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annotate OrthancFramework/Sources/DicomParsing/Internals/DicomFrameIndex.cpp @ 5814:122fd5f97d39

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fix
author Alain Mazy <am@orthanc.team>
date Wed, 25 Sep 2024 16:36:04 +0200
parents f7adfb22e20e
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) 2017-2023 Osimis S.A., Belgium
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6 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium
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7 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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8 *
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9 * This program is free software: you can redistribute it and/or
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10 * modify it under the terms of the GNU Lesser General Public License
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11 * as published by the Free Software Foundation, either version 3 of
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12 * the License, or (at your option) any later version.
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13 *
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14 * This program is distributed in the hope that it will be useful, but
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15 * WITHOUT ANY WARRANTY; without even the implied warranty of
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16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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17 * Lesser General Public License for more details.
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18 *
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19 * You should have received a copy of the GNU Lesser General Public
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20 * License along with this program. If not, see
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21 * <http://www.gnu.org/licenses/>.
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22 **/
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25 #include "../../PrecompiledHeaders.h"
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26 #include "DicomFrameIndex.h"
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27
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28 #include "../../OrthancException.h"
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29 #include "../../DicomFormat/DicomImageInformation.h"
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30 #include "../FromDcmtkBridge.h"
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31 #include "../../Endianness.h"
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32 #include "DicomImageDecoder.h"
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34 #include <boost/lexical_cast.hpp>
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36 #include <dcmtk/dcmdata/dcdeftag.h>
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37 #include <dcmtk/dcmdata/dcpxitem.h>
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38 #include <dcmtk/dcmdata/dcpixseq.h>
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39
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40 namespace Orthanc
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41 {
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42 class DicomFrameIndex::FragmentIndex : public DicomFrameIndex::IIndex
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43 {
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44 private:
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45 DcmPixelSequence* pixelSequence_;
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46 std::vector<DcmPixelItem*> startFragment_;
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47 std::vector<unsigned int> countFragments_;
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48 std::vector<unsigned int> frameSize_;
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49
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50 void GetOffsetTable(std::vector<uint32_t>& table)
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51 {
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52 DcmPixelItem* item = NULL;
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53 if (!pixelSequence_->getItem(item, 0).good() ||
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54 item == NULL)
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55 {
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56 throw OrthancException(ErrorCode_BadFileFormat);
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57 }
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58
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59 uint32_t length = item->getLength();
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60 if (length == 0)
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61 {
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62 // Degenerate case: Empty offset table means only one frame
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63 // that overlaps all the fragments
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64 table.resize(1);
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65 table[0] = 0;
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66 return;
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67 }
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69 if (length % 4 != 0)
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70 {
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71 // Error: Each fragment is index with 4 bytes (uint32_t)
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72 throw OrthancException(ErrorCode_BadFileFormat);
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73 }
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75 uint8_t* content = NULL;
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76 if (!item->getUint8Array(content).good() ||
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77 content == NULL)
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78 {
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79 throw OrthancException(ErrorCode_InternalError);
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80 }
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81
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82 table.resize(length / 4);
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84 // The offset table is always in little endian in the DICOM
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85 // file. Swap it to host endianness if needed.
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86 const uint32_t* offset = reinterpret_cast<const uint32_t*>(content);
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87 for (size_t i = 0; i < table.size(); i++, offset++)
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88 {
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89 table[i] = le32toh(*offset);
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90 }
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91 }
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94 public:
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95 FragmentIndex(DcmPixelSequence* pixelSequence,
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96 unsigned int countFrames) :
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97 pixelSequence_(pixelSequence)
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98 {
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99 assert(pixelSequence != NULL);
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100
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101 startFragment_.resize(countFrames);
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102 countFragments_.resize(countFrames);
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103 frameSize_.resize(countFrames);
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104
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105 // The first fragment corresponds to the offset table
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106 unsigned int countFragments = static_cast<unsigned int>(pixelSequence_->card());
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107 if (countFragments < countFrames + 1)
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108 {
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109 throw OrthancException(ErrorCode_BadFileFormat);
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110 }
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diff changeset
111
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diff changeset
112 if (countFragments == countFrames + 1)
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diff changeset
113 {
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114 // Simple case: There is one fragment per frame.
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115
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116 DcmObject* fragment = pixelSequence_->nextInContainer(NULL); // Skip the offset table
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117 if (fragment == NULL)
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118 {
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119 throw OrthancException(ErrorCode_InternalError);
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120 }
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121
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122 for (unsigned int i = 0; i < countFrames; i++)
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123 {
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124 fragment = pixelSequence_->nextInContainer(fragment);
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125 startFragment_[i] = dynamic_cast<DcmPixelItem*>(fragment);
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126 frameSize_[i] = fragment->getLength();
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127 countFragments_[i] = 1;
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128 }
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129
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130 return;
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131 }
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132
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133 // Parse the offset table
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134 std::vector<uint32_t> offsetOfFrame;
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135 GetOffsetTable(offsetOfFrame);
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136
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137 if (offsetOfFrame.size() != countFrames ||
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138 offsetOfFrame[0] != 0)
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139 {
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140 throw OrthancException(ErrorCode_BadFileFormat);
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141 }
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parents:
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142
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143 // Loop over the fragments (ignoring the offset table). This is
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144 // an alternative, faster implementation to DCMTK's
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145 // "DcmCodec::determineStartFragment()".
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146 DcmObject* fragment = pixelSequence_->nextInContainer(NULL);
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147 if (fragment == NULL)
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148 {
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149 throw OrthancException(ErrorCode_InternalError);
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150 }
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parents:
diff changeset
151
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diff changeset
152 fragment = pixelSequence_->nextInContainer(fragment); // Skip the offset table
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153 if (fragment == NULL)
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diff changeset
154 {
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parents:
diff changeset
155 throw OrthancException(ErrorCode_InternalError);
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parents:
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156 }
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parents:
diff changeset
157
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158 uint32_t offset = 0;
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diff changeset
159 unsigned int currentFrame = 0;
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diff changeset
160 startFragment_[0] = dynamic_cast<DcmPixelItem*>(fragment);
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161
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diff changeset
162 unsigned int currentFragment = 1;
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diff changeset
163 while (fragment != NULL)
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diff changeset
164 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
165 if (currentFrame + 1 < countFrames &&
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diff changeset
166 offset == offsetOfFrame[currentFrame + 1])
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diff changeset
167 {
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diff changeset
168 currentFrame += 1;
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diff changeset
169 startFragment_[currentFrame] = dynamic_cast<DcmPixelItem*>(fragment);
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170 }
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parents:
diff changeset
171
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parents:
diff changeset
172 frameSize_[currentFrame] += fragment->getLength();
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diff changeset
173 countFragments_[currentFrame]++;
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diff changeset
174
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parents:
diff changeset
175 // 8 bytes = overhead for the item tag and length field
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parents:
diff changeset
176 offset += fragment->getLength() + 8;
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diff changeset
177
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diff changeset
178 currentFragment++;
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diff changeset
179 fragment = pixelSequence_->nextInContainer(fragment);
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180 }
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parents:
diff changeset
181
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parents:
diff changeset
182 if (currentFragment != countFragments ||
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parents:
diff changeset
183 currentFrame + 1 != countFrames ||
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parents:
diff changeset
184 fragment != NULL)
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diff changeset
185 {
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parents:
diff changeset
186 throw OrthancException(ErrorCode_BadFileFormat);
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diff changeset
187 }
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parents:
diff changeset
188
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diff changeset
189 assert(startFragment_.size() == countFragments_.size() &&
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diff changeset
190 startFragment_.size() == frameSize_.size());
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parents:
diff changeset
191 }
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parents:
diff changeset
192
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parents:
diff changeset
193
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diff changeset
194 virtual void GetRawFrame(std::string& frame,
4200
7112a8af0b63 cppcheck
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4184
diff changeset
195 unsigned int index) const ORTHANC_OVERRIDE
1924
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196 {
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diff changeset
197 if (index >= startFragment_.size())
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diff changeset
198 {
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diff changeset
199 throw OrthancException(ErrorCode_ParameterOutOfRange);
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200 }
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parents:
diff changeset
201
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parents:
diff changeset
202 frame.resize(frameSize_[index]);
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diff changeset
203 if (frame.size() == 0)
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parents:
diff changeset
204 {
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parents:
diff changeset
205 return;
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diff changeset
206 }
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parents:
diff changeset
207
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diff changeset
208 uint8_t* target = reinterpret_cast<uint8_t*>(&frame[0]);
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diff changeset
209
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diff changeset
210 size_t offset = 0;
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diff changeset
211 DcmPixelItem* fragment = startFragment_[index];
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diff changeset
212 for (unsigned int i = 0; i < countFragments_[index]; i++)
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diff changeset
213 {
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parents:
diff changeset
214 uint8_t* content = NULL;
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215 if (!fragment->getUint8Array(content).good() ||
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216 content == NULL)
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217 {
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218 throw OrthancException(ErrorCode_InternalError);
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219 }
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220
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221 assert(offset + fragment->getLength() <= frame.size());
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222
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223 memcpy(target + offset, content, fragment->getLength());
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224 offset += fragment->getLength();
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225
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226 fragment = dynamic_cast<DcmPixelItem*>(pixelSequence_->nextInContainer(fragment));
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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
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233 class DicomFrameIndex::UncompressedIndex : public DicomFrameIndex::IIndex
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234 {
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235 private:
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236 uint8_t* pixelData_;
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237 size_t frameSize_;
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238
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239 public:
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240 UncompressedIndex(DcmDataset& dataset,
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241 unsigned int countFrames,
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242 size_t frameSize) :
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243 pixelData_(NULL),
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244 frameSize_(frameSize)
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245 {
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246 size_t size = 0;
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247
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248 DcmElement* e;
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249 if (dataset.findAndGetElement(DCM_PixelData, e).good() &&
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250 e != NULL)
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251 {
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252 size = e->getLength();
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253
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254 if (size > 0)
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255 {
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256 pixelData_ = NULL;
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257 if (!e->getUint8Array(pixelData_).good() ||
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258 pixelData_ == NULL)
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259 {
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260 throw OrthancException(ErrorCode_BadFileFormat);
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261 }
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262 }
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263 }
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parents:
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264
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265 if (size < frameSize_ * countFrames)
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266 {
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267 throw OrthancException(ErrorCode_BadFileFormat);
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268 }
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269 }
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270
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271 virtual void GetRawFrame(std::string& frame,
4200
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272 unsigned int index) const ORTHANC_OVERRIDE
1924
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273 {
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274 frame.resize(frameSize_);
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275 if (frameSize_ > 0)
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276 {
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277 memcpy(&frame[0], pixelData_ + index * frameSize_, frameSize_);
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278 }
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279 }
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280 };
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281
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parents:
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282
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283 class DicomFrameIndex::PsmctRle1Index : public DicomFrameIndex::IIndex
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diff changeset
284 {
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285 private:
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286 std::string pixelData_;
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287 size_t frameSize_;
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288
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289 public:
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290 PsmctRle1Index(DcmDataset& dataset,
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291 unsigned int countFrames,
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292 size_t frameSize) :
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293 frameSize_(frameSize)
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294 {
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diff changeset
295 if (!DicomImageDecoder::DecodePsmctRle1(pixelData_, dataset) ||
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diff changeset
296 pixelData_.size() < frameSize * countFrames)
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diff changeset
297 {
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diff changeset
298 throw OrthancException(ErrorCode_BadFileFormat);
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299 }
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300 }
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diff changeset
301
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diff changeset
302 virtual void GetRawFrame(std::string& frame,
4200
7112a8af0b63 cppcheck
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diff changeset
303 unsigned int index) const ORTHANC_OVERRIDE
1924
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diff changeset
304 {
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diff changeset
305 frame.resize(frameSize_);
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diff changeset
306 if (frameSize_ > 0)
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diff changeset
307 {
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diff changeset
308 memcpy(&frame[0], reinterpret_cast<const uint8_t*>(&pixelData_[0]) + index * frameSize_, frameSize_);
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309 }
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310 }
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diff changeset
311 };
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312
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diff changeset
313
3745
113a7b994a12 extracting the raw frame in the transcoder
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parents: 3640
diff changeset
314 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
315 {
4334
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diff changeset
316 DicomTransferSyntax transferSyntax;
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diff changeset
317 if (FromDcmtkBridge::LookupOrthancTransferSyntax(transferSyntax, dicom) &&
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diff changeset
318 (transferSyntax == DicomTransferSyntax_MPEG2MainProfileAtMainLevel ||
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diff changeset
319 transferSyntax == DicomTransferSyntax_MPEG2MainProfileAtHighLevel ||
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parents: 4312
diff changeset
320 transferSyntax == DicomTransferSyntax_MPEG4HighProfileLevel4_1 ||
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parents: 4312
diff changeset
321 transferSyntax == DicomTransferSyntax_MPEG4BDcompatibleHighProfileLevel4_1 ||
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parents: 4312
diff changeset
322 transferSyntax == DicomTransferSyntax_MPEG4HighProfileLevel4_2_For2DVideo ||
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parents: 4312
diff changeset
323 transferSyntax == DicomTransferSyntax_MPEG4HighProfileLevel4_2_For3DVideo ||
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parents: 4312
diff changeset
324 transferSyntax == DicomTransferSyntax_MPEG4StereoHighProfileLevel4_2 ||
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325 transferSyntax == DicomTransferSyntax_HEVCMainProfileLevel5_1 ||
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326 transferSyntax == DicomTransferSyntax_HEVCMain10ProfileLevel5_1))
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327 {
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328 /**
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329 * Fixes an issue that was present from Orthanc 1.6.0 until
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330 * 1.8.0 for the special case of the videos: In a video, the
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331 * number of frames doesn't correspond to the number of
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332 * fragments. We consider that there is one single frame (the
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333 * video itself).
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334 **/
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335 return 1;
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336 }
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337
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338 const char* tmp = NULL;
3745
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339 if (!dicom.findAndGetString(DCM_NumberOfFrames, tmp).good() ||
1924
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340 tmp == NULL)
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341 {
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342 return 1;
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343 }
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344
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345 int count = -1;
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346 try
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347 {
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348 count = boost::lexical_cast<int>(tmp);
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349 }
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350 catch (boost::bad_lexical_cast&)
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351 {
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352 }
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353
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354 if (count < 0)
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355 {
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356 throw OrthancException(ErrorCode_BadFileFormat);
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357 }
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358 else
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359 {
3745
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360 return static_cast<unsigned int>(count);
1924
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361 }
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362 }
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parents:
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363
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diff changeset
364
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diff changeset
365 DicomFrameIndex::DicomFrameIndex(DcmDataset& dicom)
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366 {
1956
fc16ee04e71b refactoring
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diff changeset
367 countFrames_ = GetFramesCount(dicom);
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368 if (countFrames_ == 0)
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369 {
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370 // The image has no frame. No index is to be built.
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371 return;
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372 }
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diff changeset
373
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374 // Extract information about the image structure
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diff changeset
375 DicomMap tags;
4137
6774605d4341 keep only one signature for FromDcmtkBridge::ExtractDicomSummary()
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diff changeset
376 std::set<DicomTag> ignoreTagLength;
4312
6d49e3b6ff77 fix abi of DicomImageInformation
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diff changeset
377 FromDcmtkBridge::ExtractDicomSummary(tags, dicom, DicomImageInformation::GetUsefulTagLength(), ignoreTagLength);
1924
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diff changeset
378
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379 DicomImageInformation information(tags);
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diff changeset
380
4184
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diff changeset
381 // Test whether this image is composed of a sequence of fragments
4475
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parents: 4437
diff changeset
382 if (dicom.tagExists(DCM_PixelData))
4184
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diff changeset
383 {
dbd74fa2f446 Enable the access to raw frames in Philips ELSCINT1 proprietary compression
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4138
diff changeset
384 DcmPixelSequence* pixelSequence = FromDcmtkBridge::GetPixelSequence(dicom);
dbd74fa2f446 Enable the access to raw frames in Philips ELSCINT1 proprietary compression
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diff changeset
385 if (pixelSequence != NULL)
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parents: 4138
diff changeset
386 {
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diff changeset
387 index_.reset(new FragmentIndex(pixelSequence, countFrames_));
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388 }
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diff changeset
389 else
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diff changeset
390 {
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diff changeset
391 // Access to the raw pixel data
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parents: 4138
diff changeset
392 index_.reset(new UncompressedIndex(dicom, countFrames_, information.GetFrameSize()));
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parents: 4138
diff changeset
393 }
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parents: 4138
diff changeset
394 }
dbd74fa2f446 Enable the access to raw frames in Philips ELSCINT1 proprietary compression
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parents: 4138
diff changeset
395 else if (DicomImageDecoder::IsPsmctRle1(dicom))
1924
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
396 {
3745
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diff changeset
397 index_.reset(new PsmctRle1Index(dicom, countFrames_, information.GetFrameSize()));
1924
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diff changeset
398 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
399 }
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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
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
402 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
403 unsigned int index) const
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
404 {
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
405 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
406 {
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
407 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
408 }
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
409 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
410 {
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
411 return index_->GetRawFrame(frame, index);
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diff changeset
412 }
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
413 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
414 {
4184
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diff changeset
415 throw OrthancException(ErrorCode_BadFileFormat, "Cannot access a raw frame");
1924
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diff changeset
416 }
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diff changeset
417 }
6c73df12ca51 New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff changeset
418 }