Mercurial > hg > orthanc
annotate OrthancCppClient/Series.cpp @ 1185:cbd1f05b4ef2 db-changes
plugin callbacks are executed in mutual exclusion
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 25 Sep 2014 16:40:15 +0200 |
parents | de18e90d5507 |
children | 6e7e5ed91c2d |
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 "../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 |
986 | 56 * http://dicomiseasy.blogspot.be/2013/06/getting-oriented-using-image-plane.html |
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57 * http://www.itk.org/pipermail/insight-users/2003-September/004762.html |
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58 **/ |
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59 |
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60 std::vector<float> cosines; |
986 | 61 someSlice.SplitVectorOfFloats(cosines, "ImageOrientationPatient"); // 0020-0037 |
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62 |
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63 if (cosines.size() != 6) |
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64 { |
504 | 65 throw OrthancClientException(Orthanc::ErrorCode_BadFileFormat); |
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66 } |
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67 |
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68 normal_[0] = cosines[1] * cosines[5] - cosines[2] * cosines[4]; |
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69 normal_[1] = cosines[2] * cosines[3] - cosines[0] * cosines[5]; |
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70 normal_[2] = cosines[0] * cosines[4] - cosines[1] * cosines[3]; |
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71 } |
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72 |
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73 |
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74 /** |
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75 * Compute the distance of some slice along the slice normal. |
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76 **/ |
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77 float ComputeSliceLocation(Instance& instance) const |
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78 { |
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79 std::vector<float> ipp; |
986 | 80 instance.SplitVectorOfFloats(ipp, "ImagePositionPatient"); // 0020-0032 |
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81 if (ipp.size() != 3) |
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82 { |
504 | 83 throw OrthancClientException(Orthanc::ErrorCode_BadFileFormat); |
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84 } |
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85 |
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86 float dist = 0; |
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87 |
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88 for (int i = 0; i < 3; i++) |
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89 { |
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90 dist += normal_[i] * ipp[i]; |
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91 } |
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92 |
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93 return dist; |
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94 } |
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95 }; |
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96 |
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97 class ImageDownloadCommand : public Orthanc::ICommand |
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98 { |
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99 private: |
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100 Orthanc::PixelFormat format_; |
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101 Orthanc::ImageExtractionMode mode_; |
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102 Instance& instance_; |
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103 void* target_; |
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104 size_t lineStride_; |
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105 |
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106 public: |
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107 ImageDownloadCommand(Instance& instance, |
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108 Orthanc::PixelFormat format, |
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109 Orthanc::ImageExtractionMode mode, |
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110 void* target, |
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111 size_t lineStride) : |
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112 format_(format), |
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113 mode_(mode), |
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114 instance_(instance), |
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115 target_(target), |
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116 lineStride_(lineStride) |
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117 { |
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118 instance_.SetImageExtractionMode(mode); |
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119 } |
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120 |
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121 virtual bool Execute() |
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122 { |
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123 using namespace Orthanc; |
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124 |
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125 unsigned int width = instance_.GetHeight(); |
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126 |
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127 for (unsigned int y = 0; y < instance_.GetHeight(); y++) |
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128 { |
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129 uint8_t* p = reinterpret_cast<uint8_t*>(target_) + y * lineStride_; |
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130 |
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131 if (instance_.GetPixelFormat() == format_) |
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132 { |
986 | 133 memcpy(p, instance_.GetBuffer(y), GetBytesPerPixel(instance_.GetPixelFormat()) * instance_.GetWidth()); |
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134 } |
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135 else if (instance_.GetPixelFormat() == PixelFormat_Grayscale8 && |
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136 format_ == PixelFormat_RGB24) |
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137 { |
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138 const uint8_t* s = reinterpret_cast<const uint8_t*>(instance_.GetBuffer(y)); |
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139 for (unsigned int x = 0; x < width; x++, s++, p += 3) |
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140 { |
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141 p[0] = *s; |
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142 p[1] = *s; |
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143 p[2] = *s; |
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144 } |
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145 } |
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146 else |
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147 { |
504 | 148 throw OrthancClientException(ErrorCode_NotImplemented); |
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149 } |
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150 } |
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151 |
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152 // Do not keep the image in memory, as we are loading 3D images |
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153 instance_.DiscardImage(); |
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154 |
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155 return true; |
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156 } |
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157 }; |
548 | 158 |
159 | |
160 class ProgressToFloatListener : public Orthanc::ThreadedCommandProcessor::IListener | |
161 { | |
162 private: | |
163 float* target_; | |
164 | |
165 public: | |
166 ProgressToFloatListener(float* target) : target_(target) | |
167 { | |
168 } | |
169 | |
170 virtual void SignalProgress(unsigned int current, | |
171 unsigned int total) | |
172 { | |
173 if (total == 0) | |
174 { | |
175 *target_ = 0; | |
176 } | |
177 else | |
178 { | |
179 *target_ = static_cast<float>(current) / static_cast<float>(total); | |
180 } | |
181 } | |
182 | |
183 virtual void SignalSuccess(unsigned int total) | |
184 { | |
185 *target_ = 1; | |
186 } | |
187 | |
188 virtual void SignalFailure() | |
189 { | |
190 *target_ = 0; | |
191 } | |
192 | |
193 virtual void SignalCancel() | |
194 { | |
195 *target_ = 0; | |
196 } | |
197 }; | |
198 | |
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199 } |
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200 |
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201 |
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202 void Series::Check3DImage() |
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203 { |
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204 if (!Is3DImage()) |
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205 { |
504 | 206 throw OrthancClientException(Orthanc::ErrorCode_NotImplemented); |
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207 } |
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208 } |
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209 |
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210 bool Series::Is3DImageInternal() |
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211 { |
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212 try |
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213 { |
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214 if (GetInstanceCount() == 0) |
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215 { |
986 | 216 // Empty image, use some default value (should never happen) |
217 voxelSizeX_ = 1; | |
218 voxelSizeY_ = 1; | |
219 voxelSizeZ_ = 1; | |
220 sliceThickness_ = 1; | |
221 | |
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222 return true; |
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223 } |
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224 |
986 | 225 // Choose a reference slice |
226 Instance& reference = GetInstance(0); | |
502
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227 |
986 | 228 // Check that all the child instances share the same 3D parameters |
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229 for (unsigned int i = 0; i < GetInstanceCount(); i++) |
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230 { |
548 | 231 Instance& i2 = GetInstance(i); |
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232 |
986 | 233 if (std::string(reference.GetTagAsString("Columns")) != std::string(i2.GetTagAsString("Columns")) || |
234 std::string(reference.GetTagAsString("Rows")) != std::string(i2.GetTagAsString("Rows")) || | |
235 std::string(reference.GetTagAsString("ImageOrientationPatient")) != std::string(i2.GetTagAsString("ImageOrientationPatient")) || | |
236 std::string(reference.GetTagAsString("SliceThickness")) != std::string(i2.GetTagAsString("SliceThickness")) || | |
237 std::string(reference.GetTagAsString("PixelSpacing")) != std::string(i2.GetTagAsString("PixelSpacing"))) | |
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238 { |
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239 return false; |
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240 } |
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241 } |
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242 |
986 | 243 |
244 // Extract X/Y voxel size and slice thickness | |
245 std::string s = GetInstance(0).GetTagAsString("PixelSpacing"); // 0028-0030 | |
246 size_t pos = s.find('\\'); | |
247 assert(pos != std::string::npos); | |
248 std::string sy = s.substr(0, pos); | |
249 std::string sx = s.substr(pos + 1); | |
250 | |
251 try | |
252 { | |
253 voxelSizeX_ = boost::lexical_cast<float>(sx); | |
254 voxelSizeY_ = boost::lexical_cast<float>(sy); | |
255 } | |
256 catch (boost::bad_lexical_cast) | |
257 { | |
258 throw OrthancClientException(Orthanc::ErrorCode_BadFileFormat); | |
259 } | |
260 | |
261 sliceThickness_ = GetInstance(0).GetTagAsFloat("SliceThickness"); // 0018-0050 | |
262 | |
263 | |
264 // Compute the location of each slice to extract the voxel size along Z | |
265 voxelSizeZ_ = std::numeric_limits<float>::infinity(); | |
266 | |
267 SliceLocator locator(reference); | |
268 float referenceSliceLocation = locator.ComputeSliceLocation(reference); | |
269 | |
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270 std::set<float> l; |
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271 for (unsigned int i = 0; i < GetInstanceCount(); i++) |
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272 { |
986 | 273 float location = locator.ComputeSliceLocation(GetInstance(i)); |
274 float distanceToReferenceSlice = fabs(location - referenceSliceLocation); | |
275 | |
276 l.insert(location); | |
277 | |
278 if (distanceToReferenceSlice > std::numeric_limits<float>::epsilon() && | |
279 distanceToReferenceSlice < voxelSizeZ_) | |
280 { | |
281 voxelSizeZ_ = distanceToReferenceSlice; | |
282 } | |
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283 } |
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284 |
986 | 285 |
286 // Make sure that 2 slices do not share the same Z location | |
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287 return l.size() == GetInstanceCount(); |
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288 } |
504 | 289 catch (OrthancClientException) |
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290 { |
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291 return false; |
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292 } |
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293 } |
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294 |
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295 void Series::ReadSeries() |
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296 { |
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297 Orthanc::HttpClient client(connection_.GetHttpClient()); |
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298 |
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299 client.SetUrl(std::string(connection_.GetOrthancUrl()) + "/series/" + id_); |
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300 Json::Value v; |
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301 if (!client.Apply(series_)) |
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302 { |
504 | 303 throw OrthancClientException(Orthanc::ErrorCode_NetworkProtocol); |
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304 } |
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305 } |
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306 |
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307 Orthanc::IDynamicObject* Series::GetFillerItem(size_t index) |
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308 { |
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309 Json::Value::ArrayIndex tmp = static_cast<Json::Value::ArrayIndex>(index); |
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310 std::string id = series_["Instances"][tmp].asString(); |
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311 return new Instance(connection_, id.c_str()); |
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312 } |
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313 |
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314 Series::Series(const OrthancConnection& connection, |
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315 const char* id) : |
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316 connection_(connection), |
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317 id_(id), |
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318 instances_(*this) |
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319 { |
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320 ReadSeries(); |
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321 status_ = Status3DImage_NotTested; |
500 | 322 url_ = std::string(connection_.GetOrthancUrl()) + "/series/" + id_; |
656 | 323 |
324 voxelSizeX_ = 0; | |
325 voxelSizeY_ = 0; | |
326 voxelSizeZ_ = 0; | |
986 | 327 sliceThickness_ = 0; |
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328 |
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329 instances_.SetThreadCount(connection.GetThreadCount()); |
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330 } |
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331 |
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332 |
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333 bool Series::Is3DImage() |
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334 { |
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335 if (status_ == Status3DImage_NotTested) |
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336 { |
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337 status_ = Is3DImageInternal() ? Status3DImage_True : Status3DImage_False; |
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338 } |
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339 |
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340 return status_ == Status3DImage_True; |
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341 } |
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342 |
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343 unsigned int Series::GetInstanceCount() |
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344 { |
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345 return instances_.GetSize(); |
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346 } |
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347 |
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348 Instance& Series::GetInstance(unsigned int index) |
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349 { |
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350 return dynamic_cast<Instance&>(instances_.GetItem(index)); |
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351 } |
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352 |
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353 unsigned int Series::GetWidth() |
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354 { |
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355 Check3DImage(); |
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356 |
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357 if (GetInstanceCount() == 0) |
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358 return 0; |
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359 else |
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360 return GetInstance(0).GetTagAsInt("Columns"); |
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361 } |
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362 |
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363 unsigned int Series::GetHeight() |
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364 { |
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365 Check3DImage(); |
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366 |
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367 if (GetInstanceCount() == 0) |
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368 return 0; |
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369 else |
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370 return GetInstance(0).GetTagAsInt("Rows"); |
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371 } |
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372 |
500 | 373 const char* Series::GetMainDicomTag(const char* tag, const char* defaultValue) const |
479
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374 { |
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375 if (series_["MainDicomTags"].isMember(tag)) |
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376 { |
500 | 377 return series_["MainDicomTags"][tag].asCString(); |
479
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378 } |
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379 else |
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380 { |
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381 return defaultValue; |
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382 } |
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383 } |
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384 |
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385 |
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386 |
548 | 387 void Series::Load3DImageInternal(void* target, |
388 Orthanc::PixelFormat format, | |
389 size_t lineStride, | |
390 size_t stackStride, | |
391 Orthanc::ThreadedCommandProcessor::IListener* listener) | |
479
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392 { |
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393 using namespace Orthanc; |
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394 |
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395 // Choose the extraction mode, depending on the format of the |
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396 // target image. |
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397 |
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398 uint8_t bytesPerPixel; |
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399 ImageExtractionMode mode; |
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400 |
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401 switch (format) |
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402 { |
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403 case PixelFormat_RGB24: |
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404 bytesPerPixel = 3; |
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405 mode = ImageExtractionMode_Preview; |
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406 break; |
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407 |
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408 case PixelFormat_Grayscale8: |
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409 bytesPerPixel = 1; |
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410 mode = ImageExtractionMode_UInt8; // Preview ??? |
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411 break; |
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412 |
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413 case PixelFormat_Grayscale16: |
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414 bytesPerPixel = 2; |
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415 mode = ImageExtractionMode_UInt16; |
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416 break; |
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417 |
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418 case PixelFormat_SignedGrayscale16: |
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419 bytesPerPixel = 2; |
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420 mode = ImageExtractionMode_UInt16; |
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421 format = PixelFormat_Grayscale16; |
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422 break; |
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423 |
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424 default: |
504 | 425 throw OrthancClientException(ErrorCode_NotImplemented); |
479
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426 } |
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427 |
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428 |
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429 // Check that the target image is properly sized |
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430 unsigned int sx = GetWidth(); |
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431 unsigned int sy = GetHeight(); |
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432 |
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433 if (lineStride < sx * bytesPerPixel || |
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434 stackStride < sx * sy * bytesPerPixel) |
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435 { |
504 | 436 throw OrthancClientException(ErrorCode_BadRequest); |
479
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437 } |
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438 |
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439 if (sx == 0 || sy == 0 || GetInstanceCount() == 0) |
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440 { |
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441 // Empty image, nothing to do |
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442 if (listener) |
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443 listener->SignalSuccess(0); |
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444 return; |
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445 } |
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446 |
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447 |
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448 /** |
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449 * Order the stacks according to their distance along the slice |
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450 * normal (using the "Image Position Patient" tag). This works |
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451 * even if the "SliceLocation" tag is absent. |
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452 **/ |
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453 SliceLocator locator(GetInstance(0)); |
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454 |
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455 typedef std::map<float, Instance*> Instances; |
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456 Instances instances; |
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457 for (unsigned int i = 0; i < GetInstanceCount(); i++) |
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458 { |
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459 float dist = locator.ComputeSliceLocation(GetInstance(i)); |
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460 instances[dist] = &GetInstance(i); |
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461 } |
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462 |
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463 if (instances.size() != GetInstanceCount()) |
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464 { |
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465 // Several instances have the same Z coordinate |
504 | 466 throw OrthancClientException(ErrorCode_NotImplemented); |
479
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467 } |
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468 |
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469 |
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470 // Submit the download of each stack as a set of commands |
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471 ThreadedCommandProcessor processor(connection_.GetThreadCount()); |
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472 |
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473 if (listener != NULL) |
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474 { |
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475 processor.SetListener(*listener); |
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476 } |
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477 |
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478 uint8_t* stackTarget = reinterpret_cast<uint8_t*>(target); |
656 | 479 for (Instances::iterator it = instances.begin(); it != instances.end(); ++it) |
479
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480 { |
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481 processor.Post(new ImageDownloadCommand(*it->second, format, mode, stackTarget, lineStride)); |
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482 stackTarget += stackStride; |
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483 } |
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484 |
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485 |
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486 // Wait for all the stacks to be downloaded |
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487 if (!processor.Join()) |
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488 { |
504 | 489 throw OrthancClientException(ErrorCode_NetworkProtocol); |
479
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490 } |
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491 } |
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492 |
502
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493 float Series::GetVoxelSizeX() |
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494 { |
986 | 495 Check3DImage(); // Is3DImageInternal() will compute the voxel sizes |
502
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496 return voxelSizeX_; |
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497 } |
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498 |
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499 float Series::GetVoxelSizeY() |
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500 { |
986 | 501 Check3DImage(); // Is3DImageInternal() will compute the voxel sizes |
502
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502 return voxelSizeY_; |
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503 } |
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504 |
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505 float Series::GetVoxelSizeZ() |
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506 { |
986 | 507 Check3DImage(); // Is3DImageInternal() will compute the voxel sizes |
502
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508 return voxelSizeZ_; |
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509 } |
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510 |
986 | 511 float Series::GetSliceThickness() |
512 { | |
513 Check3DImage(); // Is3DImageInternal() will compute the voxel sizes | |
514 return sliceThickness_; | |
515 } | |
516 | |
548 | 517 void Series::Load3DImage(void* target, |
518 Orthanc::PixelFormat format, | |
519 int64_t lineStride, | |
520 int64_t stackStride, | |
521 float* progress) | |
522 { | |
523 ProgressToFloatListener listener(progress); | |
585 | 524 Load3DImageInternal(target, format, static_cast<size_t>(lineStride), |
525 static_cast<size_t>(stackStride), &listener); | |
548 | 526 } |
479
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527 } |