrthancMultiframeVolumeLoader& that) :
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133 State(that)
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134 {
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135 }
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136
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137 virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message)
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138 {
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139 GetLoader<OrthancMultiframeVolumeLoader>().SetUncompressedPixelData(message.GetAnswer());
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140 }
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141 };
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142
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143 const std::string& OrthancMultiframeVolumeLoader::GetInstanceId() const
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144 {
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145 if (IsActive())
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146 {
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147 return instanceId_;
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148 }
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149 else
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150 {
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151 LOG(ERROR) << "OrthancMultiframeVolumeLoader::GetInstanceId(): (!IsActive())";
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152 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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153 }
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154 }
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155
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156 void OrthancMultiframeVolumeLoader::ScheduleFrameDownloads()
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157 {
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158 if (transferSyntaxUid_.empty() ||
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159 !volume_->HasGeometry())
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160 {
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161 return;
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162 }
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163 /*
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164 1.2.840.10008.1.2 Implicit VR Endian: Default Transfer Syntax for DICOM
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165 1.2.840.10008.1.2.1 Explicit VR Little Endian
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166 1.2.840.10008.1.2.2 Explicit VR Big Endian
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167
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168 See https://www.dicomlibrary.com/dicom/transfer-syntax/
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169 */
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170 if (transferSyntaxUid_ == "1.2.840.10008.1.2" ||
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171 transferSyntaxUid_ == "1.2.840.10008.1.2.1" ||
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172 transferSyntaxUid_ == "1.2.840.10008.1.2.2")
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173 {
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174 std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand);
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175 command->SetHttpHeader("Accept-Encoding", "gzip");
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176 command->SetUri("/instances/" + instanceId_ + "/content/" +
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177 Orthanc::DICOM_TAG_PIXEL_DATA.Format() + "/0");
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178 command->AcquirePayload(new LoadUncompressedPixelData(*this));
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179 Schedule(command.release());
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180 }
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181 else
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182 {
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183 throw Orthanc::OrthancException(
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184 Orthanc::ErrorCode_NotImplemented,
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185 "No support for multiframe instances with transfer syntax: " + transferSyntaxUid_);
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186 }
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187 }
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188
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189 void OrthancMultiframeVolumeLoader::SetTransferSyntax(const std::string& transferSyntax)
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190 {
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191 transferSyntaxUid_ = Orthanc::Toolbox::StripSpaces(transferSyntax);
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192 ScheduleFrameDownloads();
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193 }
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194
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195 void OrthancMultiframeVolumeLoader::SetGeometry(const Orthanc::DicomMap& dicom)
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196 {
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197 OrthancStone::DicomInstanceParameters parameters(dicom);
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198 volume_->SetDicomParameters(parameters);
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199
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200 Orthanc::PixelFormat format;
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201 if (!parameters.GetImageInformation().ExtractPixelFormat(format, true))
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202 {
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203 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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204 }
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205
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206 double spacingZ;
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207 switch (parameters.GetSopClassUid())
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208 {
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209 case OrthancStone::SopClassUid_RTDose:
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210 spacingZ = parameters.GetThickness();
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211 break;
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212
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213 default:
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214 throw Orthanc::OrthancException(
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215 Orthanc::ErrorCode_NotImplemented,
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216 "No support for multiframe instances with SOP class UID: " + GetSopClassUid(dicom));
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217 }
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218
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219 const unsigned int width = parameters.GetImageInformation().GetWidth();
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220 const unsigned int height = parameters.GetImageInformation().GetHeight();
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221 const unsigned int depth = parameters.GetImageInformation().GetNumberOfFrames();
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222
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223 {
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224 OrthancStone::VolumeImageGeometry geometry;
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225 geometry.SetSizeInVoxels(width, height, depth);
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226 geometry.SetAxialGeometry(parameters.GetGeometry());
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227 geometry.SetVoxelDimensions(parameters.GetPixelSpacingX(),
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228 parameters.GetPixelSpacingY(), spacingZ);
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229 volume_->Initialize(geometry, format, true /* Do compute range */);
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230 }
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231
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232 volume_->GetPixelData().Clear();
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233
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234 ScheduleFrameDownloads();
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235
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236
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237
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238 BroadcastMessage(OrthancStone::DicomVolumeImage::GeometryReadyMessage(*volume_));
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239 }
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240
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241
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242 ORTHANC_FORCE_INLINE
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243 static void CopyPixel(uint32_t& target, const void* source)
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244 {
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245 // TODO - check alignement?
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246 target = le32toh(*reinterpret_cast<const uint32_t*>(source));
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247 }
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248
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249 ORTHANC_FORCE_INLINE
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250 static void CopyPixel(uint16_t& target, const void* source)
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251 {
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252 // TODO - check alignement?
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253 target = le16toh(*reinterpret_cast<const uint16_t*>(source));
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254 }
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255
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256 ORTHANC_FORCE_INLINE
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257 static void CopyPixel(int16_t& target, const void* source)
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258 {
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259 // byte swapping is the same for unsigned and signed integers
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260 // (the sign bit is always stored with the MSByte)
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261 uint16_t* targetUp = reinterpret_cast<uint16_t*>(&target);
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262 CopyPixel(*targetUp, source);
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263 }
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264
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265 template <typename T>
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266 void OrthancMultiframeVolumeLoader::CopyPixelDataAndComputeDistribution(
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267 const std::string& pixelData, std::map<T,uint64_t>& distribution)
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268 {
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269 OrthancStone::ImageBuffer3D& target = volume_->GetPixelData();
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270
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271 const unsigned int bpp = target.GetBytesPerPixel();
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272 const unsigned int width = target.GetWidth();
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273 const unsigned int height = target.GetHeight();
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274 const unsigned int depth = target.GetDepth();
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275
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276 if (pixelData.size() != bpp * width * height * depth)
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277 {
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278 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
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279 "The pixel data has not the proper size");
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280 }
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281
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282 if (pixelData.empty())
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283 {
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284 return;
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285 }
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286
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287 // first pass to initialize map
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288 {
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289 const uint8_t* source = reinterpret_cast<const uint8_t*>(pixelData.c_str());
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290
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291 for (unsigned int z = 0; z < depth; z++)
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292 {
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293 for (unsigned int y = 0; y < height; y++)
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diff changeset
294 {
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295 for (unsigned int x = 0; x < width; x++)
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296 {
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diff changeset
297 T value;
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298 CopyPixel(value, source);
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diff changeset
299 distribution[value] = 0;
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300 source += bpp;
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301 }
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302 }
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303 }
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304 }
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305
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306 {
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307 const uint8_t* source = reinterpret_cast<const uint8_t*>(pixelData.c_str());
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308
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309 for (unsigned int z = 0; z < depth; z++)
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310 {
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311 OrthancStone::ImageBuffer3D::SliceWriter writer(target, OrthancStone::VolumeProjection_Axial, z);
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312
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313 assert(writer.GetAccessor().GetWidth() == width &&
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314 writer.GetAccessor().GetHeight() == height);
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315 #if 0
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316 for (unsigned int y = 0; y < height; y++)
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317 {
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318 assert(sizeof(T) == Orthanc::GetBytesPerPixel(target.GetFormat()));
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319
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320 T* target = reinterpret_cast<T*>(writer.GetAccessor().GetRow(y));
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321
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322 for (unsigned int x = 0; x < width; x++)
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323 {
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324 CopyPixel(*target, source);
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325
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326 distribution[*target] += 1;
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327
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328 target++;
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329 source += bpp;
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330 }
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331 }
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332 #else
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333 // optimized version (fixed) as of 2020-04-15
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334 unsigned int pitch = writer.GetAccessor().GetPitch();
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335 T* targetAddrLine = reinterpret_cast<T*>(writer.GetAccessor().GetRow(0));
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336 assert(sizeof(T) == Orthanc::GetBytesPerPixel(target.GetFormat()));
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337
1337
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338 for (unsigned int y = 0; y < height; y++)
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339 {
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340 T* targetAddrPix = targetAddrLine;
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341 for (unsigned int x = 0; x < width; x++)
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342 {
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343 CopyPixel(*targetAddrPix, source);
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344
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345 distribution[*targetAddrPix] += 1;
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346
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347 targetAddrPix++;
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348 source += bpp;
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349 }
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350 uint8_t* targetAddrLineBytes = reinterpret_cast<uint8_t*>(targetAddrLine) + pitch;
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351 targetAddrLine = reinterpret_cast<T*>(targetAddrLineBytes);
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352 }
1362
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353 #endif
1337
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354 }
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355 }
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diff changeset
356 }
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357
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358 template <typename T>
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359 void OrthancMultiframeVolumeLoader::ComputeMinMaxWithOutlierRejection(
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360 const std::map<T, uint64_t>& distribution)
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361 {
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362 if (distribution.size() == 0)
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diff changeset
363 {
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364 LOG(ERROR) << "ComputeMinMaxWithOutlierRejection -- Volume image empty.";
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diff changeset
365 }
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366 else
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diff changeset
367 {
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diff changeset
368 OrthancStone::ImageBuffer3D& target = volume_->GetPixelData();
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369
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370 const uint64_t width = target.GetWidth();
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371 const uint64_t height = target.GetHeight();
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372 const uint64_t depth = target.GetDepth();
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373 const uint64_t voxelCount = width * height * depth;
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374
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375 // now that we have distribution[pixelValue] == numberOfPixelsWithValue
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376 // compute number of values and check (assertion) that it is equal to
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377 // width * height * depth
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diff changeset
378 {
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379 typename std::map<T, uint64_t>::const_iterator it = distribution.begin();
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diff changeset
380 uint64_t totalCount = 0;
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381 distributionRawMin_ = static_cast<float>(it->first);
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diff changeset
382
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diff changeset
383 while (it != distribution.end())
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diff changeset
384 {
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diff changeset
385 T pixelValue = it->first;
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diff changeset
386 uint64_t count = it->second;
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diff changeset
387 totalCount += count;
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diff changeset
388 it++;
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diff changeset
389 if (it == distribution.end())
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diff changeset
390 distributionRawMax_ = static_cast<float>(pixelValue);
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diff changeset
391 }
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diff changeset
392 LOG(INFO) << "Volume image. First distribution value = "
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diff changeset
393 << static_cast<float>(distributionRawMin_)
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394 << " | Last distribution value = "
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diff changeset
395 << static_cast<float>(distributionRawMax_);
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diff changeset
396
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diff changeset
397 if (totalCount != voxelCount)
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diff changeset
398 {
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diff changeset
399 LOG(ERROR) << "Internal error in dose distribution computation. TC ("
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400 << totalCount << ") != VoxC (" << voxelCount;
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401 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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diff changeset
402 }
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diff changeset
403 }
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parents:
diff changeset
404
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diff changeset
405 // compute the number of voxels to reject at each end of the distribution
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diff changeset
406 uint64_t endRejectionCount = static_cast<uint64_t>(
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diff changeset
407 outliersHalfRejectionRate_ * voxelCount);
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diff changeset
408
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diff changeset
409 if (endRejectionCount > voxelCount)
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parents:
diff changeset
410 {
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diff changeset
411 LOG(ERROR) << "Internal error in dose distribution computation."
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parents:
diff changeset
412 << " endRejectionCount = " << endRejectionCount
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diff changeset
413 << " | voxelCount = " << voxelCount;
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diff changeset
414 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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parents:
diff changeset
415 }
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parents:
diff changeset
416
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parents:
diff changeset
417 // this will contain the actual distribution minimum after outlier
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diff changeset
418 // rejection
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diff changeset
419 T resultMin = 0;
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parents:
diff changeset
420
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diff changeset
421 // then start from start and remove pixel values up to
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diff changeset
422 // endRejectionCount voxels rejected
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diff changeset
423 {
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diff changeset
424 typename std::map<T, uint64_t>::const_iterator it = distribution.begin();
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diff changeset
425
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diff changeset
426 uint64_t currentCount = 0;
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parents:
diff changeset
427
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diff changeset
428 while (it != distribution.end())
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diff changeset
429 {
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diff changeset
430 T pixelValue = it->first;
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diff changeset
431 uint64_t count = it->second;
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diff changeset
432
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parents:
diff changeset
433 // if this pixelValue crosses the rejection threshold, let's set it
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Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
434 // and exit the loop
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
435 if ((currentCount <= endRejectionCount) &&
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
436 (currentCount + count > endRejectionCount))
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
437 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
438 resultMin = pixelValue;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
439 break;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
440 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
441 else
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
442 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
443 currentCount += count;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
444 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
445 // and continue walking along the distribution
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
446 it++;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
447 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
448 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
449
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
450 // this will contain the actual distribution maximum after outlier
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
451 // rejection
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
452 T resultMax = 0;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
453 // now start from END and remove pixel values up to
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
454 // endRejectionCount voxels rejected
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
455 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
456 typename std::map<T, uint64_t>::const_reverse_iterator it = distribution.rbegin();
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
457
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
458 uint64_t currentCount = 0;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
459
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
460 while (it != distribution.rend())
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
461 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
462 T pixelValue = it->first;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
463 uint64_t count = it->second;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
464
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
465 if ((currentCount <= endRejectionCount) &&
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
466 (currentCount + count > endRejectionCount))
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
467 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
468 resultMax = pixelValue;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
469 break;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
470 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
471 else
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
472 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
473 currentCount += count;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
474 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
475 // and continue walking along the distribution
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
476 it++;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
477 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
478 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
479 if (resultMin > resultMax)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
480 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
481 LOG(ERROR) << "Internal error in dose distribution computation! " <<
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
482 "resultMin (" << resultMin << ") > resultMax (" << resultMax << ")";
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
483 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
484 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
485 computedDistributionMin_ = static_cast<float>(resultMin);
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
486 computedDistributionMax_ = static_cast<float>(resultMax);
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
487 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
488 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
489
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
490 template <typename T>
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
491 void OrthancMultiframeVolumeLoader::CopyPixelDataAndComputeMinMax(
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
492 const std::string& pixelData)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
493 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
494 std::map<T, uint64_t> distribution;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
495 CopyPixelDataAndComputeDistribution(pixelData, distribution);
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
496 ComputeMinMaxWithOutlierRejection(distribution);
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
497 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
498
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
499 void OrthancMultiframeVolumeLoader::SetUncompressedPixelData(const std::string& pixelData)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
500 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
501 switch (volume_->GetPixelData().GetFormat())
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
502 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
503 case Orthanc::PixelFormat_Grayscale32:
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
504 CopyPixelDataAndComputeMinMax<uint32_t>(pixelData);
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
505 break;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
506 case Orthanc::PixelFormat_Grayscale16:
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
507 CopyPixelDataAndComputeMinMax<uint16_t>(pixelData);
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
508 break;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
509 case Orthanc::PixelFormat_SignedGrayscale16:
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
510 CopyPixelDataAndComputeMinMax<int16_t>(pixelData);
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
511 break;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
512 default:
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
513 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
514 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
515
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
516 volume_->IncrementRevision();
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
517
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
518 pixelDataLoaded_ = true;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
519 BroadcastMessage(OrthancStone::DicomVolumeImage::ContentUpdatedMessage(*volume_));
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
520 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
521
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
522 bool OrthancMultiframeVolumeLoader::HasGeometry() const
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
523 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
524 return volume_->HasGeometry();
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
525 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
526
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
527 const OrthancStone::VolumeImageGeometry& OrthancMultiframeVolumeLoader::GetImageGeometry() const
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
528 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
529 return volume_->GetGeometry();
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
530 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
531
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
532 OrthancMultiframeVolumeLoader::OrthancMultiframeVolumeLoader(
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
533 OrthancStone::ILoadersContext& loadersContext,
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
534 boost::shared_ptr<OrthancStone::DicomVolumeImage> volume,
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
535 float outliersHalfRejectionRate)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
536 : LoaderStateMachine(loadersContext)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
537 , volume_(volume)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
538 , pixelDataLoaded_(false)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
539 , outliersHalfRejectionRate_(outliersHalfRejectionRate)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
540 , distributionRawMin_(0)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
541 , distributionRawMax_(0)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
542 , computedDistributionMin_(0)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
543 , computedDistributionMax_(0)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
544 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
545 if (volume.get() == NULL)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
546 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
547 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer);
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
548 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
549 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
550
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
551
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
552 boost::shared_ptr<OrthancMultiframeVolumeLoader>
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
553 OrthancMultiframeVolumeLoader::Create(
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
554 OrthancStone::ILoadersContext& loadersContext,
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
555 boost::shared_ptr<OrthancStone::DicomVolumeImage> volume,
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
556 float outliersHalfRejectionRate /*= 0.0005*/)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
557 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
558 boost::shared_ptr<OrthancMultiframeVolumeLoader> obj(
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
559 new OrthancMultiframeVolumeLoader(
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
560 loadersContext,
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
561 volume,
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
562 outliersHalfRejectionRate));
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
563 obj->LoaderStateMachine::PostConstructor();
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
564 return obj;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
565 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
566
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
567 OrthancMultiframeVolumeLoader::~OrthancMultiframeVolumeLoader()
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
568 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
569 LOG(TRACE) << "OrthancMultiframeVolumeLoader::~OrthancMultiframeVolumeLoader()";
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
570 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
571
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
572 void OrthancMultiframeVolumeLoader::GetDistributionMinMax
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
573 (float& minValue, float& maxValue) const
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
574 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
575 if (distributionRawMin_ == 0 && distributionRawMax_ == 0)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
576 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
577 LOG(WARNING) << "GetDistributionMinMaxWithOutliersRejection called before computation!";
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
578 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
579 minValue = distributionRawMin_;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
580 maxValue = distributionRawMax_;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
581 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
582
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
583 void OrthancMultiframeVolumeLoader::GetDistributionMinMaxWithOutliersRejection
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584 (float& minValue, float& maxValue) const
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585 {
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586 if (computedDistributionMin_ == 0 && computedDistributionMax_ == 0)
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587 {
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588 LOG(WARNING) << "GetDistributionMinMaxWithOutliersRejection called before computation!";
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589 }
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590 minValue = computedDistributionMin_;
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591 maxValue = computedDistributionMax_;
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592 }
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593
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594 void OrthancMultiframeVolumeLoader::LoadInstance(const std::string& instanceId)
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595 {
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596 Start();
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597
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598 instanceId_ = instanceId;
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599
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600 {
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601 std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand);
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602 command->SetHttpHeader("Accept-Encoding", "gzip");
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603 command->SetUri("/instances/" + instanceId + "/tags");
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604 command->AcquirePayload(new LoadGeometry(*this));
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605 Schedule(command.release());
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606 }
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607
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608 {
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609 std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand);
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610 command->SetUri("/instances/" + instanceId + "/metadata/TransferSyntax");
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611 command->AcquirePayload(new LoadTransferSyntax(*this));
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612 Schedule(command.release());
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613 }
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614 }
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615 }