Mercurial > hg > orthanc-wsi

annotate Framework/Inputs/DicomPyramidInstance.cpp @ 62:f45cec2c32e2

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Speed-up in the Web viewer plugin
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 25 Nov 2016 18:21:15 +0100
parents 147bd6dc28db
children 63d0a5c74460
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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
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33 namespace OrthancWSI
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34 {
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35 static ImageCompression DetectImageCompression(OrthancPlugins::IOrthancConnection& orthanc,
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36 const std::string& instanceId)
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37 {
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38 using namespace OrthancPlugins;
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39
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40 DicomDatasetReader header(new FullOrthancDataset
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41 (orthanc, "/instances/" + instanceId + "/header"));
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42
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43 std::string s = Orthanc::Toolbox::StripSpaces
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44 (header.GetMandatoryStringValue(DICOM_TAG_TRANSFER_SYNTAX_UID));
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45
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46 if (s == "1.2.840.10008.1.2" ||
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47 s == "1.2.840.10008.1.2.1")
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48 {
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49 return ImageCompression_None;
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50 }
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51 else if (s == "1.2.840.10008.1.2.4.50")
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52 {
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53 return ImageCompression_Jpeg;
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54 }
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55 else if (s == "1.2.840.10008.1.2.4.90" ||
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56 s == "1.2.840.10008.1.2.4.91")
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57 {
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58 return ImageCompression_Jpeg2000;
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59 }
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60 else
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61 {
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62 LOG(ERROR) << "Unsupported transfer syntax: " << s;
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63 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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64 }
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65 }
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66
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67
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68 static Orthanc::PixelFormat DetectPixelFormat(OrthancPlugins::DicomDatasetReader& reader)
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69 {
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70 using namespace OrthancPlugins;
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71
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72 std::string photometric = Orthanc::Toolbox::StripSpaces
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73 (reader.GetMandatoryStringValue(DICOM_TAG_PHOTOMETRIC_INTERPRETATION));
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74
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75 if (photometric == "PALETTE")
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76 {
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77 LOG(ERROR) << "Unsupported photometric interpretation: " << photometric;
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78 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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79 }
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80
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81 unsigned int bitsStored = reader.GetUnsignedIntegerValue(DICOM_TAG_BITS_STORED);
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82 unsigned int samplesPerPixel = reader.GetUnsignedIntegerValue(DICOM_TAG_SAMPLES_PER_PIXEL);
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83 bool isSigned = (reader.GetUnsignedIntegerValue(DICOM_TAG_PIXEL_REPRESENTATION) != 0);
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84
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85 if (bitsStored == 8 &&
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86 samplesPerPixel == 1 &&
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87 !isSigned)
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88 {
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89 return Orthanc::PixelFormat_Grayscale8;
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90 }
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91 else if (bitsStored == 8 &&
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92 samplesPerPixel == 3 &&
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93 !isSigned)
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94 {
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95 return Orthanc::PixelFormat_RGB24;
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96 }
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97 else
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98 {
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99 LOG(ERROR) << "Unsupported pixel format";
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100 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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101 }
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102 }
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103
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104
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105 ImageCompression DicomPyramidInstance::GetImageCompression(OrthancPlugins::IOrthancConnection& orthanc)
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106 {
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107 /**
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108 * Lazy detection of the image compression using the transfer
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109 * syntax stored inside the DICOM header. Given the fact that
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110 * reading the header is a time-consuming operation (it implies
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111 * the decoding of the DICOM image by Orthanc, whereas the "/tags"
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112 * endpoint only reads the "DICOM-as-JSON" attachment), the
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113 * "/header" REST call is delayed until it is really required.
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114 **/
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115
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116 if (!hasCompression_)
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117 {
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118 compression_ = DetectImageCompression(orthanc, instanceId_);
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119 hasCompression_ = true;
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120 }
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121
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122 return compression_;
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123 }
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124
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125
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126 DicomPyramidInstance::DicomPyramidInstance(OrthancPlugins::IOrthancConnection& orthanc,
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127 const std::string& instanceId) :
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128 instanceId_(instanceId),
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129 hasCompression_(false)
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130 {
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131 using namespace OrthancPlugins;
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132
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133 DicomDatasetReader reader(new FullOrthancDataset(orthanc, "/instances/" + instanceId + "/tags"));
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134
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135 if (reader.GetMandatoryStringValue(DICOM_TAG_SOP_CLASS_UID) != "1.2.840.10008.5.1.4.1.1.77.1.6" ||
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136 reader.GetMandatoryStringValue(DICOM_TAG_MODALITY) != "SM")
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137 {
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138 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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139 }
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140
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141 format_ = DetectPixelFormat(reader);
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142 tileWidth_ = reader.GetUnsignedIntegerValue(DICOM_TAG_COLUMNS);
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143 tileHeight_ = reader.GetUnsignedIntegerValue(DICOM_TAG_ROWS);
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144 totalWidth_ = reader.GetUnsignedIntegerValue(DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS);
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145 totalHeight_ = reader.GetUnsignedIntegerValue(DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS);
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146
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147 size_t countFrames;
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148 if (!reader.GetDataset().GetSequenceSize(countFrames, DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE))
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149 {
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150 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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151 }
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152
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153 if (countFrames != reader.GetUnsignedIntegerValue(DICOM_TAG_NUMBER_OF_FRAMES))
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154 {
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155 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId;
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156 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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157 }
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158
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159 frames_.resize(countFrames);
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160
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161 for (size_t i = 0; i < countFrames; i++)
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162 {
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163 int xx = reader.GetIntegerValue(DicomPath(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i,
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164 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0,
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165 DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX));
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166
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167 int yy = reader.GetIntegerValue(DicomPath(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i,
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168 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0,
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169 DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX));
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170
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171 // "-1", because coordinates are shifted by 1 in DICOM
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172 xx -= 1;
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173 yy -= 1;
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174
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175 unsigned int x = static_cast<unsigned int>(xx);
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176 unsigned int y = static_cast<unsigned int>(yy);
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177
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178 if (xx < 0 ||
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179 yy < 0 ||
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180 x % tileWidth_ != 0 ||
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181 y % tileHeight_ != 0 ||
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182 x >= totalWidth_ ||
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183 y >= totalHeight_)
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184 {
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185 LOG(ERROR) << "Frame " << i << " with unexpected tile location ("
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186 << x << "," << y << ") in instance: " << instanceId;
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187 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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188 }
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189
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190 frames_[i].first = x / tileWidth_;
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191 frames_[i].second = y / tileHeight_;
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192 }
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193 }
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194
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195
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196 unsigned int DicomPyramidInstance::GetFrameLocationX(size_t frame) const
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197 {
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198 assert(frame < frames_.size());
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199 return frames_[frame].first;
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200 }
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201
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202
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203 unsigned int DicomPyramidInstance::GetFrameLocationY(size_t frame) const
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204 {
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205 assert(frame < frames_.size());
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206 return frames_[frame].second;
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207 }
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208 }