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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 *
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6 * This program is free software: you can redistribute it and/or
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7 * modify it under the terms of the GNU Affero General Public License
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8 * as published by the Free Software Foundation, either version 3 of
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9 * the License, or (at your option) any later version.
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10 *
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11 * This program is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty of
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13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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14 * Affero General Public License for more details.
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15 *
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16 * You should have received a copy of the GNU Affero General Public License
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17 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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18 **/
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19
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20
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21 #include "MultiframeDicomWriter.h"
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22
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23 #include "../Orthanc/Core/OrthancException.h"
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24 #include "../Orthanc/Core/Logging.h"
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25 #include "../DicomToolbox.h"
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26
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27 #include <dcmtk/dcmdata/dcuid.h>
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28 #include <dcmtk/dcmdata/dcdeftag.h>
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29 #include <dcmtk/dcmdata/dcostrmb.h>
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30 #include <dcmtk/dcmdata/dcpxitem.h>
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31 #include <dcmtk/dcmdata/dcpixel.h>
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32 #include <dcmtk/dcmdata/dcvrat.h>
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33
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34 #include <boost/lexical_cast.hpp>
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35
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36 namespace OrthancWSI
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37 {
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38 static void SaveDicomToMemory(std::string& target,
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39 DcmFileFormat& dicom,
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40 E_TransferSyntax transferSyntax)
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41 {
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42 dicom.validateMetaInfo(transferSyntax);
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43 dicom.removeInvalidGroups();
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44
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45 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength;
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46
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47 // Create a memory buffer with the proper size
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48 {
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49 const uint32_t estimatedSize = dicom.calcElementLength(transferSyntax, encodingType); // (*)
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50 target.resize(estimatedSize);
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51 }
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52
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53 DcmOutputBufferStream ob(&target[0], target.size());
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54
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55 // Fill the memory buffer with the meta-header and the dataset
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56 dicom.transferInit();
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57 OFCondition c = dicom.write(ob, transferSyntax, encodingType, NULL,
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58 /*opt_groupLength*/ EGL_recalcGL,
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59 /*opt_paddingType*/ EPD_withoutPadding);
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60 dicom.transferEnd();
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61
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62 if (!c.good())
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63 {
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64 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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65 }
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66
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67 // The DICOM file is successfully written, truncate the target
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68 // buffer if its size was overestimated by (*)
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69 ob.flush();
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70
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71 size_t effectiveSize = static_cast<size_t>(ob.tell());
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72 if (effectiveSize < target.size())
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73 {
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74 target.resize(effectiveSize);
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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 void MultiframeDicomWriter::ResetImage()
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80 {
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81 perFrameFunctionalGroups_.reset(new DcmSequenceOfItems(DCM_PerFrameFunctionalGroupsSequence));
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82
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83 if (compression_ != ImageCompression_None)
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84 {
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85 compressedPixelSequence_.reset(new DcmPixelSequence(DcmTag(DCM_PixelData, EVR_OB)));
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86
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87 offsetTable_ = new DcmPixelItem(DCM_Item, EVR_OB);
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88 compressedPixelSequence_->insert(offsetTable_);
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89 offsetList_.reset(new DcmOffsetList);
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90 }
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91
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92 writtenSize_ = 0;
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93 framesCount_ = 0;
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94 }
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95
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96
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97 void MultiframeDicomWriter::InjectUncompressedPixelData(DcmFileFormat& dicom)
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98 {
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99 static const size_t GIGABYTE = 1024 * 1024 * 1024;
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100
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101 std::string pixelData;
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102 uncompressedPixelData_.Flatten(pixelData);
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103
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104 // Prevent the creation of too large DICOM files
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105 // (uncompressed DICOM files are limited to 2GB)
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106 if (pixelData.size() > GIGABYTE)
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107 {
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108 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotEnoughMemory);
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109 }
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110
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111 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(DCM_PixelData));
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112
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113 uint8_t* target = NULL;
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114 if (!pixels->createUint8Array(pixelData.size(), target).good())
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115 {
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116 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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117 }
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118
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119 if (pixelData.size() > 0)
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120 {
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121 if (target == NULL)
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122 {
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123 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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124 }
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125
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126 // TODO Avoid this memcpy()
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127 memcpy(target, pixelData.c_str(), pixelData.size());
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128 }
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129
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130 if (!dicom.getDataset()->insert(pixels.release(), false, false).good())
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131 {
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132 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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133 }
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134 }
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135
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136
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137 MultiframeDicomWriter::MultiframeDicomWriter(const DcmDataset& dataset,
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138 ImageCompression compression,
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139 Orthanc::PixelFormat pixelFormat,
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140 unsigned int width,
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141 unsigned int height,
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142 unsigned int tileWidth,
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143 unsigned int tileHeight) :
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144 compression_(compression),
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145 width_(width),
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146 height_(height)
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147 {
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148 switch (compression)
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149 {
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150 case ImageCompression_None:
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151 transferSyntax_ = EXS_LittleEndianImplicit;
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152 break;
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153
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154 case ImageCompression_Jpeg:
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155 // Default transfer syntax for lossy JPEG 8bit compression
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156 transferSyntax_ = EXS_JPEGProcess1TransferSyntax;
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157 break;
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158
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159 case ImageCompression_Jpeg2000:
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160 // JPEG2000 compression (lossless only)
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161 transferSyntax_ = EXS_JPEG2000LosslessOnly;
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162 break;
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163
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164 default:
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165 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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166 }
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167
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168 if (!sharedTags_.copyFrom(dataset).good())
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169 {
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170 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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171 }
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172
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173 // We only take care of grayscale or RGB images in 8bpp
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174 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixColumns, width);
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175 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixRows, height);
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176 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PlanarConfiguration, 0); // Interleaved RGB values
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177 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Columns, tileWidth);
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178 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Rows, tileHeight);
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179 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsAllocated, 8);
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180 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsStored, 8);
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181 DicomToolbox::SetUint16Tag(sharedTags_, DCM_HighBit, 7);
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182 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PixelRepresentation, 0); // Unsigned values
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183
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184 switch (pixelFormat)
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185 {
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186 case Orthanc::PixelFormat_RGB24:
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187 uncompressedFrameSize_ = 3 * tileWidth * tileHeight;
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188 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 3);
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189
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190 if (compression_ == ImageCompression_Jpeg)
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191 {
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192 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, "YBR_FULL_422");
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193 }
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194 else
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195 {
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196 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, "RGB");
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197 }
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198
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199 break;
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200
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201 case Orthanc::PixelFormat_Grayscale8:
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202 uncompressedFrameSize_ = tileWidth * tileHeight;
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203 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 1);
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204 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, "MONOCHROME2");
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205 break;
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206
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207 default:
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208 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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209 }
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210
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211 ResetImage();
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212 }
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213
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214
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215 void MultiframeDicomWriter::AddFrame(const std::string& frame,
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216 DcmItem* functionalGroup) // This takes the ownership
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217 {
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218 // Free the functional group on error
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219 std::auto_ptr<DcmItem> functionalGroupRaii(functionalGroup);
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220
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221 if (compression_ == ImageCompression_None)
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222 {
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223 if (frame.size() != uncompressedFrameSize_)
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224 {
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225 LOG(ERROR) << "An uncompressed frame has not the proper size: "
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226 << frame.size() << " instead of " << uncompressedFrameSize_;
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227 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize);
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228 }
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229
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230 uncompressedPixelData_.AddChunk(frame);
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231 }
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232 else
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233 {
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234 uint8_t* bytes = const_cast<uint8_t*>(reinterpret_cast<const uint8_t*>(frame.c_str()));
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235
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236 compressedPixelSequence_->storeCompressedFrame(*offsetList_, bytes, frame.size(),
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237 0 /* unlimited fragment size */);
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238 }
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239
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240 if (functionalGroup != NULL)
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241 {
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242 perFrameFunctionalGroups_->insert(functionalGroupRaii.release());
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243 }
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244 else
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245 {
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246 perFrameFunctionalGroups_->insert(new DcmItem);
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247 }
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248
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249 writtenSize_ += frame.size();
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250 framesCount_ += 1;
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251 }
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252
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253
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254 void MultiframeDicomWriter::Flush(std::string& target,
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255 unsigned int instanceNumber)
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256 {
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257 if (instanceNumber <= 0)
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258 {
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259 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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260 }
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261
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262 std::string tmp = boost::lexical_cast<std::string>(instanceNumber);
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263
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264 std::auto_ptr<DcmFileFormat> dicom(new DcmFileFormat);
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265
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266 char uid[100];
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267 dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT);
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268
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269 if (!dicom->getDataset()->copyFrom(sharedTags_).good() ||
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270 !dicom->getDataset()->insert(perFrameFunctionalGroups_.release(), false, false).good() ||
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271 !dicom->getDataset()->putAndInsertString(DCM_SOPInstanceUID, uid).good() ||
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272 !dicom->getDataset()->putAndInsertString(DCM_InstanceNumber, tmp.c_str()).good())
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273 {
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274 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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275 }
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276
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277 DicomToolbox::SetStringTag(*dicom->getDataset(), DCM_NumberOfFrames, boost::lexical_cast<std::string>(framesCount_));
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278
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279 switch (compression_)
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280 {
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281 case ImageCompression_None:
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282 InjectUncompressedPixelData(*dicom);
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283 break;
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284
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285 case ImageCompression_Jpeg:
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286 case ImageCompression_Jpeg2000:
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287 offsetTable_->createOffsetTable(*offsetList_);
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288 dicom->getDataset()->insert(compressedPixelSequence_.release());
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289 break;
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290
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291 default:
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292 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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293 }
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294
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295 ResetImage();
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296
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297 SaveDicomToMemory(target, *dicom, transferSyntax_);
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298 }
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299 }
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