Mercurial > hg > orthanc

annotate Core/DicomParsing/Internals/DicomFrameIndex.cpp @ 3745:113a7b994a12

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extracting the raw frame in the transcoder
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 12 Mar 2020 21:48:35 +0100
parents 94f4a18a79cc
children
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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 * Copyright (C) 2017-2020 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 General Public License as
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9 * published by the Free Software Foundation, either version 3 of the
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10 * License, or (at your option) any later version.
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11 *
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12 * In addition, as a special exception, the copyright holders of this
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13 * program give permission to link the code of its release with the
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14 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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15 * that use the same license as the "OpenSSL" library), and distribute
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16 * the linked executables. You must obey the GNU General Public License
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17 * in all respects for all of the code used other than "OpenSSL". If you
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18 * modify file(s) with this exception, you may extend this exception to
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19 * your version of the file(s), but you are not obligated to do so. If
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20 * you do not wish to do so, delete this exception statement from your
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21 * version. If you delete this exception statement from all source files
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22 * in the program, then also delete it here.
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23 *
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24 * This program is distributed in the hope that it will be useful, but
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25 * WITHOUT ANY WARRANTY; without even the implied warranty of
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26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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27 * General Public License for more details.
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28 *
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29 * You should have received a copy of the GNU General Public License
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30 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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31 **/
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33
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34 #include "../../PrecompiledHeaders.h"
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35 #include "DicomFrameIndex.h"
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36
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37 #include "../../OrthancException.h"
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38 #include "../../DicomFormat/DicomImageInformation.h"
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39 #include "../FromDcmtkBridge.h"
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40 #include "../../Endianness.h"
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41 #include "DicomImageDecoder.h"
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43 #include <boost/lexical_cast.hpp>
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45 #include <dcmtk/dcmdata/dcdeftag.h>
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46 #include <dcmtk/dcmdata/dcpxitem.h>
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47 #include <dcmtk/dcmdata/dcpixseq.h>
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48
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49 namespace Orthanc
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50 {
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51 class DicomFrameIndex::FragmentIndex : public DicomFrameIndex::IIndex
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52 {
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53 private:
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54 DcmPixelSequence* pixelSequence_;
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55 std::vector<DcmPixelItem*> startFragment_;
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56 std::vector<unsigned int> countFragments_;
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57 std::vector<unsigned int> frameSize_;
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58
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59 void GetOffsetTable(std::vector<uint32_t>& table)
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60 {
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61 DcmPixelItem* item = NULL;
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62 if (!pixelSequence_->getItem(item, 0).good() ||
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63 item == NULL)
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64 {
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65 throw OrthancException(ErrorCode_BadFileFormat);
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66 }
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67
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68 uint32_t length = item->getLength();
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69 if (length == 0)
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70 {
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71 // Degenerate case: Empty offset table means only one frame
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72 // that overlaps all the fragments
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73 table.resize(1);
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74 table[0] = 0;
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75 return;
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76 }
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77
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78 if (length % 4 != 0)
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79 {
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80 // Error: Each fragment is index with 4 bytes (uint32_t)
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81 throw OrthancException(ErrorCode_BadFileFormat);
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82 }
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83
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84 uint8_t* content = NULL;
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85 if (!item->getUint8Array(content).good() ||
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86 content == NULL)
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87 {
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88 throw OrthancException(ErrorCode_InternalError);
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89 }
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90
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91 table.resize(length / 4);
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93 // The offset table is always in little endian in the DICOM
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94 // file. Swap it to host endianness if needed.
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95 const uint32_t* offset = reinterpret_cast<const uint32_t*>(content);
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96 for (size_t i = 0; i < table.size(); i++, offset++)
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97 {
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98 table[i] = le32toh(*offset);
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99 }
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100 }
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101
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102
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103 public:
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104 FragmentIndex(DcmPixelSequence* pixelSequence,
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105 unsigned int countFrames) :
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106 pixelSequence_(pixelSequence)
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107 {
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108 assert(pixelSequence != NULL);
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109
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110 startFragment_.resize(countFrames);
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111 countFragments_.resize(countFrames);
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112 frameSize_.resize(countFrames);
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113
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114 // The first fragment corresponds to the offset table
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115 unsigned int countFragments = static_cast<unsigned int>(pixelSequence_->card());
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116 if (countFragments < countFrames + 1)
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117 {
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118 throw OrthancException(ErrorCode_BadFileFormat);
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119 }
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120
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121 if (countFragments == countFrames + 1)
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122 {
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123 // Simple case: There is one fragment per frame.
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124
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125 DcmObject* fragment = pixelSequence_->nextInContainer(NULL); // Skip the offset table
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126 if (fragment == NULL)
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127 {
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128 throw OrthancException(ErrorCode_InternalError);
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129 }
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130
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131 for (unsigned int i = 0; i < countFrames; i++)
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132 {
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133 fragment = pixelSequence_->nextInContainer(fragment);
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134 startFragment_[i] = dynamic_cast<DcmPixelItem*>(fragment);
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135 frameSize_[i] = fragment->getLength();
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136 countFragments_[i] = 1;
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137 }
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138
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139 return;
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140 }
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141
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142 // Parse the offset table
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143 std::vector<uint32_t> offsetOfFrame;
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144 GetOffsetTable(offsetOfFrame);
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145
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146 if (offsetOfFrame.size() != countFrames ||
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147 offsetOfFrame[0] != 0)
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148 {
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149 throw OrthancException(ErrorCode_BadFileFormat);
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150 }
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151
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152 // Loop over the fragments (ignoring the offset table). This is
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153 // an alternative, faster implementation to DCMTK's
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154 // "DcmCodec::determineStartFragment()".
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155 DcmObject* fragment = pixelSequence_->nextInContainer(NULL);
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156 if (fragment == NULL)
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157 {
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158 throw OrthancException(ErrorCode_InternalError);
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159 }
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160
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161 fragment = pixelSequence_->nextInContainer(fragment); // Skip the offset table
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162 if (fragment == NULL)
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163 {
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164 throw OrthancException(ErrorCode_InternalError);
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165 }
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166
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167 uint32_t offset = 0;
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168 unsigned int currentFrame = 0;
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169 startFragment_[0] = dynamic_cast<DcmPixelItem*>(fragment);
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170
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171 unsigned int currentFragment = 1;
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172 while (fragment != NULL)
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173 {
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174 if (currentFrame + 1 < countFrames &&
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175 offset == offsetOfFrame[currentFrame + 1])
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176 {
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177 currentFrame += 1;
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178 startFragment_[currentFrame] = dynamic_cast<DcmPixelItem*>(fragment);
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179 }
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180
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181 frameSize_[currentFrame] += fragment->getLength();
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182 countFragments_[currentFrame]++;
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183
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184 // 8 bytes = overhead for the item tag and length field
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185 offset += fragment->getLength() + 8;
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186
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187 currentFragment++;
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188 fragment = pixelSequence_->nextInContainer(fragment);
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189 }
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190
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191 if (currentFragment != countFragments ||
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192 currentFrame + 1 != countFrames ||
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193 fragment != NULL)
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194 {
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195 throw OrthancException(ErrorCode_BadFileFormat);
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196 }
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197
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198 assert(startFragment_.size() == countFragments_.size() &&
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199 startFragment_.size() == frameSize_.size());
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200 }
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parents:
diff changeset
201
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parents:
diff changeset
202
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203 virtual void GetRawFrame(std::string& frame,
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204 unsigned int index) const
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205 {
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206 if (index >= startFragment_.size())
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207 {
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208 throw OrthancException(ErrorCode_ParameterOutOfRange);
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209 }
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210
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211 frame.resize(frameSize_[index]);
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212 if (frame.size() == 0)
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213 {
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diff changeset
214 return;
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215 }
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216
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diff changeset
217 uint8_t* target = reinterpret_cast<uint8_t*>(&frame[0]);
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218
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diff changeset
219 size_t offset = 0;
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diff changeset
220 DcmPixelItem* fragment = startFragment_[index];
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parents:
diff changeset
221 for (unsigned int i = 0; i < countFragments_[index]; i++)
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parents:
diff changeset
222 {
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diff changeset
223 uint8_t* content = NULL;
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diff changeset
224 if (!fragment->getUint8Array(content).good() ||
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parents:
diff changeset
225 content == NULL)
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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parents:
diff changeset
226 {
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diff changeset
227 throw OrthancException(ErrorCode_InternalError);
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diff changeset
228 }
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diff changeset
229
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diff changeset
230 assert(offset + fragment->getLength() <= frame.size());
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diff changeset
231
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diff changeset
232 memcpy(target + offset, content, fragment->getLength());
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diff changeset
233 offset += fragment->getLength();
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234
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diff changeset
235 fragment = dynamic_cast<DcmPixelItem*>(pixelSequence_->nextInContainer(fragment));
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diff changeset
236 }
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff changeset
237 }
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diff changeset
238 };
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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parents:
diff changeset
239
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parents:
diff changeset
240
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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parents:
diff changeset
241
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diff changeset
242 class DicomFrameIndex::UncompressedIndex : public DicomFrameIndex::IIndex
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diff changeset
243 {
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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244 private:
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diff changeset
245 uint8_t* pixelData_;
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff changeset
246 size_t frameSize_;
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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247
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diff changeset
248 public:
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diff changeset
249 UncompressedIndex(DcmDataset& dataset,
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250 unsigned int countFrames,
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251 size_t frameSize) :
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diff changeset
252 pixelData_(NULL),
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diff changeset
253 frameSize_(frameSize)
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254 {
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255 size_t size = 0;
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256
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diff changeset
257 DcmElement* e;
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diff changeset
258 if (dataset.findAndGetElement(DCM_PixelData, e).good() &&
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diff changeset
259 e != NULL)
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diff changeset
260 {
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diff changeset
261 size = e->getLength();
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parents:
diff changeset
262
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parents:
diff changeset
263 if (size > 0)
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parents:
diff changeset
264 {
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parents:
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265 pixelData_ = NULL;
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diff changeset
266 if (!e->getUint8Array(pixelData_).good() ||
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parents:
diff changeset
267 pixelData_ == NULL)
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parents:
diff changeset
268 {
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diff changeset
269 throw OrthancException(ErrorCode_BadFileFormat);
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diff changeset
270 }
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parents:
diff changeset
271 }
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parents:
diff changeset
272 }
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parents:
diff changeset
273
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diff changeset
274 if (size < frameSize_ * countFrames)
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diff changeset
275 {
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diff changeset
276 throw OrthancException(ErrorCode_BadFileFormat);
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277 }
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diff changeset
278 }
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parents:
diff changeset
279
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diff changeset
280 virtual void GetRawFrame(std::string& frame,
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diff changeset
281 unsigned int index) const
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diff changeset
282 {
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diff changeset
283 frame.resize(frameSize_);
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diff changeset
284 if (frameSize_ > 0)
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parents:
diff changeset
285 {
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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parents:
diff changeset
286 memcpy(&frame[0], pixelData_ + index * frameSize_, frameSize_);
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diff changeset
287 }
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parents:
diff changeset
288 }
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parents:
diff changeset
289 };
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parents:
diff changeset
290
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
291
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parents:
diff changeset
292 class DicomFrameIndex::PsmctRle1Index : public DicomFrameIndex::IIndex
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
293 {
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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parents:
diff changeset
294 private:
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parents:
diff changeset
295 std::string pixelData_;
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parents:
diff changeset
296 size_t frameSize_;
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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parents:
diff changeset
297
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parents:
diff changeset
298 public:
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parents:
diff changeset
299 PsmctRle1Index(DcmDataset& dataset,
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parents:
diff changeset
300 unsigned int countFrames,
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parents:
diff changeset
301 size_t frameSize) :
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
302 frameSize_(frameSize)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
303 {
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
304 if (!DicomImageDecoder::DecodePsmctRle1(pixelData_, dataset) ||
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
305 pixelData_.size() < frameSize * countFrames)
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
306 {
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
307 throw OrthancException(ErrorCode_BadFileFormat);
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
308 }
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
309 }
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
310
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
311 virtual void GetRawFrame(std::string& frame,
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parents:
diff changeset
312 unsigned int index) const
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parents:
diff changeset
313 {
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parents:
diff changeset
314 frame.resize(frameSize_);
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parents:
diff changeset
315 if (frameSize_ > 0)
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parents:
diff changeset
316 {
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
317 memcpy(&frame[0], reinterpret_cast<const uint8_t*>(&pixelData_[0]) + index * frameSize_, frameSize_);
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff changeset
318 }
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parents:
diff changeset
319 }
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parents:
diff changeset
320 };
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
321
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
322
3745
113a7b994a12 extracting the raw frame in the transcoder
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3640
diff changeset
323 unsigned int DicomFrameIndex::GetFramesCount(DcmDataset& dicom)
1950
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324 {
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325 const char* tmp = NULL;
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326 if (!dicom.findAndGetString(DCM_NumberOfFrames, tmp).good() ||
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327 tmp == NULL)
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328 {
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329 return 1;
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330 }
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331
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332 int count = -1;
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333 try
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334 {
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335 count = boost::lexical_cast<int>(tmp);
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336 }
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337 catch (boost::bad_lexical_cast&)
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338 {
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339 }
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340
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341 if (count < 0)
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342 {
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343 throw OrthancException(ErrorCode_BadFileFormat);
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344 }
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345 else
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346 {
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347 return static_cast<unsigned int>(count);
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348 }
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349 }
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350
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351
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352 DicomFrameIndex::DicomFrameIndex(DcmDataset& dicom)
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353 {
1956
fc16ee04e71b refactoring
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354 countFrames_ = GetFramesCount(dicom);
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355 if (countFrames_ == 0)
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356 {
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357 // The image has no frame. No index is to be built.
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358 return;
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359 }
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360
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361 // Test whether this image is composed of a sequence of fragments
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362 DcmPixelSequence* pixelSequence = FromDcmtkBridge::GetPixelSequence(dicom);
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363 if (pixelSequence != NULL)
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364 {
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365 index_.reset(new FragmentIndex(pixelSequence, countFrames_));
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366 return;
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367 }
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368
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369 // Extract information about the image structure
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370 DicomMap tags;
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371 FromDcmtkBridge::ExtractDicomSummary(tags, dicom);
1924
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372
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373 DicomImageInformation information(tags);
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374
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375 // Access to the raw pixel data
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376 if (DicomImageDecoder::IsPsmctRle1(dicom))
1924
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377 {
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378 index_.reset(new PsmctRle1Index(dicom, countFrames_, information.GetFrameSize()));
1924
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379 }
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380 else
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381 {
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382 index_.reset(new UncompressedIndex(dicom, countFrames_, information.GetFrameSize()));
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383 }
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384 }
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385
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386
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387 void DicomFrameIndex::GetRawFrame(std::string& frame,
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388 unsigned int index) const
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389 {
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390 if (index >= countFrames_)
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391 {
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392 throw OrthancException(ErrorCode_ParameterOutOfRange);
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393 }
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394 else if (index_.get() != NULL)
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395 {
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396 return index_->GetRawFrame(frame, index);
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397 }
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398 else
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parents:
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399 {
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400 frame.clear();
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401 }
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402 }
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403 }