Mercurial > hg > orthanc

annotate Core/DicomFormat/DicomIntegerPixelAccessor.cpp @ 823:da4c30a8bcdd templating

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 28 May 2014 16:21:48 +0200
parents ecedd89055db
children a811bdf8b8eb
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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 #ifndef NOMINMAX
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34 #define NOMINMAX
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35 #endif
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36
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37 #include "DicomIntegerPixelAccessor.h"
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38
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39 #include "../OrthancException.h"
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40 #include <boost/lexical_cast.hpp>
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41 #include <limits>
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42 #include <cassert>
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43 #include <stdio.h>
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44
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45 namespace Orthanc
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46 {
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47 DicomIntegerPixelAccessor::DicomIntegerPixelAccessor(const DicomMap& values,
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48 const void* pixelData,
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49 size_t size) :
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50 pixelData_(pixelData),
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51 size_(size)
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52 {
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53 unsigned int bitsAllocated;
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54 unsigned int bitsStored;
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55 unsigned int highBit;
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56 unsigned int pixelRepresentation;
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57 planarConfiguration_ = 0;
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59 try
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60 {
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61 width_ = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_COLUMNS).AsString());
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62 height_ = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_ROWS).AsString());
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63 samplesPerPixel_ = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_SAMPLES_PER_PIXEL).AsString());
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64 bitsAllocated = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_BITS_ALLOCATED).AsString());
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65 bitsStored = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_BITS_STORED).AsString());
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66 highBit = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_HIGH_BIT).AsString());
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67 pixelRepresentation = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_PIXEL_REPRESENTATION).AsString());
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69 if (samplesPerPixel_ > 1)
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70 {
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71 // The "Planar Configuration" is only set when "Samples per Pixels" is greater than 1
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72 // https://www.dabsoft.ch/dicom/3/C.7.6.3.1.3/
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73 planarConfiguration_ = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_PLANAR_CONFIGURATION).AsString());
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74 }
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75 }
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76 catch (boost::bad_lexical_cast)
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77 {
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78 throw OrthancException(ErrorCode_NotImplemented);
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79 }
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80 catch (OrthancException)
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81 {
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82 throw OrthancException(ErrorCode_NotImplemented);
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83 }
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84
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85 frame_ = 0;
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86 try
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87 {
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88 numberOfFrames_ = boost::lexical_cast<unsigned int>(values.GetValue(DICOM_TAG_NUMBER_OF_FRAMES).AsString());
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89 }
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90 catch (OrthancException)
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91 {
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92 // If the tag "NumberOfFrames" is absent, assume there is a single frame
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93 numberOfFrames_ = 1;
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94 }
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95 catch (boost::bad_lexical_cast)
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96 {
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97 throw OrthancException(ErrorCode_NotImplemented);
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98 }
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99
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100 if ((bitsAllocated != 8 && bitsAllocated != 16 &&
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101 bitsAllocated != 24 && bitsAllocated != 32) ||
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102 numberOfFrames_ == 0 ||
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103 (planarConfiguration_ != 0 && planarConfiguration_ != 1))
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104 {
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105 throw OrthancException(ErrorCode_NotImplemented);
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106 }
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107
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108 if (bitsAllocated > 32 ||
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109 bitsStored >= 32)
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110 {
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111 // Not available, as the accessor internally uses int32_t values
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112 throw OrthancException(ErrorCode_NotImplemented);
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113 }
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114
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115 if (samplesPerPixel_ == 0)
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116 {
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117 throw OrthancException(ErrorCode_NotImplemented);
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118 }
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119
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120 bytesPerPixel_ = bitsAllocated / 8;
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121 shift_ = highBit + 1 - bitsStored;
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122 frameOffset_ = height_ * width_ * bytesPerPixel_ * samplesPerPixel_;
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123
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124 if (numberOfFrames_ * frameOffset_ > size)
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125 {
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126 throw OrthancException(ErrorCode_BadFileFormat);
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127 }
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128
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129 /*printf("%d %d %d %d %d %d %d %d\n", width_, height_, samplesPerPixel_, bitsAllocated,
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130 bitsStored, highBit, pixelRepresentation, numberOfFrames_);*/
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131
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132 if (pixelRepresentation)
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133 {
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134 // Pixels are signed
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135 mask_ = (1 << (bitsStored - 1)) - 1;
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136 signMask_ = (1 << (bitsStored - 1));
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137 }
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138 else
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139 {
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140 // Pixels are unsigned
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141 mask_ = (1 << bitsStored) - 1;
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142 signMask_ = 0;
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143 }
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144
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145 if (planarConfiguration_ == 0)
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146 {
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147 /**
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148 * The sample values for the first pixel are followed by the
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149 * sample values for the second pixel, etc. For RGB images, this
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150 * means the order of the pixel values sent shall be R1, G1, B1,
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151 * R2, G2, B2, ..., etc.
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152 **/
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153 rowOffset_ = width_ * bytesPerPixel_ * samplesPerPixel_;
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154 }
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155 else
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156 {
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157 /**
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158 * Each color plane shall be sent contiguously. For RGB images,
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159 * this means the order of the pixel values sent is R1, R2, R3,
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160 * ..., G1, G2, G3, ..., B1, B2, B3, etc.
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161 **/
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162 rowOffset_ = width_ * bytesPerPixel_;
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163 }
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164 }
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165
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166
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167 void DicomIntegerPixelAccessor::GetExtremeValues(int32_t& min,
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168 int32_t& max) const
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169 {
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170 if (height_ == 0 || width_ == 0)
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171 {
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172 min = max = 0;
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173 return;
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174 }
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175
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176 min = std::numeric_limits<int32_t>::max();
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177 max = std::numeric_limits<int32_t>::min();
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178
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179 for (unsigned int y = 0; y < height_; y++)
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180 {
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181 for (unsigned int x = 0; x < width_; x++)
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182 {
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183 for (unsigned int c = 0; c < GetChannelCount(); c++)
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184 {
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185 int32_t v = GetValue(x, y);
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186 if (v < min)
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187 min = v;
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188 if (v > max)
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189 max = v;
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190 }
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191 }
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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 int32_t DicomIntegerPixelAccessor::GetValue(unsigned int x,
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197 unsigned int y,
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198 unsigned int channel) const
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199 {
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200 assert(x < width_ && y < height_ && channel < samplesPerPixel_);
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201
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202 const uint8_t* pixel = reinterpret_cast<const uint8_t*>(pixelData_) +
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203 y * rowOffset_ + frame_ * frameOffset_;
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204
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205 // https://www.dabsoft.ch/dicom/3/C.7.6.3.1.3/
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206 if (planarConfiguration_ == 0)
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207 {
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208 /**
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209 * The sample values for the first pixel are followed by the
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210 * sample values for the second pixel, etc. For RGB images, this
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211 * means the order of the pixel values sent shall be R1, G1, B1,
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212 * R2, G2, B2, ..., etc.
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213 **/
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214 pixel += channel * bytesPerPixel_ + x * samplesPerPixel_ * bytesPerPixel_;
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215 }
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216 else
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217 {
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218 /**
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219 * Each color plane shall be sent contiguously. For RGB images,
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220 * this means the order of the pixel values sent is R1, R2, R3,
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221 * ..., G1, G2, G3, ..., B1, B2, B3, etc.
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222 **/
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223 assert(frameOffset_ % samplesPerPixel_ == 0);
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224 pixel += channel * frameOffset_ / samplesPerPixel_ + x * bytesPerPixel_;
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225 }
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226
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227 uint32_t v;
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228 v = pixel[0];
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229 if (bytesPerPixel_ >= 2)
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230 v = v + (static_cast<uint32_t>(pixel[1]) << 8);
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231 if (bytesPerPixel_ >= 3)
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232 v = v + (static_cast<uint32_t>(pixel[2]) << 16);
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233 if (bytesPerPixel_ >= 4)
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234 v = v + (static_cast<uint32_t>(pixel[3]) << 24);
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235
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236 v = v >> shift_;
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237
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238 if (v & signMask_)
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239 {
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240 // Signed value
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241 // http://en.wikipedia.org/wiki/Two%27s_complement#Subtraction_from_2N
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242 return -static_cast<int32_t>(mask_) + static_cast<int32_t>(v & mask_) - 1;
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243 }
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244 else
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245 {
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246 // Unsigned value
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247 return static_cast<int32_t>(v & mask_);
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248 }
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249 }
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250
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251
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252 void DicomIntegerPixelAccessor::SetCurrentFrame(unsigned int frame)
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253 {
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254 if (frame >= numberOfFrames_)
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255 {
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256 throw OrthancException(ErrorCode_ParameterOutOfRange);
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257 }
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258
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259 frame_ = frame;
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260 }
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261
0
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262 }