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comparison Framework/Loaders/OrthancMultiframeVolumeLoader.cpp @ 860:238693c3bc51 am-dev

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merge default -> am-dev
author Alain Mazy <alain@mazy.be>
date Mon, 24 Jun 2019 14:35:00 +0200
parents 1f85e9c7d020
children 81d30cd93b65
comparison
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856:a6e17a5a39e7 860:238693c3bc51
1 /**
2 * Stone of Orthanc
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
4 * Department, University Hospital of Liege, Belgium
5 * Copyright (C) 2017-2019 Osimis S.A., Belgium
6 *
7 * This program is free software: you can redistribute it and/or
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.
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
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
18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
19 **/
20
21
22 #include "OrthancMultiframeVolumeLoader.h"
23
24 #include <Core/Endianness.h>
25 #include <Core/Toolbox.h>
26
27 namespace OrthancStone
28 {
29 class OrthancMultiframeVolumeLoader::LoadRTDoseGeometry : public LoaderStateMachine::State
30 {
31 private:
32 std::auto_ptr<Orthanc::DicomMap> dicom_;
33
34 public:
35 LoadRTDoseGeometry(OrthancMultiframeVolumeLoader& that,
36 Orthanc::DicomMap* dicom) :
37 State(that),
38 dicom_(dicom)
39 {
40 if (dicom == NULL)
41 {
42 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer);
43 }
44
45 }
46
47 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message)
48 {
49 // Complete the DICOM tags with just-received "Grid Frame Offset Vector"
50 std::string s = Orthanc::Toolbox::StripSpaces(message.GetAnswer());
51 dicom_->SetValue(Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR, s, false);
52
53 GetLoader<OrthancMultiframeVolumeLoader>().SetGeometry(*dicom_);
54 }
55 };
56
57
58 static std::string GetSopClassUid(const Orthanc::DicomMap& dicom)
59 {
60 std::string s;
61 if (!dicom.CopyToString(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false))
62 {
63 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
64 "DICOM file without SOP class UID");
65 }
66 else
67 {
68 return s;
69 }
70 }
71
72
73 class OrthancMultiframeVolumeLoader::LoadGeometry : public State
74 {
75 public:
76 LoadGeometry(OrthancMultiframeVolumeLoader& that) :
77 State(that)
78 {
79 }
80
81 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message)
82 {
83 OrthancMultiframeVolumeLoader& loader = GetLoader<OrthancMultiframeVolumeLoader>();
84
85 Json::Value body;
86 message.ParseJsonBody(body);
87
88 if (body.type() != Json::objectValue)
89 {
90 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol);
91 }
92
93 std::auto_ptr<Orthanc::DicomMap> dicom(new Orthanc::DicomMap);
94 dicom->FromDicomAsJson(body);
95
96 if (StringToSopClassUid(GetSopClassUid(*dicom)) == SopClassUid_RTDose)
97 {
98 // Download the "Grid Frame Offset Vector" DICOM tag, that is
99 // mandatory for RT-DOSE, but is too long to be returned by default
100
101 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand);
102 command->SetUri("/instances/" + loader.GetInstanceId() + "/content/" +
103 Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR.Format());
104 command->SetPayload(new LoadRTDoseGeometry(loader, dicom.release()));
105
106 Schedule(command.release());
107 }
108 else
109 {
110 loader.SetGeometry(*dicom);
111 }
112 }
113 };
114
115
116
117 class OrthancMultiframeVolumeLoader::LoadTransferSyntax : public State
118 {
119 public:
120 LoadTransferSyntax(OrthancMultiframeVolumeLoader& that) :
121 State(that)
122 {
123 }
124
125 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message)
126 {
127 GetLoader<OrthancMultiframeVolumeLoader>().SetTransferSyntax(message.GetAnswer());
128 }
129 };
130
131
132 class OrthancMultiframeVolumeLoader::LoadUncompressedPixelData : public State
133 {
134 public:
135 LoadUncompressedPixelData(OrthancMultiframeVolumeLoader& that) :
136 State(that)
137 {
138 }
139
140 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message)
141 {
142 GetLoader<OrthancMultiframeVolumeLoader>().SetUncompressedPixelData(message.GetAnswer());
143 }
144 };
145
146
147 const std::string& OrthancMultiframeVolumeLoader::GetInstanceId() const
148 {
149 if (IsActive())
150 {
151 return instanceId_;
152 }
153 else
154 {
155 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
156 }
157 }
158
159
160 void OrthancMultiframeVolumeLoader::ScheduleFrameDownloads()
161 {
162 if (transferSyntaxUid_.empty() ||
163 !volume_->HasGeometry())
164 {
165 return;
166 }
167 /*
168 1.2.840.10008.1.2 Implicit VR Endian: Default Transfer Syntax for DICOM
169 1.2.840.10008.1.2.1 Explicit VR Little Endian
170 1.2.840.10008.1.2.2 Explicit VR Big Endian
171
172 See https://www.dicomlibrary.com/dicom/transfer-syntax/
173 */
174 if (transferSyntaxUid_ == "1.2.840.10008.1.2" ||
175 transferSyntaxUid_ == "1.2.840.10008.1.2.1" ||
176 transferSyntaxUid_ == "1.2.840.10008.1.2.2")
177 {
178 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand);
179 command->SetHttpHeader("Accept-Encoding", "gzip");
180 command->SetUri("/instances/" + instanceId_ + "/content/" +
181 Orthanc::DICOM_TAG_PIXEL_DATA.Format() + "/0");
182 command->SetPayload(new LoadUncompressedPixelData(*this));
183 Schedule(command.release());
184 }
185 else
186 {
187 throw Orthanc::OrthancException(
188 Orthanc::ErrorCode_NotImplemented,
189 "No support for multiframe instances with transfer syntax: " + transferSyntaxUid_);
190 }
191 }
192
193
194 void OrthancMultiframeVolumeLoader::SetTransferSyntax(const std::string& transferSyntax)
195 {
196 transferSyntaxUid_ = Orthanc::Toolbox::StripSpaces(transferSyntax);
197 ScheduleFrameDownloads();
198 }
199
200
201 void OrthancMultiframeVolumeLoader::SetGeometry(const Orthanc::DicomMap& dicom)
202 {
203 DicomInstanceParameters parameters(dicom);
204 volume_->SetDicomParameters(parameters);
205
206 Orthanc::PixelFormat format;
207 if (!parameters.GetImageInformation().ExtractPixelFormat(format, true))
208 {
209 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
210 }
211
212 double spacingZ;
213 switch (parameters.GetSopClassUid())
214 {
215 case SopClassUid_RTDose:
216 spacingZ = parameters.GetThickness();
217 break;
218
219 default:
220 throw Orthanc::OrthancException(
221 Orthanc::ErrorCode_NotImplemented,
222 "No support for multiframe instances with SOP class UID: " + GetSopClassUid(dicom));
223 }
224
225 const unsigned int width = parameters.GetImageInformation().GetWidth();
226 const unsigned int height = parameters.GetImageInformation().GetHeight();
227 const unsigned int depth = parameters.GetImageInformation().GetNumberOfFrames();
228
229 {
230 VolumeImageGeometry geometry;
231 geometry.SetSize(width, height, depth);
232 geometry.SetAxialGeometry(parameters.GetGeometry());
233 geometry.SetVoxelDimensions(parameters.GetPixelSpacingX(),
234 parameters.GetPixelSpacingY(), spacingZ);
235 volume_->Initialize(geometry, format);
236 }
237
238 volume_->GetPixelData().Clear();
239
240 ScheduleFrameDownloads();
241
242 BroadcastMessage(DicomVolumeImage::GeometryReadyMessage(*volume_));
243 }
244
245
246 ORTHANC_FORCE_INLINE
247 static void CopyPixel(uint32_t& target,
248 const void* source)
249 {
250 // TODO - check alignement?
251 target = le32toh(*reinterpret_cast<const uint32_t*>(source));
252 }
253
254
255 template <typename T>
256 void OrthancMultiframeVolumeLoader::CopyPixelData(const std::string& pixelData)
257 {
258 ImageBuffer3D& target = volume_->GetPixelData();
259
260 const unsigned int bpp = target.GetBytesPerPixel();
261 const unsigned int width = target.GetWidth();
262 const unsigned int height = target.GetHeight();
263 const unsigned int depth = target.GetDepth();
264
265 if (pixelData.size() != bpp * width * height * depth)
266 {
267 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
268 "The pixel data has not the proper size");
269 }
270
271 if (pixelData.empty())
272 {
273 return;
274 }
275
276 const uint8_t* source = reinterpret_cast<const uint8_t*>(pixelData.c_str());
277
278 for (unsigned int z = 0; z < depth; z++)
279 {
280 ImageBuffer3D::SliceWriter writer(target, VolumeProjection_Axial, z);
281
282 assert (writer.GetAccessor().GetWidth() == width &&
283 writer.GetAccessor().GetHeight() == height);
284
285 for (unsigned int y = 0; y < height; y++)
286 {
287 assert(sizeof(T) == Orthanc::GetBytesPerPixel(target.GetFormat()));
288
289 T* target = reinterpret_cast<T*>(writer.GetAccessor().GetRow(y));
290
291 for (unsigned int x = 0; x < width; x++)
292 {
293 CopyPixel(*target, source);
294
295 target ++;
296 source += bpp;
297 }
298 }
299 }
300 }
301
302
303 void OrthancMultiframeVolumeLoader::SetUncompressedPixelData(const std::string& pixelData)
304 {
305 switch (volume_->GetPixelData().GetFormat())
306 {
307 case Orthanc::PixelFormat_Grayscale32:
308 CopyPixelData<uint32_t>(pixelData);
309 break;
310
311 default:
312 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
313 }
314
315 volume_->IncrementRevision();
316
317 BroadcastMessage(DicomVolumeImage::ContentUpdatedMessage(*volume_));
318 }
319
320
321 OrthancMultiframeVolumeLoader::OrthancMultiframeVolumeLoader(const boost::shared_ptr<DicomVolumeImage>& volume,
322 IOracle& oracle,
323 IObservable& oracleObservable) :
324 LoaderStateMachine(oracle, oracleObservable),
325 IObservable(oracleObservable.GetBroker()),
326 volume_(volume)
327 {
328 if (volume.get() == NULL)
329 {
330 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer);
331 }
332 }
333
334
335 void OrthancMultiframeVolumeLoader::LoadInstance(const std::string& instanceId)
336 {
337 Start();
338
339 instanceId_ = instanceId;
340
341 {
342 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand);
343 command->SetHttpHeader("Accept-Encoding", "gzip");
344 command->SetUri("/instances/" + instanceId + "/tags");
345 command->SetPayload(new LoadGeometry(*this));
346 Schedule(command.release());
347 }
348
349 {
350 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand);
351 command->SetUri("/instances/" + instanceId + "/metadata/TransferSyntax");
352 command->SetPayload(new LoadTransferSyntax(*this));
353 Schedule(command.release());
354 }
355 }
356 }