Mercurial > hg > orthanc

annotate OrthancFramework/Sources/DicomParsing/Internals/DicomFrameIndex.cpp @ 4844:55e8fb8e8028

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tagging a pre-release of the Orthanc framework for WSI 1.1
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 07 Dec 2021 14:01:17 +0100
parents 7053502fbf97
children 43e613a7756b
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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) 2017-2021 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2021 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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7 *
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8 * This program is free software: you can redistribute it and/or
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9 * modify it under the terms of the GNU Lesser General Public License
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10 * as published by the Free Software Foundation, either version 3 of
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11 * the License, or (at your option) any later version.
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12 *
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13 * This program is distributed in the hope that it will be useful, but
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 * Lesser General Public License for more details.
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17 *
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18 * You should have received a copy of the GNU Lesser General Public
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19 * License along with this program. If not, see
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20 * <http://www.gnu.org/licenses/>.
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21 **/
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24 #include "../../PrecompiledHeaders.h"
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25 #include "DicomFrameIndex.h"
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27 #include "../../OrthancException.h"
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28 #include "../../DicomFormat/DicomImageInformation.h"
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29 #include "../FromDcmtkBridge.h"
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30 #include "../../Endianness.h"
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31 #include "DicomImageDecoder.h"
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33 #include <boost/lexical_cast.hpp>
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35 #include <dcmtk/dcmdata/dcdeftag.h>
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36 #include <dcmtk/dcmdata/dcpxitem.h>
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37 #include <dcmtk/dcmdata/dcpixseq.h>
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39 namespace Orthanc
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40 {
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41 class DicomFrameIndex::FragmentIndex : public DicomFrameIndex::IIndex
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42 {
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43 private:
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44 DcmPixelSequence* pixelSequence_;
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45 std::vector<DcmPixelItem*> startFragment_;
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46 std::vector<unsigned int> countFragments_;
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47 std::vector<unsigned int> frameSize_;
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49 void GetOffsetTable(std::vector<uint32_t>& table)
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50 {
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51 DcmPixelItem* item = NULL;
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52 if (!pixelSequence_->getItem(item, 0).good() ||
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53 item == NULL)
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54 {
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55 throw OrthancException(ErrorCode_BadFileFormat);
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56 }
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58 uint32_t length = item->getLength();
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59 if (length == 0)
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60 {
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61 // Degenerate case: Empty offset table means only one frame
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62 // that overlaps all the fragments
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63 table.resize(1);
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64 table[0] = 0;
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65 return;
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66 }
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67
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68 if (length % 4 != 0)
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69 {
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70 // Error: Each fragment is index with 4 bytes (uint32_t)
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71 throw OrthancException(ErrorCode_BadFileFormat);
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72 }
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74 uint8_t* content = NULL;
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75 if (!item->getUint8Array(content).good() ||
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76 content == NULL)
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77 {
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78 throw OrthancException(ErrorCode_InternalError);
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79 }
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81 table.resize(length / 4);
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83 // The offset table is always in little endian in the DICOM
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84 // file. Swap it to host endianness if needed.
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85 const uint32_t* offset = reinterpret_cast<const uint32_t*>(content);
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86 for (size_t i = 0; i < table.size(); i++, offset++)
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87 {
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88 table[i] = le32toh(*offset);
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89 }
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90 }
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93 public:
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94 FragmentIndex(DcmPixelSequence* pixelSequence,
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95 unsigned int countFrames) :
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96 pixelSequence_(pixelSequence)
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97 {
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98 assert(pixelSequence != NULL);
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99
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100 startFragment_.resize(countFrames);
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101 countFragments_.resize(countFrames);
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102 frameSize_.resize(countFrames);
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103
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104 // The first fragment corresponds to the offset table
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105 unsigned int countFragments = static_cast<unsigned int>(pixelSequence_->card());
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106 if (countFragments < countFrames + 1)
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107 {
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108 throw OrthancException(ErrorCode_BadFileFormat);
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109 }
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110
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111 if (countFragments == countFrames + 1)
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112 {
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113 // Simple case: There is one fragment per frame.
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114
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115 DcmObject* fragment = pixelSequence_->nextInContainer(NULL); // Skip the offset table
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116 if (fragment == NULL)
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117 {
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118 throw OrthancException(ErrorCode_InternalError);
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119 }
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120
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diff changeset
121 for (unsigned int i = 0; i < countFrames; i++)
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122 {
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123 fragment = pixelSequence_->nextInContainer(fragment);
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124 startFragment_[i] = dynamic_cast<DcmPixelItem*>(fragment);
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125 frameSize_[i] = fragment->getLength();
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126 countFragments_[i] = 1;
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127 }
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128
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129 return;
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130 }
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131
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132 // Parse the offset table
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133 std::vector<uint32_t> offsetOfFrame;
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134 GetOffsetTable(offsetOfFrame);
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135
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136 if (offsetOfFrame.size() != countFrames ||
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137 offsetOfFrame[0] != 0)
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138 {
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139 throw OrthancException(ErrorCode_BadFileFormat);
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140 }
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parents:
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141
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142 // Loop over the fragments (ignoring the offset table). This is
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143 // an alternative, faster implementation to DCMTK's
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144 // "DcmCodec::determineStartFragment()".
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145 DcmObject* fragment = pixelSequence_->nextInContainer(NULL);
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146 if (fragment == NULL)
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147 {
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diff changeset
148 throw OrthancException(ErrorCode_InternalError);
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149 }
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150
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diff changeset
151 fragment = pixelSequence_->nextInContainer(fragment); // Skip the offset table
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152 if (fragment == NULL)
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diff changeset
153 {
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154 throw OrthancException(ErrorCode_InternalError);
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155 }
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parents:
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156
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157 uint32_t offset = 0;
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158 unsigned int currentFrame = 0;
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159 startFragment_[0] = dynamic_cast<DcmPixelItem*>(fragment);
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160
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161 unsigned int currentFragment = 1;
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diff changeset
162 while (fragment != NULL)
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parents:
diff changeset
163 {
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164 if (currentFrame + 1 < countFrames &&
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165 offset == offsetOfFrame[currentFrame + 1])
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diff changeset
166 {
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diff changeset
167 currentFrame += 1;
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168 startFragment_[currentFrame] = dynamic_cast<DcmPixelItem*>(fragment);
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169 }
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diff changeset
170
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parents:
diff changeset
171 frameSize_[currentFrame] += fragment->getLength();
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diff changeset
172 countFragments_[currentFrame]++;
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173
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parents:
diff changeset
174 // 8 bytes = overhead for the item tag and length field
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diff changeset
175 offset += fragment->getLength() + 8;
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diff changeset
176
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diff changeset
177 currentFragment++;
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178 fragment = pixelSequence_->nextInContainer(fragment);
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179 }
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parents:
diff changeset
180
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parents:
diff changeset
181 if (currentFragment != countFragments ||
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diff changeset
182 currentFrame + 1 != countFrames ||
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diff changeset
183 fragment != NULL)
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diff changeset
184 {
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parents:
diff changeset
185 throw OrthancException(ErrorCode_BadFileFormat);
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parents:
diff changeset
186 }
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parents:
diff changeset
187
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diff changeset
188 assert(startFragment_.size() == countFragments_.size() &&
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diff changeset
189 startFragment_.size() == frameSize_.size());
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diff changeset
190 }
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parents:
diff changeset
191
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parents:
diff changeset
192
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diff changeset
193 virtual void GetRawFrame(std::string& frame,
4200
7112a8af0b63 cppcheck
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4184
diff changeset
194 unsigned int index) const ORTHANC_OVERRIDE
1924
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195 {
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diff changeset
196 if (index >= startFragment_.size())
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diff changeset
197 {
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parents:
diff changeset
198 throw OrthancException(ErrorCode_ParameterOutOfRange);
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199 }
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parents:
diff changeset
200
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parents:
diff changeset
201 frame.resize(frameSize_[index]);
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diff changeset
202 if (frame.size() == 0)
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parents:
diff changeset
203 {
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parents:
diff changeset
204 return;
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diff changeset
205 }
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parents:
diff changeset
206
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diff changeset
207 uint8_t* target = reinterpret_cast<uint8_t*>(&frame[0]);
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parents:
diff changeset
208
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diff changeset
209 size_t offset = 0;
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210 DcmPixelItem* fragment = startFragment_[index];
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diff changeset
211 for (unsigned int i = 0; i < countFragments_[index]; i++)
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diff changeset
212 {
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diff changeset
213 uint8_t* content = NULL;
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214 if (!fragment->getUint8Array(content).good() ||
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215 content == NULL)
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216 {
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217 throw OrthancException(ErrorCode_InternalError);
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218 }
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219
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220 assert(offset + fragment->getLength() <= frame.size());
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221
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222 memcpy(target + offset, content, fragment->getLength());
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223 offset += fragment->getLength();
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224
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225 fragment = dynamic_cast<DcmPixelItem*>(pixelSequence_->nextInContainer(fragment));
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226 }
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227 }
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228 };
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229
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230
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231
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232 class DicomFrameIndex::UncompressedIndex : public DicomFrameIndex::IIndex
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233 {
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234 private:
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235 uint8_t* pixelData_;
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236 size_t frameSize_;
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237
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238 public:
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239 UncompressedIndex(DcmDataset& dataset,
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240 unsigned int countFrames,
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241 size_t frameSize) :
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242 pixelData_(NULL),
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243 frameSize_(frameSize)
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244 {
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245 size_t size = 0;
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246
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247 DcmElement* e;
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248 if (dataset.findAndGetElement(DCM_PixelData, e).good() &&
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249 e != NULL)
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250 {
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251 size = e->getLength();
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252
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253 if (size > 0)
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254 {
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255 pixelData_ = NULL;
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256 if (!e->getUint8Array(pixelData_).good() ||
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257 pixelData_ == NULL)
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258 {
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259 throw OrthancException(ErrorCode_BadFileFormat);
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260 }
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261 }
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262 }
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263
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264 if (size < frameSize_ * countFrames)
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265 {
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266 throw OrthancException(ErrorCode_BadFileFormat);
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267 }
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268 }
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269
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270 virtual void GetRawFrame(std::string& frame,
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271 unsigned int index) const ORTHANC_OVERRIDE
1924
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272 {
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273 frame.resize(frameSize_);
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274 if (frameSize_ > 0)
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275 {
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276 memcpy(&frame[0], pixelData_ + index * frameSize_, frameSize_);
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277 }
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278 }
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279 };
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280
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281
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282 class DicomFrameIndex::PsmctRle1Index : public DicomFrameIndex::IIndex
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283 {
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284 private:
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285 std::string pixelData_;
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286 size_t frameSize_;
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287
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288 public:
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289 PsmctRle1Index(DcmDataset& dataset,
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290 unsigned int countFrames,
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291 size_t frameSize) :
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292 frameSize_(frameSize)
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293 {
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diff changeset
294 if (!DicomImageDecoder::DecodePsmctRle1(pixelData_, dataset) ||
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295 pixelData_.size() < frameSize * countFrames)
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296 {
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297 throw OrthancException(ErrorCode_BadFileFormat);
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298 }
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299 }
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300
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diff changeset
301 virtual void GetRawFrame(std::string& frame,
4200
7112a8af0b63 cppcheck
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diff changeset
302 unsigned int index) const ORTHANC_OVERRIDE
1924
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303 {
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diff changeset
304 frame.resize(frameSize_);
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diff changeset
305 if (frameSize_ > 0)
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diff changeset
306 {
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diff changeset
307 memcpy(&frame[0], reinterpret_cast<const uint8_t*>(&pixelData_[0]) + index * frameSize_, frameSize_);
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308 }
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309 }
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310 };
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311
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diff changeset
312
3745
113a7b994a12 extracting the raw frame in the transcoder
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parents: 3640
diff changeset
313 unsigned int DicomFrameIndex::GetFramesCount(DcmDataset& dicom)
1950
533ff46e944b return a single raw frame from DICOM videos
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1929
diff changeset
314 {
4334
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diff changeset
315 DicomTransferSyntax transferSyntax;
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diff changeset
316 if (FromDcmtkBridge::LookupOrthancTransferSyntax(transferSyntax, dicom) &&
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diff changeset
317 (transferSyntax == DicomTransferSyntax_MPEG2MainProfileAtMainLevel ||
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diff changeset
318 transferSyntax == DicomTransferSyntax_MPEG2MainProfileAtHighLevel ||
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diff changeset
319 transferSyntax == DicomTransferSyntax_MPEG4HighProfileLevel4_1 ||
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parents: 4312
diff changeset
320 transferSyntax == DicomTransferSyntax_MPEG4BDcompatibleHighProfileLevel4_1 ||
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parents: 4312
diff changeset
321 transferSyntax == DicomTransferSyntax_MPEG4HighProfileLevel4_2_For2DVideo ||
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diff changeset
322 transferSyntax == DicomTransferSyntax_MPEG4HighProfileLevel4_2_For3DVideo ||
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parents: 4312
diff changeset
323 transferSyntax == DicomTransferSyntax_MPEG4StereoHighProfileLevel4_2 ||
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324 transferSyntax == DicomTransferSyntax_HEVCMainProfileLevel5_1 ||
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325 transferSyntax == DicomTransferSyntax_HEVCMain10ProfileLevel5_1))
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diff changeset
326 {
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327 /**
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328 * Fixes an issue that was present from Orthanc 1.6.0 until
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diff changeset
329 * 1.8.0 for the special case of the videos: In a video, the
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330 * number of frames doesn't correspond to the number of
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331 * fragments. We consider that there is one single frame (the
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332 * video itself).
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333 **/
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334 return 1;
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335 }
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336
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337 const char* tmp = NULL;
3745
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338 if (!dicom.findAndGetString(DCM_NumberOfFrames, tmp).good() ||
1924
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339 tmp == NULL)
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340 {
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341 return 1;
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342 }
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343
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344 int count = -1;
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345 try
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346 {
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347 count = boost::lexical_cast<int>(tmp);
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348 }
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349 catch (boost::bad_lexical_cast&)
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350 {
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351 }
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352
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353 if (count < 0)
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354 {
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355 throw OrthancException(ErrorCode_BadFileFormat);
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356 }
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357 else
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358 {
3745
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359 return static_cast<unsigned int>(count);
1924
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360 }
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diff changeset
361 }
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parents:
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362
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diff changeset
363
3745
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diff changeset
364 DicomFrameIndex::DicomFrameIndex(DcmDataset& dicom)
1924
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365 {
1956
fc16ee04e71b refactoring
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diff changeset
366 countFrames_ = GetFramesCount(dicom);
1924
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367 if (countFrames_ == 0)
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diff changeset
368 {
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369 // The image has no frame. No index is to be built.
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370 return;
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371 }
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diff changeset
372
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373 // Extract information about the image structure
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diff changeset
374 DicomMap tags;
4137
6774605d4341 keep only one signature for FromDcmtkBridge::ExtractDicomSummary()
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diff changeset
375 std::set<DicomTag> ignoreTagLength;
4312
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diff changeset
376 FromDcmtkBridge::ExtractDicomSummary(tags, dicom, DicomImageInformation::GetUsefulTagLength(), ignoreTagLength);
1924
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diff changeset
377
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diff changeset
378 DicomImageInformation information(tags);
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diff changeset
379
4184
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diff changeset
380 // Test whether this image is composed of a sequence of fragments
4475
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parents: 4437
diff changeset
381 if (dicom.tagExists(DCM_PixelData))
4184
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diff changeset
382 {
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diff changeset
383 DcmPixelSequence* pixelSequence = FromDcmtkBridge::GetPixelSequence(dicom);
dbd74fa2f446 Enable the access to raw frames in Philips ELSCINT1 proprietary compression
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diff changeset
384 if (pixelSequence != NULL)
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parents: 4138
diff changeset
385 {
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diff changeset
386 index_.reset(new FragmentIndex(pixelSequence, countFrames_));
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387 }
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diff changeset
388 else
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diff changeset
389 {
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diff changeset
390 // Access to the raw pixel data
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parents: 4138
diff changeset
391 index_.reset(new UncompressedIndex(dicom, countFrames_, information.GetFrameSize()));
dbd74fa2f446 Enable the access to raw frames in Philips ELSCINT1 proprietary compression
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parents: 4138
diff changeset
392 }
dbd74fa2f446 Enable the access to raw frames in Philips ELSCINT1 proprietary compression
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parents: 4138
diff changeset
393 }
dbd74fa2f446 Enable the access to raw frames in Philips ELSCINT1 proprietary compression
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parents: 4138
diff changeset
394 else if (DicomImageDecoder::IsPsmctRle1(dicom))
1924
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
395 {
3745
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diff changeset
396 index_.reset(new PsmctRle1Index(dicom, countFrames_, information.GetFrameSize()));
1924
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diff changeset
397 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
398 }
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
399
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
400
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
401 void DicomFrameIndex::GetRawFrame(std::string& frame,
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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parents:
diff changeset
402 unsigned int index) const
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
403 {
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
404 if (index >= countFrames_)
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
405 {
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
406 throw OrthancException(ErrorCode_ParameterOutOfRange);
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
407 }
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
408 else if (index_.get() != NULL)
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
409 {
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
410 return index_->GetRawFrame(frame, index);
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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parents:
diff changeset
411 }
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
412 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
413 {
4184
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diff changeset
414 throw OrthancException(ErrorCode_BadFileFormat, "Cannot access a raw frame");
1924
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diff changeset
415 }
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parents:
diff changeset
416 }
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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parents:
diff changeset
417 }