Mercurial > hg > orthanc-stone

annotate OrthancStone/Sources/Loaders/OrthancMultiframeVolumeLoader.cpp @ 1739:9ac2a65d4172

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upgrade to year 2021
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 06 Jan 2021 17:50:00 +0100
parents 52b8b96cb55f
children 946eb7200b82
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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) 2017-2021 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 Lesser 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 * Lesser 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 Lesser General Public
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18 * License along with this program. If not, see
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19 * <http://www.gnu.org/licenses/>.
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20 **/
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23 #include "OrthancMultiframeVolumeLoader.h"
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24
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25 #include <Endianness.h>
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26 #include <Toolbox.h>
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28 namespace OrthancStone
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29 {
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30 class OrthancMultiframeVolumeLoader::LoadRTDoseGeometry : public LoaderStateMachine::State
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31 {
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32 private:
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33 std::unique_ptr<Orthanc::DicomMap> dicom_;
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34
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35 public:
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36 LoadRTDoseGeometry(OrthancMultiframeVolumeLoader& that,
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37 Orthanc::DicomMap* dicom) :
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38 State(that),
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39 dicom_(dicom)
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40 {
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41 if (dicom == NULL)
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42 {
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43 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer);
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44 }
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45
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46 }
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47
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48 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) ORTHANC_OVERRIDE
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49 {
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50 // Complete the DICOM tags with just-received "Grid Frame Offset Vector"
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51 std::string s = Orthanc::Toolbox::StripSpaces(message.GetAnswer());
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52 dicom_->SetValue(Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR, s, false);
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53
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54 GetLoader<OrthancMultiframeVolumeLoader>().SetGeometry(*dicom_);
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55 }
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56 };
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57
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58
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59 static std::string GetSopClassUid(const Orthanc::DicomMap& dicom)
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60 {
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61 std::string s;
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62 if (!dicom.LookupStringValue(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false))
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63 {
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64 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
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65 "DICOM file without SOP class UID");
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66 }
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67 else
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68 {
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69 return s;
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70 }
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71 }
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72
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73
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74 class OrthancMultiframeVolumeLoader::LoadGeometry : public State
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75 {
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76 public:
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77 explicit LoadGeometry(OrthancMultiframeVolumeLoader& that) :
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78 State(that)
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79 {
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80 }
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81
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82 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message)
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83 {
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84 OrthancMultiframeVolumeLoader& loader = GetLoader<OrthancMultiframeVolumeLoader>();
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85
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86 Json::Value body;
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87 message.ParseJsonBody(body);
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88
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89 if (body.type() != Json::objectValue)
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90 {
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91 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol);
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92 }
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93
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94 std::unique_ptr<Orthanc::DicomMap> dicom(new Orthanc::DicomMap);
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95 dicom->FromDicomAsJson(body);
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96
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97 if (StringToSopClassUid(GetSopClassUid(*dicom)) == SopClassUid_RTDose)
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98 {
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99 // Download the "Grid Frame Offset Vector" DICOM tag, that is
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100 // mandatory for RT-DOSE, but is too long to be returned by default
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101
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102 std::unique_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand);
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103 command->SetUri("/instances/" + loader.GetInstanceId() + "/content/" +
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104 Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR.Format());
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105 command->AcquirePayload(new LoadRTDoseGeometry(loader, dicom.release()));
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106
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107 Schedule(command.release());
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108 }
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109 else
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110 {
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111 loader.SetGeometry(*dicom);
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112 }
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113 }
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114 };
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115
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116 class OrthancMultiframeVolumeLoader::LoadTransferSyntax : public State
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117 {
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118 public:
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119 explicit LoadTransferSyntax(OrthancMultiframeVolumeLoader& that) :
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120 State(that)
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121 {
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122 }
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123
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124 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message)
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125 {
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126 GetLoader<OrthancMultiframeVolumeLoader>().SetTransferSyntax(message.GetAnswer());
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127 }
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128 };
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129
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130 class OrthancMultiframeVolumeLoader::LoadUncompressedPixelData : public State
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131 {
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132 public:
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133 explicit LoadUncompressedPixelData(OrthancMultiframeVolumeLoader& that) :
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134 State(that)
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135 {
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136 }
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137
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138 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message)
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139 {
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140 GetLoader<OrthancMultiframeVolumeLoader>().SetUncompressedPixelData(message.GetAnswer());
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141 }
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142 };
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143
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144 const std::string& OrthancMultiframeVolumeLoader::GetInstanceId() const
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145 {
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146 if (IsActive())
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147 {
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148 return instanceId_;
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149 }
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150 else
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151 {
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152 LOG(ERROR) << "OrthancMultiframeVolumeLoader::GetInstanceId(): (!IsActive())";
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153 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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154 }
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155 }
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156
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157 void OrthancMultiframeVolumeLoader::ScheduleFrameDownloads()
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158 {
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159 if (transferSyntaxUid_.empty() ||
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160 !volume_->HasGeometry())
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161 {
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162 return;
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163 }
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164 /*
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165 1.2.840.10008.1.2 Implicit VR Endian: Default Transfer Syntax for DICOM
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166 1.2.840.10008.1.2.1 Explicit VR Little Endian
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167 1.2.840.10008.1.2.2 Explicit VR Big Endian
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168
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169 See https://www.dicomlibrary.com/dicom/transfer-syntax/
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170 */
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171 if (transferSyntaxUid_ == "1.2.840.10008.1.2" ||
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172 transferSyntaxUid_ == "1.2.840.10008.1.2.1" ||
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173 transferSyntaxUid_ == "1.2.840.10008.1.2.2")
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174 {
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175 std::unique_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand);
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176 command->SetHttpHeader("Accept-Encoding", "gzip");
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177 command->SetUri("/instances/" + instanceId_ + "/content/" +
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178 Orthanc::DICOM_TAG_PIXEL_DATA.Format() + "/0");
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179 command->AcquirePayload(new LoadUncompressedPixelData(*this));
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180 Schedule(command.release());
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181 }
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182 else
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183 {
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184 throw Orthanc::OrthancException(
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185 Orthanc::ErrorCode_NotImplemented,
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186 "No support for multiframe instances with transfer syntax: " + transferSyntaxUid_);
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187 }
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188 }
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189
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190 void OrthancMultiframeVolumeLoader::SetTransferSyntax(const std::string& transferSyntax)
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191 {
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192 transferSyntaxUid_ = Orthanc::Toolbox::StripSpaces(transferSyntax);
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193 ScheduleFrameDownloads();
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194 }
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195
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196 void OrthancMultiframeVolumeLoader::SetGeometry(const Orthanc::DicomMap& dicom)
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197 {
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198 DicomInstanceParameters parameters(dicom);
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199 volume_->SetDicomParameters(parameters);
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200
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201 Orthanc::PixelFormat format;
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202 if (!parameters.GetImageInformation().ExtractPixelFormat(format, true))
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203 {
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204 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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205 }
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206
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207 double spacingZ;
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208 switch (parameters.GetSopClassUid())
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209 {
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210 case SopClassUid_RTDose:
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211 spacingZ = parameters.GetSliceThickness();
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212 break;
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213
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214 default:
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215 throw Orthanc::OrthancException(
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216 Orthanc::ErrorCode_NotImplemented,
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217 "No support for multiframe instances with SOP class UID: " + GetSopClassUid(dicom));
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218 }
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219
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220 const unsigned int width = parameters.GetImageInformation().GetWidth();
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221 const unsigned int height = parameters.GetImageInformation().GetHeight();
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222 const unsigned int depth = parameters.GetImageInformation().GetNumberOfFrames();
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223
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224 {
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225 VolumeImageGeometry geometry;
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226 geometry.SetSizeInVoxels(width, height, depth);
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227 geometry.SetAxialGeometry(parameters.GetGeometry());
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228 geometry.SetVoxelDimensions(parameters.GetPixelSpacingX(),
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229 parameters.GetPixelSpacingY(), spacingZ);
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230 volume_->Initialize(geometry, format, true /* Do compute range */);
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231 }
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232
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233 volume_->GetPixelData().Clear();
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234
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235 ScheduleFrameDownloads();
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236
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237
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238
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239 BroadcastMessage(DicomVolumeImage::GeometryReadyMessage(*volume_));
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240 }
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241
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242
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243 ORTHANC_FORCE_INLINE
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244 static void CopyPixel(uint32_t& target, const void* source)
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245 {
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246 // TODO - check alignement?
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247 target = le32toh(*reinterpret_cast<const uint32_t*>(source));
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248 }
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249
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250 ORTHANC_FORCE_INLINE
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251 static void CopyPixel(uint16_t& target, const void* source)
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252 {
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253 // TODO - check alignement?
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254 target = le16toh(*reinterpret_cast<const uint16_t*>(source));
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255 }
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256
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257 ORTHANC_FORCE_INLINE
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258 static void CopyPixel(int16_t& target, const void* source)
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259 {
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260 // byte swapping is the same for unsigned and signed integers
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261 // (the sign bit is always stored with the MSByte)
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262 uint16_t* targetUp = reinterpret_cast<uint16_t*>(&target);
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263 CopyPixel(*targetUp, source);
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264 }
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265
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266 template <typename T>
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267 void OrthancMultiframeVolumeLoader::CopyPixelDataAndComputeDistribution(
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268 const std::string& pixelData, std::map<T,uint64_t>& distribution)
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269 {
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270 ImageBuffer3D& target = volume_->GetPixelData();
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271
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272 const unsigned int bpp = target.GetBytesPerPixel();
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273 const unsigned int width = target.GetWidth();
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274 const unsigned int height = target.GetHeight();
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275 const unsigned int depth = target.GetDepth();
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276
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277 if (pixelData.size() != bpp * width * height * depth)
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278 {
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279 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
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280 "The pixel data has not the proper size");
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281 }
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282
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283 if (pixelData.empty())
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284 {
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285 return;
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diff changeset
286 }
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diff changeset
287
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288 // first pass to initialize map
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289 {
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290 const uint8_t* source = reinterpret_cast<const uint8_t*>(pixelData.c_str());
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291
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diff changeset
292 for (unsigned int z = 0; z < depth; z++)
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diff changeset
293 {
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294 for (unsigned int y = 0; y < height; y++)
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diff changeset
295 {
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296 for (unsigned int x = 0; x < width; x++)
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297 {
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298 T value;
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299 CopyPixel(value, source);
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300 distribution[value] = 0;
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301 source += bpp;
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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 {
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308 const uint8_t* source = reinterpret_cast<const uint8_t*>(pixelData.c_str());
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309
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310 for (unsigned int z = 0; z < depth; z++)
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311 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1634
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312 ImageBuffer3D::SliceWriter writer(target, VolumeProjection_Axial, z);
1337
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313
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314 assert(writer.GetAccessor().GetWidth() == width &&
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315 writer.GetAccessor().GetHeight() == height);
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316 #if 0
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317 for (unsigned int y = 0; y < height; y++)
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318 {
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319 assert(sizeof(T) == Orthanc::GetBytesPerPixel(target.GetFormat()));
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320
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321 T* target = reinterpret_cast<T*>(writer.GetAccessor().GetRow(y));
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322
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323 for (unsigned int x = 0; x < width; x++)
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324 {
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325 CopyPixel(*target, source);
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326
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327 distribution[*target] += 1;
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328
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329 target++;
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Benjamin Golinvaux <bgo@osimis.io>
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330 source += bpp;
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331 }
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332 }
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333 #else
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334 // optimized version (fixed) as of 2020-04-15
1349
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335 unsigned int pitch = writer.GetAccessor().GetPitch();
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336 T* targetAddrLine = reinterpret_cast<T*>(writer.GetAccessor().GetRow(0));
1349
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337 assert(sizeof(T) == Orthanc::GetBytesPerPixel(target.GetFormat()));
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Benjamin Golinvaux <bgo@osimis.io>
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diff changeset
338
1337
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339 for (unsigned int y = 0; y < height; y++)
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340 {
1362
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341 T* targetAddrPix = targetAddrLine;
1337
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342 for (unsigned int x = 0; x < width; x++)
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343 {
1362
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344 CopyPixel(*targetAddrPix, source);
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345
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346 distribution[*targetAddrPix] += 1;
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347
1362
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348 targetAddrPix++;
1337
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349 source += bpp;
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350 }
1362
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351 uint8_t* targetAddrLineBytes = reinterpret_cast<uint8_t*>(targetAddrLine) + pitch;
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352 targetAddrLine = reinterpret_cast<T*>(targetAddrLineBytes);
1337
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353 }
1362
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354 #endif
1337
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355 }
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diff changeset
356 }
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diff changeset
357 }
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358
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359 template <typename T>
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360 void OrthancMultiframeVolumeLoader::ComputeMinMaxWithOutlierRejection(
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361 const std::map<T, uint64_t>& distribution)
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362 {
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363 if (distribution.size() == 0)
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diff changeset
364 {
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365 LOG(ERROR) << "ComputeMinMaxWithOutlierRejection -- Volume image empty.";
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diff changeset
366 }
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367 else
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parents:
diff changeset
368 {
1640
52b8b96cb55f cleaning namespaces
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1634
diff changeset
369 ImageBuffer3D& target = volume_->GetPixelData();
1337
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diff changeset
370
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371 const uint64_t width = target.GetWidth();
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diff changeset
372 const uint64_t height = target.GetHeight();
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373 const uint64_t depth = target.GetDepth();
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374 const uint64_t voxelCount = width * height * depth;
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375
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376 // now that we have distribution[pixelValue] == numberOfPixelsWithValue
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diff changeset
377 // compute number of values and check (assertion) that it is equal to
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diff changeset
378 // width * height * depth
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diff changeset
379 {
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diff changeset
380 typename std::map<T, uint64_t>::const_iterator it = distribution.begin();
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diff changeset
381 uint64_t totalCount = 0;
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diff changeset
382 distributionRawMin_ = static_cast<float>(it->first);
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diff changeset
383
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diff changeset
384 while (it != distribution.end())
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diff changeset
385 {
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diff changeset
386 T pixelValue = it->first;
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diff changeset
387 uint64_t count = it->second;
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diff changeset
388 totalCount += count;
1571
85e117739eca cppcheck
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1512
diff changeset
389 ++it;
1337
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diff changeset
390 if (it == distribution.end())
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diff changeset
391 distributionRawMax_ = static_cast<float>(pixelValue);
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diff changeset
392 }
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diff changeset
393 LOG(INFO) << "Volume image. First distribution value = "
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diff changeset
394 << static_cast<float>(distributionRawMin_)
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diff changeset
395 << " | Last distribution value = "
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diff changeset
396 << static_cast<float>(distributionRawMax_);
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parents:
diff changeset
397
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diff changeset
398 if (totalCount != voxelCount)
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diff changeset
399 {
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diff changeset
400 LOG(ERROR) << "Internal error in dose distribution computation. TC ("
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diff changeset
401 << totalCount << ") != VoxC (" << voxelCount;
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diff changeset
402 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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parents:
diff changeset
403 }
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parents:
diff changeset
404 }
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parents:
diff changeset
405
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parents:
diff changeset
406 // compute the number of voxels to reject at each end of the distribution
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parents:
diff changeset
407 uint64_t endRejectionCount = static_cast<uint64_t>(
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parents:
diff changeset
408 outliersHalfRejectionRate_ * voxelCount);
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parents:
diff changeset
409
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parents:
diff changeset
410 if (endRejectionCount > voxelCount)
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parents:
diff changeset
411 {
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parents:
diff changeset
412 LOG(ERROR) << "Internal error in dose distribution computation."
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parents:
diff changeset
413 << " endRejectionCount = " << endRejectionCount
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parents:
diff changeset
414 << " | voxelCount = " << voxelCount;
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parents:
diff changeset
415 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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parents:
diff changeset
416 }
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parents:
diff changeset
417
b1396be5aa27 Moved the fixed loaders back from the dead
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parents:
diff changeset
418 // this will contain the actual distribution minimum after outlier
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parents:
diff changeset
419 // rejection
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parents:
diff changeset
420 T resultMin = 0;
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parents:
diff changeset
421
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parents:
diff changeset
422 // then start from start and remove pixel values up to
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parents:
diff changeset
423 // endRejectionCount voxels rejected
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parents:
diff changeset
424 {
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parents:
diff changeset
425 typename std::map<T, uint64_t>::const_iterator it = distribution.begin();
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parents:
diff changeset
426
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
427 uint64_t currentCount = 0;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
428
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Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
429 while (it != distribution.end())
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
430 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
431 T pixelValue = it->first;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
432 uint64_t count = it->second;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
433
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
434 // if this pixelValue crosses the rejection threshold, let's set it
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
435 // and exit the loop
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
436 if ((currentCount <= endRejectionCount) &&
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
437 (currentCount + count > endRejectionCount))
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
438 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
439 resultMin = pixelValue;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
440 break;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
441 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
442 else
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
443 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
444 currentCount += count;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
445 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
446 // and continue walking along the distribution
1571
85e117739eca cppcheck
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1512
diff changeset
447 ++it;
1337
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
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
451 // 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
452 // rejection
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
453 T resultMax = 0;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
454 // 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
455 // endRejectionCount voxels rejected
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
456 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
457 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
458
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
459 uint64_t currentCount = 0;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
460
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
461 while (it != distribution.rend())
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Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
462 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
463 T pixelValue = it->first;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
464 uint64_t count = it->second;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
465
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
466 if ((currentCount <= endRejectionCount) &&
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
467 (currentCount + count > endRejectionCount))
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
468 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
469 resultMax = pixelValue;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
470 break;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
471 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
472 else
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
473 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
474 currentCount += count;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
475 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
476 // and continue walking along the distribution
1571
85e117739eca cppcheck
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1512
diff changeset
477 ++it;
1337
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 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
480 if (resultMin > resultMax)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
481 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
482 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
483 "resultMin (" << resultMin << ") > resultMax (" << resultMax << ")";
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
484 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
485 }
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
486 computedDistributionMin_ = static_cast<float>(resultMin);
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
487 computedDistributionMax_ = static_cast<float>(resultMax);
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
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
491 template <typename T>
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
492 void OrthancMultiframeVolumeLoader::CopyPixelDataAndComputeMinMax(
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
493 const std::string& pixelData)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
494 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
495 std::map<T, uint64_t> distribution;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
496 CopyPixelDataAndComputeDistribution(pixelData, distribution);
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
497 ComputeMinMaxWithOutlierRejection(distribution);
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
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
500 void OrthancMultiframeVolumeLoader::SetUncompressedPixelData(const std::string& pixelData)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
501 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
502 switch (volume_->GetPixelData().GetFormat())
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
503 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
504 case Orthanc::PixelFormat_Grayscale32:
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
505 CopyPixelDataAndComputeMinMax<uint32_t>(pixelData);
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
506 break;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
507 case Orthanc::PixelFormat_Grayscale16:
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
508 CopyPixelDataAndComputeMinMax<uint16_t>(pixelData);
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
509 break;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
510 case Orthanc::PixelFormat_SignedGrayscale16:
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
511 CopyPixelDataAndComputeMinMax<int16_t>(pixelData);
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
512 break;
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
513 default:
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
514 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
517 volume_->IncrementRevision();
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
518
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
519 pixelDataLoaded_ = true;
1640
52b8b96cb55f cleaning namespaces
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1634
diff changeset
520 BroadcastMessage(DicomVolumeImage::ContentUpdatedMessage(*volume_));
1337
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
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
523 bool OrthancMultiframeVolumeLoader::HasGeometry() const
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
524 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
525 return volume_->HasGeometry();
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
1640
52b8b96cb55f cleaning namespaces
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1634
diff changeset
528 const VolumeImageGeometry& OrthancMultiframeVolumeLoader::GetImageGeometry() const
1337
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
529 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
530 return volume_->GetGeometry();
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
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
533 OrthancMultiframeVolumeLoader::OrthancMultiframeVolumeLoader(
1640
52b8b96cb55f cleaning namespaces
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1634
diff changeset
534 ILoadersContext& loadersContext,
52b8b96cb55f cleaning namespaces
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1634
diff changeset
535 boost::shared_ptr<DicomVolumeImage> volume,
1337
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
536 float outliersHalfRejectionRate)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
537 : LoaderStateMachine(loadersContext)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
538 , volume_(volume)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
539 , pixelDataLoaded_(false)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
540 , outliersHalfRejectionRate_(outliersHalfRejectionRate)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
541 , distributionRawMin_(0)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
542 , distributionRawMax_(0)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
543 , computedDistributionMin_(0)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
544 , computedDistributionMax_(0)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
545 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
546 if (volume.get() == NULL)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
547 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
548 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer);
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
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
553 boost::shared_ptr<OrthancMultiframeVolumeLoader>
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
554 OrthancMultiframeVolumeLoader::Create(
1640
52b8b96cb55f cleaning namespaces
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1634
diff changeset
555 ILoadersContext& loadersContext,
52b8b96cb55f cleaning namespaces
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1634
diff changeset
556 boost::shared_ptr<DicomVolumeImage> volume,
1337
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
557 float outliersHalfRejectionRate /*= 0.0005*/)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
558 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
559 boost::shared_ptr<OrthancMultiframeVolumeLoader> obj(
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
560 new OrthancMultiframeVolumeLoader(
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
561 loadersContext,
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
562 volume,
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
563 outliersHalfRejectionRate));
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
564 obj->LoaderStateMachine::PostConstructor();
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
565 return obj;
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
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
568 OrthancMultiframeVolumeLoader::~OrthancMultiframeVolumeLoader()
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
569 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
570 LOG(TRACE) << "OrthancMultiframeVolumeLoader::~OrthancMultiframeVolumeLoader()";
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
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
573 void OrthancMultiframeVolumeLoader::GetDistributionMinMax
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
574 (float& minValue, float& maxValue) const
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
575 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
576 if (distributionRawMin_ == 0 && distributionRawMax_ == 0)
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
577 {
b1396be5aa27 Moved the fixed loaders back from the dead
Benjamin Golinvaux <bgo@osimis.io>
parents:
diff changeset
578 LOG(WARNING) << "GetDistributionMinMaxWithOutliersRejection called before computation!";
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579 }
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580 minValue = distributionRawMin_;
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581 maxValue = distributionRawMax_;
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582 }
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583
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584 void OrthancMultiframeVolumeLoader::GetDistributionMinMaxWithOutliersRejection
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585 (float& minValue, float& maxValue) const
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586 {
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587 if (computedDistributionMin_ == 0 && computedDistributionMax_ == 0)
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588 {
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589 LOG(WARNING) << "GetDistributionMinMaxWithOutliersRejection called before computation!";
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590 }
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591 minValue = computedDistributionMin_;
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592 maxValue = computedDistributionMax_;
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593 }
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594
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595 void OrthancMultiframeVolumeLoader::LoadInstance(const std::string& instanceId)
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596 {
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597 Start();
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598
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599 instanceId_ = instanceId;
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600
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601 {
1640
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602 std::unique_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand);
1337
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603 command->SetHttpHeader("Accept-Encoding", "gzip");
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604 command->SetUri("/instances/" + instanceId + "/tags");
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605 command->AcquirePayload(new LoadGeometry(*this));
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606 Schedule(command.release());
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607 }
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608
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Benjamin Golinvaux <bgo@osimis.io>
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609 {
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parents: 1634
diff changeset
610 std::unique_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand);
1337
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611 command->SetUri("/instances/" + instanceId + "/metadata/TransferSyntax");
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612 command->AcquirePayload(new LoadTransferSyntax(*this));
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613 Schedule(command.release());
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614 }
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615 }
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616 }