1 /*=========================================================================
4 Module: $RCSfile: gdcmFile.cxx,v $
6 Date: $Date: 2004/11/25 16:35:17 $
7 Version: $Revision: 1.165 $
9 Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
10 l'Image). All rights reserved. See Doc/License.txt or
11 http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
13 This software is distributed WITHOUT ANY WARRANTY; without even
14 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 PURPOSE. See the above copyright notices for more information.
17 =========================================================================*/
20 #include "gdcmDocument.h"
21 #include "gdcmDebug.h"
23 #include "gdcmBinEntry.h"
28 typedef std::pair<TagDocEntryHT::iterator,TagDocEntryHT::iterator> IterHT;
30 //-------------------------------------------------------------------------
31 // Constructor / Destructor
33 * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
34 * file (Header only deals with the ... header)
35 * Opens (in read only and when possible) an existing file and checks
36 * for DICOM compliance. Returns NULL on failure.
37 * It will be up to the user to load the pixels into memory
38 * (see GetImageData, GetImageDataRaw)
39 * \note the in-memory representation of all available tags found in
40 * the DICOM header is post-poned to first header information access.
41 * This avoid a double parsing of public part of the header when
42 * user sets an a posteriori shadow dictionary (efficiency can be
43 * seen as a side effect).
44 * @param header already built Header
46 File::File(Header *header)
48 HeaderInternal = header;
54 * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
55 * file (Header only deals with the ... header)
56 * Opens (in read only and when possible) an existing file and checks
57 * for DICOM compliance. Returns NULL on failure.
58 * It will be up to the user to load the pixels into memory
59 * (see GetImageData, GetImageDataRaw)
60 * \note the in-memory representation of all available tags found in
61 * the DICOM header is post-poned to first header information access.
62 * This avoid a double parsing of public part of the header when
63 * one sets an a posteriori shadow dictionary (efficiency can be
64 * seen as a side effect).
65 * @param filename file to be opened for parsing
67 File::File(std::string const & filename )
69 HeaderInternal = new Header( filename );
75 * \brief Factorization for various forms of constructors.
77 void File::Initialise()
79 WriteMode = WMODE_DECOMPRESSED;
80 WriteType = WTYPE_IMPL_VR;
82 PixelConverter = new PixelConvert;
83 Archive = new DocEntryArchive( HeaderInternal );
85 if ( HeaderInternal->IsReadable() )
87 PixelConverter->GrabInformationsFromHeader( HeaderInternal );
95 * \brief canonical destructor
96 * \note If the Header was created by the File constructor,
97 * it is destroyed by the File
103 delete PixelConverter;
112 delete HeaderInternal;
117 //-----------------------------------------------------------------------------
120 //-----------------------------------------------------------------------------
123 * \brief Get the size of the image data
125 * If the image can be RGB (with a lut or by default), the size
126 * corresponds to the RGB image
127 * @return The image size
129 size_t File::GetImageDataSize()
131 return PixelConverter->GetRGBSize();
135 * \brief Get the size of the image data
137 * If the image can be RGB by transformation in a LUT, this
138 * transformation isn't considered
139 * @return The raw image size
141 size_t File::GetImageDataRawSize()
143 return PixelConverter->GetDecompressedSize();
147 * \brief - Allocates necessary memory,
148 * - Reads the pixels from disk (uncompress if necessary),
149 * - Transforms YBR pixels, if any, into RGB pixels
150 * - Transforms 3 planes R, G, B, if any, into a single RGB Plane
151 * - Transforms single Grey plane + 3 Palettes into a RGB Plane
152 * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
153 * @return Pointer to newly allocated pixel data.
154 * NULL if alloc fails
156 uint8_t* File::GetImageData()
158 if ( ! GetDecompressed() )
160 // If the decompression failed nothing can be done.
164 if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
166 return PixelConverter->GetRGB();
170 // When no LUT or LUT conversion fails, return the decompressed
171 return PixelConverter->GetDecompressed();
177 * Read the pixels from disk (uncompress if necessary),
178 * Transforms YBR pixels, if any, into RGB pixels
179 * Transforms 3 planes R, G, B, if any, into a single RGB Plane
180 * Transforms single Grey plane + 3 Palettes into a RGB Plane
181 * Copies at most MaxSize bytes of pixel data to caller allocated
183 * \warning This function allows people that want to build a volume
184 * from an image stack *not to* have, first to get the image pixels,
185 * and then move them to the volume area.
186 * It's absolutely useless for any VTK user since vtk chooses
187 * to invert the lines of an image, that is the last line comes first
188 * (for some axis related reasons?). Hence he will have
189 * to load the image line by line, starting from the end.
190 * VTK users have to call GetImageData
192 * @param destination Address (in caller's memory space) at which the
193 * pixel data should be copied
194 * @param maxSize Maximum number of bytes to be copied. When MaxSize
195 * is not sufficient to hold the pixel data the copy is not
196 * executed (i.e. no partial copy).
197 * @return On success, the number of bytes actually copied. Zero on
198 * failure e.g. MaxSize is lower than necessary.
200 size_t File::GetImageDataIntoVector (void* destination, size_t maxSize)
202 if ( ! GetDecompressed() )
204 // If the decompression failed nothing can be done.
208 if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
210 if ( PixelConverter->GetRGBSize() > maxSize )
212 dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
213 "than caller's expected MaxSize");
217 (void*)PixelConverter->GetRGB(),
218 PixelConverter->GetRGBSize() );
219 return PixelConverter->GetRGBSize();
222 // Either no LUT conversion necessary or LUT conversion failed
223 if ( PixelConverter->GetDecompressedSize() > maxSize )
225 dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
226 "than caller's expected MaxSize");
230 (void*)PixelConverter->GetDecompressed(),
231 PixelConverter->GetDecompressedSize() );
232 return PixelConverter->GetDecompressedSize();
236 * \brief Allocates necessary memory,
237 * Transforms YBR pixels (if any) into RGB pixels
238 * Transforms 3 planes R, G, B (if any) into a single RGB Plane
239 * Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
240 * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
241 * @return Pointer to newly allocated pixel data.
242 * \ NULL if alloc fails
244 uint8_t* File::GetImageDataRaw ()
246 return GetDecompressed();
249 uint8_t* File::GetDecompressed()
251 uint8_t* decompressed = PixelConverter->GetDecompressed();
252 if ( ! decompressed )
254 // The decompressed image migth not be loaded yet:
255 std::ifstream* fp = HeaderInternal->OpenFile();
256 PixelConverter->ReadAndDecompressPixelData( fp );
258 HeaderInternal->CloseFile();
260 decompressed = PixelConverter->GetDecompressed();
261 if ( ! decompressed )
263 dbg.Verbose(0, "File::GetDecompressed: read/decompress of "
264 "pixel data apparently went wrong.");
273 * \brief Points the internal Pixel_Data pointer to the callers inData
274 * image representation, BUT WITHOUT COPYING THE DATA.
275 * 'image' Pixels are presented as C-like 2D arrays : line per line.
276 * 'volume'Pixels are presented as C-like 3D arrays : plane per plane
277 * \warning Since the pixels are not copied, it is the caller's responsability
278 * not to deallocate it's data before gdcm uses them (e.g. with
279 * the Write() method.
280 * @param inData user supplied pixel area
281 * @param expectedSize total image size, in Bytes
285 bool File::SetImageData(uint8_t* inData, size_t expectedSize)
287 // FIXME : if already allocated, memory leak !
289 ImageDataSize = expectedSize;
290 // FIXME : 7fe0, 0010 IS NOT set ...
295 * \brief Writes on disk A SINGLE Dicom file
296 * NO test is performed on processor "Endiannity".
297 * It's up to the user to call his Reader properly
298 * @param fileName name of the file to be created
299 * (any already existing file is over written)
300 * @return false if write fails
303 bool File::WriteRawData(std::string const & fileName)
305 std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary );
308 dbg.Verbose(2, "Fail to open (write) file:", fileName.c_str());
311 fp1.write((char*)Pixel_Data, ImageDataSize);
318 * \brief Writes on disk A SINGLE Dicom file,
319 * using the Implicit Value Representation convention
320 * NO test is performed on processor "Endiannity".
321 * @param fileName name of the file to be created
322 * (any already existing file is overwritten)
323 * @return false if write fails
326 bool File::WriteDcmImplVR (std::string const & fileName)
328 SetWriteTypeToDcmImplVR();
329 return Write(fileName);
333 * \brief Writes on disk A SINGLE Dicom file,
334 * using the Explicit Value Representation convention
335 * NO test is performed on processor "Endiannity". * @param fileName name of the file to be created
336 * (any already existing file is overwritten)
337 * @return false if write fails
340 bool File::WriteDcmExplVR (std::string const & fileName)
342 SetWriteTypeToDcmExplVR();
343 return Write(fileName);
347 * \brief Writes on disk A SINGLE Dicom file,
348 * using the ACR-NEMA convention
349 * NO test is performed on processor "Endiannity".
350 * (a l'attention des logiciels cliniques
351 * qui ne prennent en entrée QUE des images ACR ...
352 * \warning if a DICOM_V3 header is supplied,
353 * groups < 0x0008 and shadow groups are ignored
354 * \warning NO TEST is performed on processor "Endiannity".
355 * @param fileName name of the file to be created
356 * (any already existing file is overwritten)
357 * @return false if write fails
360 bool File::WriteAcr (std::string const & fileName)
363 return Write(fileName);
366 bool File::Write(std::string const& fileName)
371 return WriteBase(fileName,ImplicitVR);
373 return WriteBase(fileName,ExplicitVR);
375 return WriteBase(fileName,ACR);
381 * \brief Access to the underlying \ref PixelConverter RGBA LUT
383 uint8_t* File::GetLutRGBA()
385 return PixelConverter->GetLutRGBA();
388 //-----------------------------------------------------------------------------
391 * \brief NOT a end user inteded function
392 * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc)
393 * @param fileName name of the file to be created
394 * (any already existing file is overwritten)
395 * @param type file type (ExplicitVR, ImplicitVR, ...)
396 * @return false if write fails
398 bool File::WriteBase (std::string const & fileName, FileType type)
403 SetWriteFileTypeToImplicitVR();
406 SetWriteFileTypeToExplicitVR();
409 SetWriteFileTypeToACR();
412 SetWriteFileTypeToACRLibido();
415 SetWriteFileTypeToExplicitVR();
423 case WMODE_DECOMPRESSED :
424 SetWriteToDecompressed();
431 // --------------------------------------------------------------
432 // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
434 // if recognition code tells us we dealt with a LibIDO image
435 // we reproduce on disk the switch between lineNumber and columnNumber
436 // just before writting ...
437 /// \todo the best trick would be *change* the recognition code
438 /// but pb expected if user deals with, e.g. COMPLEX images
439 /* if ( HeaderInternal->GetFileType() == ACR_LIBIDO)
443 // ----------------- End of Special Patch ----------------
445 bool check = CheckWriteIntegrity();
448 check = HeaderInternal->Write(fileName,type);
451 // --------------------------------------------------------------
452 // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
454 // ...and we restore the Header to be Dicom Compliant again
455 // just after writting
456 /* if ( HeaderInternal->GetFileType() == ACR_LIBIDO )
458 RestoreWriteFromLibido();
460 // ----------------- End of Special Patch ----------------
463 RestoreWriteFileType();
469 * \brief Check the write integrity
471 * The tests made are :
472 * - verify the size of the image to write with the possible write
473 * when the user set an image data
474 * @return true if the check successfulls
476 bool File::CheckWriteIntegrity()
480 int numberBitsAllocated = HeaderInternal->GetBitsAllocated();
481 if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
483 numberBitsAllocated = 16;
486 size_t decSize = HeaderInternal->GetXSize()
487 * HeaderInternal->GetYSize()
488 * HeaderInternal->GetZSize()
489 * ( numberBitsAllocated / 8 )
490 * HeaderInternal->GetSamplesPerPixel();
491 size_t rgbSize = decSize;
492 if( HeaderInternal->HasLUT() )
493 rgbSize = decSize * 3;
499 case WMODE_DECOMPRESSED :
500 if( decSize!=ImageDataSize )
502 dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect");
503 //std::cerr<<"Dec : "<<decSize<<" | "<<ImageDataSize<<std::endl;
508 if( rgbSize!=ImageDataSize )
510 dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect");
511 //std::cerr<<"RGB : "<<decSize<<" | "<<ImageDataSize<<std::endl;
521 void File::SetWriteToNative()
525 BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
526 pixel->SetValue(GDCM_BINLOADED);
527 pixel->SetBinArea(Pixel_Data,false);
528 pixel->SetLength(ImageDataSize);
530 Archive->Push(pixel);
534 void File::SetWriteToDecompressed()
536 if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT())
542 ValEntry* photInt = CopyValEntry(0x0028,0x0004);
543 if(HeaderInternal->HasLUT())
545 photInt->SetValue("PALETTE COLOR ");
546 photInt->SetLength(14);
550 photInt->SetValue("MONOCHROME1 ");
551 photInt->SetLength(12);
554 BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
555 pixel->SetValue(GDCM_BINLOADED);
558 pixel->SetBinArea(Pixel_Data,false);
559 pixel->SetLength(ImageDataSize);
563 pixel->SetBinArea(PixelConverter->GetDecompressed(),false);
564 pixel->SetLength(PixelConverter->GetDecompressedSize());
567 Archive->Push(photInt);
568 Archive->Push(pixel);
572 void File::SetWriteToRGB()
574 if(HeaderInternal->GetNumberOfScalarComponents()==3)
576 PixelConverter->BuildRGBImage();
578 ValEntry* spp = CopyValEntry(0x0028,0x0002);
582 ValEntry* planConfig = CopyValEntry(0x0028,0x0006);
583 planConfig->SetValue("0 ");
584 planConfig->SetLength(2);
586 ValEntry* photInt = CopyValEntry(0x0028,0x0004);
587 photInt->SetValue("RGB ");
588 photInt->SetLength(4);
590 BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
591 pixel->SetValue(GDCM_BINLOADED);
594 pixel->SetBinArea(Pixel_Data,false);
595 pixel->SetLength(ImageDataSize);
597 else if(PixelConverter->GetRGB())
599 pixel->SetBinArea(PixelConverter->GetRGB(),false);
600 pixel->SetLength(PixelConverter->GetRGBSize());
602 else // Decompressed data
604 pixel->SetBinArea(PixelConverter->GetDecompressed(),false);
605 pixel->SetLength(PixelConverter->GetDecompressedSize());
609 Archive->Push(planConfig);
610 Archive->Push(photInt);
611 Archive->Push(pixel);
614 Archive->Push(0x0028,0x1101);
615 Archive->Push(0x0028,0x1102);
616 Archive->Push(0x0028,0x1103);
617 Archive->Push(0x0028,0x1201);
618 Archive->Push(0x0028,0x1202);
619 Archive->Push(0x0028,0x1203);
622 // Thus, we have a RGB image and the bits allocated = 24 and
623 // samples per pixels = 1 (in the read file)
624 if(HeaderInternal->GetBitsAllocated()==24)
626 ValEntry* bitsAlloc = CopyValEntry(0x0028,0x0100);
627 bitsAlloc->SetValue("8 ");
628 bitsAlloc->SetLength(2);
630 ValEntry* bitsStored = CopyValEntry(0x0028,0x0101);
631 bitsStored->SetValue("8 ");
632 bitsStored->SetLength(2);
634 ValEntry* highBit = CopyValEntry(0x0028,0x0102);
635 highBit->SetValue("7 ");
636 highBit->SetLength(2);
638 Archive->Push(bitsAlloc);
639 Archive->Push(bitsStored);
640 Archive->Push(highBit);
645 SetWriteToDecompressed();
649 void File::RestoreWrite()
651 Archive->Restore(0x0028,0x0002);
652 Archive->Restore(0x0028,0x0004);
653 Archive->Restore(0x0028,0x0006);
654 Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
656 // For old ACR-NEMA (24 bits problem)
657 Archive->Restore(0x0028,0x0100);
658 Archive->Restore(0x0028,0x0101);
659 Archive->Restore(0x0028,0x0102);
662 Archive->Restore(0x0028,0x1101);
663 Archive->Restore(0x0028,0x1102);
664 Archive->Restore(0x0028,0x1103);
665 Archive->Restore(0x0028,0x1201);
666 Archive->Restore(0x0028,0x1202);
667 Archive->Restore(0x0028,0x1203);
670 void File::SetWriteFileTypeToACR()
672 Archive->Push(0x0002,0x0010);
675 void File::SetWriteFileTypeToACRLibido()
677 SetWriteFileTypeToACR();
680 void File::SetWriteFileTypeToExplicitVR()
682 std::string ts = Util::DicomString(
683 Document::GetTransferSyntaxValue(ExplicitVRLittleEndian).c_str() );
685 ValEntry* tss = CopyValEntry(0x0002,0x0010);
687 tss->SetLength(ts.length());
692 void File::SetWriteFileTypeToImplicitVR()
694 std::string ts = Util::DicomString(
695 Document::GetTransferSyntaxValue(ImplicitVRLittleEndian).c_str() );
697 ValEntry* tss = CopyValEntry(0x0002,0x0010);
699 tss->SetLength(ts.length());
702 void File::RestoreWriteFileType()
704 Archive->Restore(0x0002,0x0010);
707 void File::SetWriteToLibido()
709 ValEntry *oldRow = dynamic_cast<ValEntry *>(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010));
710 ValEntry *oldCol = dynamic_cast<ValEntry *>(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011));
712 if( oldRow && oldCol )
714 std::string rows, columns;
716 ValEntry *newRow=new ValEntry(oldRow->GetDictEntry());
717 ValEntry *newCol=new ValEntry(oldCol->GetDictEntry());
719 newRow->Copy(oldCol);
720 newCol->Copy(oldRow);
722 newRow->SetValue(oldCol->GetValue());
723 newCol->SetValue(oldRow->GetValue());
725 Archive->Push(newRow);
726 Archive->Push(newCol);
730 void File::RestoreWriteFromLibido()
732 Archive->Restore(0x0028,0x0010);
733 Archive->Restore(0x0028,0x0011);
736 ValEntry* File::CopyValEntry(uint16_t group,uint16_t element)
738 DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element);
743 newE = new ValEntry(oldE->GetDictEntry());
748 newE = GetHeader()->NewValEntryByNumber(group,element);
754 BinEntry* File::CopyBinEntry(uint16_t group,uint16_t element)
756 DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element);
761 newE = new BinEntry(oldE->GetDictEntry());
766 newE = GetHeader()->NewBinEntryByNumber(group,element);
773 //-----------------------------------------------------------------------------
776 * \brief Set the pixel datas in the good entry of the Header
778 void File::SetPixelData(uint8_t* data)
780 GetHeader()->SetEntryByNumber( GDCM_BINLOADED,
781 GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
783 // Will be 7fe0, 0010 in standard case
784 DocEntry* currentEntry = GetHeader()->GetDocEntryByNumber(GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
787 if ( BinEntry* binEntry = dynamic_cast<BinEntry *>(currentEntry) )
788 // Flag is to false because datas are kept in the gdcmPixelConvert
789 binEntry->SetBinArea( data, false );
793 //-----------------------------------------------------------------------------
794 } // end namespace gdcm