Mercurial > hg > orthanc-wsi

annotate Framework/Inputs/DicomPyramidInstance.cpp @ 217:20bc074ec19a

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Viewer can display DICOM pyramids whose tile sizes vary across levels
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 12 Jan 2021 14:24:18 +0100
parents c35a3a0627b9
children ef3f8c5126a4
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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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21
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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 #define SERIALIZED_METADATA "4201" // Was "4200" if versions <= 0.7 of this plugin
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39 namespace OrthancWSI
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40 {
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41 static const Orthanc::DicomTag DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX(0x0048, 0x021e);
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42 static const Orthanc::DicomTag DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE(0x5200, 0x9230);
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43 static const Orthanc::DicomTag DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE(0x0048, 0x021a);
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44 static const Orthanc::DicomTag DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX(0x0048, 0x021f);
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45 static const Orthanc::DicomTag DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS(0x0048, 0x0006);
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46 static const Orthanc::DicomTag DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS(0x0048, 0x0007);
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47
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48 static ImageCompression DetectImageCompression(OrthancStone::IOrthancConnection& orthanc,
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49 const std::string& instanceId)
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50 {
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51 using namespace OrthancStone;
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52
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53 FullOrthancDataset dataset(orthanc, "/instances/" + instanceId + "/header");
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54 DicomDatasetReader header(dataset);
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56 std::string s = Orthanc::Toolbox::StripSpaces
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57 (header.GetMandatoryStringValue(OrthancStone::DicomPath(Orthanc::DICOM_TAG_TRANSFER_SYNTAX_UID)));
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58
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59 if (s == "1.2.840.10008.1.2" ||
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60 s == "1.2.840.10008.1.2.1")
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61 {
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62 return ImageCompression_None;
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63 }
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64 else if (s == "1.2.840.10008.1.2.4.50")
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65 {
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66 return ImageCompression_Jpeg;
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67 }
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68 else if (s == "1.2.840.10008.1.2.4.90" ||
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69 s == "1.2.840.10008.1.2.4.91")
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70 {
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71 return ImageCompression_Jpeg2000;
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72 }
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73 else
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74 {
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75 LOG(ERROR) << "Unsupported transfer syntax: " << s;
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76 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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77 }
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78 }
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81 static void DetectPixelFormat(Orthanc::PixelFormat& format,
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82 Orthanc::PhotometricInterpretation& photometric,
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83 const OrthancStone::DicomDatasetReader& reader)
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84 {
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85 using namespace OrthancStone;
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87 std::string p = Orthanc::Toolbox::StripSpaces
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88 (reader.GetMandatoryStringValue(OrthancStone::DicomPath(Orthanc::DICOM_TAG_PHOTOMETRIC_INTERPRETATION)));
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89
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90 photometric = Orthanc::StringToPhotometricInterpretation(p.c_str());
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92 if (photometric == Orthanc::PhotometricInterpretation_Palette)
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93 {
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94 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented,
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95 "Unsupported photometric interpretation: " + p);
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96 }
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97
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98 unsigned int bitsStored, samplesPerPixel, tmp;
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99
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100 if (!reader.GetUnsignedIntegerValue(bitsStored, OrthancStone::DicomPath(Orthanc::DICOM_TAG_BITS_STORED)) ||
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101 !reader.GetUnsignedIntegerValue(samplesPerPixel, OrthancStone::DicomPath(Orthanc::DICOM_TAG_SAMPLES_PER_PIXEL)) ||
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102 !reader.GetUnsignedIntegerValue(tmp, OrthancStone::DicomPath(Orthanc::DICOM_TAG_PIXEL_REPRESENTATION)))
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103 {
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104 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag);
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105 }
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106
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107 bool isSigned = (tmp != 0);
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108
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109 if (bitsStored == 8 &&
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110 samplesPerPixel == 1 &&
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111 !isSigned)
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112 {
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113 format = Orthanc::PixelFormat_Grayscale8;
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114 }
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115 else if (bitsStored == 8 &&
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116 samplesPerPixel == 3 &&
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117 !isSigned)
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118 {
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119 format = Orthanc::PixelFormat_RGB24;
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120 }
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121 else
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122 {
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123 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "Unsupported pixel format");
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124 }
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125 }
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128 ImageCompression DicomPyramidInstance::GetImageCompression(OrthancStone::IOrthancConnection& orthanc)
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129 {
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130 /**
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131 * Lazy detection of the image compression using the transfer
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132 * syntax stored inside the DICOM header. Given the fact that
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133 * reading the header is a time-consuming operation (it implies
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134 * the decoding of the DICOM image by Orthanc, whereas the "/tags"
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135 * endpoint only reads the "DICOM-as-JSON" attachment), the
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136 * "/header" REST call is delayed until it is really required.
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137 **/
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138
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139 if (!hasCompression_)
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140 {
62
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141 compression_ = DetectImageCompression(orthanc, instanceId_);
56
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142 hasCompression_ = true;
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143 }
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144
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145 return compression_;
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146 }
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147
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148
196
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149 void DicomPyramidInstance::Load(OrthancStone::IOrthancConnection& orthanc,
68
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150 const std::string& instanceId)
0
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151 {
196
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152 using namespace OrthancStone;
0
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153
87
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154 FullOrthancDataset dataset(orthanc, "/instances/" + instanceId + "/tags");
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155 DicomDatasetReader reader(dataset);
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156
213
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157 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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158 reader.GetMandatoryStringValue(OrthancStone::DicomPath(Orthanc::DICOM_TAG_MODALITY)) != "SM")
0
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159 {
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160 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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161 }
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162
69
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163 hasCompression_ = false;
166
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164 DetectPixelFormat(format_, photometric_, reader);
89
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165
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166 unsigned int tmp;
213
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167 if (!reader.GetUnsignedIntegerValue(tileWidth_, OrthancStone::DicomPath(Orthanc::DICOM_TAG_COLUMNS)) ||
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168 !reader.GetUnsignedIntegerValue(tileHeight_, OrthancStone::DicomPath(Orthanc::DICOM_TAG_ROWS)) ||
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169 !reader.GetUnsignedIntegerValue(totalWidth_, OrthancStone::DicomPath(DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS)) ||
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170 !reader.GetUnsignedIntegerValue(totalHeight_, OrthancStone::DicomPath(DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS)) ||
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171 !reader.GetUnsignedIntegerValue(tmp, OrthancStone::DicomPath(Orthanc::DICOM_TAG_NUMBER_OF_FRAMES)))
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172 {
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173 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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174 }
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175
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176 size_t countFrames;
215
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177 if (reader.GetDataset().GetSequenceSize(countFrames, OrthancStone::DicomPath(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE)))
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178 {
215
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179 if (countFrames != tmp)
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180 {
215
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181 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId;
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182 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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183 }
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184
215
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185 frames_.resize(countFrames);
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186
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187 for (size_t i = 0; i < countFrames; i++)
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188 {
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189 DicomPath pathX(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i,
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190 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0,
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191 DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX);
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192
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193 DicomPath pathY(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_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX);
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196
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197 int xx, yy;
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198 if (!reader.GetIntegerValue(xx, pathX) ||
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199 !reader.GetIntegerValue(yy, pathY))
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200 {
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201 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag);
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202 }
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203
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204 // "-1", because coordinates are shifted by 1 in DICOM
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205 xx -= 1;
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206 yy -= 1;
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207
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208 unsigned int x = static_cast<unsigned int>(xx);
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209 unsigned int y = static_cast<unsigned int>(yy);
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210
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211 if (xx < 0 ||
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212 yy < 0 ||
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213 x % tileWidth_ != 0 ||
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214 y % tileHeight_ != 0 ||
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215 x >= totalWidth_ ||
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216 y >= totalHeight_)
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217 {
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218 LOG(ERROR) << "Frame " << i << " with unexpected tile location ("
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219 << x << "," << y << ") in instance: " << instanceId;
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220 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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221 }
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222
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223 frames_[i].first = x / tileWidth_;
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224 frames_[i].second = y / tileHeight_;
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225 }
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226 }
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227 else
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228 {
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229 // No "Per frame functional groups sequence" tag. Assume regular grid.
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230 frames_.resize(tmp);
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231
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232 // Compute "ceiling(totalWidth_ / tileWidth_)
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233 unsigned int w = totalWidth_ / tileWidth_;
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234 if (totalWidth_ % tileWidth_ != 0)
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235 {
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236 w += 1;
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237 }
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238
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239 unsigned int h = totalHeight_ / tileHeight_;
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240 if (totalHeight_ % tileHeight_ != 0)
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diff changeset
241 {
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242 h += 1;
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243 }
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diff changeset
244
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245 if (w * h != tmp)
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diff changeset
246 {
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247 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId;
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248 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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249 }
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diff changeset
250
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diff changeset
251 for (size_t i = 0; i < frames_.size(); i++)
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252 {
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253 frames_[i].first = i % w;
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254 frames_[i].second = i / w;
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255 }
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256 }
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257 }
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258
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259
196
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260 DicomPyramidInstance::DicomPyramidInstance(OrthancStone::IOrthancConnection& orthanc,
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261 const std::string& instanceId,
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262 bool useCache) :
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263 instanceId_(instanceId),
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264 hasCompression_(false),
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265 compression_(ImageCompression_None) // Dummy initialization for serialization
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266 {
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267 if (useCache)
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268 {
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269 try
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270 {
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271 // Try and deserialized the cached information about this instance
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272 std::string serialized;
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273 orthanc.RestApiGet(serialized, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA);
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274 std::cout << serialized;
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275 Deserialize(serialized);
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276 return; // Success
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277 }
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278 catch (Orthanc::OrthancException&)
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279 {
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280 // No cached information yet
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281 }
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282 }
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283
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284 // Compute information about this instance from scratch
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285 Load(orthanc, instanceId);
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286
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287 if (useCache)
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288 {
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289 // Serialize the computed information and cache it as a metadata
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290 std::string serialized, tmp;
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291 Serialize(serialized);
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292 orthanc.RestApiPut(tmp, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA, serialized);
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293 }
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294 }
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295
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296
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297 unsigned int DicomPyramidInstance::GetFrameLocationX(size_t frame) const
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298 {
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299 assert(frame < frames_.size());
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300 return frames_[frame].first;
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301 }
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302
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303
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304 unsigned int DicomPyramidInstance::GetFrameLocationY(size_t frame) const
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305 {
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306 assert(frame < frames_.size());
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307 return frames_[frame].second;
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308 }
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309
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310
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311
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312 static const char* const HAS_COMPRESSION = "HasCompression";
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313 static const char* const IMAGE_COMPRESSION = "ImageCompression";
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314 static const char* const PIXEL_FORMAT = "PixelFormat";
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315 static const char* const FRAMES = "Frames";
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316 static const char* const TILE_WIDTH = "TileWidth";
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317 static const char* const TILE_HEIGHT = "TileHeight";
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318 static const char* const TOTAL_WIDTH = "TotalWidth";
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319 static const char* const TOTAL_HEIGHT = "TotalHeight";
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320 static const char* const PHOTOMETRIC_INTERPRETATION = "PhotometricInterpretation";
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321
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322
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323 void DicomPyramidInstance::Serialize(std::string& result) const
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324 {
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325 Json::Value frames = Json::arrayValue;
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326 for (size_t i = 0; i < frames_.size(); i++)
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327 {
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328 Json::Value frame = Json::arrayValue;
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329 frame.append(frames_[i].first);
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330 frame.append(frames_[i].second);
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331 frames.append(frame);
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332 }
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333
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334 Json::Value content = Json::objectValue;
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335 content[FRAMES] = frames;
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336
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337 // "instanceId_" is set by the constructor
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338
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339 content[HAS_COMPRESSION] = hasCompression_;
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340 content[IMAGE_COMPRESSION] = static_cast<int>(compression_);
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341 content[PIXEL_FORMAT] = static_cast<int>(format_);
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342 content[TILE_WIDTH] = tileWidth_;
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343 content[TILE_HEIGHT] = tileHeight_;
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344 content[TOTAL_WIDTH] = totalWidth_;
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345 content[TOTAL_HEIGHT] = totalHeight_;
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346 content[PHOTOMETRIC_INTERPRETATION] = Orthanc::EnumerationToString(photometric_);
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347
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348 Orthanc::Toolbox::WriteFastJson(result, content);
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349 }
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350
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351
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352 void DicomPyramidInstance::Deserialize(const std::string& s)
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353 {
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354 Json::Value content;
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355 Orthanc::Toolbox::ReadJson(content, s);
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356
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357 if (content.type() != Json::objectValue ||
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358 !content.isMember(FRAMES) ||
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359 content[FRAMES].type() != Json::arrayValue)
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360 {
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361 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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362 }
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363
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364 hasCompression_ = Orthanc::SerializationToolbox::ReadBoolean(content, HAS_COMPRESSION);
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365 compression_ = static_cast<ImageCompression>(Orthanc::SerializationToolbox::ReadInteger(content, IMAGE_COMPRESSION));
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366 format_ = static_cast<Orthanc::PixelFormat>(Orthanc::SerializationToolbox::ReadInteger(content, PIXEL_FORMAT));
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367 tileWidth_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TILE_WIDTH);
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368 tileHeight_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TILE_HEIGHT);
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369 totalWidth_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TOTAL_WIDTH);
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370 totalHeight_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TOTAL_HEIGHT);
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371
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372 std::string p = Orthanc::SerializationToolbox::ReadString(content, PHOTOMETRIC_INTERPRETATION);
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373 photometric_ = Orthanc::StringToPhotometricInterpretation(p.c_str());
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374
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375 const Json::Value f = content[FRAMES];
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376 frames_.resize(f.size());
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377
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378 for (Json::Value::ArrayIndex i = 0; i < f.size(); i++)
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parents: 64
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379 {
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
380 if (f[i].type() != Json::arrayValue ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
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381 f[i].size() != 2 ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
382 f[i][0].type() != Json::intValue ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
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383 f[i][1].type() != Json::intValue ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
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384 f[i][0].asInt() < 0 ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
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385 f[i][1].asInt() < 0)
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
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386 {
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
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387 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
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388 }
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
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389
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
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390 frames_[i].first = f[i][0].asInt();
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
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391 frames_[i].second = f[i][1].asInt();
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
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392 }
64
63d0a5c74460 DicomPyramidInstance::Serialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 62
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393 }
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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394 }