Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomStructureSet.cpp @ 113:2eca030792aa wasm
using the Orthanc Framework
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Wed, 20 Sep 2017 15:32:32 +0200 |
parents | 53025eecbc95 |
children | a4d0b6c82b29 |
rev | line source |
---|---|
0 | 1 /** |
2 * Stone of Orthanc | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
40
7207a407bcd8
shared copyright with osimis
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
35
diff
changeset
|
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 |
113
2eca030792aa
using the Orthanc Framework
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
110
diff
changeset
|
26 #include <Core/Logging.h> |
2eca030792aa
using the Orthanc Framework
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
110
diff
changeset
|
27 #include <Core/OrthancException.h> |
2eca030792aa
using the Orthanc Framework
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
110
diff
changeset
|
28 #include <Plugins/Samples/Common/FullOrthancDataset.h> |
2eca030792aa
using the Orthanc Framework
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
110
diff
changeset
|
29 |
0 | 30 #include <stdio.h> |
31 #include <boost/lexical_cast.hpp> | |
32 | |
33 namespace OrthancStone | |
34 { | |
32 | 35 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
36 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
37 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
38 static const OrthancPlugins::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); | |
39 static const OrthancPlugins::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
40 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
41 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
42 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
43 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
44 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
45 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
0 | 46 |
47 | |
48 static uint8_t ConvertColor(double v) | |
49 { | |
50 if (v < 0) | |
51 { | |
52 return 0; | |
53 } | |
54 else if (v >= 255) | |
55 { | |
56 return 255; | |
57 } | |
58 else | |
59 { | |
60 return static_cast<uint8_t>(v); | |
61 } | |
62 } | |
63 | |
64 | |
110
53025eecbc95
renamed SliceGeometry as CoordinateSystem3D
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
47
diff
changeset
|
65 CoordinateSystem3D DicomStructureSet::ExtractSliceGeometry(double& sliceThickness, |
31
9aace933cb64
sharing code with the Orthanc core
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
16
diff
changeset
|
66 OrthancPlugins::IOrthancConnection& orthanc, |
32 | 67 const OrthancPlugins::IDicomDataset& tags, |
68 size_t contourIndex, | |
69 size_t sliceIndex) | |
0 | 70 { |
32 | 71 using namespace OrthancPlugins; |
0 | 72 |
32 | 73 size_t size; |
74 if (!tags.GetSequenceSize(size, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, contourIndex, | |
75 DICOM_TAG_CONTOUR_SEQUENCE, sliceIndex, | |
76 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE)) || | |
77 size != 1) | |
0 | 78 { |
79 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
80 } | |
81 | |
32 | 82 DicomDatasetReader reader(tags); |
83 std::string parentUid = reader.GetMandatoryStringValue(DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, contourIndex, | |
84 DICOM_TAG_CONTOUR_SEQUENCE, sliceIndex, | |
85 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, | |
86 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID)); | |
0 | 87 |
34 | 88 Json::Value parentLookup; |
89 MessagingToolbox::RestApiPost(parentLookup, orthanc, "/tools/lookup", parentUid); | |
0 | 90 |
34 | 91 if (parentLookup.type() != Json::arrayValue || |
92 parentLookup.size() != 1 || | |
93 !parentLookup[0].isMember("Type") || | |
94 !parentLookup[0].isMember("Path") || | |
95 parentLookup[0]["Type"].type() != Json::stringValue || | |
96 parentLookup[0]["ID"].type() != Json::stringValue || | |
97 parentLookup[0]["Type"].asString() != "Instance") | |
0 | 98 { |
99 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
100 } | |
101 | |
102 Json::Value parentInstance; | |
34 | 103 MessagingToolbox::RestApiGet(parentInstance, orthanc, "/instances/" + parentLookup[0]["ID"].asString()); |
0 | 104 |
105 if (parentInstance.type() != Json::objectValue || | |
106 !parentInstance.isMember("ParentSeries") || | |
107 parentInstance["ParentSeries"].type() != Json::stringValue) | |
108 { | |
109 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); | |
110 } | |
111 | |
112 std::string parentSeriesId = parentInstance["ParentSeries"].asString(); | |
113 bool isFirst = parentSeriesId_.empty(); | |
114 | |
115 if (isFirst) | |
116 { | |
117 parentSeriesId_ = parentSeriesId; | |
118 } | |
119 else if (parentSeriesId_ != parentSeriesId) | |
120 { | |
121 LOG(ERROR) << "This RT-STRUCT refers to several different series"; | |
122 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
123 } | |
124 | |
34 | 125 FullOrthancDataset parentTags(orthanc, "/instances/" + parentLookup[0]["ID"].asString() + "/tags"); |
110
53025eecbc95
renamed SliceGeometry as CoordinateSystem3D
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
47
diff
changeset
|
126 CoordinateSystem3D slice(parentTags); |
0 | 127 |
32 | 128 Vector v; |
129 if (GeometryToolbox::ParseVector(v, parentTags, DICOM_TAG_SLICE_THICKNESS) && | |
130 v.size() > 0) | |
0 | 131 { |
32 | 132 sliceThickness = v[0]; |
133 } | |
134 else | |
135 { | |
136 sliceThickness = 1; // 1 mm by default | |
0 | 137 } |
138 | |
139 if (isFirst) | |
140 { | |
141 normal_ = slice.GetNormal(); | |
142 } | |
143 else if (!GeometryToolbox::IsParallel(normal_, slice.GetNormal())) | |
144 { | |
145 LOG(ERROR) << "Incompatible orientation of slices in this RT-STRUCT"; | |
146 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
147 } | |
148 | |
149 return slice; | |
150 } | |
151 | |
152 | |
153 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const | |
154 { | |
155 if (index >= structures_.size()) | |
156 { | |
157 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
158 } | |
159 | |
160 return structures_[index]; | |
161 } | |
162 | |
163 | |
164 bool DicomStructureSet::IsPolygonOnSlice(const Polygon& polygon, | |
110
53025eecbc95
renamed SliceGeometry as CoordinateSystem3D
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
47
diff
changeset
|
165 const CoordinateSystem3D& geometry) const |
0 | 166 { |
167 double d = boost::numeric::ublas::inner_prod(geometry.GetOrigin(), normal_); | |
168 | |
169 return (GeometryToolbox::IsNear(d, polygon.projectionAlongNormal_, polygon.sliceThickness_ / 2.0) && | |
170 !polygon.points_.empty()); | |
171 } | |
172 | |
173 | |
31
9aace933cb64
sharing code with the Orthanc core
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
16
diff
changeset
|
174 DicomStructureSet::DicomStructureSet(OrthancPlugins::IOrthancConnection& orthanc, |
0 | 175 const std::string& instanceId) |
176 { | |
32 | 177 using namespace OrthancPlugins; |
0 | 178 |
32 | 179 FullOrthancDataset tags(orthanc, "/instances/" + instanceId + "/tags"); |
180 DicomDatasetReader reader(tags); | |
181 | |
182 size_t count, tmp; | |
183 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) || | |
184 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) || | |
185 tmp != count || | |
186 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) || | |
187 tmp != count) | |
0 | 188 { |
189 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
190 } | |
191 | |
32 | 192 structures_.resize(count); |
193 for (size_t i = 0; i < count; i++) | |
194 { | |
195 structures_[i].interpretation_ = reader.GetStringValue(DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, | |
196 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), | |
197 "No interpretation"); | |
0 | 198 |
32 | 199 structures_[i].name_ = reader.GetStringValue(DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
200 DICOM_TAG_ROI_NAME), | |
201 "No interpretation"); | |
0 | 202 |
203 Vector color; | |
32 | 204 if (GeometryToolbox::ParseVector(color, tags, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
205 DICOM_TAG_ROI_DISPLAY_COLOR)) && | |
206 color.size() == 3) | |
0 | 207 { |
32 | 208 structures_[i].red_ = ConvertColor(color[0]); |
209 structures_[i].green_ = ConvertColor(color[1]); | |
210 structures_[i].blue_ = ConvertColor(color[2]); | |
211 } | |
212 else | |
213 { | |
214 structures_[i].red_ = 255; | |
215 structures_[i].green_ = 0; | |
216 structures_[i].blue_ = 0; | |
0 | 217 } |
218 | |
32 | 219 size_t countSlices; |
220 if (!tags.GetSequenceSize(countSlices, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, | |
221 DICOM_TAG_CONTOUR_SEQUENCE))) | |
222 { | |
223 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
224 } | |
0 | 225 |
226 LOG(WARNING) << "New RT structure: \"" << structures_[i].name_ | |
227 << "\" with interpretation \"" << structures_[i].interpretation_ | |
32 | 228 << "\" containing " << countSlices << " slices (color: " |
0 | 229 << static_cast<int>(structures_[i].red_) << "," |
230 << static_cast<int>(structures_[i].green_) << "," | |
231 << static_cast<int>(structures_[i].blue_) << ")"; | |
232 | |
32 | 233 for (size_t j = 0; j < countSlices; j++) |
0 | 234 { |
32 | 235 unsigned int countPoints; |
0 | 236 |
32 | 237 if (!reader.GetUnsignedIntegerValue(countPoints, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
238 DICOM_TAG_CONTOUR_SEQUENCE, j, | |
239 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS))) | |
240 { | |
241 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
242 } | |
243 | |
244 LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; | |
0 | 245 |
32 | 246 std::string type = reader.GetMandatoryStringValue(DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
247 DICOM_TAG_CONTOUR_SEQUENCE, j, | |
248 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE)); | |
249 if (type != "CLOSED_PLANAR") | |
0 | 250 { |
32 | 251 LOG(ERROR) << "Cannot handle contour with geometry type: " << type; |
0 | 252 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
253 } | |
254 | |
32 | 255 // The "CountourData" tag (3006,0050) is too large to be |
256 // returned by the "/instances/{id}/tags" URI: Access it using | |
257 // the raw "/instances/{id}/content/{...}" endpoint | |
0 | 258 std::string slicesData; |
259 orthanc.RestApiGet(slicesData, "/instances/" + instanceId + "/content/3006-0039/" + | |
260 boost::lexical_cast<std::string>(i) + "/3006-0040/" + | |
261 boost::lexical_cast<std::string>(j) + "/3006-0050"); | |
262 | |
263 Vector points; | |
264 if (!GeometryToolbox::ParseVector(points, slicesData) || | |
32 | 265 points.size() != 3 * countPoints) |
0 | 266 { |
267 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
268 } | |
269 | |
270 Polygon polygon; | |
110
53025eecbc95
renamed SliceGeometry as CoordinateSystem3D
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
47
diff
changeset
|
271 CoordinateSystem3D geometry = ExtractSliceGeometry(polygon.sliceThickness_, orthanc, tags, i, j); |
0 | 272 polygon.projectionAlongNormal_ = geometry.ProjectAlongNormal(geometry.GetOrigin()); |
273 | |
32 | 274 for (size_t k = 0; k < countPoints; k++) |
0 | 275 { |
276 Vector v(3); | |
277 v[0] = points[3 * k]; | |
278 v[1] = points[3 * k + 1]; | |
279 v[2] = points[3 * k + 2]; | |
280 | |
281 if (!GeometryToolbox::IsNear(geometry.ProjectAlongNormal(v), | |
282 polygon.projectionAlongNormal_, | |
283 polygon.sliceThickness_ / 2.0 /* in mm */)) | |
284 { | |
285 LOG(ERROR) << "This RT-STRUCT contains a point that is off the slice of its instance"; | |
286 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
287 } | |
288 | |
289 polygon.points_.push_back(v); | |
290 } | |
291 | |
292 structures_[i].polygons_.push_back(polygon); | |
293 } | |
294 } | |
295 | |
296 if (parentSeriesId_.empty() || | |
297 normal_.size() != 3) | |
298 { | |
299 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
300 } | |
301 } | |
302 | |
303 | |
304 Vector DicomStructureSet::GetStructureCenter(size_t index) const | |
305 { | |
306 const Structure& structure = GetStructure(index); | |
307 | |
308 Vector center; | |
309 GeometryToolbox::AssignVector(center, 0, 0, 0); | |
310 if (structure.polygons_.empty()) | |
311 { | |
312 return center; | |
313 } | |
314 | |
315 double n = static_cast<double>(structure.polygons_.size()); | |
316 | |
317 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
318 polygon != structure.polygons_.end(); ++polygon) | |
319 { | |
320 if (!polygon->points_.empty()) | |
321 { | |
322 center += polygon->points_.front() / n; | |
323 } | |
324 } | |
325 | |
326 return center; | |
327 } | |
328 | |
329 | |
330 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
331 { | |
332 return GetStructure(index).name_; | |
333 } | |
334 | |
335 | |
336 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
337 { | |
338 return GetStructure(index).interpretation_; | |
339 } | |
340 | |
341 | |
342 void DicomStructureSet::GetStructureColor(uint8_t& red, | |
343 uint8_t& green, | |
344 uint8_t& blue, | |
345 size_t index) const | |
346 { | |
347 const Structure& s = GetStructure(index); | |
348 red = s.red_; | |
349 green = s.green_; | |
350 blue = s.blue_; | |
351 } | |
352 | |
353 | |
354 void DicomStructureSet::Render(CairoContext& context, | |
110
53025eecbc95
renamed SliceGeometry as CoordinateSystem3D
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
47
diff
changeset
|
355 const CoordinateSystem3D& slice) const |
0 | 356 { |
357 cairo_t* cr = context.GetObject(); | |
358 | |
359 for (Structures::const_iterator structure = structures_.begin(); | |
360 structure != structures_.end(); ++structure) | |
361 { | |
362 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
363 polygon != structure->polygons_.end(); ++polygon) | |
364 { | |
365 if (IsPolygonOnSlice(*polygon, slice)) | |
366 { | |
367 context.SetSourceColor(structure->red_, structure->green_, structure->blue_); | |
368 | |
369 Points::const_iterator p = polygon->points_.begin(); | |
370 | |
371 double x, y; | |
372 slice.ProjectPoint(x, y, *p); | |
373 cairo_move_to(cr, x, y); | |
374 ++p; | |
375 | |
376 while (p != polygon->points_.end()) | |
377 { | |
378 slice.ProjectPoint(x, y, *p); | |
379 cairo_line_to(cr, x, y); | |
380 ++p; | |
381 } | |
382 | |
383 slice.ProjectPoint(x, y, *polygon->points_.begin()); | |
384 cairo_line_to(cr, x, y); | |
385 } | |
386 } | |
387 } | |
388 | |
389 cairo_stroke(cr); | |
390 } | |
391 } |