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comparison OrthancStone/Resources/Graveyard/RTStructTentativeReimplementation-BGO/DicomStructureSet2.cpp @ 1908:affde38b84de

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moved tentative bgo reimplementation of rt-struct into graveyard
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 01 Feb 2022 08:38:32 +0100
parents OrthancStone/Sources/Toolbox/DicomStructureSet2.cpp@7053b8a0aaec
children 07964689cb0b
comparison
equal deleted inserted replaced
1907:0208f99b8bde 1908:affde38b84de
1 /**
2 * Stone of Orthanc
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
4 * Department, University Hospital of Liege, Belgium
5 * Copyright (C) 2017-2022 Osimis S.A., Belgium
6 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
7 *
8 * This program is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU Lesser General Public License
10 * as published by the Free Software Foundation, either version 3 of
11 * the License, or (at your option) any later version.
12 *
13 * This program is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty of
15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
16 * Lesser General Public License for more details.
17 *
18 * You should have received a copy of the GNU Lesser General Public
19 * License along with this program. If not, see
20 * <http://www.gnu.org/licenses/>.
21 **/
22
23 #ifdef BGO_ENABLE_DICOMSTRUCTURESETLOADER2
24
25 #include "DicomStructureSet2.h"
26
27 #include "../Toolbox/LinearAlgebra.h"
28 #include "../StoneException.h"
29
30 #include <Logging.h>
31 #include <OrthancException.h>
32 #include <Toolbox.h>
33 #include <DicomFormat/DicomTag.h>
34
35 #include "DicomStructure2.h"
36 #include "GenericToolbox.h"
37 #include "OrthancDatasets/DicomDatasetReader.h"
38
39 namespace OrthancStone
40 {
41 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042);
42 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016);
43 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040);
44 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050);
45 static const Orthanc::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046);
46 static const Orthanc::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155);
47 static const Orthanc::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039);
48 static const Orthanc::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a);
49 static const Orthanc::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026);
50 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4);
51 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080);
52 static const Orthanc::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020);
53
54 static inline uint8_t ConvertAndClipToByte(double v)
55 {
56 if (v < 0)
57 {
58 return 0;
59 }
60 else if (v >= 255)
61 {
62 return 255;
63 }
64 else
65 {
66 return static_cast<uint8_t>(v);
67 }
68 }
69
70 static bool ReadDicomToVector(Vector& target,
71 const IDicomDataset& dataset,
72 const Orthanc::DicomPath& tag)
73 {
74 std::string value;
75 return (dataset.GetStringValue(value, tag) &&
76 GenericToolbox::FastParseVector(target, value));
77 }
78
79
80 void DicomPathToString(std::string& s, const Orthanc::DicomPath& dicomPath)
81 {
82 std::stringstream tmp;
83 for (size_t i = 0; i < dicomPath.GetPrefixLength(); ++i)
84 {
85 Orthanc::DicomTag tag = dicomPath.GetPrefixTag(i);
86
87 // We use this other object to be able to use Format
88 Orthanc::DicomTag tag2(tag.GetGroup(), tag.GetElement());
89 size_t index = dicomPath.GetPrefixIndex(i);
90 tmp << " (" << tag2.Format() << ") [" << index << "] / ";
91 }
92 const Orthanc::DicomTag& tag = dicomPath.GetFinalTag();
93 Orthanc::DicomTag tag2(tag.GetGroup(), tag.GetElement());
94 tmp << " (" << tag2.Format() << ")";
95 s = tmp.str();
96 }
97
98 std::ostream& operator<<(std::ostream& s, const Orthanc::DicomPath& dicomPath)
99 {
100 std::string tmp;
101 DicomPathToString(tmp, dicomPath);
102 s << tmp;
103 return s;
104 }
105
106
107 DicomStructureSet2::DicomStructureSet2()
108 {
109
110 }
111
112
113 DicomStructureSet2::~DicomStructureSet2()
114 {
115
116 }
117
118 void DicomStructureSet2::SetContents(const FullOrthancDataset& tags)
119 {
120 FillStructuresFromDataset(tags);
121 ComputeDependentProperties();
122 }
123
124 void DicomStructureSet2::ComputeDependentProperties()
125 {
126 for (size_t i = 0; i < structures_.size(); ++i)
127 {
128 structures_[i].ComputeDependentProperties();
129 }
130 }
131
132 void DicomStructureSet2::FillStructuresFromDataset(const FullOrthancDataset& tags)
133 {
134 DicomDatasetReader reader(tags);
135
136 // a few sanity checks
137 size_t count = 0, tmp = 0;
138
139 // DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE (0x3006, 0x0080);
140 // DICOM_TAG_ROI_CONTOUR_SEQUENCE (0x3006, 0x0039);
141 // DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE (0x3006, 0x0020);
142 if (!tags.GetSequenceSize(count, Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE)) ||
143 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE)) ||
144 tmp != count ||
145 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE)) ||
146 tmp != count)
147 {
148 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
149 }
150
151 // let's now parse the structures stored in the dicom file
152 // DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE (0x3006, 0x0080)
153 // DICOM_TAG_RT_ROI_INTERPRETED_TYPE (0x3006, 0x00a4)
154 // DICOM_TAG_ROI_DISPLAY_COLOR (0x3006, 0x002a)
155 // DICOM_TAG_ROI_NAME (0x3006, 0x0026)
156 structures_.resize(count);
157 for (size_t i = 0; i < count; i++)
158 {
159 // (0x3006, 0x0080)[i]/(0x3006, 0x00a4)
160 structures_[i].interpretation_ = reader.GetStringValue
161 (Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i,
162 DICOM_TAG_RT_ROI_INTERPRETED_TYPE),
163 "No interpretation");
164
165 // (0x3006, 0x0020)[i]/(0x3006, 0x0026)
166 structures_[i].name_ = reader.GetStringValue
167 (Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i,
168 DICOM_TAG_ROI_NAME),
169 "No name");
170
171 Vector color;
172 // (0x3006, 0x0039)[i]/(0x3006, 0x002a)
173 if (ReadDicomToVector(color, tags, Orthanc::DicomPath(
174 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_ROI_DISPLAY_COLOR))
175 && color.size() == 3)
176 {
177 structures_[i].red_ = ConvertAndClipToByte(color[0]);
178 structures_[i].green_ = ConvertAndClipToByte(color[1]);
179 structures_[i].blue_ = ConvertAndClipToByte(color[2]);
180 }
181 else
182 {
183 structures_[i].red_ = 255;
184 structures_[i].green_ = 0;
185 structures_[i].blue_ = 0;
186 }
187
188 size_t countSlices;
189 // DICOM_TAG_ROI_CONTOUR_SEQUENCE (0x3006, 0x0039);
190 // DICOM_TAG_CONTOUR_SEQUENCE (0x3006, 0x0040);
191 if (!tags.GetSequenceSize(countSlices, Orthanc::DicomPath(
192 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_CONTOUR_SEQUENCE)))
193 {
194 LOG(WARNING) << "DicomStructureSet2::SetContents | structure \"" << structures_[i].name_ << "\" has no slices!";
195 countSlices = 0;
196 }
197
198 LOG(INFO) << "New RT structure: \"" << structures_[i].name_
199 << "\" with interpretation \"" << structures_[i].interpretation_
200 << "\" containing " << countSlices << " slices (color: "
201 << static_cast<int>(structures_[i].red_) << ","
202 << static_cast<int>(structures_[i].green_) << ","
203 << static_cast<int>(structures_[i].blue_) << ")";
204
205 // These temporary variables avoid allocating many vectors in the loop below
206
207 // (0x3006, 0x0039)[i]/(0x3006, 0x0040)[0]/(0x3006, 0x0046)
208 Orthanc::DicomPath countPointsPath(
209 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
210 DICOM_TAG_CONTOUR_SEQUENCE, 0,
211 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS);
212
213 Orthanc::DicomPath geometricTypePath(
214 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
215 DICOM_TAG_CONTOUR_SEQUENCE, 0,
216 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE);
217
218 Orthanc::DicomPath imageSequencePath(
219 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
220 DICOM_TAG_CONTOUR_SEQUENCE, 0,
221 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE);
222
223 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)
224 Orthanc::DicomPath referencedInstancePath(
225 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
226 DICOM_TAG_CONTOUR_SEQUENCE, 0,
227 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0,
228 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID);
229
230 Orthanc::DicomPath contourDataPath(
231 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
232 DICOM_TAG_CONTOUR_SEQUENCE, 0,
233 DICOM_TAG_CONTOUR_DATA);
234
235 for (size_t j = 0; j < countSlices; j++)
236 {
237 unsigned int countPoints = 0;
238
239 countPointsPath.SetPrefixIndex(1, j);
240 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath))
241 {
242 std::string s;
243 DicomPathToString(s, countPointsPath);
244 LOG(ERROR) << "Dicom path " << s << " is not valid (should contain an unsigned integer)";
245 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
246 }
247
248 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices";
249
250 geometricTypePath.SetPrefixIndex(1, j);
251 std::string type = reader.GetMandatoryStringValue(geometricTypePath);
252 if (type != "CLOSED_PLANAR")
253 {
254 // TODO: support points!!
255 LOG(WARNING) << "Ignoring contour with geometry type: " << type;
256 continue;
257 }
258
259 size_t size = 0;
260
261 imageSequencePath.SetPrefixIndex(1, j);
262 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1)
263 {
264 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry.";
265 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
266 }
267
268 referencedInstancePath.SetPrefixIndex(1, j);
269 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath);
270
271 contourDataPath.SetPrefixIndex(1, j);
272 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath);
273
274 Vector points;
275 if (!GenericToolbox::FastParseVector(points, slicesData) ||
276 points.size() != 3 * countPoints)
277 {
278 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
279 }
280
281 // seen in real world
282 if (Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "")
283 {
284 LOG(ERROR) << "WARNING. The following Dicom tag (Referenced SOP Instance UID) contains an empty value : // (3006,0039)[" << i << "] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)";
285 }
286
287 DicomStructurePolygon2 polygon(sopInstanceUid,type);
288 polygon.Reserve(countPoints);
289
290 for (size_t k = 0; k < countPoints; k++)
291 {
292 Vector v(3);
293 v[0] = points[3 * k];
294 v[1] = points[3 * k + 1];
295 v[2] = points[3 * k + 2];
296 polygon.AddPoint(v);
297 }
298 structures_[i].AddPolygon(polygon);
299 }
300 }
301 }
302
303
304 void DicomStructureSet2::Clear()
305 {
306 structures_.clear();
307 }
308
309 }
310
311 #endif
312 // BGO_ENABLE_DICOMSTRUCTURESETLOADER2
313