Mercurial > hg > orthanc
annotate OrthancCppClient/Series.cpp @ 803:4689e400e0fa
directory to store the results of the unit tests
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 07 May 2014 09:29:11 +0200 |
parents | 2d0a347e8cfc |
children | a811bdf8b8eb |
rev | line source |
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1 /** |
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2 * Orthanc - A Lightweight, RESTful DICOM Store |
689 | 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 { |
504 | 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 { |
504 | 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 { |
504 | 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 }; |
548 | 156 |
157 | |
158 class ProgressToFloatListener : public Orthanc::ThreadedCommandProcessor::IListener | |
159 { | |
160 private: | |
161 float* target_; | |
162 | |
163 public: | |
164 ProgressToFloatListener(float* target) : target_(target) | |
165 { | |
166 } | |
167 | |
168 virtual void SignalProgress(unsigned int current, | |
169 unsigned int total) | |
170 { | |
171 if (total == 0) | |
172 { | |
173 *target_ = 0; | |
174 } | |
175 else | |
176 { | |
177 *target_ = static_cast<float>(current) / static_cast<float>(total); | |
178 } | |
179 } | |
180 | |
181 virtual void SignalSuccess(unsigned int total) | |
182 { | |
183 *target_ = 1; | |
184 } | |
185 | |
186 virtual void SignalFailure() | |
187 { | |
188 *target_ = 0; | |
189 } | |
190 | |
191 virtual void SignalCancel() | |
192 { | |
193 *target_ = 0; | |
194 } | |
195 }; | |
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 { |
504 | 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 |
502
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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 { |
548 | 221 Instance& i2 = GetInstance(i); |
502
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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 } |
504 | 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 |
496
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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 { |
504 | 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 { |
492
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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) : |
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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; |
500 | 275 url_ = std::string(connection_.GetOrthancUrl()) + "/series/" + id_; |
656 | 276 |
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277 isVoxelSizeRead_ = false; |
656 | 278 voxelSizeX_ = 0; |
279 voxelSizeY_ = 0; | |
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() |
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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 |
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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; |
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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"); |
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355 } |
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356 catch (boost::bad_lexical_cast) |
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357 { |
504 | 358 throw OrthancClientException(Orthanc::ErrorCode_NotImplemented); |
479
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359 } |
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360 } |
502
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361 |
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362 isVoxelSizeRead_ = true; |
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363 } |
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364 |
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365 |
500 | 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 | 370 return series_["MainDicomTags"][tag].asCString(); |
479
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371 } |
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372 else |
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373 { |
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374 return defaultValue; |
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375 } |
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376 } |
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377 |
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378 |
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379 |
548 | 380 void Series::Load3DImageInternal(void* target, |
381 Orthanc::PixelFormat format, | |
382 size_t lineStride, | |
383 size_t stackStride, | |
384 Orthanc::ThreadedCommandProcessor::IListener* listener) | |
479
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385 { |
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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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394 switch (format) |
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395 { |
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396 case PixelFormat_RGB24: |
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397 bytesPerPixel = 3; |
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398 mode = ImageExtractionMode_Preview; |
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399 break; |
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400 |
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401 case PixelFormat_Grayscale8: |
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402 bytesPerPixel = 1; |
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403 mode = ImageExtractionMode_UInt8; // Preview ??? |
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404 break; |
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405 |
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406 case PixelFormat_Grayscale16: |
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407 bytesPerPixel = 2; |
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408 mode = ImageExtractionMode_UInt16; |
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409 break; |
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410 |
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411 case PixelFormat_SignedGrayscale16: |
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412 bytesPerPixel = 2; |
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413 mode = ImageExtractionMode_UInt16; |
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414 format = PixelFormat_Grayscale16; |
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415 break; |
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416 |
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417 default: |
504 | 418 throw OrthancClientException(ErrorCode_NotImplemented); |
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419 } |
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420 |
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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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424 unsigned int sy = GetHeight(); |
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425 |
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426 if (lineStride < sx * bytesPerPixel || |
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427 stackStride < sx * sy * bytesPerPixel) |
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428 { |
504 | 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 | 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); |
656 | 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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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 | 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 } |
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503 |
548 | 504 void Series::Load3DImage(void* target, |
505 Orthanc::PixelFormat format, | |
506 int64_t lineStride, | |
507 int64_t stackStride, | |
508 float* progress) | |
509 { | |
510 ProgressToFloatListener listener(progress); | |
585 | 511 Load3DImageInternal(target, format, static_cast<size_t>(lineStride), |
512 static_cast<size_t>(stackStride), &listener); | |
548 | 513 } |
479
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514 } |