Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomStructureSet.cpp @ 125:44fc253d4876 wasm
refactoring
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 08 Nov 2017 16:13:55 +0100 |
parents | e3433dabfb8d |
children | c9e88e7935a4 |
rev | line source |
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0 | 1 /** |
2 * Stone of Orthanc | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
40
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5 * Copyright (C) 2017 Osimis, Belgium |
0 | 6 * |
7 * This program is free software: you can redistribute it and/or | |
47 | 8 * modify it under the terms of the GNU Affero General Public License |
9 * as published by the Free Software Foundation, either version 3 of | |
10 * the License, or (at your option) any later version. | |
0 | 11 * |
12 * This program is distributed in the hope that it will be useful, but | |
13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
47 | 14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
15 * Affero General Public License for more details. | |
16 * | |
17 * You should have received a copy of the GNU Affero General Public License | |
0 | 18 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
19 **/ | |
20 | |
21 | |
22 #include "DicomStructureSet.h" | |
23 | |
35 | 24 #include "../Toolbox/MessagingToolbox.h" |
0 | 25 |
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26 #include <Core/Logging.h> |
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27 #include <Core/OrthancException.h> |
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28 #include <Plugins/Samples/Common/FullOrthancDataset.h> |
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29 #include <Plugins/Samples/Common/DicomDatasetReader.h> |
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30 |
0 | 31 #include <stdio.h> |
32 #include <boost/lexical_cast.hpp> | |
33 | |
34 namespace OrthancStone | |
35 { | |
32 | 36 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
37 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
38 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
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39 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050); |
32 | 40 static const OrthancPlugins::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); |
41 static const OrthancPlugins::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
42 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
43 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
44 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
45 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
46 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
47 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
0 | 48 |
49 | |
50 static uint8_t ConvertColor(double v) | |
51 { | |
52 if (v < 0) | |
53 { | |
54 return 0; | |
55 } | |
56 else if (v >= 255) | |
57 { | |
58 return 255; | |
59 } | |
60 else | |
61 { | |
62 return static_cast<uint8_t>(v); | |
63 } | |
64 } | |
65 | |
66 | |
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67 static bool ParseVector(Vector& target, |
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68 const OrthancPlugins::IDicomDataset& dataset, |
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69 const OrthancPlugins::DicomPath& tag) |
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70 { |
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71 std::string value; |
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72 return (dataset.GetStringValue(value, tag) && |
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73 GeometryToolbox::ParseVector(target, value)); |
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74 } |
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75 |
0 | 76 |
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77 void DicomStructureSet::Polygon::CheckPoint(const Vector& v) |
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78 { |
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79 if (hasSlice_) |
0 | 80 { |
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81 if (!GeometryToolbox::IsNear(GeometryToolbox::ProjectAlongNormal(v, normal_), |
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82 projectionAlongNormal_, |
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83 sliceThickness_ / 2.0 /* in mm */)) |
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84 { |
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85 LOG(ERROR) << "This RT-STRUCT contains a point that is off the slice of its instance"; |
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86 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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87 } |
0 | 88 } |
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89 } |
0 | 90 |
91 | |
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92 void DicomStructureSet::Polygon::AddPoint(const Vector& v) |
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93 { |
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94 CheckPoint(v); |
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95 points_.push_back(v); |
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96 } |
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97 |
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98 |
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99 bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices) |
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100 { |
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101 if (hasSlice_) |
0 | 102 { |
122
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103 return true; |
32 | 104 } |
105 else | |
106 { | |
122
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107 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_); |
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108 |
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109 if (it == slices.end()) |
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110 { |
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111 return false; |
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112 } |
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113 else |
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114 { |
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115 const CoordinateSystem3D& geometry = it->second.geometry_; |
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116 |
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117 hasSlice_ = true; |
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118 normal_ = geometry.GetNormal(); |
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119 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), normal_); |
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120 sliceThickness_ = it->second.thickness_; |
0 | 121 |
122
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122 for (Points::const_iterator it = points_.begin(); it != points_.end(); ++it) |
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123 { |
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124 CheckPoint(*it); |
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125 } |
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126 |
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127 return true; |
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128 } |
0 | 129 } |
130 } | |
131 | |
132 | |
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133 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const |
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134 { |
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135 bool isOpposite; |
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136 |
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137 if (points_.empty() || |
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138 !hasSlice_ || |
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139 !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), normal_)) |
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140 { |
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141 return false; |
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142 } |
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143 |
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144 double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), normal_); |
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145 |
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146 return (GeometryToolbox::IsNear(d, projectionAlongNormal_, |
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147 sliceThickness_ / 2.0)); |
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148 } |
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149 |
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150 |
0 | 151 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const |
152 { | |
153 if (index >= structures_.size()) | |
154 { | |
125 | 155 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
156 } | |
157 | |
158 return structures_[index]; | |
159 } | |
160 | |
161 | |
162 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) | |
163 { | |
164 if (index >= structures_.size()) | |
165 { | |
166 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
0 | 167 } |
168 | |
169 return structures_[index]; | |
170 } | |
171 | |
172 | |
122
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173 DicomStructureSet::DicomStructureSet(const OrthancPlugins::FullOrthancDataset& tags) |
0 | 174 { |
32 | 175 using namespace OrthancPlugins; |
0 | 176 |
32 | 177 DicomDatasetReader reader(tags); |
178 | |
179 size_t count, tmp; | |
180 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) || | |
181 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) || | |
182 tmp != count || | |
183 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) || | |
184 tmp != count) | |
0 | 185 { |
186 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
187 } | |
188 | |
32 | 189 structures_.resize(count); |
190 for (size_t i = 0; i < count; i++) | |
191 { | |
122
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192 structures_[i].interpretation_ = reader.GetStringValue |
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193 (DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
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194 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
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195 "No interpretation"); |
0 | 196 |
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197 structures_[i].name_ = reader.GetStringValue |
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198 (DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
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199 DICOM_TAG_ROI_NAME), |
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200 "No interpretation"); |
0 | 201 |
202 Vector color; | |
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203 if (ParseVector(color, tags, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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204 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
32 | 205 color.size() == 3) |
0 | 206 { |
32 | 207 structures_[i].red_ = ConvertColor(color[0]); |
208 structures_[i].green_ = ConvertColor(color[1]); | |
209 structures_[i].blue_ = ConvertColor(color[2]); | |
210 } | |
211 else | |
212 { | |
213 structures_[i].red_ = 255; | |
214 structures_[i].green_ = 0; | |
215 structures_[i].blue_ = 0; | |
0 | 216 } |
217 | |
32 | 218 size_t countSlices; |
219 if (!tags.GetSequenceSize(countSlices, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, | |
220 DICOM_TAG_CONTOUR_SEQUENCE))) | |
221 { | |
121
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222 countSlices = 0; |
32 | 223 } |
0 | 224 |
225 LOG(WARNING) << "New RT structure: \"" << structures_[i].name_ | |
226 << "\" with interpretation \"" << structures_[i].interpretation_ | |
32 | 227 << "\" containing " << countSlices << " slices (color: " |
0 | 228 << static_cast<int>(structures_[i].red_) << "," |
229 << static_cast<int>(structures_[i].green_) << "," | |
230 << static_cast<int>(structures_[i].blue_) << ")"; | |
231 | |
32 | 232 for (size_t j = 0; j < countSlices; j++) |
0 | 233 { |
32 | 234 unsigned int countPoints; |
0 | 235 |
122
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236 if (!reader.GetUnsignedIntegerValue |
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237 (countPoints, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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238 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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239 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS))) |
32 | 240 { |
241 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
242 } | |
243 | |
121
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244 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
0 | 245 |
122
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246 std::string type = reader.GetMandatoryStringValue |
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247 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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248 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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249 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE)); |
32 | 250 if (type != "CLOSED_PLANAR") |
0 | 251 { |
32 | 252 LOG(ERROR) << "Cannot handle contour with geometry type: " << type; |
0 | 253 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
254 } | |
255 | |
122
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256 size_t size; |
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257 if (!tags.GetSequenceSize(size, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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258 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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259 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE)) || |
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260 size != 1) |
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261 { |
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262 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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263 } |
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264 |
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265 std::string sopInstanceUid = reader.GetMandatoryStringValue |
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266 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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267 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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268 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
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269 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID)); |
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270 |
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271 std::string slicesData = reader.GetMandatoryStringValue |
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272 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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273 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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274 DICOM_TAG_CONTOUR_DATA)); |
0 | 275 |
276 Vector points; | |
277 if (!GeometryToolbox::ParseVector(points, slicesData) || | |
32 | 278 points.size() != 3 * countPoints) |
0 | 279 { |
280 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
281 } | |
282 | |
122
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283 Polygon polygon(sopInstanceUid); |
0 | 284 |
32 | 285 for (size_t k = 0; k < countPoints; k++) |
0 | 286 { |
287 Vector v(3); | |
288 v[0] = points[3 * k]; | |
289 v[1] = points[3 * k + 1]; | |
290 v[2] = points[3 * k + 2]; | |
122
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291 polygon.AddPoint(v); |
0 | 292 } |
293 | |
294 structures_[i].polygons_.push_back(polygon); | |
295 } | |
296 } | |
297 } | |
298 | |
299 | |
300 Vector DicomStructureSet::GetStructureCenter(size_t index) const | |
301 { | |
302 const Structure& structure = GetStructure(index); | |
303 | |
304 Vector center; | |
305 GeometryToolbox::AssignVector(center, 0, 0, 0); | |
306 if (structure.polygons_.empty()) | |
307 { | |
308 return center; | |
309 } | |
310 | |
311 double n = static_cast<double>(structure.polygons_.size()); | |
312 | |
313 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
314 polygon != structure.polygons_.end(); ++polygon) | |
315 { | |
122
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316 if (!polygon->GetPoints().empty()) |
0 | 317 { |
122
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318 center += polygon->GetPoints().front() / n; |
0 | 319 } |
320 } | |
321 | |
322 return center; | |
323 } | |
324 | |
325 | |
326 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
327 { | |
328 return GetStructure(index).name_; | |
329 } | |
330 | |
331 | |
332 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
333 { | |
334 return GetStructure(index).interpretation_; | |
335 } | |
336 | |
337 | |
338 void DicomStructureSet::GetStructureColor(uint8_t& red, | |
339 uint8_t& green, | |
340 uint8_t& blue, | |
341 size_t index) const | |
342 { | |
343 const Structure& s = GetStructure(index); | |
344 red = s.red_; | |
345 green = s.green_; | |
346 blue = s.blue_; | |
347 } | |
348 | |
349 | |
122
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350 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) |
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351 { |
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352 for (Structures::const_iterator structure = structures_.begin(); |
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353 structure != structures_.end(); ++structure) |
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354 { |
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355 for (Polygons::const_iterator polygon = structure->polygons_.begin(); |
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356 polygon != structure->polygons_.end(); ++polygon) |
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357 { |
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358 instances.insert(polygon->GetSopInstanceUid()); |
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359 } |
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360 } |
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361 } |
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362 |
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363 |
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364 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, |
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365 const std::string& seriesInstanceUid, |
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366 const CoordinateSystem3D& geometry, |
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367 double thickness) |
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368 { |
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369 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) |
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370 { |
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371 // This geometry is already known |
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372 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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373 } |
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374 else |
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375 { |
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376 if (thickness < 0) |
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377 { |
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378 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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379 } |
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380 |
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381 if (!referencedSlices_.empty()) |
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382 { |
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383 const ReferencedSlice& reference = referencedSlices_.begin()->second; |
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384 |
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385 if (reference.seriesInstanceUid_ != seriesInstanceUid) |
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386 { |
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387 LOG(ERROR) << "This RT-STRUCT refers to several different series"; |
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388 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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389 } |
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390 |
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391 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) |
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392 { |
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393 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; |
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394 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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395 } |
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396 } |
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397 |
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398 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); |
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399 } |
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400 } |
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401 |
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402 |
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403 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) |
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404 { |
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405 CoordinateSystem3D slice(dataset); |
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406 |
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407 double thickness = 1; // 1 mm by default |
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408 |
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409 std::string s; |
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410 Vector v; |
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411 if (dataset.CopyToString(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && |
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412 GeometryToolbox::ParseVector(v, s) && |
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413 v.size() > 0) |
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414 { |
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415 thickness = v[0]; |
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416 } |
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417 |
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418 std::string instance, series; |
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419 if (dataset.CopyToString(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) && |
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420 dataset.CopyToString(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) |
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421 { |
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422 AddReferencedSlice(instance, series, slice, thickness); |
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423 } |
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424 else |
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425 { |
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426 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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427 } |
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428 } |
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429 |
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430 |
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431 void DicomStructureSet::CheckReferencedSlices() |
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432 { |
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433 for (Structures::iterator structure = structures_.begin(); |
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434 structure != structures_.end(); ++structure) |
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435 { |
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436 for (Polygons::iterator polygon = structure->polygons_.begin(); |
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437 polygon != structure->polygons_.end(); ++polygon) |
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438 { |
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439 if (!polygon->UpdateReferencedSlice(referencedSlices_)) |
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440 { |
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441 LOG(ERROR) << "Missing information about referenced instance: " |
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442 << polygon->GetSopInstanceUid(); |
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443 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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444 } |
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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 |
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450 Vector DicomStructureSet::GetNormal() const |
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451 { |
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452 if (!referencedSlices_.empty()) |
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453 { |
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454 Vector v; |
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455 GeometryToolbox::AssignVector(v, 0, 0, 1); |
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456 return v; |
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457 } |
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458 else |
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459 { |
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460 return referencedSlices_.begin()->second.geometry_.GetNormal(); |
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461 } |
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462 } |
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463 |
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464 |
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465 DicomStructureSet* DicomStructureSet::SynchronousLoad(OrthancPlugins::IOrthancConnection& orthanc, |
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466 const std::string& instanceId) |
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467 { |
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468 const std::string uri = "/instances/" + instanceId + "/tags?ignore-length=3006-0050"; |
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469 OrthancPlugins::FullOrthancDataset dataset(orthanc, uri); |
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470 |
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471 std::auto_ptr<DicomStructureSet> result(new DicomStructureSet(dataset)); |
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472 |
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473 std::set<std::string> instances; |
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474 result->GetReferencedInstances(instances); |
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475 |
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476 for (std::set<std::string>::const_iterator it = instances.begin(); |
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477 it != instances.end(); ++it) |
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478 { |
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479 Json::Value lookup; |
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480 MessagingToolbox::RestApiPost(lookup, orthanc, "/tools/lookup", *it); |
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481 |
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482 if (lookup.type() != Json::arrayValue || |
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483 lookup.size() != 1 || |
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484 !lookup[0].isMember("Type") || |
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485 !lookup[0].isMember("Path") || |
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486 lookup[0]["Type"].type() != Json::stringValue || |
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487 lookup[0]["ID"].type() != Json::stringValue || |
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488 lookup[0]["Type"].asString() != "Instance") |
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489 { |
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490 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
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491 } |
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492 |
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493 OrthancPlugins::FullOrthancDataset slice |
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494 (orthanc, "/instances/" + lookup[0]["ID"].asString() + "/tags"); |
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495 Orthanc::DicomMap m; |
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496 MessagingToolbox::ConvertDataset(m, slice); |
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497 result->AddReferencedSlice(m); |
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498 } |
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499 |
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500 result->CheckReferencedSlices(); |
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501 |
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502 return result.release(); |
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503 } |
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504 |
125 | 505 |
506 bool DicomStructureSet::ProjectStructure(std::vector< std::vector<PolygonPoint> >& polygons, | |
507 Structure& structure, | |
508 const CoordinateSystem3D& slice) | |
509 { | |
510 polygons.clear(); | |
511 | |
512 Vector normal = GetNormal(); | |
513 | |
514 bool isOpposite; | |
515 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal())) | |
516 { | |
517 // This is an axial projection | |
518 | |
519 for (Polygons::iterator polygon = structure.polygons_.begin(); | |
520 polygon != structure.polygons_.end(); ++polygon) | |
521 { | |
522 polygon->UpdateReferencedSlice(referencedSlices_); | |
523 | |
524 if (polygon->IsOnSlice(slice)) | |
525 { | |
526 polygons.push_back(std::vector<PolygonPoint>()); | |
527 | |
528 for (Points::const_iterator p = polygon->GetPoints().begin(); | |
529 p != polygon->GetPoints().end(); ++p) | |
530 { | |
531 double x, y; | |
532 slice.ProjectPoint(x, y, *p); | |
533 polygons.back().push_back(std::make_pair(x, y)); | |
534 } | |
535 } | |
536 } | |
537 | |
538 return true; | |
539 } | |
540 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) || | |
541 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY())) | |
542 { | |
543 // Sagittal or coronal projections | |
544 | |
545 return false; | |
546 } | |
547 else | |
548 { | |
549 return false; | |
550 } | |
551 } | |
0 | 552 } |