0
|
1 /**
|
|
2 * Orthanc - A Lightweight, RESTful DICOM Store
|
|
3 * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics
|
|
4 * Department, University Hospital of Liege, Belgium
|
|
5 *
|
|
6 * This program is free software: you can redistribute it and/or
|
|
7 * modify it under the terms of the GNU Affero General Public License
|
|
8 * as published by the Free Software Foundation, either version 3 of
|
|
9 * the License, or (at your option) any later version.
|
|
10 *
|
|
11 * This program is distributed in the hope that it will be useful, but
|
|
12 * WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
|
|
14 * Affero General Public License for more details.
|
|
15 *
|
|
16 * You should have received a copy of the GNU Affero General Public License
|
|
17 * along with this program. If not, see <http://www.gnu.org/licenses/>.
|
|
18 **/
|
|
19
|
|
20
|
|
21 #include "ParsedDicomImage.h"
|
|
22
|
|
23 #include "../Orthanc/OrthancException.h"
|
|
24 #include "../Orthanc/Toolbox.h"
|
|
25 #include "../Orthanc/ImageFormats/ImageProcessing.h"
|
|
26 #include "../Orthanc/ImageFormats/ImageBuffer.h"
|
|
27 #include "JpegWriter.h"
|
|
28 #include "ViewerToolbox.h"
|
|
29
|
|
30 #include <gdcmImageReader.h>
|
|
31 #include <gdcmImageChangePlanarConfiguration.h>
|
|
32 #include <gdcmImageChangePhotometricInterpretation.h>
|
|
33 #include <boost/lexical_cast.hpp>
|
|
34 #include <boost/math/special_functions/round.hpp>
|
|
35
|
|
36 #include "../Resources/ThirdParty/base64/base64.h"
|
|
37
|
|
38
|
|
39 namespace OrthancPlugins
|
|
40 {
|
|
41 struct ParsedDicomImage::PImpl
|
|
42 {
|
|
43 gdcm::ImageReader reader_;
|
|
44 std::auto_ptr<gdcm::ImageChangePhotometricInterpretation> photometric_;
|
|
45 std::auto_ptr<gdcm::ImageChangePlanarConfiguration> interleaved_;
|
|
46 std::string decoded_;
|
|
47
|
|
48 const gdcm::Image& GetImage() const
|
|
49 {
|
|
50 if (interleaved_.get() != NULL)
|
|
51 {
|
|
52 return interleaved_->GetOutput();
|
|
53 }
|
|
54
|
|
55 if (photometric_.get() != NULL)
|
|
56 {
|
|
57 return photometric_->GetOutput();
|
|
58 }
|
|
59
|
|
60 return reader_.GetImage();
|
|
61 }
|
|
62
|
|
63
|
|
64 const gdcm::DataSet& GetDataSet() const
|
|
65 {
|
|
66 return reader_.GetFile().GetDataSet();
|
|
67 }
|
|
68 };
|
|
69
|
|
70
|
|
71 template <typename TargetType, typename SourceType>
|
|
72 static void ChangeDynamics(Orthanc::ImageAccessor& target,
|
|
73 const Orthanc::ImageAccessor& source,
|
|
74 SourceType source1, TargetType target1,
|
|
75 SourceType source2, TargetType target2)
|
|
76 {
|
|
77 if (source.GetWidth() != target.GetWidth() ||
|
|
78 source.GetHeight() != target.GetHeight())
|
|
79 {
|
|
80 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize);
|
|
81 }
|
|
82
|
|
83 float scale = static_cast<float>(target2 - target1) / static_cast<float>(source2 - source1);
|
|
84 float offset = static_cast<float>(target1) - scale * static_cast<float>(source1);
|
|
85
|
|
86 const float minValue = static_cast<float>(std::numeric_limits<TargetType>::min());
|
|
87 const float maxValue = static_cast<float>(std::numeric_limits<TargetType>::max());
|
|
88
|
|
89 for (unsigned int y = 0; y < source.GetHeight(); y++)
|
|
90 {
|
|
91 const SourceType* p = reinterpret_cast<const SourceType*>(source.GetConstRow(y));
|
|
92 TargetType* q = reinterpret_cast<TargetType*>(target.GetRow(y));
|
|
93
|
|
94 for (unsigned int x = 0; x < source.GetWidth(); x++, p++, q++)
|
|
95 {
|
|
96 float v = (scale * static_cast<float>(*p)) + offset;
|
|
97
|
|
98 if (v > maxValue)
|
|
99 {
|
|
100 *q = std::numeric_limits<TargetType>::max();
|
|
101 }
|
|
102 else if (v < minValue)
|
|
103 {
|
|
104 *q = std::numeric_limits<TargetType>::min();
|
|
105 }
|
|
106 else
|
|
107 {
|
|
108 *q = static_cast<TargetType>(boost::math::iround(v));
|
|
109 }
|
|
110 }
|
|
111 }
|
|
112 }
|
|
113
|
|
114
|
|
115 void ParsedDicomImage::Setup(const std::string& dicom)
|
|
116 {
|
|
117 // Prepare a memory stream over the DICOM instance
|
|
118 std::stringstream stream(dicom);
|
|
119
|
|
120 // Parse the DICOM instance using GDCM
|
|
121 pimpl_->reader_.SetStream(stream);
|
|
122 if (!pimpl_->reader_.Read())
|
|
123 {
|
|
124 throw Orthanc::OrthancException("GDCM cannot extract an image from this DICOM instance");
|
|
125 }
|
|
126
|
|
127 // Change photometric interpretation, if required
|
|
128 {
|
|
129 const gdcm::Image& image = pimpl_->GetImage();
|
|
130 if (image.GetPixelFormat().GetSamplesPerPixel() == 1)
|
|
131 {
|
|
132 if (image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME1 &&
|
|
133 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::MONOCHROME2)
|
|
134 {
|
|
135 pimpl_->photometric_.reset(new gdcm::ImageChangePhotometricInterpretation());
|
|
136 pimpl_->photometric_->SetInput(image);
|
|
137 pimpl_->photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::MONOCHROME2);
|
|
138 if (!pimpl_->photometric_->Change())
|
|
139 {
|
|
140 throw Orthanc::OrthancException("GDCM cannot change the photometric interpretation");
|
|
141 }
|
|
142 }
|
|
143 }
|
|
144 else
|
|
145 {
|
|
146 if (image.GetPixelFormat().GetSamplesPerPixel() == 3 &&
|
|
147 image.GetPhotometricInterpretation() != gdcm::PhotometricInterpretation::RGB)
|
|
148 {
|
|
149 pimpl_->photometric_.reset(new gdcm::ImageChangePhotometricInterpretation());
|
|
150 pimpl_->photometric_->SetInput(image);
|
|
151 pimpl_->photometric_->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::RGB);
|
|
152 if (!pimpl_->photometric_->Change())
|
|
153 {
|
|
154 throw Orthanc::OrthancException("GDCM cannot change the photometric interpretation");
|
|
155 }
|
|
156 }
|
|
157 }
|
|
158 }
|
|
159
|
|
160 // Possibly convert planar configuration to interleaved
|
|
161 {
|
|
162 const gdcm::Image& image = pimpl_->GetImage();
|
|
163 if (image.GetPlanarConfiguration() != 0 &&
|
|
164 image.GetPixelFormat().GetSamplesPerPixel() != 1)
|
|
165 {
|
|
166 pimpl_->interleaved_.reset(new gdcm::ImageChangePlanarConfiguration());
|
|
167 pimpl_->interleaved_->SetInput(image);
|
|
168 if (!pimpl_->interleaved_->Change())
|
|
169 {
|
|
170 throw Orthanc::OrthancException("GDCM cannot change the planar configuration to interleaved");
|
|
171 }
|
|
172 }
|
|
173 }
|
|
174
|
|
175 // Decode the image to the memory buffer
|
|
176 {
|
|
177 const gdcm::Image& image = pimpl_->GetImage();
|
|
178 pimpl_->decoded_.resize(image.GetBufferLength());
|
|
179
|
|
180 if (pimpl_->decoded_.size() > 0)
|
|
181 {
|
|
182 image.GetBuffer(&pimpl_->decoded_[0]);
|
|
183 }
|
|
184 }
|
|
185 }
|
|
186
|
|
187
|
|
188 ParsedDicomImage::ParsedDicomImage(const std::string& dicom) : pimpl_(new PImpl)
|
|
189 {
|
|
190 Setup(dicom);
|
|
191 }
|
|
192
|
|
193
|
|
194 bool ParsedDicomImage::GetTag(std::string& result,
|
|
195 uint16_t group,
|
|
196 uint16_t element,
|
|
197 bool stripSpaces)
|
|
198 {
|
|
199 const gdcm::Tag tag(group, element);
|
|
200
|
|
201 if (pimpl_->GetDataSet().FindDataElement(tag))
|
|
202 {
|
|
203 const gdcm::ByteValue* value = pimpl_->GetDataSet().GetDataElement(tag).GetByteValue();
|
|
204 if (value)
|
|
205 {
|
|
206 result = std::string(value->GetPointer(), value->GetLength());
|
|
207
|
|
208 if (stripSpaces)
|
|
209 {
|
|
210 result = Orthanc::Toolbox::StripSpaces(result);
|
|
211 }
|
|
212
|
|
213 return true;
|
|
214 }
|
|
215 }
|
|
216
|
|
217 return false;
|
|
218 }
|
|
219
|
|
220
|
|
221 bool ParsedDicomImage::GetAccessor(Orthanc::ImageAccessor& accessor)
|
|
222 {
|
|
223 const gdcm::Image& image = pimpl_->GetImage();
|
|
224
|
|
225 size_t size = pimpl_->decoded_.size();
|
|
226 void* buffer = (size ? &pimpl_->decoded_[0] : NULL);
|
|
227 unsigned int height = image.GetRows();
|
|
228 unsigned int width = image.GetColumns();
|
|
229
|
|
230 if (image.GetPixelFormat().GetSamplesPerPixel() == 1 &&
|
|
231 (image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME1 ||
|
|
232 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME2))
|
|
233 {
|
|
234 switch (image.GetPixelFormat())
|
|
235 {
|
|
236 case gdcm::PixelFormat::UINT16:
|
|
237 accessor.AssignWritable(Orthanc::PixelFormat_Grayscale16, width, height, 2 * width, buffer);
|
|
238 return true;
|
|
239
|
|
240 case gdcm::PixelFormat::INT16:
|
|
241 accessor.AssignWritable(Orthanc::PixelFormat_SignedGrayscale16, width, height, 2 * width, buffer);
|
|
242 return true;
|
|
243
|
|
244 case gdcm::PixelFormat::UINT8:
|
|
245 accessor.AssignWritable(Orthanc::PixelFormat_Grayscale8, width, height, width, buffer);
|
|
246 return true;
|
|
247 }
|
|
248 }
|
|
249 else if (image.GetPixelFormat().GetSamplesPerPixel() == 3 &&
|
|
250 image.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::RGB)
|
|
251 {
|
|
252 switch (image.GetPixelFormat())
|
|
253 {
|
|
254 case gdcm::PixelFormat::UINT8:
|
|
255 accessor.AssignWritable(Orthanc::PixelFormat_RGB24, width, height, 3 * width, buffer);
|
|
256 return true;
|
|
257 }
|
|
258 }
|
|
259
|
|
260 return false;
|
|
261 }
|
|
262
|
|
263 bool ParsedDicomImage::GetCornerstoneMetadata(Json::Value& json)
|
|
264 {
|
|
265 using namespace Orthanc;
|
|
266
|
|
267 ImageAccessor accessor;
|
|
268 if (!GetAccessor(accessor))
|
|
269 {
|
|
270 return false;
|
|
271 }
|
|
272
|
|
273 float windowCenter, windowWidth;
|
|
274
|
|
275 switch (accessor.GetFormat())
|
|
276 {
|
|
277 case PixelFormat_Grayscale8:
|
|
278 case PixelFormat_Grayscale16:
|
|
279 case PixelFormat_SignedGrayscale16:
|
|
280 {
|
|
281 int64_t a, b;
|
|
282 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor);
|
|
283 json["minPixelValue"] = (a < 0 ? static_cast<int32_t>(a) : 0);
|
|
284 json["maxPixelValue"] = (b > 0 ? static_cast<int32_t>(b) : 1);
|
|
285 json["color"] = false;
|
|
286
|
|
287 windowCenter = static_cast<float>(a + b) / 2.0f;
|
|
288
|
|
289 if (a == b)
|
|
290 {
|
|
291 windowWidth = 127.5f; // Arbitrary value
|
|
292 }
|
|
293 else
|
|
294 {
|
|
295 windowWidth = static_cast<float>(b - a) / 2.0f;
|
|
296 }
|
|
297
|
|
298 break;
|
|
299 }
|
|
300
|
|
301 case PixelFormat_RGB24:
|
|
302 json["minPixelValue"] = 0;
|
|
303 json["maxPixelValue"] = 255;
|
|
304 json["color"] = true;
|
|
305 windowCenter = 127.5f;
|
|
306 windowWidth = 127.5f;
|
|
307 break;
|
|
308
|
|
309 default:
|
|
310 return false;
|
|
311 }
|
|
312
|
|
313 const gdcm::Image& image = pimpl_->GetImage();
|
|
314 json["slope"] = image.GetSlope();
|
|
315 json["intercept"] = image.GetIntercept();
|
|
316 json["rows"] = image.GetRows();
|
|
317 json["columns"] = image.GetColumns();
|
|
318 json["height"] = image.GetRows();
|
|
319 json["width"] = image.GetColumns();
|
|
320 json["columnPixelSpacing"] = image.GetSpacing(1);
|
|
321 json["rowPixelSpacing"] = image.GetSpacing(0);
|
|
322
|
|
323 json["windowCenter"] = windowCenter * image.GetSlope() + image.GetIntercept();
|
|
324 json["windowWidth"] = windowWidth * image.GetSlope();
|
|
325
|
|
326 try
|
|
327 {
|
|
328 std::string width, center;
|
|
329 if (GetTag(center, 0x0028, 0x1050 /*DICOM_TAG_WINDOW_CENTER*/) &&
|
|
330 GetTag(width, 0x0028, 0x1051 /*DICOM_TAG_WINDOW_WIDTH*/))
|
|
331 {
|
|
332 float a = boost::lexical_cast<float>(width);
|
|
333 float b = boost::lexical_cast<float>(center);
|
|
334 json["windowWidth"] = a;
|
|
335 json["windowCenter"] = b;
|
|
336 }
|
|
337 }
|
|
338 catch (boost::bad_lexical_cast&)
|
|
339 {
|
|
340 }
|
|
341
|
|
342 return true;
|
|
343 }
|
|
344
|
|
345
|
|
346 bool ParsedDicomImage::EncodeUsingDeflate(Json::Value& result,
|
|
347 uint8_t compressionLevel /* between 0 and 9 */)
|
|
348 {
|
|
349 using namespace Orthanc;
|
|
350
|
|
351 ImageAccessor accessor;
|
|
352 if (!GetAccessor(accessor))
|
|
353 {
|
|
354 return false;
|
|
355 }
|
|
356
|
|
357 result = Json::objectValue;
|
|
358 result["Orthanc"] = Json::objectValue;
|
|
359 if (!GetCornerstoneMetadata(result))
|
|
360 {
|
|
361 return false;
|
|
362 }
|
|
363
|
|
364 ImageBuffer buffer;
|
|
365 buffer.SetMinimalPitchForced(true);
|
|
366
|
|
367 ImageAccessor converted;
|
|
368
|
|
369
|
|
370 switch (accessor.GetFormat())
|
|
371 {
|
|
372 case Orthanc::PixelFormat_RGB24:
|
|
373 converted = accessor;
|
|
374 break;
|
|
375
|
|
376 case Orthanc::PixelFormat_Grayscale8:
|
|
377 case Orthanc::PixelFormat_Grayscale16:
|
|
378 buffer.SetFormat(Orthanc::PixelFormat_SignedGrayscale16);
|
|
379 buffer.SetWidth(accessor.GetWidth());
|
|
380 buffer.SetHeight(accessor.GetHeight());
|
|
381 converted = buffer.GetAccessor();
|
|
382 ImageProcessing::Convert(converted, accessor);
|
|
383 break;
|
|
384
|
|
385 case Orthanc::PixelFormat_SignedGrayscale16:
|
|
386 converted = accessor;
|
|
387 break;
|
|
388
|
|
389 default:
|
|
390 // Unsupported pixel format
|
|
391 return false;
|
|
392 }
|
|
393
|
|
394 // Sanity check: The pitch must be minimal
|
|
395 assert(converted.GetSize() == converted.GetWidth() * converted.GetHeight() *
|
|
396 GetBytesPerPixel(converted.GetFormat()));
|
|
397 result["Orthanc"]["Compression"] = "Deflate";
|
|
398 result["sizeInBytes"] = converted.GetSize();
|
|
399
|
|
400 std::string z;
|
|
401 if (!CompressUsingDeflate(z, converted.GetConstBuffer(), converted.GetSize(), compressionLevel))
|
|
402 {
|
|
403 return false;
|
|
404 }
|
|
405
|
|
406 result["Orthanc"]["PixelData"] = base64_encode(z);
|
|
407
|
|
408 return true;
|
|
409 }
|
|
410
|
|
411
|
|
412
|
|
413 bool ParsedDicomImage::EncodeUsingJpeg(Json::Value& result,
|
|
414 uint8_t quality /* between 0 and 100 */)
|
|
415 {
|
|
416 using namespace Orthanc;
|
|
417
|
|
418 ImageAccessor accessor;
|
|
419 if (!GetAccessor(accessor))
|
|
420 {
|
|
421 return false;
|
|
422 }
|
|
423
|
|
424 result = Json::objectValue;
|
|
425 result["Orthanc"] = Json::objectValue;
|
|
426 GetCornerstoneMetadata(result);
|
|
427
|
|
428 ImageBuffer buffer;
|
|
429 buffer.SetMinimalPitchForced(true);
|
|
430
|
|
431 ImageAccessor converted;
|
|
432
|
|
433 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale8 ||
|
|
434 accessor.GetFormat() == Orthanc::PixelFormat_RGB24)
|
|
435 {
|
|
436 result["Orthanc"]["Stretched"] = false;
|
|
437 converted = accessor;
|
|
438 }
|
|
439 else if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16 ||
|
|
440 accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16)
|
|
441 {
|
|
442 result["Orthanc"]["Stretched"] = true;
|
|
443 buffer.SetFormat(Orthanc::PixelFormat_Grayscale8);
|
|
444 buffer.SetWidth(accessor.GetWidth());
|
|
445 buffer.SetHeight(accessor.GetHeight());
|
|
446 converted = buffer.GetAccessor();
|
|
447
|
|
448 int64_t a, b;
|
|
449 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor);
|
|
450 result["Orthanc"]["StretchLow"] = static_cast<int32_t>(a);
|
|
451 result["Orthanc"]["StretchHigh"] = static_cast<int32_t>(b);
|
|
452
|
|
453 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16)
|
|
454 {
|
|
455 ChangeDynamics<uint8_t, uint16_t>(converted, accessor, a, 0, b, 255);
|
|
456 }
|
|
457 else
|
|
458 {
|
|
459 ChangeDynamics<uint8_t, int16_t>(converted, accessor, a, 0, b, 255);
|
|
460 }
|
|
461 }
|
|
462 else
|
|
463 {
|
|
464 return false;
|
|
465 }
|
|
466
|
|
467 result["Orthanc"]["Compression"] = "Jpeg";
|
|
468 result["sizeInBytes"] = converted.GetSize();
|
|
469
|
|
470 std::string jpeg;
|
|
471 OrthancPlugins::JpegWriter writer;
|
|
472 writer.SetQuality(quality);
|
|
473 writer.WriteToMemory(jpeg, converted);
|
|
474 result["Orthanc"]["PixelData"] = base64_encode(jpeg);
|
|
475 return true;
|
|
476 }
|
|
477 };
|