Mercurial > hg > orthanc
annotate OrthancServer/FromDcmtkBridge.cpp @ 188:090cefdab1d1
fix because of Windows macros
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 12 Nov 2012 17:43:12 +0100 |
| parents | 81f11fb357f2 |
| children | 4031f73fe0e4 |
| 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. | |
| 136 | 10 * |
| 11 * In addition, as a special exception, the copyright holders of this | |
| 12 * program give permission to link the code of its release with the | |
| 13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 14 * that use the same license as the "OpenSSL" library), and distribute | |
| 15 * the linked executables. You must obey the GNU General Public License | |
| 16 * in all respects for all of the code used other than "OpenSSL". If you | |
| 17 * modify file(s) with this exception, you may extend this exception to | |
| 18 * your version of the file(s), but you are not obligated to do so. If | |
| 19 * you do not wish to do so, delete this exception statement from your | |
| 20 * version. If you delete this exception statement from all source files | |
| 21 * in the program, then also delete it here. | |
| 0 | 22 * |
| 23 * This program is distributed in the hope that it will be useful, but | |
| 24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 26 * General Public License for more details. | |
| 27 * | |
| 28 * You should have received a copy of the GNU General Public License | |
| 29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 30 **/ | |
| 31 | |
| 71 | 32 #ifndef NOMINMAX |
| 33 #define NOMINMAX | |
| 34 #endif | |
| 0 | 35 |
| 36 #include "FromDcmtkBridge.h" | |
| 37 | |
| 38 #include "ToDcmtkBridge.h" | |
|
107
3b45473c0a73
replace boost::locale with iconv for debian
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
106
diff
changeset
|
39 #include "../Core/Toolbox.h" |
| 62 | 40 #include "../Core/OrthancException.h" |
| 0 | 41 #include "../Core/PngWriter.h" |
| 42 #include "../Core/DicomFormat/DicomString.h" | |
| 43 #include "../Core/DicomFormat/DicomNullValue.h" | |
| 79 | 44 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" |
| 0 | 45 |
| 71 | 46 #include <limits> |
| 47 | |
| 0 | 48 #include <boost/lexical_cast.hpp> |
| 49 | |
| 50 #include <dcmtk/dcmdata/dcdicent.h> | |
| 51 #include <dcmtk/dcmdata/dcdict.h> | |
| 52 #include <dcmtk/dcmdata/dcfilefo.h> | |
| 53 #include <dcmtk/dcmdata/dcistrmb.h> | |
| 54 #include <dcmtk/dcmdata/dcvrfd.h> | |
| 55 #include <dcmtk/dcmdata/dcvrfl.h> | |
| 56 #include <dcmtk/dcmdata/dcvrsl.h> | |
| 57 #include <dcmtk/dcmdata/dcvrss.h> | |
| 58 #include <dcmtk/dcmdata/dcvrul.h> | |
| 59 #include <dcmtk/dcmdata/dcvrus.h> | |
| 176 | 60 #include <dcmtk/dcmdata/dcuid.h> |
| 0 | 61 |
| 2 | 62 #include <boost/math/special_functions/round.hpp> |
| 0 | 63 |
| 62 | 64 namespace Orthanc |
| 0 | 65 { |
| 66 void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) | |
| 67 { | |
| 68 target.Clear(); | |
| 69 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 70 { | |
| 71 DcmElement* element = dataset.getElement(i); | |
| 72 if (element && element->isLeaf()) | |
| 73 { | |
| 74 target.SetValue(element->getTag().getGTag(), | |
| 75 element->getTag().getETag(), | |
| 76 ConvertLeafElement(*element)); | |
| 77 } | |
| 78 } | |
| 79 } | |
| 80 | |
| 81 | |
| 82 DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) | |
| 83 { | |
| 84 return DicomTag(element.getGTag(), element.getETag()); | |
| 85 } | |
| 86 | |
| 87 | |
| 88 DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element) | |
| 89 { | |
| 90 if (!element.isLeaf()) | |
| 91 { | |
| 62 | 92 throw OrthancException("Only applicable to leaf elements"); |
| 0 | 93 } |
| 94 | |
| 95 if (element.isaString()) | |
| 96 { | |
| 97 char *c; | |
| 98 if (element.getString(c).good() && | |
| 99 c != NULL) | |
| 100 { | |
| 101 std::string s(c); | |
|
107
3b45473c0a73
replace boost::locale with iconv for debian
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
106
diff
changeset
|
102 std::string utf8 = Toolbox::ConvertToUtf8(s, "ISO-8859-1"); // TODO Parameter? |
| 0 | 103 return new DicomString(utf8); |
| 104 } | |
| 105 else | |
| 106 { | |
| 107 return new DicomNullValue; | |
| 108 } | |
| 109 } | |
| 110 | |
| 111 try | |
| 112 { | |
| 113 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 114 switch (element.getVR()) | |
| 115 { | |
| 116 | |
| 117 /** | |
| 118 * TODO. | |
| 119 **/ | |
| 120 | |
| 121 case EVR_DS: // decimal string | |
| 122 case EVR_IS: // integer string | |
| 123 case EVR_OB: // other byte | |
| 124 case EVR_OF: // other float | |
| 125 case EVR_OW: // other word | |
| 126 case EVR_AS: // age string | |
| 127 case EVR_AT: // attribute tag | |
| 128 case EVR_DA: // date string | |
| 129 case EVR_DT: // date time string | |
| 130 case EVR_TM: // time string | |
| 131 case EVR_UN: // unknown value representation | |
| 132 return new DicomNullValue(); | |
| 133 | |
| 134 | |
| 135 /** | |
| 136 * String types, should never happen at this point because of | |
| 137 * "element.isaString()". | |
| 138 **/ | |
| 139 | |
| 140 case EVR_AE: // application entity title | |
| 141 case EVR_CS: // code string | |
| 142 case EVR_SH: // short string | |
| 143 case EVR_LO: // long string | |
| 144 case EVR_ST: // short text | |
| 145 case EVR_LT: // long text | |
| 146 case EVR_UT: // unlimited text | |
| 147 case EVR_PN: // person name | |
| 148 case EVR_UI: // unique identifier | |
| 149 return new DicomNullValue(); | |
| 150 | |
| 151 | |
| 152 /** | |
| 153 * Numerical types | |
| 154 **/ | |
| 155 | |
| 156 case EVR_SL: // signed long | |
| 157 { | |
| 158 Sint32 f; | |
| 159 if (dynamic_cast<DcmSignedLong&>(element).getSint32(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_SS: // signed short | |
| 170 { | |
| 171 Sint16 f; | |
| 172 if (dynamic_cast<DcmSignedShort&>(element).getSint16(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_UL: // unsigned long | |
| 183 { | |
| 184 Uint32 f; | |
| 185 if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(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_US: // unsigned short | |
| 196 { | |
| 197 Uint16 f; | |
| 198 if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(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_FL: // float single-precision | |
| 209 { | |
| 210 Float32 f; | |
| 211 if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(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 case EVR_FD: // float double-precision | |
| 222 { | |
| 223 Float64 f; | |
| 224 if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) | |
| 225 { | |
| 226 return new DicomString(boost::lexical_cast<std::string>(f)); | |
| 227 } | |
| 228 else | |
| 229 { | |
| 230 return new DicomNullValue(); | |
| 231 } | |
| 232 } | |
| 233 | |
| 234 | |
| 235 /** | |
| 236 * Sequence types, should never occur at this point because of | |
| 237 * "element.isLeaf()". | |
| 238 **/ | |
| 239 | |
| 240 case EVR_SQ: // sequence of items | |
| 241 return new DicomNullValue; | |
| 242 | |
| 243 | |
| 244 /** | |
| 245 * Internal to DCMTK. | |
| 246 **/ | |
| 247 | |
| 248 case EVR_ox: // OB or OW depending on context | |
| 249 case EVR_xs: // SS or US depending on context | |
| 250 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 251 case EVR_na: // na="not applicable", for data which has no VR | |
| 252 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 253 case EVR_item: // used internally for items | |
| 254 case EVR_metainfo: // used internally for meta info datasets | |
| 255 case EVR_dataset: // used internally for datasets | |
| 256 case EVR_fileFormat: // used internally for DICOM files | |
| 257 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 258 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 259 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 260 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 261 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 262 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 263 case EVR_OverlayData: // used internally for overlay data | |
| 264 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 265 return new DicomNullValue; | |
| 266 | |
| 267 | |
| 268 /** | |
| 269 * Default case. | |
| 270 **/ | |
| 271 | |
| 272 default: | |
| 273 return new DicomNullValue; | |
| 274 } | |
| 275 } | |
| 276 catch (boost::bad_lexical_cast) | |
| 277 { | |
| 278 return new DicomNullValue; | |
| 279 } | |
| 280 } | |
| 281 | |
| 282 | |
| 283 static void StoreElement(Json::Value& target, | |
| 284 DcmElement& element, | |
| 285 unsigned int maxStringLength); | |
| 286 | |
| 287 static void StoreItem(Json::Value& target, | |
| 288 DcmItem& item, | |
| 289 unsigned int maxStringLength) | |
| 290 { | |
| 291 target = Json::Value(Json::objectValue); | |
| 292 | |
| 293 for (unsigned long i = 0; i < item.card(); i++) | |
| 294 { | |
| 295 DcmElement* element = item.getElement(i); | |
| 296 StoreElement(target, *element, maxStringLength); | |
| 297 } | |
| 298 } | |
| 299 | |
| 300 | |
| 301 static void StoreElement(Json::Value& target, | |
| 302 DcmElement& element, | |
| 303 unsigned int maxStringLength) | |
| 304 { | |
| 305 assert(target.type() == Json::objectValue); | |
| 306 | |
|
35
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
307 DicomTag tag(FromDcmtkBridge::GetTag(element)); |
|
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
308 const std::string tagName = FromDcmtkBridge::GetName(tag); |
|
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
309 const std::string formattedTag = tag.Format(); |
| 0 | 310 |
| 311 if (element.isLeaf()) | |
| 312 { | |
|
35
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
313 Json::Value value(Json::objectValue); |
|
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
314 value["Name"] = tagName; |
|
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
315 |
| 0 | 316 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); |
| 317 if (v->IsNull()) | |
| 318 { | |
|
35
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
319 value["Type"] = "Null"; |
|
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
320 value["Value"] = Json::nullValue; |
| 0 | 321 } |
| 322 else | |
| 323 { | |
| 324 std::string s = v->AsString(); | |
| 325 if (maxStringLength == 0 || | |
| 326 s.size() <= maxStringLength) | |
| 327 { | |
|
35
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
328 value["Type"] = "String"; |
|
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
329 value["Value"] = s; |
| 0 | 330 } |
| 331 else | |
| 332 { | |
|
35
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
333 value["Type"] = "TooLong"; |
|
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
334 value["Value"] = Json::nullValue; |
| 0 | 335 } |
| 336 } | |
|
35
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
337 |
|
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
338 target[formattedTag] = value; |
| 0 | 339 } |
| 340 else | |
| 341 { | |
|
35
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
342 Json::Value children(Json::arrayValue); |
| 0 | 343 |
| 344 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
| 345 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
| 346 // etc. are not." The following cast is thus OK. | |
| 347 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
| 348 | |
| 349 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 350 { | |
| 351 DcmItem* child = sequence.getItem(i); | |
|
35
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
352 Json::Value& v = children.append(Json::objectValue); |
| 0 | 353 StoreItem(v, *child, maxStringLength); |
| 354 } | |
|
35
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
355 |
|
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
356 target[formattedTag]["Name"] = tagName; |
|
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
357 target[formattedTag]["Type"] = "Sequence"; |
|
f6d12037f886
full json vs. simplified json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
358 target[formattedTag]["Value"] = children; |
| 0 | 359 } |
| 360 } | |
| 361 | |
| 362 | |
| 363 void FromDcmtkBridge::ToJson(Json::Value& root, | |
| 364 DcmDataset& dataset, | |
| 365 unsigned int maxStringLength) | |
| 366 { | |
| 367 StoreItem(root, dataset, maxStringLength); | |
| 368 } | |
| 369 | |
| 370 | |
| 371 | |
| 372 void FromDcmtkBridge::ToJson(Json::Value& target, | |
| 373 const std::string& path, | |
| 374 unsigned int maxStringLength) | |
| 375 { | |
| 376 DcmFileFormat dicom; | |
| 377 if (!dicom.loadFile(path.c_str()).good()) | |
| 378 { | |
| 62 | 379 throw OrthancException(ErrorCode_BadFileFormat); |
| 0 | 380 } |
| 381 else | |
| 382 { | |
| 383 FromDcmtkBridge::ToJson(target, *dicom.getDataset(), maxStringLength); | |
| 384 } | |
| 385 } | |
| 386 | |
| 387 | |
|
42
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
388 static void ExtractPngImagePreview(std::string& result, |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
389 DicomIntegerPixelAccessor& accessor) |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
390 { |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
391 PngWriter w; |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
392 |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
393 int32_t min, max; |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
394 accessor.GetExtremeValues(min, max); |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
395 |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
396 std::vector<uint8_t> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
397 if (min != max) |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
398 { |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
399 uint8_t* pixel = &image[0]; |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
400 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
401 { |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
402 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
403 { |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
404 int32_t v = accessor.GetValue(x, y); |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
405 *pixel = static_cast<uint8_t>( |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
406 boost::math::lround(static_cast<float>(v - min) / |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
407 static_cast<float>(max - min) * 255.0f)); |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
408 } |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
409 } |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
410 } |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
411 |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
412 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
413 accessor.GetWidth(), PixelFormat_Grayscale8, &image[0]); |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
414 } |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
415 |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
416 |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
417 template <typename T> |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
418 static void ExtractPngImageTruncate(std::string& result, |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
419 DicomIntegerPixelAccessor& accessor, |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
420 PixelFormat format) |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
421 { |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
422 PngWriter w; |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
423 |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
424 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0); |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
425 T* pixel = &image[0]; |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
426 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
427 { |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
428 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
429 { |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
430 int32_t v = accessor.GetValue(x, y); |
| 73 | 431 if (v < std::numeric_limits<T>::min()) |
|
42
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
432 *pixel = std::numeric_limits<T>::min(); |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
433 else if (v > std::numeric_limits<T>::max()) |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
434 *pixel = std::numeric_limits<T>::max(); |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
435 else |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
436 *pixel = static_cast<T>(v); |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
437 } |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
438 } |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
439 |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
440 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
441 accessor.GetWidth() * sizeof(T), format, &image[0]); |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
442 } |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
443 |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
444 |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
445 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
446 DcmDataset& dataset, |
|
53
293038baf8f1
access to multi-frame images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
50
diff
changeset
|
447 unsigned int frame, |
|
42
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
448 ImageExtractionMode mode) |
| 0 | 449 { |
| 450 // See also: http://support.dcmtk.org/wiki/dcmtk/howto/accessing-compressed-data | |
| 451 | |
| 452 std::auto_ptr<DicomIntegerPixelAccessor> accessor; | |
| 453 | |
| 454 DicomMap m; | |
| 455 FromDcmtkBridge::Convert(m, dataset); | |
| 456 | |
| 457 DcmElement* e; | |
| 80 | 458 if (dataset.findAndGetElement(ToDcmtkBridge::Convert(DICOM_TAG_PIXEL_DATA), e).good() && |
| 0 | 459 e != NULL) |
| 460 { | |
| 461 Uint8* pixData = NULL; | |
| 462 if (e->getUint8Array(pixData) == EC_Normal) | |
| 463 { | |
| 464 accessor.reset(new DicomIntegerPixelAccessor(m, pixData, e->getLength())); | |
|
53
293038baf8f1
access to multi-frame images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
50
diff
changeset
|
465 accessor->SetCurrentFrame(frame); |
| 0 | 466 } |
| 467 } | |
| 468 | |
|
42
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
469 PixelFormat format; |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
470 switch (mode) |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
471 { |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
472 case ImageExtractionMode_Preview: |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
473 case ImageExtractionMode_UInt8: |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
474 format = PixelFormat_Grayscale8; |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
475 break; |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
476 |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
477 case ImageExtractionMode_UInt16: |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
478 format = PixelFormat_Grayscale16; |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
479 break; |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
480 |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
481 default: |
| 62 | 482 throw OrthancException(ErrorCode_NotImplemented); |
|
42
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
483 } |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
484 |
| 0 | 485 if (accessor.get() == NULL || |
| 486 accessor->GetWidth() == 0 || | |
| 487 accessor->GetHeight() == 0) | |
| 488 { | |
|
42
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
489 PngWriter w; |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
490 w.WriteToMemory(result, 0, 0, 0, format, NULL); |
| 0 | 491 } |
| 492 else | |
| 493 { | |
|
42
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
494 switch (mode) |
| 0 | 495 { |
|
42
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
496 case ImageExtractionMode_Preview: |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
497 ExtractPngImagePreview(result, *accessor); |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
498 break; |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
499 |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
500 case ImageExtractionMode_UInt8: |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
501 ExtractPngImageTruncate<uint8_t>(result, *accessor, format); |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
502 break; |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
503 |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
504 case ImageExtractionMode_UInt16: |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
505 ExtractPngImageTruncate<uint16_t>(result, *accessor, format); |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
506 break; |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
507 |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
508 default: |
| 62 | 509 throw OrthancException(ErrorCode_NotImplemented); |
| 0 | 510 } |
| 511 } | |
| 512 } | |
| 513 | |
| 514 | |
|
42
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
515 void FromDcmtkBridge::ExtractPngImage(std::string& result, |
|
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
516 const std::string& dicomContent, |
|
53
293038baf8f1
access to multi-frame images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
50
diff
changeset
|
517 unsigned int frame, |
|
42
ea48f38afe5f
access to raw images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
41
diff
changeset
|
518 ImageExtractionMode mode) |
| 0 | 519 { |
| 520 DcmInputBufferStream is; | |
| 521 if (dicomContent.size() > 0) | |
| 522 { | |
| 523 is.setBuffer(&dicomContent[0], dicomContent.size()); | |
| 524 } | |
| 525 is.setEos(); | |
| 526 | |
| 527 DcmFileFormat dicom; | |
| 528 if (dicom.read(is).good()) | |
| 529 { | |
|
53
293038baf8f1
access to multi-frame images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
50
diff
changeset
|
530 ExtractPngImage(result, *dicom.getDataset(), frame, mode); |
| 0 | 531 } |
| 532 else | |
| 533 { | |
| 62 | 534 throw OrthancException(ErrorCode_BadFileFormat); |
| 0 | 535 } |
| 536 } | |
| 537 | |
| 538 | |
| 539 | |
| 540 std::string FromDcmtkBridge::GetName(const DicomTag& t) | |
| 541 { | |
| 106 | 542 // Some patches for important tags because of different DICOM |
| 543 // dictionaries between DCMTK versions | |
| 544 if (t == DICOM_TAG_PATIENT_NAME) | |
| 545 return "PatientName"; | |
| 546 | |
| 547 if (t == DicomTag(0x0010, 0x0030)) | |
| 548 return "PatientBirthDate"; | |
| 549 | |
| 550 if (t == DicomTag(0x0010, 0x0040)) | |
| 551 return "PatientSex"; | |
| 552 | |
| 553 // End of patches | |
| 554 | |
| 0 | 555 DcmTagKey tag(t.GetGroup(), t.GetElement()); |
| 556 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
| 557 const DcmDictEntry* entry = dict.findEntry(tag, NULL); | |
| 558 | |
| 559 std::string s("Unknown"); | |
| 560 if (entry != NULL) | |
| 561 { | |
| 562 s = std::string(entry->getTagName()); | |
| 563 } | |
| 564 | |
| 565 dcmDataDict.unlock(); | |
| 566 return s; | |
| 567 } | |
| 568 | |
| 569 | |
| 570 DicomTag FromDcmtkBridge::FindTag(const char* name) | |
| 571 { | |
| 572 const DcmDataDictionary& dict = dcmDataDict.rdlock(); | |
| 573 const DcmDictEntry* entry = dict.findEntry(name); | |
| 574 | |
| 575 if (entry == NULL) | |
| 576 { | |
| 577 dcmDataDict.unlock(); | |
| 62 | 578 throw OrthancException("Unknown DICOM tag"); |
| 0 | 579 } |
| 580 else | |
| 581 { | |
| 582 DcmTagKey key = entry->getKey(); | |
| 583 DicomTag tag(key.getGroup(), key.getElement()); | |
| 584 dcmDataDict.unlock(); | |
| 585 return tag; | |
| 586 } | |
| 587 } | |
| 588 | |
| 589 | |
| 590 void FromDcmtkBridge::Print(FILE* fp, const DicomMap& m) | |
| 591 { | |
| 592 for (DicomMap::Map::const_iterator | |
| 593 it = m.map_.begin(); it != m.map_.end(); it++) | |
| 594 { | |
| 595 DicomTag t = it->first; | |
| 596 std::string s = it->second->AsString(); | |
| 597 printf("0x%04x 0x%04x (%s) [%s]\n", t.GetGroup(), t.GetElement(), GetName(t).c_str(), s.c_str()); | |
| 598 } | |
| 599 } | |
| 600 | |
| 601 | |
| 602 void FromDcmtkBridge::ToJson(Json::Value& result, | |
| 603 const DicomMap& values) | |
| 604 { | |
| 605 if (result.type() != Json::objectValue) | |
| 606 { | |
| 62 | 607 throw OrthancException(ErrorCode_BadParameterType); |
| 0 | 608 } |
| 609 | |
| 610 result.clear(); | |
| 611 | |
| 612 for (DicomMap::Map::const_iterator | |
| 613 it = values.map_.begin(); it != values.map_.end(); it++) | |
| 614 { | |
| 615 result[GetName(it->first)] = it->second->AsString(); | |
| 616 } | |
| 617 } | |
| 176 | 618 |
| 619 | |
| 620 std::string FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel level) | |
| 621 { | |
| 622 char uid[100]; | |
| 623 | |
| 624 switch (level) | |
| 625 { | |
| 626 case DicomRootLevel_Instance: | |
| 627 return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); | |
| 628 | |
| 629 case DicomRootLevel_Series: | |
| 630 return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT); | |
| 631 | |
| 632 case DicomRootLevel_Study: | |
| 633 return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT); | |
| 634 | |
| 635 default: | |
| 636 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 637 } | |
| 638 } | |
| 639 | |
| 0 | 640 } |