Mercurial > hg > orthanc
annotate OrthancServer/FromDcmtkBridge.cpp @ 122:e759f777cb72
removal of some dcmtk includes
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 05 Oct 2012 09:55:16 +0200 |
| parents | 3b45473c0a73 |
| children | fe180eae201d |
| 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" | |
|
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27 #include "../Core/Toolbox.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" | |
| 79 | 32 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" |
| 0 | 33 |
| 71 | 34 #include <limits> |
| 35 | |
| 0 | 36 #include <boost/lexical_cast.hpp> |
| 37 | |
| 38 #include <dcmtk/dcmdata/dcdicent.h> | |
| 39 #include <dcmtk/dcmdata/dcdict.h> | |
| 40 #include <dcmtk/dcmdata/dcfilefo.h> | |
| 41 #include <dcmtk/dcmdata/dcistrmb.h> | |
| 42 #include <dcmtk/dcmdata/dcvrfd.h> | |
| 43 #include <dcmtk/dcmdata/dcvrfl.h> | |
| 44 #include <dcmtk/dcmdata/dcvrsl.h> | |
| 45 #include <dcmtk/dcmdata/dcvrss.h> | |
| 46 #include <dcmtk/dcmdata/dcvrul.h> | |
| 47 #include <dcmtk/dcmdata/dcvrus.h> | |
| 48 | |
| 2 | 49 #include <boost/math/special_functions/round.hpp> |
| 0 | 50 |
| 62 | 51 namespace Orthanc |
| 0 | 52 { |
| 53 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) | |
| 54 { | |
| 55 target.Clear(); | |
| 56 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 57 { | |
| 58 DcmElement* element = dataset.getElement(i); | |
| 59 if (element && element->isLeaf()) | |
| 60 { | |
| 61 target.SetValue(element->getTag().getGTag(), | |
| 62 element->getTag().getETag(), | |
| 63 ConvertLeafElement(*element)); | |
| 64 } | |
| 65 } | |
| 66 } | |
| 67 | |
| 68 | |
| 69 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) | |
| 70 { | |
| 71 return DicomTag(element.getGTag(), element.getETag()); | |
| 72 } | |
| 73 | |
| 74 | |
| 75 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element) | |
| 76 { | |
| 77 if (!element.isLeaf()) | |
| 78 { | |
| 62 | 79 throw OrthancException("Only applicable to leaf elements"); |
| 0 | 80 } |
| 81 | |
| 82 if (element.isaString()) | |
| 83 { | |
| 84 char *c; | |
| 85 if (element.getString(c).good() && | |
| 86 c != NULL) | |
| 87 { | |
| 88 std::string s(c); | |
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89 std::string utf8 = Toolbox::ConvertToUtf8(s, "ISO-8859-1"); // TODO Parameter? |
| 0 | 90 return new DicomString(utf8); |
| 91 } | |
| 92 else | |
| 93 { | |
| 94 return new DicomNullValue; | |
| 95 } | |
| 96 } | |
| 97 | |
| 98 try | |
| 99 { | |
| 100 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 101 switch (element.getVR()) | |
| 102 { | |
| 103 | |
| 104 /** | |
| 105 * TODO. | |
| 106 **/ | |
| 107 | |
| 108 case EVR_DS: // decimal string | |
| 109 case EVR_IS: // integer string | |
| 110 case EVR_OB: // other byte | |
| 111 case EVR_OF: // other float | |
| 112 case EVR_OW: // other word | |
| 113 case EVR_AS: // age string | |
| 114 case EVR_AT: // attribute tag | |
| 115 case EVR_DA: // date string | |
| 116 case EVR_DT: // date time string | |
| 117 case EVR_TM: // time string | |
| 118 case EVR_UN: // unknown value representation | |
| 119 return new DicomNullValue(); | |
| 120 | |
| 121 | |
| 122 /** | |
| 123 * String types, should never happen at this point because of | |
| 124 * "element.isaString()". | |
| 125 **/ | |
| 126 | |
| 127 case EVR_AE: // application entity title | |
| 128 case EVR_CS: // code string | |
| 129 case EVR_SH: // short string | |
| 130 case EVR_LO: // long string | |
| 131 case EVR_ST: // short text | |
| 132 case EVR_LT: // long text | |
| 133 case EVR_UT: // unlimited text | |
| 134 case EVR_PN: // person name | |
| 135 case EVR_UI: // unique identifier | |
| 136 return new DicomNullValue(); | |
| 137 | |
| 138 | |
| 139 /** | |
| 140 * Numerical types | |
| 141 **/ | |
| 142 | |
| 143 case EVR_SL: // signed long | |
| 144 { | |
| 145 Sint32 f; | |
| 146 if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) | |
| 147 { | |
| 148 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 149 } | |
| 150 else | |
| 151 { | |
| 152 return new DicomNullValue(); | |
| 153 } | |
| 154 } | |
| 155 | |
| 156 case EVR_SS: // signed short | |
| 157 { | |
| 158 Sint16 f; | |
| 159 if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) | |
| 160 { | |
| 161 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 162 } | |
| 163 else | |
| 164 { | |
| 165 return new DicomNullValue(); | |
| 166 } | |
| 167 } | |
| 168 | |
| 169 case EVR_UL: // unsigned long | |
| 170 { | |
| 171 Uint32 f; | |
| 172 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) | |
| 173 { | |
| 174 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 175 } | |
| 176 else | |
| 177 { | |
| 178 return new DicomNullValue(); | |
| 179 } | |
| 180 } | |
| 181 | |
| 182 case EVR_US: // unsigned short | |
| 183 { | |
| 184 Uint16 f; | |
| 185 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) | |
| 186 { | |
| 187 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 188 } | |
| 189 else | |
| 190 { | |
| 191 return new DicomNullValue(); | |
| 192 } | |
| 193 } | |
| 194 | |
| 195 case EVR_FL: // float single-precision | |
| 196 { | |
| 197 Float32 f; | |
| 198 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) | |
| 199 { | |
| 200 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 201 } | |
| 202 else | |
| 203 { | |
| 204 return new DicomNullValue(); | |
| 205 } | |
| 206 } | |
| 207 | |
| 208 case EVR_FD: // float double-precision | |
| 209 { | |
| 210 Float64 f; | |
| 211 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) | |
| 212 { | |
| 213 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 214 } | |
| 215 else | |
| 216 { | |
| 217 return new DicomNullValue(); | |
| 218 } | |
| 219 } | |
| 220 | |
| 221 | |
| 222 /** | |
| 223 * Sequence types, should never occur at this point because of | |
| 224 * "element.isLeaf()". | |
| 225 **/ | |
| 226 | |
| 227 case EVR_SQ: // sequence of items | |
| 228 return new DicomNullValue; | |
| 229 | |
| 230 | |
| 231 /** | |
| 232 * Internal to DCMTK. | |
| 233 **/ | |
| 234 | |
| 235 case EVR_ox: // OB or OW depending on context | |
| 236 case EVR_xs: // SS or US depending on context | |
| 237 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 238 case EVR_na: // na="not applicable", for data which has no VR | |
| 239 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 240 case EVR_item: // used internally for items | |
| 241 case EVR_metainfo: // used internally for meta info datasets | |
| 242 case EVR_dataset: // used internally for datasets | |
| 243 case EVR_fileFormat: // used internally for DICOM files | |
| 244 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 245 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 246 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 247 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 248 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 249 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 250 case EVR_OverlayData: // used internally for overlay data | |
| 251 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 252 return new DicomNullValue; | |
| 253 | |
| 254 | |
| 255 /** | |
| 256 * Default case. | |
| 257 **/ | |
| 258 | |
| 259 default: | |
| 260 return new DicomNullValue; | |
| 261 } | |
| 262 } | |
| 263 catch (boost::bad_lexical_cast) | |
| 264 { | |
| 265 return new DicomNullValue; | |
| 266 } | |
| 267 } | |
| 268 | |
| 269 | |
| 270 static void StoreElement(Json::Value& target, | |
| 271 DcmElement& element, | |
| 272 unsigned int maxStringLength); | |
| 273 | |
| 274 static void StoreItem(Json::Value& target, | |
| 275 DcmItem& item, | |
| 276 unsigned int maxStringLength) | |
| 277 { | |
| 278 target = Json::Value(Json::objectValue); | |
| 279 | |
| 280 for (unsigned long i = 0; i < item.card(); i++) | |
| 281 { | |
| 282 DcmElement* element = item.getElement(i); | |
| 283 StoreElement(target, *element, maxStringLength); | |
| 284 } | |
| 285 } | |
| 286 | |
| 287 | |
| 288 static void StoreElement(Json::Value& target, | |
| 289 DcmElement& element, | |
| 290 unsigned int maxStringLength) | |
| 291 { | |
| 292 assert(target.type() == Json::objectValue); | |
| 293 | |
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294 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
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295 const std::string tagName = FromDcmtkBridge::GetName(tag); |
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296 const std::string formattedTag = tag.Format(); |
| 0 | 297 |
| 298 if (element.isLeaf()) | |
| 299 { | |
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300 Json::Value value(Json::objectValue); |
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301 value["Name"] = tagName; |
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302 |
| 0 | 303 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); |
| 304 if (v->IsNull()) | |
| 305 { | |
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306 value["Type"] = "Null"; |
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307 value["Value"] = Json::nullValue; |
| 0 | 308 } |
| 309 else | |
| 310 { | |
| 311 std::string s = v->AsString(); | |
| 312 if (maxStringLength == 0 || | |
| 313 s.size() <= maxStringLength) | |
| 314 { | |
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315 value["Type"] = "String"; |
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316 value["Value"] = s; |
| 0 | 317 } |
| 318 else | |
| 319 { | |
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320 value["Type"] = "TooLong"; |
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321 value["Value"] = Json::nullValue; |
| 0 | 322 } |
| 323 } | |
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324 |
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325 target[formattedTag] = value; |
| 0 | 326 } |
| 327 else | |
| 328 { | |
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329 Json::Value children(Json::arrayValue); |
| 0 | 330 |
| 331 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
| 332 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
| 333 // etc. are not." The following cast is thus OK. | |
| 334 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
| 335 | |
| 336 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 337 { | |
| 338 DcmItem* child = sequence.getItem(i); | |
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339 Json::Value& v = children.append(Json::objectValue); |
| 0 | 340 StoreItem(v, *child, maxStringLength); |
| 341 } | |
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342 |
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343 target[formattedTag]["Name"] = tagName; |
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344 target[formattedTag]["Type"] = "Sequence"; |
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345 target[formattedTag]["Value"] = children; |
| 0 | 346 } |
| 347 } | |
| 348 | |
| 349 | |
| 350 void FromDcmtkBridge::ToJson(Json::Value& root, | |
| 351 DcmDataset& dataset, | |
| 352 unsigned int maxStringLength) | |
| 353 { | |
| 354 StoreItem(root, dataset, maxStringLength); | |
| 355 } | |
| 356 | |
| 357 | |
| 358 | |
| 359 void FromDcmtkBridge::ToJson(Json::Value& target, | |
| 360 const std::string& path, | |
| 361 unsigned int maxStringLength) | |
| 362 { | |
| 363 DcmFileFormat dicom; | |
| 364 if (!dicom.loadFile(path.c_str()).good()) | |
| 365 { | |
| 62 | 366 throw OrthancException(ErrorCode_BadFileFormat); |
| 0 | 367 } |
| 368 else | |
| 369 { | |
| 370 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength); | |
| 371 } | |
| 372 } | |
| 373 | |
| 374 | |
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375 static void ExtractPngImagePreview(std::string& result, |
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376 DicomIntegerPixelAccessor& accessor) |
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377 { |
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378 PngWriter w; |
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379 |
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380 int32_t min, max; |
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381 accessor.GetExtremeValues(min, max); |
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382 |
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383 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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384 if (min != max) |
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385 { |
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386 uint8_t* pixel = &image[0]; |
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387 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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388 { |
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389 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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390 { |
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391 int32_t v = accessor.GetValue(x, y); |
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392 *pixel = static_cast<uint8_t>( |
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393 boost::math::lround(static_cast<float>(v - min) / |
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394 static_cast<float>(max - min) * 255.0f)); |
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395 } |
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396 } |
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397 } |
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398 |
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399 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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400 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]); |
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401 } |
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402 |
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403 |
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404 template <typename T> |
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405 static void ExtractPngImageTruncate(std::string& result, |
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406 DicomIntegerPixelAccessor& accessor, |
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407 PixelFormat format) |
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408 { |
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409 PngWriter w; |
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410 |
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411 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
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412 T* pixel = &image[0]; |
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413 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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414 { |
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415 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
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416 { |
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417 int32_t v = accessor.GetValue(x, y); |
| 73 | 418 if (v < std::numeric_limits<T>::min()) |
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419 *pixel = std::numeric_limits<T>::min(); |
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420 else if (v > std::numeric_limits<T>::max()) |
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421 *pixel = std::numeric_limits<T>::max(); |
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422 else |
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423 *pixel = static_cast<T>(v); |
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424 } |
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425 } |
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426 |
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427 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
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428 accessor.GetWidth() * sizeof(T), format, &image[0]); |
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429 } |
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430 |
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431 |
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432 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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433 DcmDataset& dataset, |
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434 unsigned int frame, |
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435 ImageExtractionMode mode) |
| 0 | 436 { |
| 437 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data | |
| 438 | |
| 439 std::auto_ptr<DicomIntegerPixelAccessor> accessor; | |
| 440 | |
| 441 DicomMap m; | |
| 442 FromDcmtkBridge::Convert(m, dataset); | |
| 443 | |
| 444 DcmElement* e; | |
| 80 | 445 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() && |
| 0 | 446 e != NULL) |
| 447 { | |
| 448 Uint8* pixData = NULL; | |
| 449 if (e->getUint8Array(pixData) == EC_Normal) | |
| 450 { | |
| 451 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); | |
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452 accessor->SetCurrentFrame(frame); |
| 0 | 453 } |
| 454 } | |
| 455 | |
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456 PixelFormat format; |
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457 switch (mode) |
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458 { |
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459 case ImageExtractionMode_Preview: |
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460 case ImageExtractionMode_UInt8: |
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461 format = PixelFormat_Grayscale8; |
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462 break; |
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463 |
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464 case ImageExtractionMode_UInt16: |
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465 format = PixelFormat_Grayscale16; |
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466 break; |
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467 |
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468 default: |
| 62 | 469 throw OrthancException(ErrorCode_NotImplemented); |
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470 } |
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471 |
| 0 | 472 if (accessor.get() == NULL || |
| 473 accessor->GetWidth() == 0 || | |
| 474 accessor->GetHeight() == 0) | |
| 475 { | |
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476 PngWriter w; |
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477 w.WriteToMemory(result, 0, 0, 0, format, NULL); |
| 0 | 478 } |
| 479 else | |
| 480 { | |
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481 switch (mode) |
| 0 | 482 { |
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483 case ImageExtractionMode_Preview: |
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484 ExtractPngImagePreview(result, *accessor); |
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485 break; |
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486 |
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487 case ImageExtractionMode_UInt8: |
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488 ExtractPngImageTruncate<uint8_t>(result, *accessor, format); |
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489 break; |
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490 |
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491 case ImageExtractionMode_UInt16: |
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492 ExtractPngImageTruncate<uint16_t>(result, *accessor, format); |
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493 break; |
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494 |
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495 default: |
| 62 | 496 throw OrthancException(ErrorCode_NotImplemented); |
| 0 | 497 } |
| 498 } | |
| 499 } | |
| 500 | |
| 501 | |
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502 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
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503 const std::string& dicomContent, |
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504 unsigned int frame, |
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505 ImageExtractionMode mode) |
| 0 | 506 { |
| 507 DcmInputBufferStream is; | |
| 508 if (dicomContent.size() > 0) | |
| 509 { | |
| 510 is.setBuffer(&dicomContent[0], dicomContent.size()); | |
| 511 } | |
| 512 is.setEos(); | |
| 513 | |
| 514 DcmFileFormat dicom; | |
| 515 if (dicom.read(is).good()) | |
| 516 { | |
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517 ExtractPngImage(result, *dicom.getDataset(), frame, mode); |
| 0 | 518 } |
| 519 else | |
| 520 { | |
| 62 | 521 throw OrthancException(ErrorCode_BadFileFormat); |
| 0 | 522 } |
| 523 } | |
| 524 | |
| 525 | |
| 526 | |
| 527 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
| 528 { | |
| 106 | 529 // Some patches for important tags because of different DICOM |
| 530 // dictionaries between DCMTK versions | |
| 531 if (t == DICOM_TAG_PATIENT_NAME) | |
| 532 return "PatientName"; | |
| 533 | |
| 534 if (t == DicomTag(0x0010, 0x0030)) | |
| 535 return "PatientBirthDate"; | |
| 536 | |
| 537 if (t == DicomTag(0x0010, 0x0040)) | |
| 538 return "PatientSex"; | |
| 539 | |
| 540 // End of patches | |
| 541 | |
| 0 | 542 DcmTagKey tag(t.GetGroup(), t.GetElement()); |
| 543 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
| 544 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
| 545 | |
| 546 std::string s("Unknown"); | |
| 547 if (entry != NULL) | |
| 548 { | |
| 549 s = std::string(entry->getTagName()); | |
| 550 } | |
| 551 | |
| 552 dcmDataDict.unlock(); | |
| 553 return s; | |
| 554 } | |
| 555 | |
| 556 | |
| 557 DicomTag FromDcmtkBridge::FindTag(const char* name) | |
| 558 { | |
| 559 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
| 560 const DcmDictEntry* entry = dict.findEntry(name); | |
| 561 | |
| 562 if (entry == NULL) | |
| 563 { | |
| 564 dcmDataDict.unlock(); | |
| 62 | 565 throw OrthancException("Unknown DICOM tag"); |
| 0 | 566 } |
| 567 else | |
| 568 { | |
| 569 DcmTagKey key = entry->getKey(); | |
| 570 DicomTag tag(key.getGroup(), key.getElement()); | |
| 571 dcmDataDict.unlock(); | |
| 572 return tag; | |
| 573 } | |
| 574 } | |
| 575 | |
| 576 | |
| 577 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m) | |
| 578 { | |
| 579 for (DicomMap::Map::const_iterator | |
| 580 it = m.map_.begin(); it != m.map_.end(); it++) | |
| 581 { | |
| 582 DicomTag t = it->first; | |
| 583 std::string s = it->second->AsString(); | |
| 584 printf("0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str()); | |
| 585 } | |
| 586 } | |
| 587 | |
| 588 | |
| 589 void FromDcmtkBridge::ToJson(Json::Value& result, | |
| 590 const DicomMap& values) | |
| 591 { | |
| 592 if (result.type() != Json::objectValue) | |
| 593 { | |
| 62 | 594 throw OrthancException(ErrorCode_BadParameterType); |
| 0 | 595 } |
| 596 | |
| 597 result.clear(); | |
| 598 | |
| 599 for (DicomMap::Map::const_iterator | |
| 600 it = values.map_.begin(); it != values.map_.end(); it++) | |
| 601 { | |
| 602 result[GetName(it->first)] = it->second->AsString(); | |
| 603 } | |
| 604 } | |
| 605 } |