Mercurial > hg > orthanc
annotate OrthancServer/FromDcmtkBridge.cpp @ 71:aa65ced5f0f0
fix for visual studio
| author | jodogne |
|---|---|
| date | Mon, 17 Sep 2012 12:34:55 +0200 |
| parents | a70bb32802ae |
| children | cb5ad233c336 |
| rev | line source |
|---|---|
| 0 | 1 /** |
| 62 | 2 * Orthanc - A Lightweight, RESTful DICOM Store |
| 0 | 3 * Copyright (C) 2012 Medical Physics Department, CHU of Liege, |
| 4 * Belgium | |
| 5 * | |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU General Public License as | |
| 8 * published by the Free Software Foundation, either version 3 of the | |
| 9 * 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 * General Public License for more details. | |
| 15 * | |
| 16 * You should have received a copy of the GNU General Public License | |
| 17 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 18 **/ | |
| 19 | |
| 71 | 20 #ifndef NOMINMAX |
| 21 #define NOMINMAX | |
| 22 #endif | |
| 0 | 23 |
| 24 #include "FromDcmtkBridge.h" | |
| 25 | |
| 26 #include "ToDcmtkBridge.h" | |
| 27 #include "DicomIntegerPixelAccessor.h" | |
| 62 | 28 #include "../Core/OrthancException.h" |
| 0 | 29 #include "../Core/PngWriter.h" |
| 30 #include "../Core/DicomFormat/DicomString.h" | |
| 31 #include "../Core/DicomFormat/DicomNullValue.h" | |
| 32 | |
| 71 | 33 #include <limits> |
| 34 | |
| 0 | 35 #include <boost/locale.hpp> |
| 36 #include <boost/lexical_cast.hpp> | |
| 37 | |
| 38 #include <dcmtk/dcmdata/dcdicent.h> | |
| 39 #include <dcmtk/dcmdata/dcdict.h> | |
| 40 #include <dcmtk/dcmdata/dcelem.h> | |
| 41 #include <dcmtk/dcmdata/dcfilefo.h> | |
| 42 #include <dcmtk/dcmdata/dcistrmb.h> | |
| 43 #include <dcmtk/dcmdata/dcsequen.h> | |
| 44 #include <dcmtk/dcmdata/dcvrfd.h> | |
| 45 #include <dcmtk/dcmdata/dcvrfl.h> | |
| 46 #include <dcmtk/dcmdata/dcvrsl.h> | |
| 47 #include <dcmtk/dcmdata/dcvrss.h> | |
| 48 #include <dcmtk/dcmdata/dcvrul.h> | |
| 49 #include <dcmtk/dcmdata/dcvrus.h> | |
| 50 | |
| 2 | 51 #include <boost/math/special_functions/round.hpp> |
| 0 | 52 |
| 62 | 53 namespace Orthanc |
| 0 | 54 { |
| 55 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) | |
| 56 { | |
| 57 target.Clear(); | |
| 58 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 59 { | |
| 60 DcmElement* element = dataset.getElement(i); | |
| 61 if (element && element->isLeaf()) | |
| 62 { | |
| 63 target.SetValue(element->getTag().getGTag(), | |
| 64 element->getTag().getETag(), | |
| 65 ConvertLeafElement(*element)); | |
| 66 } | |
| 67 } | |
| 68 } | |
| 69 | |
| 70 | |
| 71 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) | |
| 72 { | |
| 73 return DicomTag(element.getGTag(), element.getETag()); | |
| 74 } | |
| 75 | |
| 76 | |
| 77 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element) | |
| 78 { | |
| 79 if (!element.isLeaf()) | |
| 80 { | |
| 62 | 81 throw OrthancException("Only applicable to leaf elements"); |
| 0 | 82 } |
| 83 | |
| 84 if (element.isaString()) | |
| 85 { | |
| 86 char *c; | |
| 87 if (element.getString(c).good() && | |
| 88 c != NULL) | |
| 89 { | |
| 90 std::string s(c); | |
| 91 std::string utf8; | |
| 92 try | |
| 93 { | |
| 94 utf8 = boost::locale::conv::to_utf<char>(s, "ISO-8859-1"); // TODO Parameter? | |
| 95 } | |
| 2 | 96 catch (std::runtime_error&) |
| 0 | 97 { |
| 98 // Bad input string or bad encoding | |
| 99 utf8 = s; | |
| 100 } | |
| 101 | |
| 102 return new DicomString(utf8); | |
| 103 } | |
| 104 else | |
| 105 { | |
| 106 return new DicomNullValue; | |
| 107 } | |
| 108 } | |
| 109 | |
| 110 try | |
| 111 { | |
| 112 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 113 switch (element.getVR()) | |
| 114 { | |
| 115 | |
| 116 /** | |
| 117 * TODO. | |
| 118 **/ | |
| 119 | |
| 120 case EVR_DS: // decimal string | |
| 121 case EVR_IS: // integer string | |
| 122 case EVR_OB: // other byte | |
| 123 case EVR_OF: // other float | |
| 124 case EVR_OW: // other word | |
| 125 case EVR_AS: // age string | |
| 126 case EVR_AT: // attribute tag | |
| 127 case EVR_DA: // date string | |
| 128 case EVR_DT: // date time string | |
| 129 case EVR_TM: // time string | |
| 130 case EVR_UN: // unknown value representation | |
| 131 return new DicomNullValue(); | |
| 132 | |
| 133 | |
| 134 /** | |
| 135 * String types, should never happen at this point because of | |
| 136 * "element.isaString()". | |
| 137 **/ | |
| 138 | |
| 139 case EVR_AE: // application entity title | |
| 140 case EVR_CS: // code string | |
| 141 case EVR_SH: // short string | |
| 142 case EVR_LO: // long string | |
| 143 case EVR_ST: // short text | |
| 144 case EVR_LT: // long text | |
| 145 case EVR_UT: // unlimited text | |
| 146 case EVR_PN: // person name | |
| 147 case EVR_UI: // unique identifier | |
| 148 return new DicomNullValue(); | |
| 149 | |
| 150 | |
| 151 /** | |
| 152 * Numerical types | |
| 153 **/ | |
| 154 | |
| 155 case EVR_SL: // signed long | |
| 156 { | |
| 157 Sint32 f; | |
| 158 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) | |
| 159 { | |
| 160 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 161 } | |
| 162 else | |
| 163 { | |
| 164 return new DicomNullValue(); | |
| 165 } | |
| 166 } | |
| 167 | |
| 168 case EVR_SS: // signed short | |
| 169 { | |
| 170 Sint16 f; | |
| 171 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) | |
| 172 { | |
| 173 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 174 } | |
| 175 else | |
| 176 { | |
| 177 return new DicomNullValue(); | |
| 178 } | |
| 179 } | |
| 180 | |
| 181 case EVR_UL: // unsigned long | |
| 182 { | |
| 183 Uint32 f; | |
| 184 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) | |
| 185 { | |
| 186 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 187 } | |
| 188 else | |
| 189 { | |
| 190 return new DicomNullValue(); | |
| 191 } | |
| 192 } | |
| 193 | |
| 194 case EVR_US: // unsigned short | |
| 195 { | |
| 196 Uint16 f; | |
| 197 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) | |
| 198 { | |
| 199 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 200 } | |
| 201 else | |
| 202 { | |
| 203 return new DicomNullValue(); | |
| 204 } | |
| 205 } | |
| 206 | |
| 207 case EVR_FL: // float single-precision | |
| 208 { | |
| 209 Float32 f; | |
| 210 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) | |
| 211 { | |
| 212 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 213 } | |
| 214 else | |
| 215 { | |
| 216 return new DicomNullValue(); | |
| 217 } | |
| 218 } | |
| 219 | |
| 220 case EVR_FD: // float double-precision | |
| 221 { | |
| 222 Float64 f; | |
| 223 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) | |
| 224 { | |
| 225 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 226 } | |
| 227 else | |
| 228 { | |
| 229 return new DicomNullValue(); | |
| 230 } | |
| 231 } | |
| 232 | |
| 233 | |
| 234 /** | |
| 235 * Sequence types, should never occur at this point because of | |
| 236 * "element.isLeaf()". | |
| 237 **/ | |
| 238 | |
| 239 case EVR_SQ: // sequence of items | |
| 240 return new DicomNullValue; | |
| 241 | |
| 242 | |
| 243 /** | |
| 244 * Internal to DCMTK. | |
| 245 **/ | |
| 246 | |
| 247 case EVR_ox: // OB or OW depending on context | |
| 248 case EVR_xs: // SS or US depending on context | |
| 249 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 250 case EVR_na: // na="not applicable", for data which has no VR | |
| 251 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 252 case EVR_item: // used internally for items | |
| 253 case EVR_metainfo: // used internally for meta info datasets | |
| 254 case EVR_dataset: // used internally for datasets | |
| 255 case EVR_fileFormat: // used internally for DICOM files | |
| 256 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 257 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 258 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 259 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 260 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 261 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 262 case EVR_OverlayData: // used internally for overlay data | |
| 263 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 264 return new DicomNullValue; | |
| 265 | |
| 266 | |
| 267 /** | |
| 268 * Default case. | |
| 269 **/ | |
| 270 | |
| 271 default: | |
| 272 return new DicomNullValue; | |
| 273 } | |
| 274 } | |
| 275 catch (boost::bad_lexical_cast) | |
| 276 { | |
| 277 return new DicomNullValue; | |
| 278 } | |
| 279 } | |
| 280 | |
| 281 | |
| 282 static void StoreElement(Json::Value& target, | |
| 283 DcmElement& element, | |
| 284 unsigned int maxStringLength); | |
| 285 | |
| 286 static void StoreItem(Json::Value& target, | |
| 287 DcmItem& item, | |
| 288 unsigned int maxStringLength) | |
| 289 { | |
| 290 target = Json::Value(Json::objectValue); | |
| 291 | |
| 292 for (unsigned long i = 0; i < item.card(); i++) | |
| 293 { | |
| 294 DcmElement* element = item.getElement(i); | |
| 295 StoreElement(target, *element, maxStringLength); | |
| 296 } | |
| 297 } | |
| 298 | |
| 299 | |
| 300 static void StoreElement(Json::Value& target, | |
| 301 DcmElement& element, | |
| 302 unsigned int maxStringLength) | |
| 303 { | |
| 304 assert(target.type() == Json::objectValue); | |
| 305 | |
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306 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
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307 const std::string tagName = FromDcmtkBridge::GetName(tag); |
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308 const std::string formattedTag = tag.Format(); |
| 0 | 309 |
| 310 if (element.isLeaf()) | |
| 311 { | |
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312 Json::Value value(Json::objectValue); |
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313 value["Name"] = tagName; |
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314 |
| 0 | 315 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); |
| 316 if (v->IsNull()) | |
| 317 { | |
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318 value["Type"] = "Null"; |
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319 value["Value"] = Json::nullValue; |
| 0 | 320 } |
| 321 else | |
| 322 { | |
| 323 std::string s = v->AsString(); | |
| 324 if (maxStringLength == 0 || | |
| 325 s.size() <= maxStringLength) | |
| 326 { | |
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327 value["Type"] = "String"; |
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328 value["Value"] = s; |
| 0 | 329 } |
| 330 else | |
| 331 { | |
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332 value["Type"] = "TooLong"; |
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333 value["Value"] = Json::nullValue; |
| 0 | 334 } |
| 335 } | |
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336 |
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337 target[formattedTag] = value; |
| 0 | 338 } |
| 339 else | |
| 340 { | |
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341 Json::Value children(Json::arrayValue); |
| 0 | 342 |
| 343 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
| 344 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
| 345 // etc. are not." The following cast is thus OK. | |
| 346 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
| 347 | |
| 348 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 349 { | |
| 350 DcmItem* child = sequence.getItem(i); | |
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351 Json::Value& v = children.append(Json::objectValue); |
| 0 | 352 StoreItem(v, *child, maxStringLength); |
| 353 } | |
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354 |
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355 target[formattedTag]["Name"] = tagName; |
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356 target[formattedTag]["Type"] = "Sequence"; |
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357 target[formattedTag]["Value"] = children; |
| 0 | 358 } |
| 359 } | |
| 360 | |
| 361 | |
| 362 void FromDcmtkBridge::ToJson(Json::Value& root, | |
| 363 DcmDataset& dataset, | |
| 364 unsigned int maxStringLength) | |
| 365 { | |
| 366 StoreItem(root, dataset, maxStringLength); | |
| 367 } | |
| 368 | |
| 369 | |
| 370 | |
| 371 void FromDcmtkBridge::ToJson(Json::Value& target, | |
| 372 const std::string& path, | |
| 373 unsigned int maxStringLength) | |
| 374 { | |
| 375 DcmFileFormat dicom; | |
| 376 if (!dicom.loadFile(path.c_str()).good()) | |
| 377 { | |
| 62 | 378 throw OrthancException(ErrorCode_BadFileFormat); |
| 0 | 379 } |
| 380 else | |
| 381 { | |
| 382 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength); | |
| 383 } | |
| 384 } | |
| 385 | |
| 386 | |
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387 static void ExtractPngImagePreview(std::string& result, |
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388 DicomIntegerPixelAccessor& accessor) |
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389 { |
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390 PngWriter w; |
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391 |
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392 int32_t min, max; |
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393 accessor.GetExtremeValues(min, max); |
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394 |
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395 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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396 if (min != max) |
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397 { |
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398 uint8_t* pixel = &image[0]; |
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399 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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400 { |
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401 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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402 { |
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403 int32_t v = accessor.GetValue(x, y); |
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404 *pixel = static_cast<uint8_t>( |
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405 boost::math::lround(static_cast<float>(v - min) / |
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406 static_cast<float>(max - min) * 255.0f)); |
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407 } |
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408 } |
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409 } |
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410 |
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411 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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412 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]); |
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413 } |
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414 |
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415 |
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416 template <typename T> |
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417 static void ExtractPngImageTruncate(std::string& result, |
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418 DicomIntegerPixelAccessor& accessor, |
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419 PixelFormat format) |
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420 { |
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421 PngWriter w; |
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422 |
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423 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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424 T* pixel = &image[0]; |
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425 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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426 { |
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427 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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428 { |
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429 int32_t v = accessor.GetValue(x, y); |
| 71 | 430 if (v < typename std::numeric_limits<T>::min()) |
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431 *pixel = std::numeric_limits<T>::min(); |
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432 else if (v > std::numeric_limits<T>::max()) |
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433 *pixel = std::numeric_limits<T>::max(); |
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434 else |
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435 *pixel = static_cast<T>(v); |
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436 } |
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437 } |
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438 |
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439 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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440 accessor.GetWidth() * sizeof(T), format, &image[0]); |
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441 } |
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442 |
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443 |
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444 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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445 DcmDataset& dataset, |
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446 unsigned int frame, |
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447 ImageExtractionMode mode) |
| 0 | 448 { |
| 449 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data | |
| 450 | |
| 451 std::auto_ptr<DicomIntegerPixelAccessor> accessor; | |
| 452 | |
| 453 DicomMap m; | |
| 454 FromDcmtkBridge::Convert(m, dataset); | |
| 455 | |
| 456 DcmElement* e; | |
| 457 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DicomTag::PIXEL_DATA), e).good() && | |
| 458 e != NULL) | |
| 459 { | |
| 460 Uint8* pixData = NULL; | |
| 461 if (e->getUint8Array(pixData) == EC_Normal) | |
| 462 { | |
| 463 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); | |
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464 accessor->SetCurrentFrame(frame); |
| 0 | 465 } |
| 466 } | |
| 467 | |
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468 PixelFormat format; |
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469 switch (mode) |
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470 { |
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471 case ImageExtractionMode_Preview: |
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472 case ImageExtractionMode_UInt8: |
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473 format = PixelFormat_Grayscale8; |
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474 break; |
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475 |
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476 case ImageExtractionMode_UInt16: |
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477 format = PixelFormat_Grayscale16; |
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478 break; |
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479 |
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480 default: |
| 62 | 481 throw OrthancException(ErrorCode_NotImplemented); |
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482 } |
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483 |
| 0 | 484 if (accessor.get() == NULL || |
| 485 accessor->GetWidth() == 0 || | |
| 486 accessor->GetHeight() == 0) | |
| 487 { | |
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488 PngWriter w; |
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489 w.WriteToMemory(result, 0, 0, 0, format, NULL); |
| 0 | 490 } |
| 491 else | |
| 492 { | |
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493 switch (mode) |
| 0 | 494 { |
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495 case ImageExtractionMode_Preview: |
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496 ExtractPngImagePreview(result, *accessor); |
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497 break; |
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498 |
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499 case ImageExtractionMode_UInt8: |
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500 ExtractPngImageTruncate<uint8_t>(result, *accessor, format); |
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501 break; |
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502 |
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503 case ImageExtractionMode_UInt16: |
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504 ExtractPngImageTruncate<uint16_t>(result, *accessor, format); |
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505 break; |
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506 |
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507 default: |
| 62 | 508 throw OrthancException(ErrorCode_NotImplemented); |
| 0 | 509 } |
| 510 } | |
| 511 } | |
| 512 | |
| 513 | |
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514 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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515 const std::string& dicomContent, |
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516 unsigned int frame, |
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517 ImageExtractionMode mode) |
| 0 | 518 { |
| 519 DcmInputBufferStream is; | |
| 520 if (dicomContent.size() > 0) | |
| 521 { | |
| 522 is.setBuffer(&dicomContent[0], dicomContent.size()); | |
| 523 } | |
| 524 is.setEos(); | |
| 525 | |
| 526 DcmFileFormat dicom; | |
| 527 if (dicom.read(is).good()) | |
| 528 { | |
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529 ExtractPngImage(result, *dicom.getDataset(), frame, mode); |
| 0 | 530 } |
| 531 else | |
| 532 { | |
| 62 | 533 throw OrthancException(ErrorCode_BadFileFormat); |
| 0 | 534 } |
| 535 } | |
| 536 | |
| 537 | |
| 538 | |
| 539 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
| 540 { | |
| 541 DcmTagKey tag(t.GetGroup(), t.GetElement()); | |
| 542 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
| 543 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
| 544 | |
| 545 std::string s("Unknown"); | |
| 546 if (entry != NULL) | |
| 547 { | |
| 548 s = std::string(entry->getTagName()); | |
| 549 } | |
| 550 | |
| 551 dcmDataDict.unlock(); | |
| 552 return s; | |
| 553 } | |
| 554 | |
| 555 | |
| 556 DicomTag FromDcmtkBridge::FindTag(const char* name) | |
| 557 { | |
| 558 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
| 559 const DcmDictEntry* entry = dict.findEntry(name); | |
| 560 | |
| 561 if (entry == NULL) | |
| 562 { | |
| 563 dcmDataDict.unlock(); | |
| 62 | 564 throw OrthancException("Unknown DICOM tag"); |
| 0 | 565 } |
| 566 else | |
| 567 { | |
| 568 DcmTagKey key = entry->getKey(); | |
| 569 DicomTag tag(key.getGroup(), key.getElement()); | |
| 570 dcmDataDict.unlock(); | |
| 571 return tag; | |
| 572 } | |
| 573 } | |
| 574 | |
| 575 | |
| 576 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m) | |
| 577 { | |
| 578 for (DicomMap::Map::const_iterator | |
| 579 it = m.map_.begin(); it != m.map_.end(); it++) | |
| 580 { | |
| 581 DicomTag t = it->first; | |
| 582 std::string s = it->second->AsString(); | |
| 583 printf("0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str()); | |
| 584 } | |
| 585 } | |
| 586 | |
| 587 | |
| 588 void FromDcmtkBridge::ToJson(Json::Value& result, | |
| 589 const DicomMap& values) | |
| 590 { | |
| 591 if (result.type() != Json::objectValue) | |
| 592 { | |
| 62 | 593 throw OrthancException(ErrorCode_BadParameterType); |
| 0 | 594 } |
| 595 | |
| 596 result.clear(); | |
| 597 | |
| 598 for (DicomMap::Map::const_iterator | |
| 599 it = values.map_.begin(); it != values.map_.end(); it++) | |
| 600 { | |
| 601 result[GetName(it->first)] = it->second->AsString(); | |
| 602 } | |
| 603 } | |
| 604 } |