annotate OrthancServer/Internals/DicomImageDecoder.cpp @ 858:ebc41566f742 jpeg

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 06 Jun 2014 15:25:31 +0200
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege,
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4 * Belgium
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5 *
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6 * This program is free software: you can redistribute it and/or
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7 * modify it under the terms of the GNU General Public License as
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8 * published by the Free Software Foundation, either version 3 of the
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9 * License, or (at your option) any later version.
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10 *
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11 * In addition, as a special exception, the copyright holders of this
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12 * program give permission to link the code of its release with the
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13 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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14 * that use the same license as the "OpenSSL" library), and distribute
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15 * the linked executables. You must obey the GNU General Public License
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16 * in all respects for all of the code used other than "OpenSSL". If you
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17 * modify file(s) with this exception, you may extend this exception to
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18 * your version of the file(s), but you are not obligated to do so. If
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19 * you do not wish to do so, delete this exception statement from your
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20 * version. If you delete this exception statement from all source files
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21 * in the program, then also delete it here.
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22 *
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23 * This program is distributed in the hope that it will be useful, but
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24 * WITHOUT ANY WARRANTY; without even the implied warranty of
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25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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26 * General Public License for more details.
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27 *
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28 * You should have received a copy of the GNU General Public License
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29 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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30 **/
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31
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32
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33 #include "../PrecompiledHeadersServer.h"
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34 #include "DicomImageDecoder.h"
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35
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36
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37 /*=========================================================================
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38
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39 This file is based on portions of the following project
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40 (cf. function "DecodePsmctRle1()"):
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41
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42 Program: GDCM (Grassroots DICOM). A DICOM library
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43 Module: http://gdcm.sourceforge.net/Copyright.html
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44
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45 Copyright (c) 2006-2011 Mathieu Malaterre
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46 Copyright (c) 1993-2005 CREATIS
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47 (CREATIS = Centre de Recherche et d'Applications en Traitement de l'Image)
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48 All rights reserved.
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49
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50 Redistribution and use in source and binary forms, with or without
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51 modification, are permitted provided that the following conditions are met:
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52
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53 * Redistributions of source code must retain the above copyright notice,
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54 this list of conditions and the following disclaimer.
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55
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56 * Redistributions in binary form must reproduce the above copyright notice,
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57 this list of conditions and the following disclaimer in the documentation
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58 and/or other materials provided with the distribution.
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59
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60 * Neither name of Mathieu Malaterre, or CREATIS, nor the names of any
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61 contributors (CNRS, INSERM, UCB, Universite Lyon I), may be used to
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62 endorse or promote products derived from this software without specific
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63 prior written permission.
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64
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65 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS''
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66 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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67 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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68 ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR
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69 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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70 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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71 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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72 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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73 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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74 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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75
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76 =========================================================================*/
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77
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78
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79
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80 #include "../../Core/OrthancException.h"
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81 #include "../../Core/ImageFormats/ImageProcessing.h"
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82 #include "../../Core/DicomFormat/DicomIntegerPixelAccessor.h"
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83 #include "../ToDcmtkBridge.h"
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84 #include "../FromDcmtkBridge.h"
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85
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86 #include <glog/logging.h>
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87
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88 #include <boost/lexical_cast.hpp>
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89
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90 #if ORTHANC_JPEG_LOSSLESS_ENABLED == 1
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91 #include <dcmtk/dcmjpls/djcodecd.h>
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92 #include <dcmtk/dcmjpls/djcparam.h>
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93 #include <dcmtk/dcmjpeg/djrplol.h>
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94 #endif
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95
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96
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97 namespace Orthanc
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98 {
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99 class DicomImageDecoder::ImageSource
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100 {
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101 private:
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102 std::string psmct_;
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103 std::auto_ptr<DicomIntegerPixelAccessor> slowAccessor_;
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104 std::auto_ptr<ImageAccessor> fastAccessor_;
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105
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106 public:
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107 void Setup(DcmDataset& dataset,
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108 unsigned int frame)
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109 {
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110 psmct_.clear();
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111 slowAccessor_.reset(NULL);
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112 fastAccessor_.reset(NULL);
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113
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114 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data
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115
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116 DicomMap m;
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117 FromDcmtkBridge::Convert(m, dataset);
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118
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119 /**
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120 * Create an accessor to the raw values of the DICOM image.
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121 **/
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122
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123 DcmElement* e;
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124 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() &&
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125 e != NULL)
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126 {
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127 Uint8* pixData = NULL;
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128 if (e->getUint8Array(pixData) == EC_Normal)
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129 {
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130 slowAccessor_.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength()));
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131 }
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132 }
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133 else if (DicomImageDecoder::DecodePsmctRle1(psmct_, dataset))
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134 {
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135 LOG(INFO) << "The PMSCT_RLE1 decoding has succeeded";
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136 Uint8* pixData = NULL;
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137 if (psmct_.size() > 0)
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138 {
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139 pixData = reinterpret_cast<Uint8*>(&psmct_[0]);
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140 }
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141
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142 slowAccessor_.reset(new DicomIntegerPixelAccessor(m, pixData, psmct_.size()));
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143 }
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144
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145 if (slowAccessor_.get() == NULL)
852
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146 {
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147 throw OrthancException(ErrorCode_BadFileFormat);
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148 }
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149
853
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150 slowAccessor_->SetCurrentFrame(frame);
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151
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152
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153 /**
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154 * If possible, create a fast ImageAccessor to the image buffer.
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155 **/
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156
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157
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158 }
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159
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160 unsigned int GetWidth() const
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161 {
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162 assert(slowAccessor_.get() != NULL);
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163 return slowAccessor_->GetInformation().GetWidth();
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164 }
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165
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166 unsigned int GetHeight() const
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167 {
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168 assert(slowAccessor_.get() != NULL);
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169 return slowAccessor_->GetInformation().GetHeight();
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170 }
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171
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172 unsigned int GetBytesPerPixel() const
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173 {
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174 assert(slowAccessor_.get() != NULL);
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175 return slowAccessor_->GetInformation().GetBytesPerPixel();
852
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176 }
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177
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178 unsigned int GetChannelCount() const
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179 {
853
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180 assert(slowAccessor_.get() != NULL);
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181 return slowAccessor_->GetInformation().GetChannelCount();
852
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182 }
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183
854
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184 const DicomIntegerPixelAccessor& GetAccessor() const
852
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185 {
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186 assert(slowAccessor_.get() != NULL);
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187 return *slowAccessor_;
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188 }
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189
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190 bool HasFastAccessor() const
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191 {
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192 return fastAccessor_.get() != NULL;
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193 }
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194
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195 const ImageAccessor& GetFastAccessor() const
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196 {
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197 assert(HasFastAccessor());
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198 return *fastAccessor_;
852
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199 }
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200 };
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201
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202
846
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203 static const DicomTag DICOM_TAG_CONTENT(0x07a1, 0x100a);
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204 static const DicomTag DICOM_TAG_COMPRESSION_TYPE(0x07a1, 0x1011);
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205
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206 bool DicomImageDecoder::IsPsmctRle1(DcmDataset& dataset)
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207 {
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208 DcmElement* e;
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209 char* c;
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210
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211 // Check whether the DICOM instance contains an image encoded with
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212 // the PMSCT_RLE1 scheme.
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213 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_COMPRESSION_TYPE), e).good() ||
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214 e == NULL ||
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215 !e->isaString() ||
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216 !e->getString(c).good() ||
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217 c == NULL ||
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218 strcmp("PMSCT_RLE1", c))
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219 {
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220 return false;
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221 }
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222 else
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223 {
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224 return true;
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225 }
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226 }
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227
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228
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229 bool DicomImageDecoder::DecodePsmctRle1(std::string& output,
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230 DcmDataset& dataset)
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231 {
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232 // Check whether the DICOM instance contains an image encoded with
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233 // the PMSCT_RLE1 scheme.
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234 if (!IsPsmctRle1(dataset))
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235 {
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236 return false;
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237 }
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238
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239 // OK, this is a custom RLE encoding from Philips. Get the pixel
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240 // data from the appropriate private DICOM tag.
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241 Uint8* pixData = NULL;
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242 DcmElement* e;
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243 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_CONTENT), e).good() ||
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244 e == NULL ||
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245 e->getUint8Array(pixData) != EC_Normal)
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246 {
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247 return false;
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248 }
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249
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250 // The "unsigned" below IS VERY IMPORTANT
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251 const uint8_t* inbuffer = reinterpret_cast<const uint8_t*>(pixData);
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252 const size_t length = e->getLength();
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253
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254 /**
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255 * The code below is an adaptation of a sample code for GDCM by
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256 * Mathieu Malaterre (under a BSD license).
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257 * http://gdcm.sourceforge.net/html/rle2img_8cxx-example.html
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258 **/
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259
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260 // RLE pass
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261 std::vector<uint8_t> temp;
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262 temp.reserve(length);
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263 for (size_t i = 0; i < length; i++)
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264 {
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265 if (inbuffer[i] == 0xa5)
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266 {
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267 temp.push_back(inbuffer[i+2]);
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268 for (uint8_t repeat = inbuffer[i + 1]; repeat != 0; repeat--)
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269 {
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diff changeset
270 temp.push_back(inbuffer[i+2]);
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271 }
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272 i += 2;
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273 }
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274 else
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275 {
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276 temp.push_back(inbuffer[i]);
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277 }
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278 }
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279
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280 // Delta encoding pass
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281 uint16_t delta = 0;
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282 output.clear();
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283 output.reserve(temp.size());
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284 for (size_t i = 0; i < temp.size(); i++)
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285 {
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286 uint16_t value;
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287
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288 if (temp[i] == 0x5a)
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289 {
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290 uint16_t v1 = temp[i + 1];
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291 uint16_t v2 = temp[i + 2];
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diff changeset
292 value = (v2 << 8) + v1;
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293 i += 2;
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294 }
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295 else
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296 {
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diff changeset
297 value = delta + (int8_t) temp[i];
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298 }
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299
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300 output.push_back(value & 0xff);
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301 output.push_back(value >> 8);
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302 delta = value;
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303 }
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304
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305 if (output.size() % 2)
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306 {
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307 output.resize(output.size() - 1);
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308 }
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309
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310 return true;
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311 }
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312
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313
845
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314 void DicomImageDecoder::SetupImageBuffer(ImageBuffer& target,
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315 DcmDataset& dataset)
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316 {
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317 DicomMap m;
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318 FromDcmtkBridge::Convert(m, dataset);
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319
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320 DicomImageInformation info(m);
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321 PixelFormat format;
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322
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323 if (!info.ExtractPixelFormat(format))
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324 {
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325 LOG(WARNING) << "Unsupported DICOM image: " << info.GetBitsStored()
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326 << "bpp, " << info.GetChannelCount() << " channels, "
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327 << (info.IsSigned() ? "signed" : "unsigned");
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328 throw OrthancException(ErrorCode_NotImplemented);
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329 }
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330
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331 target.SetHeight(info.GetHeight());
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332 target.SetWidth(info.GetWidth());
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333 target.SetFormat(format);
845
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334 }
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335
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336
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337 bool DicomImageDecoder::IsJpegLossless(const DcmDataset& dataset)
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338 {
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339 // http://support.dcmtk.org/docs/dcxfer_8h-source.html
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340 return (dataset.getOriginalXfer() == EXS_JPEGLSLossless ||
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341 dataset.getOriginalXfer() == EXS_JPEGLSLossy);
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342 }
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343
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344
847
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345 bool DicomImageDecoder::IsUncompressedImage(const DcmDataset& dataset)
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346 {
851
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347 // http://support.dcmtk.org/docs/dcxfer_8h-source.html
847
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348 return (dataset.getOriginalXfer() == EXS_Unknown ||
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349 dataset.getOriginalXfer() == EXS_LittleEndianImplicit ||
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350 dataset.getOriginalXfer() == EXS_BigEndianImplicit ||
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351 dataset.getOriginalXfer() == EXS_LittleEndianExplicit ||
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352 dataset.getOriginalXfer() == EXS_BigEndianExplicit);
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353 }
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354
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355
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356 template <typename PixelType>
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357 static void CopyPixels(ImageAccessor& target,
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358 const DicomIntegerPixelAccessor& source)
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359 {
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360 const PixelType minValue = std::numeric_limits<PixelType>::min();
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361 const PixelType maxValue = std::numeric_limits<PixelType>::max();
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362
853
839be3022203 DicomImageInformation
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363 for (unsigned int y = 0; y < source.GetInformation().GetHeight(); y++)
847
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364 {
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365 PixelType* pixel = reinterpret_cast<PixelType*>(target.GetRow(y));
853
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366 for (unsigned int x = 0; x < source.GetInformation().GetWidth(); x++)
847
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diff changeset
367 {
853
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diff changeset
368 for (unsigned int c = 0; c < source.GetInformation().GetChannelCount(); c++, pixel++)
847
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369 {
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diff changeset
370 int32_t v = source.GetValue(x, y, c);
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diff changeset
371 if (v < static_cast<int32_t>(minValue))
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diff changeset
372 {
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373 *pixel = minValue;
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diff changeset
374 }
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diff changeset
375 else if (v > static_cast<int32_t>(maxValue))
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diff changeset
376 {
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diff changeset
377 *pixel = maxValue;
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diff changeset
378 }
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diff changeset
379 else
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diff changeset
380 {
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diff changeset
381 *pixel = static_cast<PixelType>(v);
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diff changeset
382 }
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diff changeset
383 }
03ea55da7429 fully functional JPEG-LS conversion
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diff changeset
384 }
03ea55da7429 fully functional JPEG-LS conversion
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diff changeset
385 }
03ea55da7429 fully functional JPEG-LS conversion
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diff changeset
386 }
03ea55da7429 fully functional JPEG-LS conversion
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parents: 846
diff changeset
387
03ea55da7429 fully functional JPEG-LS conversion
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diff changeset
388
03ea55da7429 fully functional JPEG-LS conversion
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diff changeset
389 void DicomImageDecoder::DecodeUncompressedImage(ImageBuffer& target,
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diff changeset
390 DcmDataset& dataset,
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diff changeset
391 unsigned int frame)
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diff changeset
392 {
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parents: 846
diff changeset
393 if (!IsUncompressedImage(dataset))
03ea55da7429 fully functional JPEG-LS conversion
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parents: 846
diff changeset
394 {
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diff changeset
395 throw OrthancException(ErrorCode_BadParameterType);
03ea55da7429 fully functional JPEG-LS conversion
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diff changeset
396 }
03ea55da7429 fully functional JPEG-LS conversion
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diff changeset
397
03ea55da7429 fully functional JPEG-LS conversion
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parents: 846
diff changeset
398 DecodeUncompressedImageInternal(target, dataset, frame);
03ea55da7429 fully functional JPEG-LS conversion
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diff changeset
399 }
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parents: 846
diff changeset
400
03ea55da7429 fully functional JPEG-LS conversion
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parents: 846
diff changeset
401
03ea55da7429 fully functional JPEG-LS conversion
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parents: 846
diff changeset
402 void DicomImageDecoder::DecodeUncompressedImageInternal(ImageBuffer& target,
03ea55da7429 fully functional JPEG-LS conversion
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diff changeset
403 DcmDataset& dataset,
03ea55da7429 fully functional JPEG-LS conversion
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diff changeset
404 unsigned int frame)
03ea55da7429 fully functional JPEG-LS conversion
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diff changeset
405 {
852
5944b8b80842 refactoring
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diff changeset
406 ImageSource source;
5944b8b80842 refactoring
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parents: 851
diff changeset
407 source.Setup(dataset, frame);
847
03ea55da7429 fully functional JPEG-LS conversion
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diff changeset
408
858
ebc41566f742 removed unneeded check
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parents: 854
diff changeset
409
847
03ea55da7429 fully functional JPEG-LS conversion
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diff changeset
410 /**
858
ebc41566f742 removed unneeded check
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 854
diff changeset
411 * Resize the target image.
847
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
412 **/
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
413
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
414 SetupImageBuffer(target, dataset);
03ea55da7429 fully functional JPEG-LS conversion
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parents: 846
diff changeset
415
854
ff530685e46a fast version of image copy
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diff changeset
416 if (source.GetWidth() != target.GetWidth() ||
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
417 source.GetHeight() != target.GetHeight())
847
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parents: 846
diff changeset
418 {
03ea55da7429 fully functional JPEG-LS conversion
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diff changeset
419 throw OrthancException(ErrorCode_InternalError);
03ea55da7429 fully functional JPEG-LS conversion
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parents: 846
diff changeset
420 }
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
421
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
422
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
423 /**
854
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
424 * If the format of the DICOM buffer is natively supported, use a
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
425 * direct access to copy its values.
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
426 **/
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
427
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
428 ImageAccessor targetAccessor(target.GetAccessor());
ff530685e46a fast version of image copy
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parents: 853
diff changeset
429 const DicomImageInformation& info = source.GetAccessor().GetInformation();
ff530685e46a fast version of image copy
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diff changeset
430
ff530685e46a fast version of image copy
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diff changeset
431 bool fastVersionSuccess = false;
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
432 PixelFormat sourceFormat;
ff530685e46a fast version of image copy
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parents: 853
diff changeset
433 if (info.ExtractPixelFormat(sourceFormat))
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
434 {
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
435 try
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
436 {
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
437 ImageAccessor sourceImage;
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
438 sourceImage.AssignReadOnly(sourceFormat,
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
439 info.GetWidth(),
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
440 info.GetHeight(),
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
441 info.GetWidth() * info.GetBytesPerPixel(),
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
442 source.GetAccessor().GetPixelData());
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
443
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
444 ImageProcessing::Convert(targetAccessor, sourceImage);
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
445 ImageProcessing::ShiftRight(targetAccessor, info.GetShift());
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
446 fastVersionSuccess = true;
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
447 }
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
448 catch (OrthancException&)
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
449 {
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
450 // Unsupported conversion
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
451 }
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
452 }
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
453
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
454
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
455 /**
847
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
456 * Loop over the DICOM buffer, storing its value into the target
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
457 * image.
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
458 **/
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
459
854
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
460 if (!fastVersionSuccess)
847
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
461 {
854
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
462 switch (target.GetFormat())
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
463 {
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
464 case PixelFormat_RGB24:
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
465 case PixelFormat_RGBA32:
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
466 case PixelFormat_Grayscale8:
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
467 CopyPixels<uint8_t>(targetAccessor, source.GetAccessor());
847
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
468 break;
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
469
854
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
470 case PixelFormat_Grayscale16:
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
471 CopyPixels<uint16_t>(targetAccessor, source.GetAccessor());
847
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
472 break;
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
473
854
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
474 case PixelFormat_SignedGrayscale16:
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
475 CopyPixels<int16_t>(targetAccessor, source.GetAccessor());
847
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
476 break;
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
477
854
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
478 default:
847
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
479 throw OrthancException(ErrorCode_InternalError);
854
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
480 }
847
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
481 }
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
482 }
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
483
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
484
845
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
485 #if ORTHANC_JPEG_LOSSLESS_ENABLED == 1
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
486 void DicomImageDecoder::DecodeJpegLossless(ImageBuffer& target,
847
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
487 DcmDataset& dataset,
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
488 unsigned int frame)
845
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
489 {
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
490 if (!IsJpegLossless(dataset))
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
491 {
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
492 throw OrthancException(ErrorCode_BadParameterType);
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
493 }
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
494
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
495 DcmElement *element = NULL;
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
496 if (!dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), element).good())
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
497 {
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
498 throw OrthancException(ErrorCode_BadFileFormat);
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
499 }
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
500
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
501 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element);
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
502 DcmPixelSequence* pixelSequence = NULL;
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
503 if (!pixelData.getEncapsulatedRepresentation
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
504 (dataset.getOriginalXfer(), NULL, pixelSequence).good())
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
505 {
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
506 throw OrthancException(ErrorCode_BadFileFormat);
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
507 }
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
508
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
509 SetupImageBuffer(target, dataset);
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
510
854
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
511 ImageAccessor targetAccessor(target.GetAccessor());
845
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
512
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
513 /**
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
514 * The "DJLSLosslessDecoder" and "DJLSNearLosslessDecoder" in DCMTK
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
515 * are exactly the same, except for the "supportedTransferSyntax()"
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
516 * virtual function.
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
517 * http://support.dcmtk.org/docs/classDJLSDecoderBase.html
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
518 **/
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
519
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
520 DJLSLosslessDecoder decoder; DJLSCodecParameter parameters;
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
521 //DJLSNearLosslessDecoder decoder; DJLSCodecParameter parameters;
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
522
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
523 Uint32 startFragment = 0; // Default
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
524 OFString decompressedColorModel; // Out
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
525 DJ_RPLossless representationParameter;
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
526 OFCondition c = decoder.decodeFrame(&representationParameter, pixelSequence, &parameters,
854
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
527 &dataset, frame, startFragment, targetAccessor.GetBuffer(),
ff530685e46a fast version of image copy
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 853
diff changeset
528 targetAccessor.GetSize(), decompressedColorModel);
845
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
529
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
530 if (!c.good())
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
531 {
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
532 throw OrthancException(ErrorCode_InternalError);
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
533 }
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
534 }
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
535 #endif
846
715ab7674993 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 845
diff changeset
536
715ab7674993 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 845
diff changeset
537
847
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
538
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
539 bool DicomImageDecoder::Decode(ImageBuffer& target,
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
540 DcmDataset& dataset,
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
541 unsigned int frame)
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
542 {
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
543 if (IsUncompressedImage(dataset))
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
544 {
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
545 DecodeUncompressedImage(target, dataset, frame);
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
546 return true;
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
547 }
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
548
852
5944b8b80842 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 851
diff changeset
549
847
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
550 #if ORTHANC_JPEG_LOSSLESS_ENABLED == 1
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
551 if (IsJpegLossless(dataset))
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
552 {
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
553 LOG(INFO) << "Decoding a JPEG-LS image";
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
554 DecodeJpegLossless(target, dataset, frame);
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
555 return true;
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
556 }
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
557 #endif
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
558
852
5944b8b80842 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 851
diff changeset
559
5944b8b80842 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 851
diff changeset
560 #if ORTHANC_JPEG_ENABLED == 1
5944b8b80842 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 851
diff changeset
561 // TODO Implement this part to speed up JPEG decompression
5944b8b80842 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 851
diff changeset
562 #endif
5944b8b80842 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 851
diff changeset
563
5944b8b80842 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 851
diff changeset
564
847
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
565 /**
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
566 * This DICOM image format is not natively supported by
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
567 * Orthanc. As a last resort, try and decode it through
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
568 * DCMTK. This will result in higher memory consumption. This is
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
569 * actually the second example of the following page:
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
570 * http://support.dcmtk.org/docs/mod_dcmjpeg.html#Examples
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
571 **/
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
572
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
573 {
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
574 LOG(INFO) << "Using DCMTK to decode a compressed image";
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
575
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
576 std::auto_ptr<DcmDataset> converted(dynamic_cast<DcmDataset*>(dataset.clone()));
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
577 converted->chooseRepresentation(EXS_LittleEndianExplicit, NULL);
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
578
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
579 if (converted->canWriteXfer(EXS_LittleEndianExplicit))
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
580 {
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
581 DecodeUncompressedImageInternal(target, *converted, frame);
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
582 return true;
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
583 }
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
584 }
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
585
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
586 return false;
03ea55da7429 fully functional JPEG-LS conversion
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 846
diff changeset
587 }
845
48016722c770 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
588 }