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790
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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
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34 /*=========================================================================
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35
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36 This file is based on portions of the following project:
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37
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38 Program: GDCM (Grassroots DICOM). A DICOM library
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39 Module: http://gdcm.sourceforge.net/Copyright.html
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40
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41 Copyright (c) 2006-2011 Mathieu Malaterre
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42 Copyright (c) 1993-2005 CREATIS
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43 (CREATIS = Centre de Recherche et d'Applications en Traitement de l'Image)
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44 All rights reserved.
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45
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46 Redistribution and use in source and binary forms, with or without
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47 modification, are permitted provided that the following conditions are met:
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48
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49 * Redistributions of source code must retain the above copyright notice,
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50 this list of conditions and the following disclaimer.
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51
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52 * Redistributions in binary form must reproduce the above copyright notice,
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53 this list of conditions and the following disclaimer in the documentation
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54 and/or other materials provided with the distribution.
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55
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56 * Neither name of Mathieu Malaterre, or CREATIS, nor the names of any
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57 contributors (CNRS, INSERM, UCB, Universite Lyon I), may be used to
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58 endorse or promote products derived from this software without specific
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59 prior written permission.
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60
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61 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS''
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62 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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63 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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64 ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR
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65 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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66 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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67 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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68 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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69 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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70 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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71
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72 =========================================================================*/
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73
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74
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75 #ifndef NOMINMAX
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76 #define NOMINMAX
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77 #endif
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78
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79 #include "ParsedDicomFile.h"
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80
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81 #include "FromDcmtkBridge.h"
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82 #include "ToDcmtkBridge.h"
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83 #include "../Core/Toolbox.h"
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84 #include "../Core/OrthancException.h"
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85 #include "../Core/FileFormats/PngWriter.h"
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86 #include "../Core/Uuid.h"
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87 #include "../Core/DicomFormat/DicomString.h"
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88 #include "../Core/DicomFormat/DicomNullValue.h"
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89 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h"
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90
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91 #include <list>
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92 #include <limits>
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93
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94 #include <boost/lexical_cast.hpp>
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95
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96 #include <dcmtk/dcmdata/dcchrstr.h>
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97 #include <dcmtk/dcmdata/dcdicent.h>
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98 #include <dcmtk/dcmdata/dcdict.h>
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99 #include <dcmtk/dcmdata/dcfilefo.h>
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100 #include <dcmtk/dcmdata/dcistrmb.h>
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101 #include <dcmtk/dcmdata/dcuid.h>
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102 #include <dcmtk/dcmdata/dcmetinf.h>
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103
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104 #include <dcmtk/dcmdata/dcvrae.h>
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105 #include <dcmtk/dcmdata/dcvras.h>
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106 #include <dcmtk/dcmdata/dcvrcs.h>
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107 #include <dcmtk/dcmdata/dcvrda.h>
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108 #include <dcmtk/dcmdata/dcvrds.h>
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109 #include <dcmtk/dcmdata/dcvrdt.h>
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110 #include <dcmtk/dcmdata/dcvrfd.h>
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111 #include <dcmtk/dcmdata/dcvrfl.h>
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112 #include <dcmtk/dcmdata/dcvris.h>
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113 #include <dcmtk/dcmdata/dcvrlo.h>
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114 #include <dcmtk/dcmdata/dcvrlt.h>
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115 #include <dcmtk/dcmdata/dcvrpn.h>
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116 #include <dcmtk/dcmdata/dcvrsh.h>
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117 #include <dcmtk/dcmdata/dcvrsl.h>
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118 #include <dcmtk/dcmdata/dcvrss.h>
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119 #include <dcmtk/dcmdata/dcvrst.h>
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120 #include <dcmtk/dcmdata/dcvrtm.h>
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121 #include <dcmtk/dcmdata/dcvrui.h>
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122 #include <dcmtk/dcmdata/dcvrul.h>
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123 #include <dcmtk/dcmdata/dcvrus.h>
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124 #include <dcmtk/dcmdata/dcvrut.h>
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125 #include <dcmtk/dcmdata/dcpixel.h>
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126 #include <dcmtk/dcmdata/dcpixseq.h>
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127 #include <dcmtk/dcmdata/dcpxitem.h>
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128
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129
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130 #include <boost/math/special_functions/round.hpp>
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131 #include <glog/logging.h>
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132 #include <dcmtk/dcmdata/dcostrmb.h>
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133
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134
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135 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream";
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136
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137
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138
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139 namespace Orthanc
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140 {
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794
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141 struct ParsedDicomFile::PImpl
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142 {
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143 std::auto_ptr<DcmFileFormat> file_;
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144 };
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145
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146
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147 // This method can only be called from the constructors!
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790
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148 void ParsedDicomFile::Setup(const char* buffer, size_t size)
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149 {
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150 DcmInputBufferStream is;
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151 if (size > 0)
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152 {
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153 is.setBuffer(buffer, size);
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154 }
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155 is.setEos();
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156
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794
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157 pimpl_->file_.reset(new DcmFileFormat);
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158 pimpl_->file_->transferInit();
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159 if (!pimpl_->file_->read(is).good())
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790
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160 {
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794
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161 delete pimpl_; // Avoid a memory leak due to exception
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162 // throwing, as we are in the constructor
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163
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790
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164 throw OrthancException(ErrorCode_BadFileFormat);
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165 }
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794
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166 pimpl_->file_->loadAllDataIntoMemory();
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167 pimpl_->file_->transferEnd();
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790
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168 }
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169
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170
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171 static void SendPathValueForDictionary(RestApiOutput& output,
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172 DcmItem& dicom)
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173 {
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174 Json::Value v = Json::arrayValue;
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175
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176 for (unsigned long i = 0; i < dicom.card(); i++)
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177 {
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178 DcmElement* element = dicom.getElement(i);
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179 if (element)
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180 {
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181 char buf[16];
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182 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag());
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183 v.append(buf);
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184 }
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185 }
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186
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187 output.AnswerJson(v);
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188 }
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189
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190 static inline uint16_t GetCharValue(char c)
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191 {
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192 if (c >= '0' && c <= '9')
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193 return c - '0';
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194 else if (c >= 'a' && c <= 'f')
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195 return c - 'a' + 10;
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196 else if (c >= 'A' && c <= 'F')
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197 return c - 'A' + 10;
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198 else
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199 return 0;
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200 }
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201
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202 static inline uint16_t GetTagValue(const char* c)
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203 {
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204 return ((GetCharValue(c[0]) << 12) +
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205 (GetCharValue(c[1]) << 8) +
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206 (GetCharValue(c[2]) << 4) +
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207 GetCharValue(c[3]));
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208 }
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209
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210 static void ParseTagAndGroup(DcmTagKey& key,
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211 const std::string& tag)
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212 {
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213 DicomTag t = FromDcmtkBridge::ParseTag(tag);
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214 key = DcmTagKey(t.GetGroup(), t.GetElement());
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215 }
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216
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217
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218 static void SendSequence(RestApiOutput& output,
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219 DcmSequenceOfItems& sequence)
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220 {
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221 // This element is a sequence
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222 Json::Value v = Json::arrayValue;
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223
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224 for (unsigned long i = 0; i < sequence.card(); i++)
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225 {
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226 v.append(boost::lexical_cast<std::string>(i));
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227 }
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228
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229 output.AnswerJson(v);
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230 }
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231
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232
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233 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData,
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234 E_TransferSyntax transferSyntax)
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235 {
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236 DcmPixelSequence* pixelSequence = NULL;
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237 if (pixelData.getEncapsulatedRepresentation
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238 (transferSyntax, NULL, pixelSequence).good() && pixelSequence)
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239 {
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240 return pixelSequence->card();
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241 }
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242 else
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243 {
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244 return 1;
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245 }
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246 }
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247
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248
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249 static void AnswerDicomField(RestApiOutput& output,
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250 DcmElement& element,
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251 E_TransferSyntax transferSyntax)
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252 {
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253 // This element is nor a sequence, neither a pixel-data
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254 std::string buffer;
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255 buffer.resize(65536);
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256 Uint32 length = element.getLength(transferSyntax);
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257 Uint32 offset = 0;
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258
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259 output.GetLowLevelOutput().SendOkHeader(CONTENT_TYPE_OCTET_STREAM, true, length, NULL);
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260
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261 while (offset < length)
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262 {
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263 Uint32 nbytes;
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264 if (length - offset < buffer.size())
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265 {
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266 nbytes = length - offset;
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267 }
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268 else
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269 {
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270 nbytes = buffer.size();
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271 }
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272
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273 OFCondition cond = element.getPartialValue(&buffer[0], offset, nbytes);
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274
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275 if (cond.good())
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276 {
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277 output.GetLowLevelOutput().Send(&buffer[0], nbytes);
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278 offset += nbytes;
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279 }
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280 else
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281 {
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282 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text();
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283 return;
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284 }
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285 }
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286
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287 output.MarkLowLevelOutputDone();
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288 }
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289
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290
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291 static bool AnswerPixelData(RestApiOutput& output,
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292 DcmItem& dicom,
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293 E_TransferSyntax transferSyntax,
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294 const std::string* blockUri)
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295 {
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296 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(),
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297 DICOM_TAG_PIXEL_DATA.GetElement());
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298
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299 DcmElement *element = NULL;
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300 if (!dicom.findAndGetElement(k, element).good() ||
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301 element == NULL)
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302 {
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303 return false;
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304 }
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305
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306 try
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307 {
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308 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element);
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309 if (blockUri == NULL)
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310 {
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311 // The user asks how many blocks are presents in this pixel data
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312 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax);
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313
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314 Json::Value result(Json::arrayValue);
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315 for (unsigned int i = 0; i < blocks; i++)
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316 {
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317 result.append(boost::lexical_cast<std::string>(i));
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318 }
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319
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320 output.AnswerJson(result);
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321 return true;
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322 }
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323
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324
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325 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri);
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326
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327 if (block < GetPixelDataBlockCount(pixelData, transferSyntax))
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328 {
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329 DcmPixelSequence* pixelSequence = NULL;
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330 if (pixelData.getEncapsulatedRepresentation
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331 (transferSyntax, NULL, pixelSequence).good() && pixelSequence)
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332 {
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333 // This is the case for JPEG transfer syntaxes
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334 if (block < pixelSequence->card())
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335 {
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336 DcmPixelItem* pixelItem = NULL;
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337 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem)
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338 {
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339 if (pixelItem->getLength() == 0)
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340 {
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341 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM);
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342 return true;
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343 }
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344
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345 Uint8* buffer = NULL;
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346 if (pixelItem->getUint8Array(buffer).good() && buffer)
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347 {
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348 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM);
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349 return true;
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350 }
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351 }
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352 }
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353 }
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354 else
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355 {
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356 // This is the case for raw, uncompressed image buffers
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357 assert(*blockUri == "0");
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358 AnswerDicomField(output, *element, transferSyntax);
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359 }
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360 }
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361 }
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362 catch (boost::bad_lexical_cast&)
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363 {
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364 // The URI entered by the user is not a number
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365 }
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366 catch (std::bad_cast&)
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367 {
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368 // This should never happen
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369 }
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370
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371 return false;
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372 }
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373
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374
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375
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376 static void SendPathValueForLeaf(RestApiOutput& output,
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377 const std::string& tag,
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378 DcmItem& dicom,
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379 E_TransferSyntax transferSyntax)
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380 {
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381 DcmTagKey k;
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382 ParseTagAndGroup(k, tag);
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383
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384 DcmSequenceOfItems* sequence = NULL;
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385 if (dicom.findAndGetSequence(k, sequence).good() &&
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386 sequence != NULL &&
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387 sequence->getVR() == EVR_SQ)
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388 {
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389 SendSequence(output, *sequence);
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390 return;
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391 }
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392
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393 DcmElement* element = NULL;
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394 if (dicom.findAndGetElement(k, element).good() &&
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395 element != NULL &&
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396 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags
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397 element->getVR() != EVR_SQ)
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398 {
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399 AnswerDicomField(output, *element, transferSyntax);
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400 }
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401 }
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402
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403 void ParsedDicomFile::SendPathValue(RestApiOutput& output,
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404 const UriComponents& uri)
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405 {
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794
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406 DcmItem* dicom = pimpl_->file_->getDataset();
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407 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer();
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790
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408
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409 // Special case: Accessing the pixel data
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410 if (uri.size() == 1 ||
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411 uri.size() == 2)
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412 {
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413 DcmTagKey tag;
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414 ParseTagAndGroup(tag, uri[0]);
|
|
|
415
|
|
|
416 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() &&
|
|
|
417 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement())
|
|
|
418 {
|
|
|
419 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]);
|
|
|
420 return;
|
|
|
421 }
|
|
|
422 }
|
|
|
423
|
|
|
424 // Go down in the tag hierarchy according to the URI
|
|
|
425 for (size_t pos = 0; pos < uri.size() / 2; pos++)
|
|
|
426 {
|
|
|
427 size_t index;
|
|
|
428 try
|
|
|
429 {
|
|
|
430 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]);
|
|
|
431 }
|
|
|
432 catch (boost::bad_lexical_cast&)
|
|
|
433 {
|
|
|
434 return;
|
|
|
435 }
|
|
|
436
|
|
|
437 DcmTagKey k;
|
|
|
438 DcmItem *child = NULL;
|
|
|
439 ParseTagAndGroup(k, uri[2 * pos]);
|
|
|
440 if (!dicom->findAndGetSequenceItem(k, child, index).good() ||
|
|
|
441 child == NULL)
|
|
|
442 {
|
|
|
443 return;
|
|
|
444 }
|
|
|
445
|
|
|
446 dicom = child;
|
|
|
447 }
|
|
|
448
|
|
|
449 // We have reached the end of the URI
|
|
|
450 if (uri.size() % 2 == 0)
|
|
|
451 {
|
|
|
452 SendPathValueForDictionary(output, *dicom);
|
|
|
453 }
|
|
|
454 else
|
|
|
455 {
|
|
|
456 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax);
|
|
|
457 }
|
|
|
458 }
|
|
|
459
|
|
|
460
|
|
|
461
|
|
|
462
|
|
|
463
|
|
|
464 static DcmElement* CreateElementForTag(const DicomTag& tag)
|
|
|
465 {
|
|
|
466 DcmTag key(tag.GetGroup(), tag.GetElement());
|
|
|
467
|
|
|
468 switch (key.getEVR())
|
|
|
469 {
|
|
|
470 // http://support.dcmtk.org/docs/dcvr_8h-source.html
|
|
|
471
|
|
|
472 /**
|
|
|
473 * TODO.
|
|
|
474 **/
|
|
|
475
|
|
|
476 case EVR_OB: // other byte
|
|
|
477 case EVR_OF: // other float
|
|
|
478 case EVR_OW: // other word
|
|
|
479 case EVR_AT: // attribute tag
|
|
|
480 throw OrthancException(ErrorCode_NotImplemented);
|
|
|
481
|
|
|
482 case EVR_UN: // unknown value representation
|
|
|
483 throw OrthancException(ErrorCode_ParameterOutOfRange);
|
|
|
484
|
|
|
485
|
|
|
486 /**
|
|
|
487 * String types.
|
|
|
488 * http://support.dcmtk.org/docs/classDcmByteString.html
|
|
|
489 **/
|
|
|
490
|
|
|
491 case EVR_AS: // age string
|
|
|
492 return new DcmAgeString(key);
|
|
|
493
|
|
|
494 case EVR_AE: // application entity title
|
|
|
495 return new DcmApplicationEntity(key);
|
|
|
496
|
|
|
497 case EVR_CS: // code string
|
|
|
498 return new DcmCodeString(key);
|
|
|
499
|
|
|
500 case EVR_DA: // date string
|
|
|
501 return new DcmDate(key);
|
|
|
502
|
|
|
503 case EVR_DT: // date time string
|
|
|
504 return new DcmDateTime(key);
|
|
|
505
|
|
|
506 case EVR_DS: // decimal string
|
|
|
507 return new DcmDecimalString(key);
|
|
|
508
|
|
|
509 case EVR_IS: // integer string
|
|
|
510 return new DcmIntegerString(key);
|
|
|
511
|
|
|
512 case EVR_TM: // time string
|
|
|
513 return new DcmTime(key);
|
|
|
514
|
|
|
515 case EVR_UI: // unique identifier
|
|
|
516 return new DcmUniqueIdentifier(key);
|
|
|
517
|
|
|
518 case EVR_ST: // short text
|
|
|
519 return new DcmShortText(key);
|
|
|
520
|
|
|
521 case EVR_LO: // long string
|
|
|
522 return new DcmLongString(key);
|
|
|
523
|
|
|
524 case EVR_LT: // long text
|
|
|
525 return new DcmLongText(key);
|
|
|
526
|
|
|
527 case EVR_UT: // unlimited text
|
|
|
528 return new DcmUnlimitedText(key);
|
|
|
529
|
|
|
530 case EVR_SH: // short string
|
|
|
531 return new DcmShortString(key);
|
|
|
532
|
|
|
533 case EVR_PN: // person name
|
|
|
534 return new DcmPersonName(key);
|
|
|
535
|
|
|
536
|
|
|
537 /**
|
|
|
538 * Numerical types
|
|
|
539 **/
|
|
|
540
|
|
|
541 case EVR_SL: // signed long
|
|
|
542 return new DcmSignedLong(key);
|
|
|
543
|
|
|
544 case EVR_SS: // signed short
|
|
|
545 return new DcmSignedShort(key);
|
|
|
546
|
|
|
547 case EVR_UL: // unsigned long
|
|
|
548 return new DcmUnsignedLong(key);
|
|
|
549
|
|
|
550 case EVR_US: // unsigned short
|
|
|
551 return new DcmUnsignedShort(key);
|
|
|
552
|
|
|
553 case EVR_FL: // float single-precision
|
|
|
554 return new DcmFloatingPointSingle(key);
|
|
|
555
|
|
|
556 case EVR_FD: // float double-precision
|
|
|
557 return new DcmFloatingPointDouble(key);
|
|
|
558
|
|
|
559
|
|
|
560 /**
|
|
|
561 * Sequence types, should never occur at this point.
|
|
|
562 **/
|
|
|
563
|
|
|
564 case EVR_SQ: // sequence of items
|
|
|
565 throw OrthancException(ErrorCode_ParameterOutOfRange);
|
|
|
566
|
|
|
567
|
|
|
568 /**
|
|
|
569 * Internal to DCMTK.
|
|
|
570 **/
|
|
|
571
|
|
|
572 case EVR_ox: // OB or OW depending on context
|
|
|
573 case EVR_xs: // SS or US depending on context
|
|
|
574 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name)
|
|
|
575 case EVR_na: // na="not applicable", for data which has no VR
|
|
|
576 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor
|
|
|
577 case EVR_item: // used internally for items
|
|
|
578 case EVR_metainfo: // used internally for meta info datasets
|
|
|
579 case EVR_dataset: // used internally for datasets
|
|
|
580 case EVR_fileFormat: // used internally for DICOM files
|
|
|
581 case EVR_dicomDir: // used internally for DICOMDIR objects
|
|
|
582 case EVR_dirRecord: // used internally for DICOMDIR records
|
|
|
583 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image
|
|
|
584 case EVR_pixelItem: // used internally for pixel items in a compressed image
|
|
|
585 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
|
|
|
586 case EVR_PixelData: // used internally for uncompressed pixeld data
|
|
|
587 case EVR_OverlayData: // used internally for overlay data
|
|
|
588 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR
|
|
|
589 default:
|
|
|
590 break;
|
|
|
591 }
|
|
|
592
|
|
|
593 throw OrthancException(ErrorCode_InternalError);
|
|
|
594 }
|
|
|
595
|
|
|
596
|
|
|
597
|
|
|
598 static void FillElementWithString(DcmElement& element,
|
|
|
599 const DicomTag& tag,
|
|
|
600 const std::string& value)
|
|
|
601 {
|
|
|
602 DcmTag key(tag.GetGroup(), tag.GetElement());
|
|
|
603 bool ok = false;
|
|
|
604
|
|
|
605 try
|
|
|
606 {
|
|
|
607 switch (key.getEVR())
|
|
|
608 {
|
|
|
609 // http://support.dcmtk.org/docs/dcvr_8h-source.html
|
|
|
610
|
|
|
611 /**
|
|
|
612 * TODO.
|
|
|
613 **/
|
|
|
614
|
|
|
615 case EVR_OB: // other byte
|
|
|
616 case EVR_OF: // other float
|
|
|
617 case EVR_OW: // other word
|
|
|
618 case EVR_AT: // attribute tag
|
|
|
619 throw OrthancException(ErrorCode_NotImplemented);
|
|
|
620
|
|
|
621 case EVR_UN: // unknown value representation
|
|
|
622 throw OrthancException(ErrorCode_ParameterOutOfRange);
|
|
|
623
|
|
|
624
|
|
|
625 /**
|
|
|
626 * String types.
|
|
|
627 **/
|
|
|
628
|
|
|
629 case EVR_DS: // decimal string
|
|
|
630 case EVR_IS: // integer string
|
|
|
631 case EVR_AS: // age string
|
|
|
632 case EVR_DA: // date string
|
|
|
633 case EVR_DT: // date time string
|
|
|
634 case EVR_TM: // time string
|
|
|
635 case EVR_AE: // application entity title
|
|
|
636 case EVR_CS: // code string
|
|
|
637 case EVR_SH: // short string
|
|
|
638 case EVR_LO: // long string
|
|
|
639 case EVR_ST: // short text
|
|
|
640 case EVR_LT: // long text
|
|
|
641 case EVR_UT: // unlimited text
|
|
|
642 case EVR_PN: // person name
|
|
|
643 case EVR_UI: // unique identifier
|
|
|
644 {
|
|
|
645 ok = element.putString(value.c_str()).good();
|
|
|
646 break;
|
|
|
647 }
|
|
|
648
|
|
|
649
|
|
|
650 /**
|
|
|
651 * Numerical types
|
|
|
652 **/
|
|
|
653
|
|
|
654 case EVR_SL: // signed long
|
|
|
655 {
|
|
|
656 ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good();
|
|
|
657 break;
|
|
|
658 }
|
|
|
659
|
|
|
660 case EVR_SS: // signed short
|
|
|
661 {
|
|
|
662 ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good();
|
|
|
663 break;
|
|
|
664 }
|
|
|
665
|
|
|
666 case EVR_UL: // unsigned long
|
|
|
667 {
|
|
|
668 ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good();
|
|
|
669 break;
|
|
|
670 }
|
|
|
671
|
|
|
672 case EVR_US: // unsigned short
|
|
|
673 {
|
|
|
674 ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good();
|
|
|
675 break;
|
|
|
676 }
|
|
|
677
|
|
|
678 case EVR_FL: // float single-precision
|
|
|
679 {
|
|
|
680 ok = element.putFloat32(boost::lexical_cast<float>(value)).good();
|
|
|
681 break;
|
|
|
682 }
|
|
|
683
|
|
|
684 case EVR_FD: // float double-precision
|
|
|
685 {
|
|
|
686 ok = element.putFloat64(boost::lexical_cast<double>(value)).good();
|
|
|
687 break;
|
|
|
688 }
|
|
|
689
|
|
|
690
|
|
|
691 /**
|
|
|
692 * Sequence types, should never occur at this point.
|
|
|
693 **/
|
|
|
694
|
|
|
695 case EVR_SQ: // sequence of items
|
|
|
696 {
|
|
|
697 ok = false;
|
|
|
698 break;
|
|
|
699 }
|
|
|
700
|
|
|
701
|
|
|
702 /**
|
|
|
703 * Internal to DCMTK.
|
|
|
704 **/
|
|
|
705
|
|
|
706 case EVR_ox: // OB or OW depending on context
|
|
|
707 case EVR_xs: // SS or US depending on context
|
|
|
708 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name)
|
|
|
709 case EVR_na: // na="not applicable", for data which has no VR
|
|
|
710 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor
|
|
|
711 case EVR_item: // used internally for items
|
|
|
712 case EVR_metainfo: // used internally for meta info datasets
|
|
|
713 case EVR_dataset: // used internally for datasets
|
|
|
714 case EVR_fileFormat: // used internally for DICOM files
|
|
|
715 case EVR_dicomDir: // used internally for DICOMDIR objects
|
|
|
716 case EVR_dirRecord: // used internally for DICOMDIR records
|
|
|
717 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image
|
|
|
718 case EVR_pixelItem: // used internally for pixel items in a compressed image
|
|
|
719 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
|
|
|
720 case EVR_PixelData: // used internally for uncompressed pixeld data
|
|
|
721 case EVR_OverlayData: // used internally for overlay data
|
|
|
722 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR
|
|
|
723 default:
|
|
|
724 break;
|
|
|
725 }
|
|
|
726 }
|
|
|
727 catch (boost::bad_lexical_cast&)
|
|
|
728 {
|
|
|
729 ok = false;
|
|
|
730 }
|
|
|
731
|
|
|
732 if (!ok)
|
|
|
733 {
|
|
|
734 throw OrthancException(ErrorCode_InternalError);
|
|
|
735 }
|
|
|
736 }
|
|
|
737
|
|
|
738
|
|
|
739 void ParsedDicomFile::Remove(const DicomTag& tag)
|
|
|
740 {
|
|
|
741 DcmTagKey key(tag.GetGroup(), tag.GetElement());
|
|
794
|
742 DcmElement* element = pimpl_->file_->getDataset()->remove(key);
|
|
790
|
743 if (element != NULL)
|
|
|
744 {
|
|
|
745 delete element;
|
|
|
746 }
|
|
|
747 }
|
|
|
748
|
|
|
749
|
|
|
750
|
|
|
751 void ParsedDicomFile::RemovePrivateTags()
|
|
|
752 {
|
|
|
753 typedef std::list<DcmElement*> Tags;
|
|
|
754
|
|
|
755 Tags privateTags;
|
|
|
756
|
|
794
|
757 DcmDataset& dataset = *pimpl_->file_->getDataset();
|
|
790
|
758 for (unsigned long i = 0; i < dataset.card(); i++)
|
|
|
759 {
|
|
|
760 DcmElement* element = dataset.getElement(i);
|
|
|
761 DcmTag tag(element->getTag());
|
|
|
762 if (!strcmp("PrivateCreator", tag.getTagName()) || // TODO - This may change with future versions of DCMTK
|
|
|
763 tag.getPrivateCreator() != NULL)
|
|
|
764 {
|
|
|
765 privateTags.push_back(element);
|
|
|
766 }
|
|
|
767 }
|
|
|
768
|
|
|
769 for (Tags::iterator it = privateTags.begin();
|
|
|
770 it != privateTags.end(); ++it)
|
|
|
771 {
|
|
|
772 DcmElement* tmp = dataset.remove(*it);
|
|
|
773 if (tmp != NULL)
|
|
|
774 {
|
|
|
775 delete tmp;
|
|
|
776 }
|
|
|
777 }
|
|
|
778 }
|
|
|
779
|
|
|
780
|
|
|
781
|
|
|
782 void ParsedDicomFile::Insert(const DicomTag& tag,
|
|
|
783 const std::string& value)
|
|
|
784 {
|
|
|
785 std::auto_ptr<DcmElement> element(CreateElementForTag(tag));
|
|
|
786 FillElementWithString(*element, tag, value);
|
|
|
787
|
|
794
|
788 if (!pimpl_->file_->getDataset()->insert(element.release(), false, false).good())
|
|
790
|
789 {
|
|
|
790 // This field already exists
|
|
|
791 throw OrthancException(ErrorCode_InternalError);
|
|
|
792 }
|
|
|
793 }
|
|
|
794
|
|
|
795
|
|
|
796 void ParsedDicomFile::Replace(const DicomTag& tag,
|
|
|
797 const std::string& value,
|
|
|
798 DicomReplaceMode mode)
|
|
|
799 {
|
|
|
800 DcmTagKey key(tag.GetGroup(), tag.GetElement());
|
|
|
801 DcmElement* element = NULL;
|
|
|
802
|
|
794
|
803 if (!pimpl_->file_->getDataset()->findAndGetElement(key, element).good() ||
|
|
790
|
804 element == NULL)
|
|
|
805 {
|
|
|
806 // This field does not exist, act wrt. the specified "mode"
|
|
|
807 switch (mode)
|
|
|
808 {
|
|
|
809 case DicomReplaceMode_InsertIfAbsent:
|
|
|
810 Insert(tag, value);
|
|
|
811 break;
|
|
|
812
|
|
|
813 case DicomReplaceMode_ThrowIfAbsent:
|
|
|
814 throw OrthancException(ErrorCode_InexistentItem);
|
|
|
815
|
|
|
816 case DicomReplaceMode_IgnoreIfAbsent:
|
|
|
817 return;
|
|
|
818 }
|
|
|
819 }
|
|
|
820 else
|
|
|
821 {
|
|
|
822 FillElementWithString(*element, tag, value);
|
|
|
823 }
|
|
|
824
|
|
|
825
|
|
|
826 /**
|
|
|
827 * dcmodify will automatically correct 'Media Storage SOP Class
|
|
|
828 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if
|
|
|
829 * you make changes to the related tags in the dataset ('SOP Class
|
|
|
830 * UID' and 'SOP Instance UID') via insert or modify mode
|
|
|
831 * options. You can disable this behaviour by using the -nmu
|
|
|
832 * option.
|
|
|
833 **/
|
|
|
834
|
|
|
835 if (tag == DICOM_TAG_SOP_CLASS_UID)
|
|
|
836 {
|
|
|
837 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent);
|
|
|
838 }
|
|
|
839
|
|
|
840 if (tag == DICOM_TAG_SOP_INSTANCE_UID)
|
|
|
841 {
|
|
|
842 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent);
|
|
|
843 }
|
|
|
844 }
|
|
|
845
|
|
|
846
|
|
|
847 void ParsedDicomFile::Answer(RestApiOutput& output)
|
|
|
848 {
|
|
|
849 std::string serialized;
|
|
794
|
850 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, pimpl_->file_->getDataset()))
|
|
790
|
851 {
|
|
|
852 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM);
|
|
|
853 }
|
|
|
854 }
|
|
|
855
|
|
|
856
|
|
|
857
|
|
|
858 bool ParsedDicomFile::GetTagValue(std::string& value,
|
|
|
859 const DicomTag& tag)
|
|
|
860 {
|
|
|
861 DcmTagKey k(tag.GetGroup(), tag.GetElement());
|
|
794
|
862 DcmDataset& dataset = *pimpl_->file_->getDataset();
|
|
790
|
863 DcmElement* element = NULL;
|
|
|
864 if (!dataset.findAndGetElement(k, element).good() ||
|
|
|
865 element == NULL)
|
|
|
866 {
|
|
|
867 return false;
|
|
|
868 }
|
|
|
869
|
|
|
870 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element));
|
|
|
871
|
|
|
872 if (v.get() == NULL)
|
|
|
873 {
|
|
|
874 value = "";
|
|
|
875 }
|
|
|
876 else
|
|
|
877 {
|
|
|
878 value = v->AsString();
|
|
|
879 }
|
|
|
880
|
|
|
881 return true;
|
|
|
882 }
|
|
|
883
|
|
|
884
|
|
|
885
|
|
|
886 DicomInstanceHasher ParsedDicomFile::GetHasher()
|
|
|
887 {
|
|
|
888 std::string patientId, studyUid, seriesUid, instanceUid;
|
|
|
889
|
|
|
890 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) ||
|
|
|
891 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) ||
|
|
|
892 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) ||
|
|
|
893 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID))
|
|
|
894 {
|
|
|
895 throw OrthancException(ErrorCode_BadFileFormat);
|
|
|
896 }
|
|
|
897
|
|
|
898 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid);
|
|
|
899 }
|
|
|
900
|
|
|
901
|
|
|
902 static void StoreElement(Json::Value& target,
|
|
|
903 DcmElement& element,
|
|
|
904 unsigned int maxStringLength);
|
|
|
905
|
|
|
906 static void StoreItem(Json::Value& target,
|
|
|
907 DcmItem& item,
|
|
|
908 unsigned int maxStringLength)
|
|
|
909 {
|
|
|
910 target = Json::Value(Json::objectValue);
|
|
|
911
|
|
|
912 for (unsigned long i = 0; i < item.card(); i++)
|
|
|
913 {
|
|
|
914 DcmElement* element = item.getElement(i);
|
|
|
915 StoreElement(target, *element, maxStringLength);
|
|
|
916 }
|
|
|
917 }
|
|
|
918
|
|
|
919
|
|
|
920 static void StoreElement(Json::Value& target,
|
|
|
921 DcmElement& element,
|
|
|
922 unsigned int maxStringLength)
|
|
|
923 {
|
|
|
924 assert(target.type() == Json::objectValue);
|
|
|
925
|
|
|
926 DicomTag tag(FromDcmtkBridge::GetTag(element));
|
|
|
927 const std::string formattedTag = tag.Format();
|
|
|
928
|
|
|
929 #if 0
|
|
|
930 const std::string tagName = FromDcmtkBridge::GetName(tag);
|
|
|
931 #else
|
|
|
932 // This version of the code gives access to the name of the private tags
|
|
|
933 DcmTag tagbis(element.getTag());
|
|
|
934 const std::string tagName(tagbis.getTagName());
|
|
|
935 #endif
|
|
|
936
|
|
|
937 if (element.isLeaf())
|
|
|
938 {
|
|
|
939 Json::Value value(Json::objectValue);
|
|
|
940 value["Name"] = tagName;
|
|
|
941
|
|
|
942 if (tagbis.getPrivateCreator() != NULL)
|
|
|
943 {
|
|
|
944 value["PrivateCreator"] = tagbis.getPrivateCreator();
|
|
|
945 }
|
|
|
946
|
|
|
947 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element));
|
|
|
948 if (v->IsNull())
|
|
|
949 {
|
|
|
950 value["Type"] = "Null";
|
|
|
951 value["Value"] = Json::nullValue;
|
|
|
952 }
|
|
|
953 else
|
|
|
954 {
|
|
|
955 std::string s = v->AsString();
|
|
|
956 if (maxStringLength == 0 ||
|
|
|
957 s.size() <= maxStringLength)
|
|
|
958 {
|
|
|
959 value["Type"] = "String";
|
|
|
960 value["Value"] = s;
|
|
|
961 }
|
|
|
962 else
|
|
|
963 {
|
|
|
964 value["Type"] = "TooLong";
|
|
|
965 value["Value"] = Json::nullValue;
|
|
|
966 }
|
|
|
967 }
|
|
|
968
|
|
|
969 target[formattedTag] = value;
|
|
|
970 }
|
|
|
971 else
|
|
|
972 {
|
|
|
973 Json::Value children(Json::arrayValue);
|
|
|
974
|
|
|
975 // "All subclasses of DcmElement except for DcmSequenceOfItems
|
|
|
976 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset
|
|
|
977 // etc. are not." The following cast is thus OK.
|
|
|
978 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element);
|
|
|
979
|
|
|
980 for (unsigned long i = 0; i < sequence.card(); i++)
|
|
|
981 {
|
|
|
982 DcmItem* child = sequence.getItem(i);
|
|
|
983 Json::Value& v = children.append(Json::objectValue);
|
|
|
984 StoreItem(v, *child, maxStringLength);
|
|
|
985 }
|
|
|
986
|
|
|
987 target[formattedTag]["Name"] = tagName;
|
|
|
988 target[formattedTag]["Type"] = "Sequence";
|
|
|
989 target[formattedTag]["Value"] = children;
|
|
|
990 }
|
|
|
991 }
|
|
|
992
|
|
|
993
|
|
|
994 template <typename T>
|
|
|
995 static void ExtractPngImageTruncate(std::string& result,
|
|
|
996 DicomIntegerPixelAccessor& accessor,
|
|
|
997 PixelFormat format)
|
|
|
998 {
|
|
|
999 assert(accessor.GetChannelCount() == 1);
|
|
|
1000
|
|
|
1001 PngWriter w;
|
|
|
1002
|
|
|
1003 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0);
|
|
|
1004 T* pixel = &image[0];
|
|
|
1005 for (unsigned int y = 0; y < accessor.GetHeight(); y++)
|
|
|
1006 {
|
|
|
1007 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++)
|
|
|
1008 {
|
|
|
1009 int32_t v = accessor.GetValue(x, y);
|
|
|
1010 if (v < static_cast<int32_t>(std::numeric_limits<T>::min()))
|
|
|
1011 *pixel = std::numeric_limits<T>::min();
|
|
|
1012 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max()))
|
|
|
1013 *pixel = std::numeric_limits<T>::max();
|
|
|
1014 else
|
|
|
1015 *pixel = static_cast<T>(v);
|
|
|
1016 }
|
|
|
1017 }
|
|
|
1018
|
|
|
1019 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(),
|
|
|
1020 accessor.GetWidth() * sizeof(T), format, &image[0]);
|
|
|
1021 }
|
|
|
1022
|
|
|
1023
|
|
|
1024 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer)
|
|
|
1025 {
|
|
794
|
1026 FromDcmtkBridge::SaveToMemoryBuffer(buffer, pimpl_->file_->getDataset());
|
|
790
|
1027 }
|
|
|
1028
|
|
|
1029
|
|
|
1030 void ParsedDicomFile::SaveToFile(const std::string& path)
|
|
|
1031 {
|
|
|
1032 // TODO Avoid using a temporary memory buffer, write directly on disk
|
|
|
1033 std::string content;
|
|
|
1034 SaveToMemoryBuffer(content);
|
|
|
1035 Toolbox::WriteFile(content, path);
|
|
|
1036 }
|
|
|
1037
|
|
|
1038
|
|
794
|
1039 ParsedDicomFile::ParsedDicomFile() : pimpl_(new PImpl)
|
|
790
|
1040 {
|
|
794
|
1041 pimpl_->file_.reset(new DcmFileFormat);
|
|
790
|
1042 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient));
|
|
|
1043 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study));
|
|
|
1044 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series));
|
|
|
1045 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance));
|
|
|
1046 }
|
|
|
1047
|
|
791
|
1048
|
|
794
|
1049 ParsedDicomFile::ParsedDicomFile(const char* content, size_t size) : pimpl_(new PImpl)
|
|
791
|
1050 {
|
|
|
1051 Setup(content, size);
|
|
|
1052 }
|
|
|
1053
|
|
794
|
1054 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl)
|
|
791
|
1055 {
|
|
|
1056 if (content.size() == 0)
|
|
|
1057 {
|
|
|
1058 Setup(NULL, 0);
|
|
|
1059 }
|
|
|
1060 else
|
|
|
1061 {
|
|
|
1062 Setup(&content[0], content.size());
|
|
|
1063 }
|
|
|
1064 }
|
|
792
|
1065
|
|
|
1066
|
|
794
|
1067 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) :
|
|
|
1068 pimpl_(new PImpl)
|
|
792
|
1069 {
|
|
794
|
1070 pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone()));
|
|
792
|
1071 }
|
|
|
1072
|
|
|
1073
|
|
|
1074 ParsedDicomFile::~ParsedDicomFile()
|
|
|
1075 {
|
|
794
|
1076 delete pimpl_;
|
|
792
|
1077 }
|
|
|
1078
|
|
793
|
1079
|
|
|
1080 void* ParsedDicomFile::GetDcmtkObject()
|
|
|
1081 {
|
|
794
|
1082 return pimpl_->file_.get();
|
|
793
|
1083 }
|
|
|
1084
|
|
|
1085
|
|
|
1086 ParsedDicomFile* ParsedDicomFile::Clone()
|
|
|
1087 {
|
|
794
|
1088 return new ParsedDicomFile(*this);
|
|
793
|
1089 }
|
|
790
|
1090 }
|
