Mercurial > hg > orthanc-webviewer
annotate Plugin/DecodedImageAdapter.cpp @ 171:b6c55352818c
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 24 Aug 2017 19:49:20 +0200 |
parents | b0910ae2ace5 |
children | 330ecfd96aec |
rev | line source |
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0 | 1 /** |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
122 | 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics |
0 | 4 * Department, University Hospital of Liege, Belgium |
159
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5 * Copyright (C) 2017 Osimis, Belgium |
0 | 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 "DecodedImageAdapter.h" | |
23 | |
96 | 24 #include "../Orthanc/Core/Images/ImageBuffer.h" |
25 #include "../Orthanc/Core/Images/ImageProcessing.h" | |
26 #include "../Orthanc/Core/OrthancException.h" | |
102 | 27 #include "../Orthanc/Core/Toolbox.h" |
96 | 28 #include "../Orthanc/Plugins/Samples/GdcmDecoder/OrthancImageWrapper.h" |
29 #include "../Orthanc/Resources/ThirdParty/base64/base64.h" | |
0 | 30 #include "ViewerToolbox.h" |
31 | |
32 #include <boost/lexical_cast.hpp> | |
33 #include <boost/algorithm/string/predicate.hpp> | |
34 #include <json/writer.h> | |
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35 #include <boost/regex.hpp> |
0 | 36 |
103 | 37 |
0 | 38 namespace OrthancPlugins |
39 { | |
160 | 40 static bool GetStringTag(std::string& value, |
41 const Json::Value& tags, | |
42 const std::string& tag) | |
43 { | |
44 if (tags.type() == Json::objectValue && | |
45 tags.isMember(tag) && | |
46 tags[tag].type() == Json::objectValue && | |
47 tags[tag].isMember("Type") && | |
48 tags[tag].isMember("Value") && | |
49 tags[tag]["Type"].type() == Json::stringValue && | |
50 tags[tag]["Value"].type() == Json::stringValue && | |
51 tags[tag]["Type"].asString() == "String") | |
52 { | |
53 value = tags[tag]["Value"].asString(); | |
54 return true; | |
55 } | |
56 else | |
57 { | |
58 return false; | |
59 } | |
60 } | |
61 | |
62 | |
63 static float GetFloatTag(const Json::Value& tags, | |
64 const std::string& tag, | |
65 float defaultValue) | |
66 { | |
67 std::string tmp; | |
68 if (GetStringTag(tmp, tags, tag)) | |
69 { | |
70 try | |
71 { | |
72 return boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tmp)); | |
73 } | |
74 catch (boost::bad_lexical_cast&) | |
75 { | |
76 } | |
77 } | |
78 | |
79 return defaultValue; | |
80 } | |
81 | |
82 | |
0 | 83 bool DecodedImageAdapter::ParseUri(CompressionType& type, |
84 uint8_t& compressionLevel, | |
85 std::string& instanceId, | |
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86 unsigned int& frameIndex, |
0 | 87 const std::string& uri) |
88 { | |
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89 boost::regex pattern("^([a-z0-9]+)-([a-z0-9-]+)_([0-9]+)$"); |
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90 |
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91 boost::cmatch what; |
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92 if (!regex_match(uri.c_str(), what, pattern)) |
0 | 93 { |
94 return false; | |
95 } | |
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96 |
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97 std::string compression(what[1]); |
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98 instanceId = what[2]; |
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99 frameIndex = boost::lexical_cast<unsigned int>(what[3]); |
0 | 100 |
101 if (compression == "deflate") | |
102 { | |
103 type = CompressionType_Deflate; | |
104 } | |
105 else if (boost::starts_with(compression, "jpeg")) | |
106 { | |
107 type = CompressionType_Jpeg; | |
108 int level = boost::lexical_cast<int>(compression.substr(4)); | |
109 if (level <= 0 || level > 100) | |
110 { | |
111 return false; | |
112 } | |
113 | |
114 compressionLevel = static_cast<uint8_t>(level); | |
115 } | |
116 else | |
117 { | |
118 return false; | |
119 } | |
120 | |
121 return true; | |
122 } | |
123 | |
124 | |
125 | |
126 bool DecodedImageAdapter::Create(std::string& content, | |
127 const std::string& uri) | |
128 { | |
129 std::string message = "Decoding DICOM instance: " + uri; | |
130 OrthancPluginLogInfo(context_, message.c_str()); | |
131 | |
132 CompressionType type; | |
133 uint8_t level; | |
134 std::string instanceId; | |
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135 unsigned int frameIndex; |
0 | 136 |
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137 if (!ParseUri(type, level, instanceId, frameIndex, uri)) |
0 | 138 { |
139 return false; | |
140 } | |
141 | |
96 | 142 |
143 bool ok = false; | |
144 | |
145 Json::Value tags; | |
146 std::string dicom; | |
147 if (!GetStringFromOrthanc(dicom, context_, "/instances/" + instanceId + "/file") || | |
148 !GetJsonFromOrthanc(tags, context_, "/instances/" + instanceId + "/tags")) | |
149 { | |
150 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
151 } | |
152 | |
102 | 153 std::auto_ptr<OrthancImageWrapper> image(new OrthancImageWrapper(context_, OrthancPluginDecodeDicomImage(context_, dicom.c_str(), dicom.size(), frameIndex))); |
96 | 154 |
155 Json::Value json; | |
156 if (GetCornerstoneMetadata(json, tags, *image)) | |
157 { | |
158 if (type == CompressionType_Deflate) | |
159 { | |
160 ok = EncodeUsingDeflate(json, *image, 9); | |
161 } | |
162 else if (type == CompressionType_Jpeg) | |
163 { | |
164 ok = EncodeUsingJpeg(json, *image, level); | |
165 } | |
166 } | |
167 | |
31 | 168 if (ok) |
169 { | |
160 | 170 std::string photometric; |
171 if (GetStringTag(photometric, tags, "0028,0004")) | |
172 { | |
173 json["Orthanc"]["PhotometricInterpretation"] = photometric; | |
174 } | |
175 | |
31 | 176 Json::FastWriter writer; |
177 content = writer.write(json); | |
178 return true; | |
0 | 179 } |
180 else | |
181 { | |
31 | 182 char msg[1024]; |
183 sprintf(msg, "Unable to decode the following instance: %s", uri.c_str()); | |
184 OrthancPluginLogWarning(context_, msg); | |
0 | 185 return false; |
186 } | |
187 } | |
96 | 188 |
189 | |
190 bool DecodedImageAdapter::GetCornerstoneMetadata(Json::Value& result, | |
191 const Json::Value& tags, | |
192 OrthancImageWrapper& image) | |
193 { | |
194 using namespace Orthanc; | |
195 | |
196 float windowCenter, windowWidth; | |
197 | |
198 Orthanc::ImageAccessor accessor; | |
199 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
200 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
201 | |
202 switch (accessor.GetFormat()) | |
203 { | |
204 case PixelFormat_Grayscale8: | |
205 case PixelFormat_Grayscale16: | |
206 case PixelFormat_SignedGrayscale16: | |
207 { | |
208 int64_t a, b; | |
209 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor); | |
210 result["minPixelValue"] = (a < 0 ? static_cast<int32_t>(a) : 0); | |
211 result["maxPixelValue"] = (b > 0 ? static_cast<int32_t>(b) : 1); | |
212 result["color"] = false; | |
213 | |
214 windowCenter = static_cast<float>(a + b) / 2.0f; | |
215 | |
216 if (a == b) | |
217 { | |
218 windowWidth = 256.0f; // Arbitrary value | |
219 } | |
220 else | |
221 { | |
222 windowWidth = static_cast<float>(b - a) / 2.0f; | |
223 } | |
224 | |
225 break; | |
226 } | |
227 | |
228 case PixelFormat_RGB24: | |
229 result["minPixelValue"] = 0; | |
230 result["maxPixelValue"] = 255; | |
231 result["color"] = true; | |
232 windowCenter = 127.5f; | |
233 windowWidth = 256.0f; | |
234 break; | |
235 | |
236 default: | |
237 return false; | |
238 } | |
239 | |
102 | 240 float slope = GetFloatTag(tags, "0028,1053", 1.0f); |
103 | 241 float intercept = GetFloatTag(tags, "0028,1052", 0.0f); |
102 | 242 |
243 result["slope"] = slope; | |
244 result["intercept"] = intercept; | |
96 | 245 result["rows"] = image.GetHeight(); |
246 result["columns"] = image.GetWidth(); | |
247 result["height"] = image.GetHeight(); | |
248 result["width"] = image.GetWidth(); | |
249 | |
102 | 250 bool ok = false; |
251 std::string pixelSpacing; | |
252 if (GetStringTag(pixelSpacing, tags, "0028,0030")) | |
96 | 253 { |
102 | 254 std::vector<std::string> tokens; |
255 Orthanc::Toolbox::TokenizeString(tokens, pixelSpacing, '\\'); | |
256 | |
257 if (tokens.size() >= 2) | |
96 | 258 { |
102 | 259 try |
260 { | |
103 | 261 result["columnPixelSpacing"] = boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tokens[1])); |
262 result["rowPixelSpacing"] = boost::lexical_cast<float>(Orthanc::Toolbox::StripSpaces(tokens[0])); | |
102 | 263 ok = true; |
264 } | |
265 catch (boost::bad_lexical_cast&) | |
266 { | |
267 } | |
96 | 268 } |
269 } | |
102 | 270 |
271 if (!ok) | |
96 | 272 { |
102 | 273 result["columnPixelSpacing"] = 1.0f; |
274 result["rowPixelSpacing"] = 1.0f; | |
96 | 275 } |
276 | |
102 | 277 result["windowCenter"] = GetFloatTag(tags, "0028,1050", windowCenter * slope + intercept); |
278 result["windowWidth"] = GetFloatTag(tags, "0028,1051", windowWidth * slope); | |
279 | |
96 | 280 return true; |
281 } | |
282 | |
283 | |
284 | |
285 bool DecodedImageAdapter::EncodeUsingDeflate(Json::Value& result, | |
286 OrthancImageWrapper& image, | |
287 uint8_t compressionLevel /* between 0 and 9 */) | |
288 { | |
289 Orthanc::ImageAccessor accessor; | |
290 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
291 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
292 | |
145 | 293 std::auto_ptr<Orthanc::ImageBuffer> buffer; |
96 | 294 |
295 Orthanc::ImageAccessor converted; | |
296 | |
297 switch (accessor.GetFormat()) | |
298 { | |
299 case Orthanc::PixelFormat_RGB24: | |
300 converted = accessor; | |
301 break; | |
302 | |
303 case Orthanc::PixelFormat_Grayscale8: | |
304 case Orthanc::PixelFormat_Grayscale16: | |
145 | 305 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_Grayscale16, |
306 accessor.GetWidth(), | |
307 accessor.GetHeight(), | |
308 true /* force minimal pitch */)); | |
309 converted = buffer->GetAccessor(); | |
96 | 310 Orthanc::ImageProcessing::Convert(converted, accessor); |
311 break; | |
312 | |
313 case Orthanc::PixelFormat_SignedGrayscale16: | |
314 converted = accessor; | |
315 break; | |
316 | |
317 default: | |
318 // Unsupported pixel format | |
319 return false; | |
320 } | |
321 | |
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322 result["Orthanc"]["IsSigned"] = (accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16); |
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323 |
96 | 324 // Sanity check: The pitch must be minimal |
325 assert(converted.GetSize() == converted.GetWidth() * converted.GetHeight() * | |
326 GetBytesPerPixel(converted.GetFormat())); | |
327 result["Orthanc"]["Compression"] = "Deflate"; | |
328 result["sizeInBytes"] = converted.GetSize(); | |
329 | |
330 std::string z; | |
331 CompressUsingDeflate(z, image.GetContext(), converted.GetConstBuffer(), converted.GetSize()); | |
332 | |
333 result["Orthanc"]["PixelData"] = base64_encode(z); | |
334 | |
335 return true; | |
336 } | |
337 | |
338 | |
339 | |
340 template <typename TargetType, typename SourceType> | |
341 static void ChangeDynamics(Orthanc::ImageAccessor& target, | |
342 const Orthanc::ImageAccessor& source, | |
343 SourceType source1, TargetType target1, | |
344 SourceType source2, TargetType target2) | |
345 { | |
346 if (source.GetWidth() != target.GetWidth() || | |
347 source.GetHeight() != target.GetHeight()) | |
348 { | |
349 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
350 } | |
351 | |
352 float scale = static_cast<float>(target2 - target1) / static_cast<float>(source2 - source1); | |
353 float offset = static_cast<float>(target1) - scale * static_cast<float>(source1); | |
354 | |
355 const float minValue = static_cast<float>(std::numeric_limits<TargetType>::min()); | |
356 const float maxValue = static_cast<float>(std::numeric_limits<TargetType>::max()); | |
357 | |
358 for (unsigned int y = 0; y < source.GetHeight(); y++) | |
359 { | |
360 const SourceType* p = reinterpret_cast<const SourceType*>(source.GetConstRow(y)); | |
361 TargetType* q = reinterpret_cast<TargetType*>(target.GetRow(y)); | |
362 | |
363 for (unsigned int x = 0; x < source.GetWidth(); x++, p++, q++) | |
364 { | |
365 float v = (scale * static_cast<float>(*p)) + offset; | |
366 | |
367 if (v > maxValue) | |
368 { | |
369 *q = std::numeric_limits<TargetType>::max(); | |
370 } | |
371 else if (v < minValue) | |
372 { | |
373 *q = std::numeric_limits<TargetType>::min(); | |
374 } | |
375 else | |
376 { | |
101 | 377 //*q = static_cast<TargetType>(boost::math::iround(v)); |
378 | |
379 // http://stackoverflow.com/a/485546/881731 | |
380 *q = static_cast<TargetType>(floor(v + 0.5f)); | |
96 | 381 } |
382 } | |
383 } | |
384 } | |
385 | |
386 | |
387 bool DecodedImageAdapter::EncodeUsingJpeg(Json::Value& result, | |
388 OrthancImageWrapper& image, | |
389 uint8_t quality /* between 0 and 100 */) | |
390 { | |
391 Orthanc::ImageAccessor accessor; | |
392 accessor.AssignReadOnly(OrthancPlugins::Convert(image.GetFormat()), image.GetWidth(), | |
393 image.GetHeight(), image.GetPitch(), image.GetBuffer()); | |
394 | |
145 | 395 std::auto_ptr<Orthanc::ImageBuffer> buffer; |
96 | 396 |
397 Orthanc::ImageAccessor converted; | |
398 | |
399 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale8 || | |
400 accessor.GetFormat() == Orthanc::PixelFormat_RGB24) | |
401 { | |
402 result["Orthanc"]["Stretched"] = false; | |
403 converted = accessor; | |
404 } | |
405 else if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16 || | |
406 accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16) | |
407 { | |
408 result["Orthanc"]["Stretched"] = true; | |
145 | 409 |
410 buffer.reset(new Orthanc::ImageBuffer(Orthanc::PixelFormat_Grayscale8, | |
411 accessor.GetWidth(), | |
412 accessor.GetHeight(), | |
413 true /* force minimal pitch */)); | |
414 converted = buffer->GetAccessor(); | |
96 | 415 |
416 int64_t a, b; | |
417 Orthanc::ImageProcessing::GetMinMaxValue(a, b, accessor); | |
418 result["Orthanc"]["StretchLow"] = static_cast<int32_t>(a); | |
419 result["Orthanc"]["StretchHigh"] = static_cast<int32_t>(b); | |
420 | |
421 if (accessor.GetFormat() == Orthanc::PixelFormat_Grayscale16) | |
422 { | |
423 ChangeDynamics<uint8_t, uint16_t>(converted, accessor, a, 0, b, 255); | |
424 } | |
425 else | |
426 { | |
427 ChangeDynamics<uint8_t, int16_t>(converted, accessor, a, 0, b, 255); | |
428 } | |
429 } | |
430 else | |
431 { | |
432 return false; | |
433 } | |
434 | |
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435 result["Orthanc"]["IsSigned"] = (accessor.GetFormat() == Orthanc::PixelFormat_SignedGrayscale16); |
96 | 436 result["Orthanc"]["Compression"] = "Jpeg"; |
437 result["sizeInBytes"] = converted.GetSize(); | |
438 | |
439 std::string jpeg; | |
440 WriteJpegToMemory(jpeg, image.GetContext(), converted, quality); | |
441 | |
442 result["Orthanc"]["PixelData"] = base64_encode(jpeg); | |
443 return true; | |
444 } | |
0 | 445 } |