annotate Framework/Inputs/DicomPyramidInstance.cpp @ 239:bab966288abe

sync
author Sebastien Jodogne <s.jodogne@gmail.com>
date Sat, 12 Jun 2021 09:20:44 +0200
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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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1e864138f0da upgrade to year 2021
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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/Stone/DicomDatasetReader.h"
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27 #include "../../Resources/Orthanc/Stone/FullOrthancDataset.h"
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29 #include <Logging.h>
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30 #include <OrthancException.h>
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31 #include <SerializationToolbox.h>
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32 #include <Toolbox.h>
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33
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34 #include <cassert>
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35
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36 #if !ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 9, 0)
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37 # include <json/writer.h>
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38 #endif
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39
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40 #define SERIALIZED_METADATA "4201" // Was "4200" if versions <= 0.7 of this plugin
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43 namespace OrthancWSI
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44 {
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45 static const Orthanc::DicomTag DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX(0x0048, 0x021e);
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46 static const Orthanc::DicomTag DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE(0x5200, 0x9230);
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47 static const Orthanc::DicomTag DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE(0x0048, 0x021a);
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48 static const Orthanc::DicomTag DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX(0x0048, 0x021f);
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49 static const Orthanc::DicomTag DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS(0x0048, 0x0006);
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50 static const Orthanc::DicomTag DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS(0x0048, 0x0007);
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51 static const Orthanc::DicomTag DICOM_TAG_IMAGE_TYPE(0x0008, 0x0008);
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53 static ImageCompression DetectImageCompression(OrthancStone::IOrthancConnection& orthanc,
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54 const std::string& instanceId)
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55 {
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56 using namespace OrthancStone;
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57
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58 FullOrthancDataset dataset(orthanc, "/instances/" + instanceId + "/header");
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59 DicomDatasetReader header(dataset);
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60
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61 std::string s = Orthanc::Toolbox::StripSpaces
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62 (header.GetMandatoryStringValue(Orthanc::DicomPath(Orthanc::DICOM_TAG_TRANSFER_SYNTAX_UID)));
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64 if (s == "1.2.840.10008.1.2" ||
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65 s == "1.2.840.10008.1.2.1")
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66 {
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67 return ImageCompression_None;
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68 }
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69 else if (s == "1.2.840.10008.1.2.4.50")
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70 {
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71 return ImageCompression_Jpeg;
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72 }
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73 else if (s == "1.2.840.10008.1.2.4.90" ||
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74 s == "1.2.840.10008.1.2.4.91")
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75 {
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76 return ImageCompression_Jpeg2000;
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77 }
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78 else
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79 {
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80 LOG(ERROR) << "Unsupported transfer syntax: " << s;
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81 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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82 }
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83 }
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86 static void DetectPixelFormat(Orthanc::PixelFormat& format,
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87 Orthanc::PhotometricInterpretation& photometric,
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88 const OrthancStone::DicomDatasetReader& reader)
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89 {
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90 using namespace OrthancStone;
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91
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92 std::string p = Orthanc::Toolbox::StripSpaces
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93 (reader.GetMandatoryStringValue(Orthanc::DicomPath(Orthanc::DICOM_TAG_PHOTOMETRIC_INTERPRETATION)));
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94
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95 photometric = Orthanc::StringToPhotometricInterpretation(p.c_str());
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96
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97 if (photometric == Orthanc::PhotometricInterpretation_Palette)
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98 {
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99 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented,
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100 "Unsupported photometric interpretation: " + p);
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101 }
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102
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103 unsigned int bitsStored, samplesPerPixel, tmp;
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104
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105 if (!reader.GetUnsignedIntegerValue(bitsStored, Orthanc::DicomPath(Orthanc::DICOM_TAG_BITS_STORED)) ||
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106 !reader.GetUnsignedIntegerValue(samplesPerPixel, Orthanc::DicomPath(Orthanc::DICOM_TAG_SAMPLES_PER_PIXEL)) ||
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107 !reader.GetUnsignedIntegerValue(tmp, Orthanc::DicomPath(Orthanc::DICOM_TAG_PIXEL_REPRESENTATION)))
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108 {
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109 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag);
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110 }
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111
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112 bool isSigned = (tmp != 0);
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113
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114 if (bitsStored == 8 &&
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115 samplesPerPixel == 1 &&
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116 !isSigned)
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117 {
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118 format = Orthanc::PixelFormat_Grayscale8;
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119 }
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120 else if (bitsStored == 8 &&
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121 samplesPerPixel == 3 &&
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122 !isSigned)
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123 {
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124 format = Orthanc::PixelFormat_RGB24;
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125 }
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126 else
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127 {
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128 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "Unsupported pixel format");
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129 }
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130 }
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131
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132
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133 ImageCompression DicomPyramidInstance::GetImageCompression(OrthancStone::IOrthancConnection& orthanc)
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134 {
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135 /**
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136 * Lazy detection of the image compression using the transfer
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137 * syntax stored inside the DICOM header. Given the fact that
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138 * reading the header is a time-consuming operation (it implies
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139 * the decoding of the DICOM image by Orthanc, whereas the "/tags"
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140 * endpoint only reads the "DICOM-as-JSON" attachment), the
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141 * "/header" REST call is delayed until it is really required.
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142 **/
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143
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144 if (!hasCompression_)
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diff changeset
145 {
62
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diff changeset
146 compression_ = DetectImageCompression(orthanc, instanceId_);
56
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147 hasCompression_ = true;
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148 }
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149
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150 return compression_;
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151 }
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152
0
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153
196
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diff changeset
154 void DicomPyramidInstance::Load(OrthancStone::IOrthancConnection& orthanc,
68
c619c8bd72ed DicomPyramidInstance::Deserialize
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155 const std::string& instanceId)
0
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156 {
196
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157 using namespace OrthancStone;
0
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158
87
3d83d34cd4db sync, optimizations
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159 FullOrthancDataset dataset(orthanc, "/instances/" + instanceId + "/tags");
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160 DicomDatasetReader reader(dataset);
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161
239
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diff changeset
162 if (reader.GetMandatoryStringValue(Orthanc::DicomPath(Orthanc::DICOM_TAG_SOP_CLASS_UID)) != "1.2.840.10008.5.1.4.1.1.77.1.6" ||
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163 reader.GetMandatoryStringValue(Orthanc::DicomPath(Orthanc::DICOM_TAG_MODALITY)) != "SM")
0
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164 {
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165 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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166 }
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167
69
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168 hasCompression_ = false;
166
f0dac1e8f736 access to photometric interpretation of source pyramids
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169 DetectPixelFormat(format_, photometric_, reader);
89
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170
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171 unsigned int tmp;
239
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172 if (!reader.GetUnsignedIntegerValue(tileWidth_, Orthanc::DicomPath(Orthanc::DICOM_TAG_COLUMNS)) ||
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173 !reader.GetUnsignedIntegerValue(tileHeight_, Orthanc::DicomPath(Orthanc::DICOM_TAG_ROWS)) ||
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174 !reader.GetUnsignedIntegerValue(totalWidth_, Orthanc::DicomPath(DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS)) ||
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175 !reader.GetUnsignedIntegerValue(totalHeight_, Orthanc::DicomPath(DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS)) ||
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176 !reader.GetUnsignedIntegerValue(tmp, Orthanc::DicomPath(Orthanc::DICOM_TAG_NUMBER_OF_FRAMES)))
89
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177 {
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178 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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179 }
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180
239
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181 imageType_ = reader.GetStringValue(Orthanc::DicomPath(DICOM_TAG_IMAGE_TYPE), "");
219
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182
62
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183 size_t countFrames;
239
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184 if (reader.GetDataset().GetSequenceSize(countFrames, Orthanc::DicomPath(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE)))
0
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185 {
215
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186 if (countFrames != tmp)
89
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diff changeset
187 {
215
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188 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId;
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189 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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190 }
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191
215
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192 frames_.resize(countFrames);
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193
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194 for (size_t i = 0; i < countFrames; i++)
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195 {
239
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196 Orthanc::DicomPath pathX(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i,
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197 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0,
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198 DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX);
215
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199
239
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200 Orthanc::DicomPath pathY(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i,
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201 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0,
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202 DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX);
215
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203
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204 int xx, yy;
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205 if (!reader.GetIntegerValue(xx, pathX) ||
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206 !reader.GetIntegerValue(yy, pathY))
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diff changeset
207 {
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208 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag);
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209 }
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diff changeset
210
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211 // "-1", because coordinates are shifted by 1 in DICOM
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212 xx -= 1;
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213 yy -= 1;
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214
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215 unsigned int x = static_cast<unsigned int>(xx);
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216 unsigned int y = static_cast<unsigned int>(yy);
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diff changeset
217
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diff changeset
218 if (xx < 0 ||
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219 yy < 0 ||
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220 x % tileWidth_ != 0 ||
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diff changeset
221 y % tileHeight_ != 0 ||
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diff changeset
222 x >= totalWidth_ ||
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diff changeset
223 y >= totalHeight_)
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diff changeset
224 {
02cb86d07966 Allow images without "Per frame functional groups sequence" tag (0x5200,0x9230)
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diff changeset
225 LOG(ERROR) << "Frame " << i << " with unexpected tile location ("
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diff changeset
226 << x << "," << y << ") in instance: " << instanceId;
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227 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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diff changeset
228 }
02cb86d07966 Allow images without "Per frame functional groups sequence" tag (0x5200,0x9230)
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diff changeset
229
02cb86d07966 Allow images without "Per frame functional groups sequence" tag (0x5200,0x9230)
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diff changeset
230 frames_[i].first = x / tileWidth_;
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diff changeset
231 frames_[i].second = y / tileHeight_;
02cb86d07966 Allow images without "Per frame functional groups sequence" tag (0x5200,0x9230)
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diff changeset
232 }
02cb86d07966 Allow images without "Per frame functional groups sequence" tag (0x5200,0x9230)
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diff changeset
233 }
02cb86d07966 Allow images without "Per frame functional groups sequence" tag (0x5200,0x9230)
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diff changeset
234 else
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diff changeset
235 {
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diff changeset
236 // No "Per frame functional groups sequence" tag. Assume regular grid.
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diff changeset
237 frames_.resize(tmp);
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diff changeset
238
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diff changeset
239 // Compute "ceiling(totalWidth_ / tileWidth_)
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diff changeset
240 unsigned int w = totalWidth_ / tileWidth_;
02cb86d07966 Allow images without "Per frame functional groups sequence" tag (0x5200,0x9230)
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diff changeset
241 if (totalWidth_ % tileWidth_ != 0)
02cb86d07966 Allow images without "Per frame functional groups sequence" tag (0x5200,0x9230)
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diff changeset
242 {
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diff changeset
243 w += 1;
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diff changeset
244 }
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diff changeset
245
02cb86d07966 Allow images without "Per frame functional groups sequence" tag (0x5200,0x9230)
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diff changeset
246 unsigned int h = totalHeight_ / tileHeight_;
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diff changeset
247 if (totalHeight_ % tileHeight_ != 0)
02cb86d07966 Allow images without "Per frame functional groups sequence" tag (0x5200,0x9230)
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diff changeset
248 {
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249 h += 1;
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diff changeset
250 }
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parents: 214
diff changeset
251
02cb86d07966 Allow images without "Per frame functional groups sequence" tag (0x5200,0x9230)
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diff changeset
252 if (w * h != tmp)
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diff changeset
253 {
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diff changeset
254 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId;
02cb86d07966 Allow images without "Per frame functional groups sequence" tag (0x5200,0x9230)
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diff changeset
255 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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diff changeset
256 }
02cb86d07966 Allow images without "Per frame functional groups sequence" tag (0x5200,0x9230)
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parents: 214
diff changeset
257
02cb86d07966 Allow images without "Per frame functional groups sequence" tag (0x5200,0x9230)
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diff changeset
258 for (size_t i = 0; i < frames_.size(); i++)
02cb86d07966 Allow images without "Per frame functional groups sequence" tag (0x5200,0x9230)
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parents: 214
diff changeset
259 {
02cb86d07966 Allow images without "Per frame functional groups sequence" tag (0x5200,0x9230)
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260 frames_[i].first = i % w;
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261 frames_[i].second = i / w;
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262 }
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263 }
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264 }
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265
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266
196
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267 DicomPyramidInstance::DicomPyramidInstance(OrthancStone::IOrthancConnection& orthanc,
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268 const std::string& instanceId,
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269 bool useCache) :
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270 instanceId_(instanceId),
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271 hasCompression_(false),
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272 compression_(ImageCompression_None) // Dummy initialization for serialization
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273 {
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274 if (useCache)
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275 {
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276 try
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277 {
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278 // Try and deserialized the cached information about this instance
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279 std::string serialized;
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280 orthanc.RestApiGet(serialized, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA);
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281 Deserialize(serialized);
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282 return; // Success
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283 }
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284 catch (Orthanc::OrthancException&)
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285 {
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286 // No cached information yet
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287 }
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288 }
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289
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290 // Compute information about this instance from scratch
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291 Load(orthanc, instanceId);
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292
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293 if (useCache)
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294 {
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295 // Serialize the computed information and cache it as a metadata
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296 std::string serialized, tmp;
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297 Serialize(serialized);
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298 orthanc.RestApiPut(tmp, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA, serialized);
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299 }
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300 }
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301
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302
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303 unsigned int DicomPyramidInstance::GetFrameLocationX(size_t frame) const
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304 {
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305 assert(frame < frames_.size());
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306 return frames_[frame].first;
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307 }
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308
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309
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310 unsigned int DicomPyramidInstance::GetFrameLocationY(size_t frame) const
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311 {
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312 assert(frame < frames_.size());
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313 return frames_[frame].second;
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314 }
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315
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316
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317
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318 static const char* const HAS_COMPRESSION = "HasCompression";
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319 static const char* const IMAGE_COMPRESSION = "ImageCompression";
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320 static const char* const PIXEL_FORMAT = "PixelFormat";
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321 static const char* const FRAMES = "Frames";
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322 static const char* const TILE_WIDTH = "TileWidth";
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323 static const char* const TILE_HEIGHT = "TileHeight";
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324 static const char* const TOTAL_WIDTH = "TotalWidth";
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325 static const char* const TOTAL_HEIGHT = "TotalHeight";
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326 static const char* const PHOTOMETRIC_INTERPRETATION = "PhotometricInterpretation";
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327 static const char* const IMAGE_TYPE = "ImageType";
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328
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329
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330 void DicomPyramidInstance::Serialize(std::string& result) const
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331 {
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332 Json::Value frames = Json::arrayValue;
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333 for (size_t i = 0; i < frames_.size(); i++)
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334 {
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335 Json::Value frame = Json::arrayValue;
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336 frame.append(frames_[i].first);
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337 frame.append(frames_[i].second);
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338 frames.append(frame);
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339 }
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340
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341 Json::Value content = Json::objectValue;
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342 content[FRAMES] = frames;
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343
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344 // "instanceId_" is set by the constructor
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345
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346 content[HAS_COMPRESSION] = hasCompression_;
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347 content[IMAGE_COMPRESSION] = static_cast<int>(compression_);
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348 content[PIXEL_FORMAT] = static_cast<int>(format_);
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349 content[TILE_WIDTH] = tileWidth_;
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350 content[TILE_HEIGHT] = tileHeight_;
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351 content[TOTAL_WIDTH] = totalWidth_;
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352 content[TOTAL_HEIGHT] = totalHeight_;
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353 content[PHOTOMETRIC_INTERPRETATION] = Orthanc::EnumerationToString(photometric_);
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354 content[IMAGE_TYPE] = imageType_;
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355
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356 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 9, 0)
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357 Orthanc::Toolbox::WriteFastJson(result, content);
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358 #else
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359 Json::FastWriter writer;
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360 result = writer.write(content);
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361 #endif
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362 }
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363
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364
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365 void DicomPyramidInstance::Deserialize(const std::string& s)
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366 {
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367 Json::Value content;
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368 OrthancStone::IOrthancConnection::ParseJson(content, s);
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369
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370 if (content.type() != Json::objectValue ||
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371 !content.isMember(FRAMES) ||
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372 content[FRAMES].type() != Json::arrayValue)
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373 {
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374 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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375 }
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376
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377 hasCompression_ = Orthanc::SerializationToolbox::ReadBoolean(content, HAS_COMPRESSION);
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378 compression_ = static_cast<ImageCompression>(Orthanc::SerializationToolbox::ReadInteger(content, IMAGE_COMPRESSION));
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379 format_ = static_cast<Orthanc::PixelFormat>(Orthanc::SerializationToolbox::ReadInteger(content, PIXEL_FORMAT));
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380 tileWidth_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TILE_WIDTH);
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381 tileHeight_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TILE_HEIGHT);
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382 totalWidth_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TOTAL_WIDTH);
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383 totalHeight_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TOTAL_HEIGHT);
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384
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385 std::string p = Orthanc::SerializationToolbox::ReadString(content, PHOTOMETRIC_INTERPRETATION);
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386 photometric_ = Orthanc::StringToPhotometricInterpretation(p.c_str());
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387
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388 imageType_ = Orthanc::SerializationToolbox::ReadString(content, IMAGE_TYPE);
217
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389
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390 const Json::Value f = content[FRAMES];
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391 frames_.resize(f.size());
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392
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393 for (Json::Value::ArrayIndex i = 0; i < f.size(); i++)
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394 {
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395 if (f[i].type() != Json::arrayValue ||
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396 f[i].size() != 2 ||
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397 f[i][0].type() != Json::intValue ||
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398 f[i][1].type() != Json::intValue ||
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399 f[i][0].asInt() < 0 ||
c619c8bd72ed DicomPyramidInstance::Deserialize
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400 f[i][1].asInt() < 0)
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401 {
c619c8bd72ed DicomPyramidInstance::Deserialize
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402 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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403 }
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404
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405 frames_[i].first = f[i][0].asInt();
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406 frames_[i].second = f[i][1].asInt();
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407 }
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408 }
0
4a7a53257c7d initial commit
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409 }