Mercurial > hg > orthanc-wsi

annotate Framework/Inputs/DicomPyramidInstance.cpp @ 68:c619c8bd72ed

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DicomPyramidInstance::Deserialize
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 25 Nov 2016 21:18:46 +0100
parents 63d0a5c74460
children d529d9ce3c7e
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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 void DicomPyramidInstance::Load(OrthancPlugins::IOrthancConnection& orthanc,
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128 const std::string& instanceId)
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129 {
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130 using namespace OrthancPlugins;
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131
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132 DicomDatasetReader reader(new FullOrthancDataset(orthanc, "/instances/" + instanceId + "/tags"));
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133
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134 if (reader.GetMandatoryStringValue(DICOM_TAG_SOP_CLASS_UID) != "1.2.840.10008.5.1.4.1.1.77.1.6" ||
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135 reader.GetMandatoryStringValue(DICOM_TAG_MODALITY) != "SM")
0
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136 {
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137 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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138 }
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139
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140 format_ = DetectPixelFormat(reader);
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141 tileWidth_ = reader.GetUnsignedIntegerValue(DICOM_TAG_COLUMNS);
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142 tileHeight_ = reader.GetUnsignedIntegerValue(DICOM_TAG_ROWS);
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143 totalWidth_ = reader.GetUnsignedIntegerValue(DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS);
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144 totalHeight_ = reader.GetUnsignedIntegerValue(DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS);
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145
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146 size_t countFrames;
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147 if (!reader.GetDataset().GetSequenceSize(countFrames, DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE))
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148 {
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149 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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150 }
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151
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152 if (countFrames != reader.GetUnsignedIntegerValue(DICOM_TAG_NUMBER_OF_FRAMES))
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153 {
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154 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId;
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155 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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156 }
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157
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158 frames_.resize(countFrames);
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159
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160 for (size_t i = 0; i < countFrames; i++)
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161 {
62
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162 int xx = reader.GetIntegerValue(DicomPath(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i,
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163 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0,
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164 DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX));
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165
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166 int yy = reader.GetIntegerValue(DicomPath(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i,
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167 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0,
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168 DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX));
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169
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170 // "-1", because coordinates are shifted by 1 in DICOM
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171 xx -= 1;
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172 yy -= 1;
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173
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174 unsigned int x = static_cast<unsigned int>(xx);
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175 unsigned int y = static_cast<unsigned int>(yy);
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176
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177 if (xx < 0 ||
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178 yy < 0 ||
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179 x % tileWidth_ != 0 ||
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180 y % tileHeight_ != 0 ||
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181 x >= totalWidth_ ||
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182 y >= totalHeight_)
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183 {
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184 LOG(ERROR) << "Frame " << i << " with unexpected tile location ("
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185 << x << "," << y << ") in instance: " << instanceId;
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186 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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187 }
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188
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189 frames_[i].first = x / tileWidth_;
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190 frames_[i].second = y / tileHeight_;
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191 }
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192 }
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193
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194
68
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195 DicomPyramidInstance::DicomPyramidInstance(OrthancPlugins::IOrthancConnection& orthanc,
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196 const std::string& instanceId) :
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197 instanceId_(instanceId),
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198 hasCompression_(false)
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199 {
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200 Load(orthanc, instanceId);
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201 }
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202
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203
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204 unsigned int DicomPyramidInstance::GetFrameLocationX(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].first;
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208 }
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209
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210
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211 unsigned int DicomPyramidInstance::GetFrameLocationY(size_t frame) const
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212 {
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213 assert(frame < frames_.size());
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214 return frames_[frame].second;
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215 }
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216
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217
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218 void DicomPyramidInstance::Serialize(std::string& result) const
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219 {
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220 Json::Value frames = Json::arrayValue;
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221 for (size_t i = 0; i < frames_.size(); i++)
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222 {
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223 Json::Value frame = Json::arrayValue;
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224 frame.append(frames_[i].first);
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225 frame.append(frames_[i].second);
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226
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227 frames.append(frame);
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228 }
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229
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230 Json::Value content;
c619c8bd72ed DicomPyramidInstance::Deserialize
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231 content["Frames"] = frames;
c619c8bd72ed DicomPyramidInstance::Deserialize
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232 content["TileHeight"] = tileHeight_;
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233 content["TileWidth"] = tileWidth_;
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234 content["TotalHeight"] = totalHeight_;
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235 content["TotalWidth"] = totalWidth_;
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236
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diff changeset
237 switch (format_)
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238 {
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239 case Orthanc::PixelFormat_RGB24:
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240 content["PixelFormat"] = 0;
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241 break;
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242
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243 case Orthanc::PixelFormat_Grayscale8:
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244 content["PixelFormat"] = 1;
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245 break;
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246
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247 default:
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248 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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249 }
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250
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251 Json::FastWriter writer;
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252 result = writer.write(content);
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253 }
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254
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255
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256 void DicomPyramidInstance::Deserialize(const std::string& s)
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257 {
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258 hasCompression_ = false;
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259
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260 Json::Value content;
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261 OrthancPlugins::IOrthancConnection::ParseJson(content, s);
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262
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263 if (content.type() != Json::objectValue ||
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264 !content.isMember("Frames") ||
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265 !content.isMember("PixelFormat") ||
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266 !content.isMember("TileHeight") ||
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267 !content.isMember("TileWidth") ||
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268 !content.isMember("TotalHeight") ||
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269 !content.isMember("TotalWidth") ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
270 content["Frames"].type() != Json::arrayValue ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
271 content["PixelFormat"].type() != Json::intValue ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
272 content["TileHeight"].type() != Json::intValue ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
273 content["TileWidth"].type() != Json::intValue ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
274 content["TotalHeight"].type() != Json::intValue ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
275 content["TotalWidth"].type() != Json::intValue ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
276 content["TileHeight"].asInt() < 0 ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
277 content["TileWidth"].asInt() < 0 ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
278 content["TotalHeight"].asInt() < 0 ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
279 content["TotalWidth"].asInt() < 0)
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
280 {
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
281 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
282 }
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
283
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
284 switch (content["Frames"].asInt())
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
285 {
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
286 case 0:
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
287 format_ = Orthanc::PixelFormat_RGB24;
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
288 break;
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
289
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
290 case 1:
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
291 format_ = Orthanc::PixelFormat_Grayscale8;
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
292 break;
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
293
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
294 default:
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
295 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
296 }
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
297
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
298 tileHeight_ = static_cast<unsigned int>(content["TileHeight"].asInt());
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
299 tileWidth_ = static_cast<unsigned int>(content["TileWidth"].asInt());
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
300 totalHeight_ = static_cast<unsigned int>(content["TotalHeight"].asInt());
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
301 totalWidth_ = static_cast<unsigned int>(content["TotalWidth"].asInt());
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
302
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
303 const Json::Value f = content["Frames"];
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
304 frames_.resize(f.size());
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
305
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
306 for (Json::Value::ArrayIndex i = 0; i < f.size(); i++)
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
307 {
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
308 if (f[i].type() != Json::arrayValue ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
309 f[i].size() != 2 ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
310 f[i][0].type() != Json::intValue ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
311 f[i][1].type() != Json::intValue ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
312 f[i][0].asInt() < 0 ||
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
313 f[i][1].asInt() < 0)
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
314 {
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
315 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
316 }
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
317
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
318 frames_[i].first = f[i][0].asInt();
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
319 frames_[i].second = f[i][1].asInt();
c619c8bd72ed DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 64
diff changeset
320 }
64
63d0a5c74460 DicomPyramidInstance::Serialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 62
diff changeset
321 }
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
322 }