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annotate OrthancCppClient/Series.cpp @ 888:d44b845c1c89 plugins

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Sat, 14 Jun 2014 19:47:51 +0200
parents a811bdf8b8eb
children de18e90d5507
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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 "../Core/PrecompiledHeaders.h"
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34 #include "Series.h"
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35
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36 #include "OrthancConnection.h"
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37
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38 #include <set>
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39 #include <boost/lexical_cast.hpp>
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40
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41 namespace OrthancClient
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42 {
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43 namespace
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44 {
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45 class SliceLocator
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46 {
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47 private:
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48 float normal_[3];
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49
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50 public:
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51 SliceLocator(Instance& someSlice)
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52 {
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53 /**
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54 * Compute the slice normal from Image Orientation Patient.
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55 * http://nipy.sourceforge.net/nibabel/dicom/dicom_orientation.html#dicom-z-from-slice
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56 * http://www.itk.org/pipermail/insight-users/2003-September/004762.html
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57 **/
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58
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59 std::vector<float> cosines;
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60 someSlice.SplitVectorOfFloats(cosines, "ImageOrientationPatient");
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61
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62 if (cosines.size() != 6)
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63 {
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64 throw OrthancClientException(Orthanc::ErrorCode_BadFileFormat);
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65 }
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66
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67 normal_[0] = cosines[1] * cosines[5] - cosines[2] * cosines[4];
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68 normal_[1] = cosines[2] * cosines[3] - cosines[0] * cosines[5];
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69 normal_[2] = cosines[0] * cosines[4] - cosines[1] * cosines[3];
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70 }
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71
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72
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73 /**
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74 * Compute the distance of some slice along the slice normal.
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75 **/
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76 float ComputeSliceLocation(Instance& instance) const
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77 {
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78 std::vector<float> ipp;
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79 instance.SplitVectorOfFloats(ipp, "ImagePositionPatient");
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80 if (ipp.size() != 3)
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81 {
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82 throw OrthancClientException(Orthanc::ErrorCode_BadFileFormat);
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83 }
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84
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85 float dist = 0;
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86
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87 for (int i = 0; i < 3; i++)
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88 {
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89 dist += normal_[i] * ipp[i];
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90 }
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91
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92 return dist;
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93 }
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94 };
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95
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96 class ImageDownloadCommand : public Orthanc::ICommand
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97 {
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98 private:
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99 Orthanc::PixelFormat format_;
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100 Orthanc::ImageExtractionMode mode_;
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101 Instance& instance_;
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102 void* target_;
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103 size_t lineStride_;
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104
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105 public:
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106 ImageDownloadCommand(Instance& instance,
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107 Orthanc::PixelFormat format,
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108 Orthanc::ImageExtractionMode mode,
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109 void* target,
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110 size_t lineStride) :
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111 format_(format),
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112 mode_(mode),
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113 instance_(instance),
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114 target_(target),
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115 lineStride_(lineStride)
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116 {
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117 instance_.SetImageExtractionMode(mode);
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118 }
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119
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120 virtual bool Execute()
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121 {
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122 using namespace Orthanc;
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123
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124 unsigned int width = instance_.GetHeight();
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125
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126 for (unsigned int y = 0; y < instance_.GetHeight(); y++)
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127 {
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128 uint8_t* p = reinterpret_cast<uint8_t*>(target_) + y * lineStride_;
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129
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130 if (instance_.GetPixelFormat() == format_)
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131 {
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132 memcpy(p, instance_.GetBuffer(y), 2 * instance_.GetWidth());
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133 }
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134 else if (instance_.GetPixelFormat() == PixelFormat_Grayscale8 &&
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135 format_ == PixelFormat_RGB24)
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136 {
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137 const uint8_t* s = reinterpret_cast<const uint8_t*>(instance_.GetBuffer(y));
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138 for (unsigned int x = 0; x < width; x++, s++, p += 3)
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139 {
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140 p[0] = *s;
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141 p[1] = *s;
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142 p[2] = *s;
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143 }
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144 }
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145 else
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146 {
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147 throw OrthancClientException(ErrorCode_NotImplemented);
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148 }
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149 }
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150
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151 // Do not keep the image in memory, as we are loading 3D images
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152 instance_.DiscardImage();
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153
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154 return true;
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155 }
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156 };
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157
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158
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159 class ProgressToFloatListener : public Orthanc::ThreadedCommandProcessor::IListener
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160 {
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161 private:
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162 float* target_;
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163
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164 public:
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165 ProgressToFloatListener(float* target) : target_(target)
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166 {
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167 }
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168
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169 virtual void SignalProgress(unsigned int current,
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170 unsigned int total)
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171 {
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172 if (total == 0)
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173 {
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174 *target_ = 0;
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175 }
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176 else
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177 {
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178 *target_ = static_cast<float>(current) / static_cast<float>(total);
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179 }
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180 }
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181
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182 virtual void SignalSuccess(unsigned int total)
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183 {
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184 *target_ = 1;
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185 }
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186
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187 virtual void SignalFailure()
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188 {
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189 *target_ = 0;
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190 }
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191
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192 virtual void SignalCancel()
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193 {
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194 *target_ = 0;
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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
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201 void Series::Check3DImage()
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202 {
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203 if (!Is3DImage())
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204 {
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205 throw OrthancClientException(Orthanc::ErrorCode_NotImplemented);
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206 }
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207 }
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208
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209 bool Series::Is3DImageInternal()
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210 {
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211 try
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212 {
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213 if (GetInstanceCount() == 0)
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214 {
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215 return true;
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216 }
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217
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218 Instance& i1 = GetInstance(0);
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219
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220 for (unsigned int i = 0; i < GetInstanceCount(); i++)
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221 {
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222 Instance& i2 = GetInstance(i);
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223
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224 if (std::string(i1.GetTagAsString("Columns")) != std::string(i2.GetTagAsString("Columns")) ||
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225 std::string(i1.GetTagAsString("Rows")) != std::string(i2.GetTagAsString("Rows")) ||
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226 std::string(i1.GetTagAsString("ImageOrientationPatient")) != std::string(i2.GetTagAsString("ImageOrientationPatient")) ||
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227 std::string(i1.GetTagAsString("SliceThickness")) != std::string(i2.GetTagAsString("SliceThickness")) ||
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228 std::string(i1.GetTagAsString("PixelSpacing")) != std::string(i2.GetTagAsString("PixelSpacing")))
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229 {
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230 return false;
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231 }
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232 }
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233
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234 SliceLocator locator(GetInstance(0));
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235 std::set<float> l;
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236 for (unsigned int i = 0; i < GetInstanceCount(); i++)
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237 {
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238 l.insert(locator.ComputeSliceLocation(GetInstance(i)));
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239 }
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240
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241 return l.size() == GetInstanceCount();
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242 }
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243 catch (OrthancClientException)
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244 {
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245 return false;
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246 }
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247 }
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248
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249 void Series::ReadSeries()
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250 {
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251 Orthanc::HttpClient client(connection_.GetHttpClient());
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252
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253 client.SetUrl(std::string(connection_.GetOrthancUrl()) + "/series/" + id_);
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254 Json::Value v;
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255 if (!client.Apply(series_))
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256 {
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257 throw OrthancClientException(Orthanc::ErrorCode_NetworkProtocol);
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258 }
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259 }
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260
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261 Orthanc::IDynamicObject* Series::GetFillerItem(size_t index)
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262 {
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263 Json::Value::ArrayIndex tmp = static_cast<Json::Value::ArrayIndex>(index);
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264 std::string id = series_["Instances"][tmp].asString();
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265 return new Instance(connection_, id.c_str());
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266 }
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267
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268 Series::Series(const OrthancConnection& connection,
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269 const char* id) :
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270 connection_(connection),
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271 id_(id),
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272 instances_(*this)
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273 {
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274 ReadSeries();
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275 status_ = Status3DImage_NotTested;
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276 url_ = std::string(connection_.GetOrthancUrl()) + "/series/" + id_;
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277
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278 isVoxelSizeRead_ = false;
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279 voxelSizeX_ = 0;
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280 voxelSizeY_ = 0;
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281 voxelSizeZ_ = 0;
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282
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283 instances_.SetThreadCount(connection.GetThreadCount());
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284 }
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285
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286
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287 bool Series::Is3DImage()
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288 {
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289 if (status_ == Status3DImage_NotTested)
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290 {
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291 status_ = Is3DImageInternal() ? Status3DImage_True : Status3DImage_False;
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292 }
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293
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294 return status_ == Status3DImage_True;
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295 }
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296
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297 unsigned int Series::GetInstanceCount()
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298 {
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299 return instances_.GetSize();
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300 }
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301
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302 Instance& Series::GetInstance(unsigned int index)
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303 {
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304 return dynamic_cast<Instance&>(instances_.GetItem(index));
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305 }
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306
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307 unsigned int Series::GetWidth()
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308 {
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309 Check3DImage();
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310
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311 if (GetInstanceCount() == 0)
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312 return 0;
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313 else
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314 return GetInstance(0).GetTagAsInt("Columns");
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315 }
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316
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317 unsigned int Series::GetHeight()
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318 {
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319 Check3DImage();
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320
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321 if (GetInstanceCount() == 0)
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322 return 0;
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323 else
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324 return GetInstance(0).GetTagAsInt("Rows");
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325 }
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326
502
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327 void Series::LoadVoxelSize()
479
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328 {
502
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329 if (isVoxelSizeRead_)
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330 {
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331 return;
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332 }
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333
479
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334 Check3DImage();
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335
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336 if (GetInstanceCount() == 0)
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337 {
502
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338 // Empty image, use some default value
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339 voxelSizeX_ = 1;
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340 voxelSizeY_ = 1;
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341 voxelSizeZ_ = 1;
479
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342 }
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343 else
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344 {
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345 try
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346 {
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347 std::string s = GetInstance(0).GetTagAsString("PixelSpacing");
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348 size_t pos = s.find('\\');
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349 assert(pos != std::string::npos);
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350 std::string sy = s.substr(0, pos);
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351 std::string sx = s.substr(pos + 1);
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352
502
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353 voxelSizeX_ = boost::lexical_cast<float>(sx);
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354 voxelSizeY_ = boost::lexical_cast<float>(sy);
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355 voxelSizeZ_ = GetInstance(0).GetTagAsFloat("SliceThickness");
479
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356 }
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357 catch (boost::bad_lexical_cast)
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358 {
504
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359 throw OrthancClientException(Orthanc::ErrorCode_NotImplemented);
479
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360 }
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361 }
502
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parents: 500
diff changeset
362
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363 isVoxelSizeRead_ = true;
479
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364 }
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365
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366
500
ec19da4a1fe7 fix api
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367 const char* Series::GetMainDicomTag(const char* tag, const char* defaultValue) const
479
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368 {
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369 if (series_["MainDicomTags"].isMember(tag))
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370 {
500
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diff changeset
371 return series_["MainDicomTags"][tag].asCString();
479
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diff changeset
372 }
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diff changeset
373 else
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374 {
0cd977e94479 initial commit of the c++ client
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375 return defaultValue;
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parents:
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376 }
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parents:
diff changeset
377 }
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parents:
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378
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379
0cd977e94479 initial commit of the c++ client
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diff changeset
380
548
ffedcc8f0938 progress
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diff changeset
381 void Series::Load3DImageInternal(void* target,
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diff changeset
382 Orthanc::PixelFormat format,
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diff changeset
383 size_t lineStride,
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diff changeset
384 size_t stackStride,
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diff changeset
385 Orthanc::ThreadedCommandProcessor::IListener* listener)
479
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diff changeset
386 {
0cd977e94479 initial commit of the c++ client
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387 using namespace Orthanc;
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388
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389 // Choose the extraction mode, depending on the format of the
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390 // target image.
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391
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392 uint8_t bytesPerPixel;
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393 ImageExtractionMode mode;
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394
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395 switch (format)
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396 {
0cd977e94479 initial commit of the c++ client
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397 case PixelFormat_RGB24:
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398 bytesPerPixel = 3;
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399 mode = ImageExtractionMode_Preview;
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400 break;
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parents:
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401
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402 case PixelFormat_Grayscale8:
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403 bytesPerPixel = 1;
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404 mode = ImageExtractionMode_UInt8; // Preview ???
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parents:
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405 break;
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parents:
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406
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407 case PixelFormat_Grayscale16:
0cd977e94479 initial commit of the c++ client
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408 bytesPerPixel = 2;
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409 mode = ImageExtractionMode_UInt16;
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parents:
diff changeset
410 break;
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parents:
diff changeset
411
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parents:
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412 case PixelFormat_SignedGrayscale16:
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413 bytesPerPixel = 2;
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414 mode = ImageExtractionMode_UInt16;
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415 format = PixelFormat_Grayscale16;
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416 break;
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parents:
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417
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418 default:
504
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diff changeset
419 throw OrthancClientException(ErrorCode_NotImplemented);
479
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420 }
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421
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diff changeset
422
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423 // Check that the target image is properly sized
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424 unsigned int sx = GetWidth();
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425 unsigned int sy = GetHeight();
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diff changeset
426
0cd977e94479 initial commit of the c++ client
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427 if (lineStride < sx * bytesPerPixel ||
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428 stackStride < sx * sy * bytesPerPixel)
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429 {
504
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430 throw OrthancClientException(ErrorCode_BadRequest);
479
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431 }
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432
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433 if (sx == 0 || sy == 0 || GetInstanceCount() == 0)
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434 {
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435 // Empty image, nothing to do
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436 if (listener)
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437 listener->SignalSuccess(0);
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438 return;
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439 }
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440
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441
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442 /**
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443 * Order the stacks according to their distance along the slice
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444 * normal (using the "Image Position Patient" tag). This works
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445 * even if the "SliceLocation" tag is absent.
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446 **/
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447 SliceLocator locator(GetInstance(0));
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448
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449 typedef std::map<float, Instance*> Instances;
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450 Instances instances;
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451 for (unsigned int i = 0; i < GetInstanceCount(); i++)
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452 {
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453 float dist = locator.ComputeSliceLocation(GetInstance(i));
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454 instances[dist] = &GetInstance(i);
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455 }
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456
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457 if (instances.size() != GetInstanceCount())
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458 {
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459 // Several instances have the same Z coordinate
504
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460 throw OrthancClientException(ErrorCode_NotImplemented);
479
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461 }
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462
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463
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464 // Submit the download of each stack as a set of commands
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465 ThreadedCommandProcessor processor(connection_.GetThreadCount());
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466
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467 if (listener != NULL)
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468 {
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469 processor.SetListener(*listener);
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470 }
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471
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472 uint8_t* stackTarget = reinterpret_cast<uint8_t*>(target);
656
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473 for (Instances::iterator it = instances.begin(); it != instances.end(); ++it)
479
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474 {
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475 processor.Post(new ImageDownloadCommand(*it->second, format, mode, stackTarget, lineStride));
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476 stackTarget += stackStride;
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477 }
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parents:
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478
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parents:
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479
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diff changeset
480 // Wait for all the stacks to be downloaded
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diff changeset
481 if (!processor.Join())
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482 {
504
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parents: 502
diff changeset
483 throw OrthancClientException(ErrorCode_NetworkProtocol);
479
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484 }
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485 }
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486
502
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487 float Series::GetVoxelSizeX()
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488 {
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489 LoadVoxelSize();
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490 return voxelSizeX_;
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491 }
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492
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493 float Series::GetVoxelSizeY()
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494 {
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parents: 500
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495 LoadVoxelSize();
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496 return voxelSizeY_;
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diff changeset
497 }
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parents: 500
diff changeset
498
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diff changeset
499 float Series::GetVoxelSizeZ()
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parents: 500
diff changeset
500 {
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parents: 500
diff changeset
501 LoadVoxelSize();
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502 return voxelSizeZ_;
ee33c7d0cda0 laaw runs correctly on the c++ api
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parents: 500
diff changeset
503 }
ee33c7d0cda0 laaw runs correctly on the c++ api
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parents: 500
diff changeset
504
548
ffedcc8f0938 progress
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parents: 504
diff changeset
505 void Series::Load3DImage(void* target,
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parents: 504
diff changeset
506 Orthanc::PixelFormat format,
ffedcc8f0938 progress
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parents: 504
diff changeset
507 int64_t lineStride,
ffedcc8f0938 progress
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diff changeset
508 int64_t stackStride,
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parents: 504
diff changeset
509 float* progress)
ffedcc8f0938 progress
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parents: 504
diff changeset
510 {
ffedcc8f0938 progress
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parents: 504
diff changeset
511 ProgressToFloatListener listener(progress);
585
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jodogne
parents: 548
diff changeset
512 Load3DImageInternal(target, format, static_cast<size_t>(lineStride),
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parents: 548
diff changeset
513 static_cast<size_t>(stackStride), &listener);
548
ffedcc8f0938 progress
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parents: 504
diff changeset
514 }
479
0cd977e94479 initial commit of the c++ client
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diff changeset
515 }