Mercurial > hg > orthanc-wsi

annotate Framework/Inputs/DicomPyramidInstance.cpp @ 64:63d0a5c74460

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DicomPyramidInstance::Serialize
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 25 Nov 2016 18:34:17 +0100
parents f45cec2c32e2
children c619c8bd72ed
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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 *
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6 * This program is free software: you can redistribute it and/or
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7 * modify it under the terms of the GNU Affero General Public License
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8 * as published by the Free Software Foundation, either version 3 of
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9 * the License, or (at your option) any later version.
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10 *
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11 * This program is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty of
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13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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14 * Affero General Public License for more details.
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15 *
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16 * You should have received a copy of the GNU Affero General Public License
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17 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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18 **/
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19
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20
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21 #include "../PrecompiledHeadersWSI.h"
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22 #include "DicomPyramidInstance.h"
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23
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24 #include "../../Resources/Orthanc/Core/Logging.h"
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25 #include "../../Resources/Orthanc/Core/OrthancException.h"
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26 #include "../../Resources/Orthanc/Core/Toolbox.h"
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27 #include "../../Resources/Orthanc/Plugins/Samples/Common/DicomDatasetReader.h"
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28 #include "../../Resources/Orthanc/Plugins/Samples/Common/FullOrthancDataset.h"
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29 #include "../DicomToolbox.h"
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30
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31 #include <cassert>
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32 #include <json/writer.h>
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33
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34 namespace OrthancWSI
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35 {
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36 static ImageCompression DetectImageCompression(OrthancPlugins::IOrthancConnection& orthanc,
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37 const std::string& instanceId)
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38 {
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39 using namespace OrthancPlugins;
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40
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41 DicomDatasetReader header(new FullOrthancDataset
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42 (orthanc, "/instances/" + instanceId + "/header"));
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43
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44 std::string s = Orthanc::Toolbox::StripSpaces
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45 (header.GetMandatoryStringValue(DICOM_TAG_TRANSFER_SYNTAX_UID));
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46
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47 if (s == "1.2.840.10008.1.2" ||
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48 s == "1.2.840.10008.1.2.1")
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49 {
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50 return ImageCompression_None;
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51 }
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52 else if (s == "1.2.840.10008.1.2.4.50")
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53 {
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54 return ImageCompression_Jpeg;
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55 }
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56 else if (s == "1.2.840.10008.1.2.4.90" ||
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57 s == "1.2.840.10008.1.2.4.91")
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58 {
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59 return ImageCompression_Jpeg2000;
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60 }
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61 else
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62 {
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63 LOG(ERROR) << "Unsupported transfer syntax: " << s;
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64 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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65 }
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66 }
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68
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69 static Orthanc::PixelFormat DetectPixelFormat(OrthancPlugins::DicomDatasetReader& reader)
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70 {
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71 using namespace OrthancPlugins;
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72
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73 std::string photometric = Orthanc::Toolbox::StripSpaces
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74 (reader.GetMandatoryStringValue(DICOM_TAG_PHOTOMETRIC_INTERPRETATION));
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75
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76 if (photometric == "PALETTE")
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77 {
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78 LOG(ERROR) << "Unsupported photometric interpretation: " << photometric;
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79 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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80 }
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81
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82 unsigned int bitsStored = reader.GetUnsignedIntegerValue(DICOM_TAG_BITS_STORED);
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83 unsigned int samplesPerPixel = reader.GetUnsignedIntegerValue(DICOM_TAG_SAMPLES_PER_PIXEL);
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84 bool isSigned = (reader.GetUnsignedIntegerValue(DICOM_TAG_PIXEL_REPRESENTATION) != 0);
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85
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86 if (bitsStored == 8 &&
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87 samplesPerPixel == 1 &&
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88 !isSigned)
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89 {
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90 return Orthanc::PixelFormat_Grayscale8;
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91 }
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92 else if (bitsStored == 8 &&
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93 samplesPerPixel == 3 &&
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94 !isSigned)
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95 {
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96 return Orthanc::PixelFormat_RGB24;
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97 }
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98 else
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99 {
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100 LOG(ERROR) << "Unsupported pixel format";
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101 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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102 }
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103 }
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104
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105
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106 ImageCompression DicomPyramidInstance::GetImageCompression(OrthancPlugins::IOrthancConnection& orthanc)
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107 {
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108 /**
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109 * Lazy detection of the image compression using the transfer
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110 * syntax stored inside the DICOM header. Given the fact that
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111 * reading the header is a time-consuming operation (it implies
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112 * the decoding of the DICOM image by Orthanc, whereas the "/tags"
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113 * endpoint only reads the "DICOM-as-JSON" attachment), the
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114 * "/header" REST call is delayed until it is really required.
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115 **/
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116
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117 if (!hasCompression_)
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118 {
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119 compression_ = DetectImageCompression(orthanc, instanceId_);
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120 hasCompression_ = true;
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121 }
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122
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123 return compression_;
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124 }
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125
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126
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127 DicomPyramidInstance::DicomPyramidInstance(OrthancPlugins::IOrthancConnection& orthanc,
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128 const std::string& instanceId) :
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129 instanceId_(instanceId),
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130 hasCompression_(false)
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131 {
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132 using namespace OrthancPlugins;
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133
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134 DicomDatasetReader reader(new FullOrthancDataset(orthanc, "/instances/" + instanceId + "/tags"));
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135
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136 if (reader.GetMandatoryStringValue(DICOM_TAG_SOP_CLASS_UID) != "1.2.840.10008.5.1.4.1.1.77.1.6" ||
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137 reader.GetMandatoryStringValue(DICOM_TAG_MODALITY) != "SM")
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138 {
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139 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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140 }
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141
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142 format_ = DetectPixelFormat(reader);
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143 tileWidth_ = reader.GetUnsignedIntegerValue(DICOM_TAG_COLUMNS);
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144 tileHeight_ = reader.GetUnsignedIntegerValue(DICOM_TAG_ROWS);
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145 totalWidth_ = reader.GetUnsignedIntegerValue(DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS);
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146 totalHeight_ = reader.GetUnsignedIntegerValue(DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS);
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147
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148 size_t countFrames;
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149 if (!reader.GetDataset().GetSequenceSize(countFrames, DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE))
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150 {
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151 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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152 }
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153
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154 if (countFrames != reader.GetUnsignedIntegerValue(DICOM_TAG_NUMBER_OF_FRAMES))
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155 {
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156 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId;
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157 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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158 }
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159
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160 frames_.resize(countFrames);
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161
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162 for (size_t i = 0; i < countFrames; i++)
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163 {
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164 int xx = reader.GetIntegerValue(DicomPath(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i,
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165 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0,
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166 DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX));
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167
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168 int yy = reader.GetIntegerValue(DicomPath(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i,
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169 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0,
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170 DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX));
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171
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172 // "-1", because coordinates are shifted by 1 in DICOM
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173 xx -= 1;
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174 yy -= 1;
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175
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176 unsigned int x = static_cast<unsigned int>(xx);
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177 unsigned int y = static_cast<unsigned int>(yy);
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178
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179 if (xx < 0 ||
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180 yy < 0 ||
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181 x % tileWidth_ != 0 ||
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182 y % tileHeight_ != 0 ||
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183 x >= totalWidth_ ||
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184 y >= totalHeight_)
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185 {
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186 LOG(ERROR) << "Frame " << i << " with unexpected tile location ("
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187 << x << "," << y << ") in instance: " << instanceId;
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188 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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189 }
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190
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191 frames_[i].first = x / tileWidth_;
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192 frames_[i].second = y / tileHeight_;
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193 }
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194 }
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195
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196
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197 unsigned int DicomPyramidInstance::GetFrameLocationX(size_t frame) const
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198 {
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199 assert(frame < frames_.size());
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200 return frames_[frame].first;
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201 }
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202
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203
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204 unsigned int DicomPyramidInstance::GetFrameLocationY(size_t frame) const
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205 {
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206 assert(frame < frames_.size());
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207 return frames_[frame].second;
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208 }
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209
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210
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211 void DicomPyramidInstance::Serialize(std::string& result) const
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212 {
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213 Json::Value frames = Json::arrayValue;
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214 for (size_t i = 0; i < frames_.size(); i++)
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215 {
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216 Json::Value frame = Json::arrayValue;
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217 frame.append(frames_[i].first);
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218 frame.append(frames_[i].second);
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219
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220 frames.append(frame);
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221 }
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222
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223 Json::Value value;
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224 value["PixelFormat"] = Orthanc::EnumerationToString(format_);
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225 value["TileHeight"] = tileHeight_;
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226 value["TileWidth"] = tileWidth_;
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227 value["TotalHeight"] = totalHeight_;
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228 value["TotalWidth"] = totalWidth_;
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229 value["Frames"] = frames;
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230
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231 Json::FastWriter writer;
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232 result = writer.write(value);
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233 }
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234 }