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annotate OrthancCppClient/Series.cpp @ 796:e7b1ca0f1e04

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creation of dicom files
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 06 May 2014 12:09:11 +0200
parents 2d0a347e8cfc
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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31
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32
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33 #include "Series.h"
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34
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35 #include "OrthancConnection.h"
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36
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37 #include <set>
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38 #include <boost/lexical_cast.hpp>
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39
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40 namespace OrthancClient
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41 {
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42 namespace
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43 {
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44 class SliceLocator
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45 {
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46 private:
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47 float normal_[3];
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48
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49 public:
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50 SliceLocator(Instance& someSlice)
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51 {
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52 /**
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53 * Compute the slice normal from Image Orientation Patient.
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54 * http://nipy.sourceforge.net/nibabel/dicom/dicom_orientation.html#dicom-z-from-slice
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55 * http://www.itk.org/pipermail/insight-users/2003-September/004762.html
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56 **/
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57
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58 std::vector<float> cosines;
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59 someSlice.SplitVectorOfFloats(cosines, "ImageOrientationPatient");
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60
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61 if (cosines.size() != 6)
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62 {
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63 throw OrthancClientException(Orthanc::ErrorCode_BadFileFormat);
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64 }
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65
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66 normal_[0] = cosines[1] * cosines[5] - cosines[2] * cosines[4];
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67 normal_[1] = cosines[2] * cosines[3] - cosines[0] * cosines[5];
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68 normal_[2] = cosines[0] * cosines[4] - cosines[1] * cosines[3];
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69 }
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70
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71
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72 /**
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73 * Compute the distance of some slice along the slice normal.
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74 **/
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75 float ComputeSliceLocation(Instance& instance) const
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76 {
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77 std::vector<float> ipp;
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78 instance.SplitVectorOfFloats(ipp, "ImagePositionPatient");
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79 if (ipp.size() != 3)
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80 {
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81 throw OrthancClientException(Orthanc::ErrorCode_BadFileFormat);
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82 }
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83
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84 float dist = 0;
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85
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86 for (int i = 0; i < 3; i++)
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87 {
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88 dist += normal_[i] * ipp[i];
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89 }
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90
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91 return dist;
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92 }
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93 };
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94
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95 class ImageDownloadCommand : public Orthanc::ICommand
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96 {
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97 private:
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98 Orthanc::PixelFormat format_;
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99 Orthanc::ImageExtractionMode mode_;
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100 Instance& instance_;
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101 void* target_;
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102 size_t lineStride_;
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103
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104 public:
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105 ImageDownloadCommand(Instance& instance,
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106 Orthanc::PixelFormat format,
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107 Orthanc::ImageExtractionMode mode,
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108 void* target,
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109 size_t lineStride) :
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110 format_(format),
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111 mode_(mode),
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112 instance_(instance),
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113 target_(target),
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114 lineStride_(lineStride)
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115 {
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116 instance_.SetImageExtractionMode(mode);
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117 }
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118
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119 virtual bool Execute()
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120 {
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121 using namespace Orthanc;
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122
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123 unsigned int width = instance_.GetHeight();
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124
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125 for (unsigned int y = 0; y < instance_.GetHeight(); y++)
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126 {
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127 uint8_t* p = reinterpret_cast<uint8_t*>(target_) + y * lineStride_;
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128
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129 if (instance_.GetPixelFormat() == format_)
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130 {
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131 memcpy(p, instance_.GetBuffer(y), 2 * instance_.GetWidth());
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132 }
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133 else if (instance_.GetPixelFormat() == PixelFormat_Grayscale8 &&
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134 format_ == PixelFormat_RGB24)
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135 {
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136 const uint8_t* s = reinterpret_cast<const uint8_t*>(instance_.GetBuffer(y));
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137 for (unsigned int x = 0; x < width; x++, s++, p += 3)
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138 {
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139 p[0] = *s;
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140 p[1] = *s;
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141 p[2] = *s;
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142 }
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143 }
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144 else
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145 {
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146 throw OrthancClientException(ErrorCode_NotImplemented);
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147 }
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148 }
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149
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150 // Do not keep the image in memory, as we are loading 3D images
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151 instance_.DiscardImage();
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152
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153 return true;
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154 }
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155 };
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156
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157
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158 class ProgressToFloatListener : public Orthanc::ThreadedCommandProcessor::IListener
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159 {
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160 private:
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161 float* target_;
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162
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163 public:
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164 ProgressToFloatListener(float* target) : target_(target)
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165 {
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166 }
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167
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168 virtual void SignalProgress(unsigned int current,
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169 unsigned int total)
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170 {
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171 if (total == 0)
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172 {
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173 *target_ = 0;
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174 }
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175 else
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176 {
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177 *target_ = static_cast<float>(current) / static_cast<float>(total);
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178 }
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179 }
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180
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181 virtual void SignalSuccess(unsigned int total)
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182 {
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183 *target_ = 1;
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184 }
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185
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186 virtual void SignalFailure()
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187 {
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188 *target_ = 0;
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189 }
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190
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191 virtual void SignalCancel()
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192 {
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193 *target_ = 0;
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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
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199
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200 void Series::Check3DImage()
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201 {
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202 if (!Is3DImage())
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203 {
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204 throw OrthancClientException(Orthanc::ErrorCode_NotImplemented);
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205 }
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206 }
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207
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208 bool Series::Is3DImageInternal()
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209 {
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210 try
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211 {
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212 if (GetInstanceCount() == 0)
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213 {
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214 return true;
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215 }
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216
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217 Instance& i1 = GetInstance(0);
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218
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219 for (unsigned int i = 0; i < GetInstanceCount(); i++)
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220 {
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221 Instance& i2 = GetInstance(i);
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222
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223 if (std::string(i1.GetTagAsString("Columns")) != std::string(i2.GetTagAsString("Columns")) ||
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224 std::string(i1.GetTagAsString("Rows")) != std::string(i2.GetTagAsString("Rows")) ||
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225 std::string(i1.GetTagAsString("ImageOrientationPatient")) != std::string(i2.GetTagAsString("ImageOrientationPatient")) ||
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226 std::string(i1.GetTagAsString("SliceThickness")) != std::string(i2.GetTagAsString("SliceThickness")) ||
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227 std::string(i1.GetTagAsString("PixelSpacing")) != std::string(i2.GetTagAsString("PixelSpacing")))
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228 {
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229 return false;
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230 }
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231 }
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232
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233 SliceLocator locator(GetInstance(0));
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234 std::set<float> l;
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235 for (unsigned int i = 0; i < GetInstanceCount(); i++)
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236 {
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237 l.insert(locator.ComputeSliceLocation(GetInstance(i)));
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238 }
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239
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240 return l.size() == GetInstanceCount();
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241 }
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242 catch (OrthancClientException)
479
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243 {
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244 return false;
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245 }
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246 }
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247
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248 void Series::ReadSeries()
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249 {
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250 Orthanc::HttpClient client(connection_.GetHttpClient());
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251
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252 client.SetUrl(std::string(connection_.GetOrthancUrl()) + "/series/" + id_);
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253 Json::Value v;
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254 if (!client.Apply(series_))
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255 {
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256 throw OrthancClientException(Orthanc::ErrorCode_NetworkProtocol);
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257 }
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258 }
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259
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260 Orthanc::IDynamicObject* Series::GetFillerItem(size_t index)
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261 {
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262 Json::Value::ArrayIndex tmp = static_cast<Json::Value::ArrayIndex>(index);
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263 std::string id = series_["Instances"][tmp].asString();
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264 return new Instance(connection_, id.c_str());
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265 }
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266
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267 Series::Series(const OrthancConnection& connection,
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268 const char* id) :
479
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269 connection_(connection),
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270 id_(id),
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271 instances_(*this)
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272 {
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273 ReadSeries();
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274 status_ = Status3DImage_NotTested;
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275 url_ = std::string(connection_.GetOrthancUrl()) + "/series/" + id_;
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276
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277 isVoxelSizeRead_ = false;
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278 voxelSizeX_ = 0;
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279 voxelSizeY_ = 0;
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280 voxelSizeZ_ = 0;
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281
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282 instances_.SetThreadCount(connection.GetThreadCount());
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283 }
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284
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285
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286 bool Series::Is3DImage()
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287 {
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288 if (status_ == Status3DImage_NotTested)
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289 {
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290 status_ = Is3DImageInternal() ? Status3DImage_True : Status3DImage_False;
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291 }
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292
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293 return status_ == Status3DImage_True;
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294 }
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295
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296 unsigned int Series::GetInstanceCount()
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297 {
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298 return instances_.GetSize();
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299 }
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300
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301 Instance& Series::GetInstance(unsigned int index)
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302 {
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303 return dynamic_cast<Instance&>(instances_.GetItem(index));
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304 }
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305
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306 unsigned int Series::GetWidth()
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307 {
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308 Check3DImage();
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309
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310 if (GetInstanceCount() == 0)
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311 return 0;
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312 else
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313 return GetInstance(0).GetTagAsInt("Columns");
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314 }
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315
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316 unsigned int Series::GetHeight()
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317 {
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318 Check3DImage();
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319
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320 if (GetInstanceCount() == 0)
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321 return 0;
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322 else
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323 return GetInstance(0).GetTagAsInt("Rows");
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324 }
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325
502
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326 void Series::LoadVoxelSize()
479
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327 {
502
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328 if (isVoxelSizeRead_)
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329 {
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330 return;
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331 }
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332
479
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333 Check3DImage();
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334
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335 if (GetInstanceCount() == 0)
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336 {
502
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337 // Empty image, use some default value
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338 voxelSizeX_ = 1;
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339 voxelSizeY_ = 1;
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340 voxelSizeZ_ = 1;
479
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341 }
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342 else
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343 {
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344 try
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345 {
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346 std::string s = GetInstance(0).GetTagAsString("PixelSpacing");
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347 size_t pos = s.find('\\');
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348 assert(pos != std::string::npos);
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349 std::string sy = s.substr(0, pos);
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350 std::string sx = s.substr(pos + 1);
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351
502
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352 voxelSizeX_ = boost::lexical_cast<float>(sx);
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353 voxelSizeY_ = boost::lexical_cast<float>(sy);
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354 voxelSizeZ_ = GetInstance(0).GetTagAsFloat("SliceThickness");
479
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355 }
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356 catch (boost::bad_lexical_cast)
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357 {
504
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358 throw OrthancClientException(Orthanc::ErrorCode_NotImplemented);
479
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359 }
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360 }
502
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parents: 500
diff changeset
361
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362 isVoxelSizeRead_ = true;
479
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363 }
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364
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365
500
ec19da4a1fe7 fix api
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366 const char* Series::GetMainDicomTag(const char* tag, const char* defaultValue) const
479
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367 {
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368 if (series_["MainDicomTags"].isMember(tag))
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369 {
500
ec19da4a1fe7 fix api
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parents: 496
diff changeset
370 return series_["MainDicomTags"][tag].asCString();
479
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diff changeset
371 }
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diff changeset
372 else
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diff changeset
373 {
0cd977e94479 initial commit of the c++ client
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374 return defaultValue;
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375 }
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parents:
diff changeset
376 }
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parents:
diff changeset
377
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diff changeset
378
0cd977e94479 initial commit of the c++ client
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diff changeset
379
548
ffedcc8f0938 progress
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diff changeset
380 void Series::Load3DImageInternal(void* target,
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parents: 504
diff changeset
381 Orthanc::PixelFormat format,
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diff changeset
382 size_t lineStride,
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diff changeset
383 size_t stackStride,
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parents: 504
diff changeset
384 Orthanc::ThreadedCommandProcessor::IListener* listener)
479
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diff changeset
385 {
0cd977e94479 initial commit of the c++ client
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386 using namespace Orthanc;
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387
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388 // Choose the extraction mode, depending on the format of the
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389 // target image.
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390
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391 uint8_t bytesPerPixel;
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392 ImageExtractionMode mode;
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393
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diff changeset
394 switch (format)
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395 {
0cd977e94479 initial commit of the c++ client
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396 case PixelFormat_RGB24:
0cd977e94479 initial commit of the c++ client
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397 bytesPerPixel = 3;
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diff changeset
398 mode = ImageExtractionMode_Preview;
0cd977e94479 initial commit of the c++ client
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diff changeset
399 break;
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parents:
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400
0cd977e94479 initial commit of the c++ client
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401 case PixelFormat_Grayscale8:
0cd977e94479 initial commit of the c++ client
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402 bytesPerPixel = 1;
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403 mode = ImageExtractionMode_UInt8; // Preview ???
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parents:
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404 break;
0cd977e94479 initial commit of the c++ client
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parents:
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405
0cd977e94479 initial commit of the c++ client
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parents:
diff changeset
406 case PixelFormat_Grayscale16:
0cd977e94479 initial commit of the c++ client
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407 bytesPerPixel = 2;
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parents:
diff changeset
408 mode = ImageExtractionMode_UInt16;
0cd977e94479 initial commit of the c++ client
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parents:
diff changeset
409 break;
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parents:
diff changeset
410
0cd977e94479 initial commit of the c++ client
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parents:
diff changeset
411 case PixelFormat_SignedGrayscale16:
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diff changeset
412 bytesPerPixel = 2;
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diff changeset
413 mode = ImageExtractionMode_UInt16;
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parents:
diff changeset
414 format = PixelFormat_Grayscale16;
0cd977e94479 initial commit of the c++ client
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parents:
diff changeset
415 break;
0cd977e94479 initial commit of the c++ client
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parents:
diff changeset
416
0cd977e94479 initial commit of the c++ client
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parents:
diff changeset
417 default:
504
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diff changeset
418 throw OrthancClientException(ErrorCode_NotImplemented);
479
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diff changeset
419 }
0cd977e94479 initial commit of the c++ client
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parents:
diff changeset
420
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diff changeset
421
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422 // Check that the target image is properly sized
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423 unsigned int sx = GetWidth();
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parents:
diff changeset
424 unsigned int sy = GetHeight();
0cd977e94479 initial commit of the c++ client
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parents:
diff changeset
425
0cd977e94479 initial commit of the c++ client
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diff changeset
426 if (lineStride < sx * bytesPerPixel ||
0cd977e94479 initial commit of the c++ client
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427 stackStride < sx * sy * bytesPerPixel)
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diff changeset
428 {
504
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429 throw OrthancClientException(ErrorCode_BadRequest);
479
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430 }
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431
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432 if (sx == 0 || sy == 0 || GetInstanceCount() == 0)
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433 {
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434 // Empty image, nothing to do
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435 if (listener)
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436 listener->SignalSuccess(0);
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437 return;
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438 }
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439
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440
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441 /**
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442 * Order the stacks according to their distance along the slice
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443 * normal (using the "Image Position Patient" tag). This works
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444 * even if the "SliceLocation" tag is absent.
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445 **/
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446 SliceLocator locator(GetInstance(0));
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447
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448 typedef std::map<float, Instance*> Instances;
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449 Instances instances;
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450 for (unsigned int i = 0; i < GetInstanceCount(); i++)
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451 {
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452 float dist = locator.ComputeSliceLocation(GetInstance(i));
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453 instances[dist] = &GetInstance(i);
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454 }
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455
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456 if (instances.size() != GetInstanceCount())
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457 {
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458 // Several instances have the same Z coordinate
504
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459 throw OrthancClientException(ErrorCode_NotImplemented);
479
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460 }
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461
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462
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463 // Submit the download of each stack as a set of commands
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464 ThreadedCommandProcessor processor(connection_.GetThreadCount());
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465
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466 if (listener != NULL)
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467 {
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468 processor.SetListener(*listener);
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469 }
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470
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471 uint8_t* stackTarget = reinterpret_cast<uint8_t*>(target);
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472 for (Instances::iterator it = instances.begin(); it != instances.end(); ++it)
479
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473 {
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474 processor.Post(new ImageDownloadCommand(*it->second, format, mode, stackTarget, lineStride));
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475 stackTarget += stackStride;
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476 }
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477
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parents:
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478
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479 // Wait for all the stacks to be downloaded
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480 if (!processor.Join())
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481 {
504
50d9660f960c laaw exception
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diff changeset
482 throw OrthancClientException(ErrorCode_NetworkProtocol);
479
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483 }
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484 }
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485
502
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486 float Series::GetVoxelSizeX()
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487 {
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488 LoadVoxelSize();
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489 return voxelSizeX_;
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490 }
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491
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492 float Series::GetVoxelSizeY()
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493 {
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494 LoadVoxelSize();
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495 return voxelSizeY_;
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496 }
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497
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498 float Series::GetVoxelSizeZ()
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499 {
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500 LoadVoxelSize();
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501 return voxelSizeZ_;
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502 }
ee33c7d0cda0 laaw runs correctly on the c++ api
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diff changeset
503
548
ffedcc8f0938 progress
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504 void Series::Load3DImage(void* target,
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505 Orthanc::PixelFormat format,
ffedcc8f0938 progress
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506 int64_t lineStride,
ffedcc8f0938 progress
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507 int64_t stackStride,
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508 float* progress)
ffedcc8f0938 progress
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parents: 504
diff changeset
509 {
ffedcc8f0938 progress
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parents: 504
diff changeset
510 ProgressToFloatListener listener(progress);
585
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511 Load3DImageInternal(target, format, static_cast<size_t>(lineStride),
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parents: 548
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512 static_cast<size_t>(stackStride), &listener);
548
ffedcc8f0938 progress
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parents: 504
diff changeset
513 }
479
0cd977e94479 initial commit of the c++ client
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514 }