Mercurial > hg > orthanc-wsi

annotate Framework/Inputs/DicomPyramidInstance.cpp @ 223:443f219a68fd

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sync, compatibility with Orthanc framework 1.8.2
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 13 Jan 2021 09:23:22 +0100
parents ef3f8c5126a4
children 4eefa34657f0
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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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 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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22 #include "../PrecompiledHeadersWSI.h"
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23 #include "DicomPyramidInstance.h"
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25 #include "../DicomToolbox.h"
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26 #include "../../Resources/Orthanc/Plugins/OrthancPluginCppWrapper.h"
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27 #include "../../Resources/Orthanc/Stone/DicomDatasetReader.h"
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28 #include "../../Resources/Orthanc/Stone/FullOrthancDataset.h"
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30 #include <Logging.h>
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31 #include <OrthancException.h>
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32 #include <SerializationToolbox.h>
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33 #include <Toolbox.h>
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34
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35 #include <cassert>
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36
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37 #define SERIALIZED_METADATA "4201" // Was "4200" if versions <= 0.7 of this plugin
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39
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40 namespace OrthancWSI
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41 {
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42 static const Orthanc::DicomTag DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX(0x0048, 0x021e);
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43 static const Orthanc::DicomTag DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE(0x5200, 0x9230);
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44 static const Orthanc::DicomTag DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE(0x0048, 0x021a);
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45 static const Orthanc::DicomTag DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX(0x0048, 0x021f);
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46 static const Orthanc::DicomTag DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS(0x0048, 0x0006);
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47 static const Orthanc::DicomTag DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS(0x0048, 0x0007);
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48 static const Orthanc::DicomTag DICOM_TAG_IMAGE_TYPE(0x0008, 0x0008);
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49
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50 static ImageCompression DetectImageCompression(OrthancStone::IOrthancConnection& orthanc,
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51 const std::string& instanceId)
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52 {
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53 using namespace OrthancStone;
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54
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55 FullOrthancDataset dataset(orthanc, "/instances/" + instanceId + "/header");
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56 DicomDatasetReader header(dataset);
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57
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58 std::string s = Orthanc::Toolbox::StripSpaces
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59 (header.GetMandatoryStringValue(OrthancStone::DicomPath(Orthanc::DICOM_TAG_TRANSFER_SYNTAX_UID)));
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61 if (s == "1.2.840.10008.1.2" ||
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62 s == "1.2.840.10008.1.2.1")
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63 {
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64 return ImageCompression_None;
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65 }
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66 else if (s == "1.2.840.10008.1.2.4.50")
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67 {
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68 return ImageCompression_Jpeg;
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69 }
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70 else if (s == "1.2.840.10008.1.2.4.90" ||
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71 s == "1.2.840.10008.1.2.4.91")
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72 {
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73 return ImageCompression_Jpeg2000;
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74 }
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75 else
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76 {
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77 LOG(ERROR) << "Unsupported transfer syntax: " << s;
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78 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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79 }
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80 }
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83 static void DetectPixelFormat(Orthanc::PixelFormat& format,
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84 Orthanc::PhotometricInterpretation& photometric,
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85 const OrthancStone::DicomDatasetReader& reader)
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86 {
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87 using namespace OrthancStone;
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88
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89 std::string p = Orthanc::Toolbox::StripSpaces
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90 (reader.GetMandatoryStringValue(OrthancStone::DicomPath(Orthanc::DICOM_TAG_PHOTOMETRIC_INTERPRETATION)));
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91
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92 photometric = Orthanc::StringToPhotometricInterpretation(p.c_str());
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94 if (photometric == Orthanc::PhotometricInterpretation_Palette)
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95 {
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96 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented,
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97 "Unsupported photometric interpretation: " + p);
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98 }
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99
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100 unsigned int bitsStored, samplesPerPixel, tmp;
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101
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102 if (!reader.GetUnsignedIntegerValue(bitsStored, OrthancStone::DicomPath(Orthanc::DICOM_TAG_BITS_STORED)) ||
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103 !reader.GetUnsignedIntegerValue(samplesPerPixel, OrthancStone::DicomPath(Orthanc::DICOM_TAG_SAMPLES_PER_PIXEL)) ||
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104 !reader.GetUnsignedIntegerValue(tmp, OrthancStone::DicomPath(Orthanc::DICOM_TAG_PIXEL_REPRESENTATION)))
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105 {
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106 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag);
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107 }
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108
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109 bool isSigned = (tmp != 0);
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110
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111 if (bitsStored == 8 &&
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112 samplesPerPixel == 1 &&
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113 !isSigned)
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114 {
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115 format = Orthanc::PixelFormat_Grayscale8;
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116 }
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117 else if (bitsStored == 8 &&
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118 samplesPerPixel == 3 &&
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119 !isSigned)
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120 {
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121 format = Orthanc::PixelFormat_RGB24;
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122 }
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123 else
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124 {
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125 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "Unsupported pixel format");
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126 }
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127 }
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129
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130 ImageCompression DicomPyramidInstance::GetImageCompression(OrthancStone::IOrthancConnection& orthanc)
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131 {
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132 /**
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133 * Lazy detection of the image compression using the transfer
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134 * syntax stored inside the DICOM header. Given the fact that
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135 * reading the header is a time-consuming operation (it implies
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136 * the decoding of the DICOM image by Orthanc, whereas the "/tags"
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137 * endpoint only reads the "DICOM-as-JSON" attachment), the
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138 * "/header" REST call is delayed until it is really required.
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139 **/
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140
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141 if (!hasCompression_)
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142 {
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143 compression_ = DetectImageCompression(orthanc, instanceId_);
56
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144 hasCompression_ = true;
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145 }
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146
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147 return compression_;
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148 }
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149
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150
196
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151 void DicomPyramidInstance::Load(OrthancStone::IOrthancConnection& orthanc,
68
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152 const std::string& instanceId)
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153 {
196
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154 using namespace OrthancStone;
0
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155
87
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156 FullOrthancDataset dataset(orthanc, "/instances/" + instanceId + "/tags");
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157 DicomDatasetReader reader(dataset);
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158
213
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159 if (reader.GetMandatoryStringValue(OrthancStone::DicomPath(Orthanc::DICOM_TAG_SOP_CLASS_UID)) != "1.2.840.10008.5.1.4.1.1.77.1.6" ||
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160 reader.GetMandatoryStringValue(OrthancStone::DicomPath(Orthanc::DICOM_TAG_MODALITY)) != "SM")
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161 {
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162 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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163 }
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164
69
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165 hasCompression_ = false;
166
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166 DetectPixelFormat(format_, photometric_, reader);
89
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167
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168 unsigned int tmp;
213
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169 if (!reader.GetUnsignedIntegerValue(tileWidth_, OrthancStone::DicomPath(Orthanc::DICOM_TAG_COLUMNS)) ||
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170 !reader.GetUnsignedIntegerValue(tileHeight_, OrthancStone::DicomPath(Orthanc::DICOM_TAG_ROWS)) ||
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171 !reader.GetUnsignedIntegerValue(totalWidth_, OrthancStone::DicomPath(DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS)) ||
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172 !reader.GetUnsignedIntegerValue(totalHeight_, OrthancStone::DicomPath(DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS)) ||
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173 !reader.GetUnsignedIntegerValue(tmp, OrthancStone::DicomPath(Orthanc::DICOM_TAG_NUMBER_OF_FRAMES)))
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174 {
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175 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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176 }
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177
219
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178 imageType_ = reader.GetStringValue(OrthancStone::DicomPath(DICOM_TAG_IMAGE_TYPE), "");
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179
62
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180 size_t countFrames;
215
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181 if (reader.GetDataset().GetSequenceSize(countFrames, OrthancStone::DicomPath(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE)))
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182 {
215
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183 if (countFrames != tmp)
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184 {
215
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185 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId;
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186 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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187 }
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188
215
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189 frames_.resize(countFrames);
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190
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191 for (size_t i = 0; i < countFrames; i++)
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192 {
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193 DicomPath pathX(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i,
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194 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0,
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195 DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX);
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196
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197 DicomPath pathY(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i,
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198 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0,
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199 DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX);
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200
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201 int xx, yy;
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202 if (!reader.GetIntegerValue(xx, pathX) ||
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203 !reader.GetIntegerValue(yy, pathY))
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204 {
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205 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag);
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206 }
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207
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208 // "-1", because coordinates are shifted by 1 in DICOM
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209 xx -= 1;
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210 yy -= 1;
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211
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212 unsigned int x = static_cast<unsigned int>(xx);
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213 unsigned int y = static_cast<unsigned int>(yy);
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214
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215 if (xx < 0 ||
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216 yy < 0 ||
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217 x % tileWidth_ != 0 ||
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218 y % tileHeight_ != 0 ||
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219 x >= totalWidth_ ||
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220 y >= totalHeight_)
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221 {
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222 LOG(ERROR) << "Frame " << i << " with unexpected tile location ("
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223 << x << "," << y << ") in instance: " << instanceId;
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224 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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225 }
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226
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227 frames_[i].first = x / tileWidth_;
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228 frames_[i].second = y / tileHeight_;
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229 }
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230 }
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231 else
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232 {
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233 // No "Per frame functional groups sequence" tag. Assume regular grid.
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234 frames_.resize(tmp);
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235
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236 // Compute "ceiling(totalWidth_ / tileWidth_)
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237 unsigned int w = totalWidth_ / tileWidth_;
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238 if (totalWidth_ % tileWidth_ != 0)
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239 {
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240 w += 1;
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241 }
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242
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243 unsigned int h = totalHeight_ / tileHeight_;
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244 if (totalHeight_ % tileHeight_ != 0)
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245 {
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246 h += 1;
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247 }
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248
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249 if (w * h != tmp)
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250 {
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251 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId;
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252 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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253 }
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254
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255 for (size_t i = 0; i < frames_.size(); i++)
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256 {
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257 frames_[i].first = i % w;
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258 frames_[i].second = i / w;
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259 }
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260 }
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261 }
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262
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263
196
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264 DicomPyramidInstance::DicomPyramidInstance(OrthancStone::IOrthancConnection& orthanc,
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265 const std::string& instanceId,
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266 bool useCache) :
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267 instanceId_(instanceId),
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268 hasCompression_(false),
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269 compression_(ImageCompression_None) // Dummy initialization for serialization
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270 {
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271 if (useCache)
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272 {
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273 try
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274 {
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275 // Try and deserialized the cached information about this instance
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276 std::string serialized;
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277 orthanc.RestApiGet(serialized, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA);
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278 Deserialize(serialized);
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279 return; // Success
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280 }
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281 catch (Orthanc::OrthancException&)
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282 {
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283 // No cached information yet
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284 }
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285 }
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286
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287 // Compute information about this instance from scratch
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288 Load(orthanc, instanceId);
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289
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290 if (useCache)
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291 {
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292 // Serialize the computed information and cache it as a metadata
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293 std::string serialized, tmp;
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294 Serialize(serialized);
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295 orthanc.RestApiPut(tmp, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA, serialized);
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296 }
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297 }
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298
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299
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300 unsigned int DicomPyramidInstance::GetFrameLocationX(size_t frame) const
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301 {
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302 assert(frame < frames_.size());
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303 return frames_[frame].first;
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304 }
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305
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306
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307 unsigned int DicomPyramidInstance::GetFrameLocationY(size_t frame) const
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308 {
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309 assert(frame < frames_.size());
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310 return frames_[frame].second;
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311 }
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312
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313
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314
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315 static const char* const HAS_COMPRESSION = "HasCompression";
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316 static const char* const IMAGE_COMPRESSION = "ImageCompression";
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317 static const char* const PIXEL_FORMAT = "PixelFormat";
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318 static const char* const FRAMES = "Frames";
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319 static const char* const TILE_WIDTH = "TileWidth";
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320 static const char* const TILE_HEIGHT = "TileHeight";
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321 static const char* const TOTAL_WIDTH = "TotalWidth";
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322 static const char* const TOTAL_HEIGHT = "TotalHeight";
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323 static const char* const PHOTOMETRIC_INTERPRETATION = "PhotometricInterpretation";
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324 static const char* const IMAGE_TYPE = "ImageType";
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325
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326
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327 void DicomPyramidInstance::Serialize(std::string& result) const
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328 {
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329 Json::Value frames = Json::arrayValue;
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330 for (size_t i = 0; i < frames_.size(); i++)
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331 {
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332 Json::Value frame = Json::arrayValue;
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333 frame.append(frames_[i].first);
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334 frame.append(frames_[i].second);
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335 frames.append(frame);
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336 }
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337
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338 Json::Value content = Json::objectValue;
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339 content[FRAMES] = frames;
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340
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341 // "instanceId_" is set by the constructor
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342
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343 content[HAS_COMPRESSION] = hasCompression_;
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344 content[IMAGE_COMPRESSION] = static_cast<int>(compression_);
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345 content[PIXEL_FORMAT] = static_cast<int>(format_);
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346 content[TILE_WIDTH] = tileWidth_;
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347 content[TILE_HEIGHT] = tileHeight_;
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348 content[TOTAL_WIDTH] = totalWidth_;
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349 content[TOTAL_HEIGHT] = totalHeight_;
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350 content[PHOTOMETRIC_INTERPRETATION] = Orthanc::EnumerationToString(photometric_);
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351 content[IMAGE_TYPE] = imageType_;
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352
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353 OrthancPlugins::WriteFastJson(result, content);
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354 }
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355
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356
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357 void DicomPyramidInstance::Deserialize(const std::string& s)
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358 {
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359 Json::Value content;
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360 OrthancPlugins::ReadJson(content, s);
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361
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362 if (content.type() != Json::objectValue ||
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363 !content.isMember(FRAMES) ||
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364 content[FRAMES].type() != Json::arrayValue)
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365 {
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366 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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367 }
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368
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369 hasCompression_ = Orthanc::SerializationToolbox::ReadBoolean(content, HAS_COMPRESSION);
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370 compression_ = static_cast<ImageCompression>(Orthanc::SerializationToolbox::ReadInteger(content, IMAGE_COMPRESSION));
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371 format_ = static_cast<Orthanc::PixelFormat>(Orthanc::SerializationToolbox::ReadInteger(content, PIXEL_FORMAT));
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372 tileWidth_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TILE_WIDTH);
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373 tileHeight_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TILE_HEIGHT);
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374 totalWidth_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TOTAL_WIDTH);
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375 totalHeight_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TOTAL_HEIGHT);
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376
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377 std::string p = Orthanc::SerializationToolbox::ReadString(content, PHOTOMETRIC_INTERPRETATION);
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378 photometric_ = Orthanc::StringToPhotometricInterpretation(p.c_str());
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ef3f8c5126a4 Don't display the thumbnail/overview instances in the Web viewer
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379
ef3f8c5126a4 Don't display the thumbnail/overview instances in the Web viewer
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380 imageType_ = Orthanc::SerializationToolbox::ReadString(content, IMAGE_TYPE);
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20bc074ec19a Viewer can display DICOM pyramids whose tile sizes vary across levels
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381
20bc074ec19a Viewer can display DICOM pyramids whose tile sizes vary across levels
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382 const Json::Value f = content[FRAMES];
68
c619c8bd72ed DicomPyramidInstance::Deserialize
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383 frames_.resize(f.size());
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
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384
c619c8bd72ed DicomPyramidInstance::Deserialize
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385 for (Json::Value::ArrayIndex i = 0; i < f.size(); i++)
c619c8bd72ed DicomPyramidInstance::Deserialize
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386 {
c619c8bd72ed DicomPyramidInstance::Deserialize
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387 if (f[i].type() != Json::arrayValue ||
c619c8bd72ed DicomPyramidInstance::Deserialize
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388 f[i].size() != 2 ||
c619c8bd72ed DicomPyramidInstance::Deserialize
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389 f[i][0].type() != Json::intValue ||
c619c8bd72ed DicomPyramidInstance::Deserialize
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390 f[i][1].type() != Json::intValue ||
c619c8bd72ed DicomPyramidInstance::Deserialize
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391 f[i][0].asInt() < 0 ||
c619c8bd72ed DicomPyramidInstance::Deserialize
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392 f[i][1].asInt() < 0)
c619c8bd72ed DicomPyramidInstance::Deserialize
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393 {
c619c8bd72ed DicomPyramidInstance::Deserialize
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394 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
c619c8bd72ed DicomPyramidInstance::Deserialize
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395 }
c619c8bd72ed DicomPyramidInstance::Deserialize
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396
c619c8bd72ed DicomPyramidInstance::Deserialize
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397 frames_[i].first = f[i][0].asInt();
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
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398 frames_[i].second = f[i][1].asInt();
c619c8bd72ed DicomPyramidInstance::Deserialize
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399 }
64
63d0a5c74460 DicomPyramidInstance::Serialize
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400 }
0
4a7a53257c7d initial commit
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401 }