Mercurial > hg > orthanc

annotate Core/DicomFormat/DicomIntegerPixelAccessor.cpp @ 835:a15ad019bbec

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 02 Jun 2014 12:21:50 +0200
parents a811bdf8b8eb
children 839be3022203
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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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32
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33 #include "../PrecompiledHeaders.h"
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34
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35 #ifndef NOMINMAX
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36 #define NOMINMAX
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37 #endif
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38
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39 #include "DicomIntegerPixelAccessor.h"
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40
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41 #include "../OrthancException.h"
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42 #include <boost/lexical_cast.hpp>
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43 #include <limits>
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44 #include <cassert>
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45 #include <stdio.h>
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46
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47 namespace Orthanc
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48 {
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49 DicomIntegerPixelAccessor::DicomIntegerPixelAccessor(const DicomMap& values,
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50 const void* pixelData,
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51 size_t size) :
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52 pixelData_(pixelData),
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53 size_(size)
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54 {
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55 unsigned int bitsAllocated;
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56 unsigned int bitsStored;
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57 unsigned int highBit;
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58 unsigned int pixelRepresentation;
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59 planarConfiguration_ = 0;
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61 try
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62 {
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63 width_ = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_COLUMNS).AsString());
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64 height_ = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_ROWS).AsString());
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65 samplesPerPixel_ = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_SAMPLES_PER_PIXEL).AsString());
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66 bitsAllocated = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_BITS_ALLOCATED).AsString());
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67 bitsStored = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_BITS_STORED).AsString());
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68 highBit = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_HIGH_BIT).AsString());
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69 pixelRepresentation = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_PIXEL_REPRESENTATION).AsString());
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71 if (samplesPerPixel_ > 1)
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72 {
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73 // The "Planar Configuration" is only set when "Samples per Pixels" is greater than 1
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74 // https://www.dabsoft.ch/dicom/3/C.7.6.3.1.3/
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75 planarConfiguration_ = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_PLANAR_CONFIGURATION).AsString());
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76 }
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77 }
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78 catch (boost::bad_lexical_cast)
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79 {
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80 throw OrthancException(ErrorCode_NotImplemented);
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81 }
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82 catch (OrthancException)
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83 {
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84 throw OrthancException(ErrorCode_NotImplemented);
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85 }
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86
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87 frame_ = 0;
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88 try
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89 {
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90 numberOfFrames_ = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_NUMBER_OF_FRAMES).AsString());
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91 }
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92 catch (OrthancException)
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93 {
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94 // If the tag "NumberOfFrames" is absent, assume there is a single frame
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95 numberOfFrames_ = 1;
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96 }
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97 catch (boost::bad_lexical_cast)
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98 {
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99 throw OrthancException(ErrorCode_NotImplemented);
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100 }
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101
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102 if ((bitsAllocated != 8 && bitsAllocated != 16 &&
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103 bitsAllocated != 24 && bitsAllocated != 32) ||
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104 numberOfFrames_ == 0 ||
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105 (planarConfiguration_ != 0 && planarConfiguration_ != 1))
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106 {
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107 throw OrthancException(ErrorCode_NotImplemented);
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108 }
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109
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110 if (bitsAllocated > 32 ||
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111 bitsStored >= 32)
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112 {
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113 // Not available, as the accessor internally uses int32_t values
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114 throw OrthancException(ErrorCode_NotImplemented);
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115 }
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116
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117 if (samplesPerPixel_ == 0)
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118 {
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119 throw OrthancException(ErrorCode_NotImplemented);
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120 }
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121
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122 bytesPerPixel_ = bitsAllocated / 8;
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123 shift_ = highBit + 1 - bitsStored;
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124 frameOffset_ = height_ * width_ * bytesPerPixel_ * samplesPerPixel_;
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125
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126 if (numberOfFrames_ * frameOffset_ > size)
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127 {
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128 throw OrthancException(ErrorCode_BadFileFormat);
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129 }
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130
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131 /*printf("%d %d %d %d %d %d %d %d\n", width_, height_, samplesPerPixel_, bitsAllocated,
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132 bitsStored, highBit, pixelRepresentation, numberOfFrames_);*/
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134 if (pixelRepresentation)
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135 {
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136 // Pixels are signed
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137 mask_ = (1 << (bitsStored - 1)) - 1;
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138 signMask_ = (1 << (bitsStored - 1));
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139 }
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140 else
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141 {
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142 // Pixels are unsigned
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143 mask_ = (1 << bitsStored) - 1;
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144 signMask_ = 0;
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145 }
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146
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147 if (planarConfiguration_ == 0)
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148 {
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149 /**
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150 * The sample values for the first pixel are followed by the
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151 * sample values for the second pixel, etc. For RGB images, this
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152 * means the order of the pixel values sent shall be R1, G1, B1,
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153 * R2, G2, B2, ..., etc.
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154 **/
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155 rowOffset_ = width_ * bytesPerPixel_ * samplesPerPixel_;
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156 }
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157 else
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158 {
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159 /**
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160 * Each color plane shall be sent contiguously. For RGB images,
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161 * this means the order of the pixel values sent is R1, R2, R3,
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162 * ..., G1, G2, G3, ..., B1, B2, B3, etc.
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163 **/
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164 rowOffset_ = width_ * bytesPerPixel_;
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165 }
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166 }
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167
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168
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169 void DicomIntegerPixelAccessor::GetExtremeValues(int32_t& min,
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170 int32_t& max) const
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171 {
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172 if (height_ == 0 || width_ == 0)
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173 {
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174 min = max = 0;
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175 return;
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176 }
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177
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178 min = std::numeric_limits<int32_t>::max();
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179 max = std::numeric_limits<int32_t>::min();
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180
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181 for (unsigned int y = 0; y < height_; y++)
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182 {
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183 for (unsigned int x = 0; x < width_; x++)
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184 {
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185 for (unsigned int c = 0; c < GetChannelCount(); c++)
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186 {
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187 int32_t v = GetValue(x, y);
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188 if (v < min)
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189 min = v;
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190 if (v > max)
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191 max = v;
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192 }
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193 }
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194 }
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195 }
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196
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197
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198 int32_t DicomIntegerPixelAccessor::GetValue(unsigned int x,
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199 unsigned int y,
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200 unsigned int channel) const
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201 {
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202 assert(x < width_ && y < height_ && channel < samplesPerPixel_);
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203
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204 const uint8_t* pixel = reinterpret_cast<const uint8_t*>(pixelData_) +
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205 y * rowOffset_ + frame_ * frameOffset_;
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206
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207 // https://www.dabsoft.ch/dicom/3/C.7.6.3.1.3/
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208 if (planarConfiguration_ == 0)
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209 {
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210 /**
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211 * The sample values for the first pixel are followed by the
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212 * sample values for the second pixel, etc. For RGB images, this
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213 * means the order of the pixel values sent shall be R1, G1, B1,
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214 * R2, G2, B2, ..., etc.
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215 **/
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216 pixel += channel * bytesPerPixel_ + x * samplesPerPixel_ * bytesPerPixel_;
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217 }
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218 else
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219 {
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220 /**
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221 * Each color plane shall be sent contiguously. For RGB images,
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222 * this means the order of the pixel values sent is R1, R2, R3,
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223 * ..., G1, G2, G3, ..., B1, B2, B3, etc.
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224 **/
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225 assert(frameOffset_ % samplesPerPixel_ == 0);
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226 pixel += channel * frameOffset_ / samplesPerPixel_ + x * bytesPerPixel_;
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227 }
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228
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229 uint32_t v;
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230 v = pixel[0];
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231 if (bytesPerPixel_ >= 2)
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232 v = v + (static_cast<uint32_t>(pixel[1]) << 8);
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233 if (bytesPerPixel_ >= 3)
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234 v = v + (static_cast<uint32_t>(pixel[2]) << 16);
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235 if (bytesPerPixel_ >= 4)
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236 v = v + (static_cast<uint32_t>(pixel[3]) << 24);
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237
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238 v = v >> shift_;
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239
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240 if (v & signMask_)
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241 {
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242 // Signed value
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243 // http://en.wikipedia.org/wiki/Two%27s_complement#Subtraction_from_2N
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244 return -static_cast<int32_t>(mask_) + static_cast<int32_t>(v & mask_) - 1;
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245 }
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246 else
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247 {
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248 // Unsigned value
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249 return static_cast<int32_t>(v & mask_);
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250 }
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251 }
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252
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253
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254 void DicomIntegerPixelAccessor::SetCurrentFrame(unsigned int frame)
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255 {
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256 if (frame >= numberOfFrames_)
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257 {
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258 throw OrthancException(ErrorCode_ParameterOutOfRange);
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259 }
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260
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261 frame_ = frame;
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262 }
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263
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264 }