1 /*=========================================================================
4 Module: $RCSfile: gdcmFileHelper.cxx,v $
7 Date: $Date: 2007/10/01 09:28:57 $
8 Version: $Revision: 1.131 $
10 Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
11 l'Image). All rights reserved. See Doc/License.txt or
12 http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
14 This software is distributed WITHOUT ANY WARRANTY; without even
15 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 PURPOSE. See the above copyright notices for more information.
18 =========================================================================*/
20 #include "gdcmFileHelper.h"
21 #include "gdcmGlobal.h"
23 #include "gdcmDocument.h"
24 #include "gdcmDebug.h"
26 #include "gdcmSeqEntry.h"
27 #include "gdcmSQItem.h"
28 #include "gdcmDataEntry.h"
29 #include "gdcmDocEntry.h"
31 #include "gdcmPixelReadConvert.h"
32 #include "gdcmPixelWriteConvert.h"
33 #include "gdcmDocEntryArchive.h"
34 #include "gdcmDictSet.h"
35 #include "gdcmOrientation.h"
37 #if defined(__BORLANDC__)
38 #include <mem.h> // for memset
44 // ----------------------------- WARNING -------------------------
46 These lines will be moved to the document-to-be 'User's Guide'
48 // To read an image, user needs a gdcm::File
49 gdcm::File *f = new gdcm::File(fileName);
51 // user may also decide he doesn't want to load some parts of the header
52 gdcm::File *f = new gdcm::File();
53 f->SetFileName(fileName);
54 f->SetLoadMode(LD_NOSEQ); // or
55 f->SetLoadMode(LD_NOSHADOW); // or
56 f->SetLoadMode(LD_NOSEQ | LD_NOSHADOW); // or
57 f->SetLoadMode(LD_NOSHADOWSEQ);
60 // To decide whether it's an 'image of interest for him, or not,
61 // user can now check some values
62 std::string v = f->GetEntryValue(groupNb,ElementNb);
64 // to get the pixels, user needs a gdcm::FileHelper
65 gdcm::FileHelper *fh = new gdcm::FileHelper(f);
67 // user may ask not to convert Palette (if any) to RGB
68 uint8_t *pixels = fh->GetImageDataRaw();
69 int imageLength = fh->GetImageDataRawSize();
71 // He can now use the pixels, create a new image, ...
72 uint8_t *userPixels = ...
74 //To re-write the image, user re-uses the gdcm::FileHelper
75 gdcm::File *fh = new gdcm::FileHelper();
77 fh->SetTypeToRaw(); // Even if it was possible to convert Palette to RGB
80 // If user wants to write the file as MONOCHROME1 (0=white)
81 fh->SetPhotometricInterpretationToMonochrome1();
83 fh->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation
84 // Little Endian is the default,
85 // bigendian not supported for writting
86 (-->SetWriteType(ExplicitVR);)
87 -->WriteType = ExplicitVR;
88 fh->SetWriteTypeToJPEG(); // lossless compression
89 fh->SetWriteTypeToJPEG2000(); // lossless compression
91 fh->SetImageData( userPixels, userPixelsLength);
93 fh->SetUserData( userPixels, userPixelsLength); // this one performs compression, when required
95 fh->Write(newFileName); // overwrites the file, if any
100 These lines will be moved to the document-to-be 'Developer's Guide'
102 WriteMode : WMODE_RAW / WMODE_RGB
103 WriteType : ImplicitVR, ExplicitVR, ACR, ACR_LIBIDO
104 PhotometricInterpretation : MONOCHROME2 (0=black), MONOCHROME2 (0=white)
106 fh->SetImageData( userPixels, userPixelsLength);
108 fh->SetUserData( userPixels, userPixelsLength);
109 PixelWriteConverter->SetUserData(inData, expectedSize);
112 fh->SetWriteMode(WMODE_RAW / WMODE_RGB)
114 fh->SetWriteType( ImplicitVR/ExplicitVR/ACR/ACR_LIBIDO/JPEG/JPEG2000)
116 fh->Write(newFileName);
117 CheckMandatoryElements(); // Checks existing ones / Add missing ones
118 Fix VR if unknown elements
119 SetWriteFileTypeToImplicitVR() / SetWriteFileTypeToExplicitVR(); /
120 SetWriteFileTypeToACR() / SetWriteFileTypeToJPEG() / SetWriteFileTypeToJ2K()
121 (Modifies TransferSyntax if any; Pushes to the Archives old one)
122 SetWriteToRaw(); / SetWriteToRGB();
123 (Modifies and pushes to the Archive, when necessary : photochr. interp.,
124 samples per pixel, Planar configuration,
125 bits allocated, bits stored, high bit -ACR 24 bits-
126 Pixels element VR, pushes out the LUT )
128 Sets Photometric Interpretation
129 DataEntry *pixel =CopyDataEntry(7fe0,0010,VR)
130 Sets VR, BinArea, Length for PixelData
133 Archive->Push(photInt);
134 Archive->Push(pixel);
138 if NumberOfScalarComponents==1
139 SetWriteToRaw(); return;
140 PixelReadConverter->BuildRGBImage()
141 DataEntry *pixel =CopyDataEntry(7fe0,0010,VR)
142 Archives spp, planConfig,photInt, pixel
144 CheckWriteIntegrity();
145 (checks user given pixels length)
146 FileInternal->Write(fileName,WriteType)
147 fp = opens file(fileName); // out|binary
148 ComputeGroup0002Length( );
149 Document::WriteContent(fp, writetype);
150 writes Dicom File Preamble not ACR-NEMA
151 ElementSet::WriteContent(fp, writetype);
152 writes recursively all DataElements
154 (moves back to the gdcm::File all the archived elements)
160 namespace GDCM_NAME_SPACE
162 typedef std::map<uint16_t, int> GroupHT; // Hash Table
163 //-------------------------------------------------------------------------
164 // Constructor / Destructor
166 * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
167 * file (gdcm::File only deals with the ... header)
168 * Opens (in read only and when possible) an existing file and checks
169 * for DICOM compliance. Returns NULL on failure.
170 * It will be up to the user to load the pixels into memory
171 * ( GetImageDataSize() + GetImageData() methods)
172 * \note the in-memory representation of all available tags found in
173 * the DICOM header is post-poned to first header information access.
174 * This avoid a double parsing of public part of the header when
175 * one sets an a posteriori shadow dictionary (efficiency can be
176 * seen as a side effect).
178 FileHelper::FileHelper( )
180 FileInternal = File::New( );
185 * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
186 * file (File only deals with the ... header)
187 * Opens (in read only and when possible) an existing file and checks
188 * for DICOM compliance. Returns NULL on failure.
189 * It will be up to the user to load the pixels into memory
190 * ( GetImageDataSize() + GetImageData() methods)
191 * \note the in-memory representation of all available tags found in
192 * the DICOM header is post-poned to first header information access.
193 * This avoid a double parsing of public part of the header when
194 * user sets an a posteriori shadow dictionary (efficiency can be
195 * seen as a side effect).
196 * @param header already built Header
198 FileHelper::FileHelper(File *header)
200 gdcmAssertMacro(header);
202 FileInternal = header;
203 FileInternal->Register();
205 if ( FileInternal->IsReadable() )
207 PixelReadConverter->GrabInformationsFromFile( FileInternal, this );
212 * \brief canonical destructor
213 * \note If the header (gdcm::File) was created by the FileHelper constructor,
214 * it is destroyed by the FileHelper
216 FileHelper::~FileHelper()
218 if ( PixelReadConverter )
220 delete PixelReadConverter;
222 if ( PixelWriteConverter )
224 delete PixelWriteConverter;
231 FileInternal->Unregister();
234 //-----------------------------------------------------------------------------
238 * \brief Sets the LoadMode of the internal gdcm::File as a boolean string.
239 * NO_SEQ, NO_SHADOW, NO_SHADOWSEQ ... (nothing more, right now)
240 * WARNING : before using NO_SHADOW, be sure *all* your files
241 * contain accurate values in the 0x0000 element (if any)
242 * of *each* Shadow Group. The parser will fail if the size is wrong !
243 * @param loadMode Load mode to be used
245 void FileHelper::SetLoadMode(int loadMode)
247 GetFile()->SetLoadMode( loadMode );
250 * \brief Sets the LoadMode of the internal gdcm::File
251 * @param fileName name of the file to be open
253 void FileHelper::SetFileName(std::string const &fileName)
255 FileInternal->SetFileName( fileName );
260 * @return false if file cannot be open or no swap info was found,
261 * or no tag was found.
263 bool FileHelper::Load()
265 if ( !FileInternal->Load() )
268 PixelReadConverter->GrabInformationsFromFile( FileInternal, this );
273 * \brief Accesses an existing DataEntry through its (group, element)
274 * and modifies its content with the given value.
275 * @param content new value (string) to substitute with
276 * @param group group number of the Dicom Element to modify
277 * @param elem element number of the Dicom Element to modify
278 * \return false if DataEntry not found
280 bool FileHelper::SetEntryString(std::string const &content,
281 uint16_t group, uint16_t elem)
283 return FileInternal->SetEntryString(content, group, elem);
288 * \brief Accesses an existing DataEntry through its (group, element)
289 * and modifies its content with the given value.
290 * @param content new value (void* -> uint8_t*) to substitute with
291 * @param lgth new value length
292 * @param group group number of the Dicom Element to modify
293 * @param elem element number of the Dicom Element to modify
294 * \return false if DataEntry not found
296 bool FileHelper::SetEntryBinArea(uint8_t *content, int lgth,
297 uint16_t group, uint16_t elem)
299 return FileInternal->SetEntryBinArea(content, lgth, group, elem);
303 * \brief Modifies the value of a given DataEntry when it exists.
304 * Creates it with the given value when unexistant.
305 * @param content (string) value to be set
306 * @param group Group number of the Entry
307 * @param elem Element number of the Entry
308 * @param vr Value Representation of the DataElement to be inserted
309 * \return pointer to the modified/created DataEntry (NULL when creation
312 DataEntry *FileHelper::InsertEntryString(std::string const &content,
313 uint16_t group, uint16_t elem,
316 return FileInternal->InsertEntryString(content, group, elem, vr);
320 * \brief Modifies the value of a given DataEntry when it exists.
321 * Creates it with the given value when unexistant.
322 * A copy of the binArea is made to be kept in the Document.
323 * @param binArea (binary) value to be set
324 * @param lgth new value length
325 * @param group Group number of the Entry
326 * @param elem Element number of the Entry
327 * @param vr Value Representation of the DataElement to be inserted
328 * \return pointer to the modified/created DataEntry (NULL when creation
331 DataEntry *FileHelper::InsertEntryBinArea(uint8_t *binArea, int lgth,
332 uint16_t group, uint16_t elem,
335 return FileInternal->InsertEntryBinArea(binArea, lgth, group, elem, vr);
339 * \brief Adds an empty SeqEntry
340 * (remove any existing entry with same group,elem)
341 * @param group Group number of the Entry
342 * @param elem Element number of the Entry
343 * \return pointer to the created SeqEntry (NULL when creation
346 SeqEntry *FileHelper::InsertSeqEntry(uint16_t group, uint16_t elem)
348 return FileInternal->InsertSeqEntry(group, elem);
352 * \brief Get the size of the image data
353 * If the image can be RGB (with a lut or by default), the size
354 * corresponds to the RGB image
355 * (use GetImageDataRawSize if you want to be sure to get *only*
356 * the size of the pixels)
357 * @return The image size
359 size_t FileHelper::GetImageDataSize()
361 if ( PixelWriteConverter->GetUserData() )
363 return PixelWriteConverter->GetUserDataSize();
365 return PixelReadConverter->GetRGBSize();
369 * \brief Get the size of the image data.
370 * If the image could be converted to RGB using a LUT,
371 * this transformation is not taken into account by GetImageDataRawSize
372 * (use GetImageDataSize if you wish)
373 * @return The raw image size
375 size_t FileHelper::GetImageDataRawSize()
377 if ( PixelWriteConverter->GetUserData() )
379 return PixelWriteConverter->GetUserDataSize();
381 return PixelReadConverter->GetRawSize();
385 * \brief brings pixels into memory :
386 * - Allocates necessary memory,
387 * - Reads the pixels from disk (uncompress if necessary),
388 * - Transforms YBR pixels, if any, into RGB pixels,
389 * - Transforms 3 planes R, G, B, if any, into a single RGB Plane
390 * - Transforms single Grey plane + 3 Palettes into a RGB Plane
391 * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
392 * @return Pointer to newly allocated pixel data.
393 * (uint8_t is just for prototyping. feel free to cast)
394 * NULL if alloc fails
396 uint8_t *FileHelper::GetImageData()
398 if ( PixelWriteConverter->GetUserData() )
400 return PixelWriteConverter->GetUserData();
405 // If the decompression failed nothing can be done.
409 if ( FileInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
411 return PixelReadConverter->GetRGB();
415 // When no LUT or LUT conversion fails, return the Raw
416 return PixelReadConverter->GetRaw();
421 * \brief brings pixels into memory :
422 * - Allocates necessary memory,
423 * - Transforms YBR pixels (if any) into RGB pixels
424 * - Transforms 3 planes R, G, B (if any) into a single RGB Plane
425 * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
426 * - DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
427 * @return Pointer to newly allocated pixel data.
428 * (uint8_t is just for prototyping. feel free to cast)
429 * NULL if alloc fails
431 uint8_t *FileHelper::GetImageDataRaw ()
436 //#ifndef GDCM_LEGACY_REMOVE
438 * \brief Useless function, since PixelReadConverter forces us
439 * copy the Pixels anyway.
440 * Reads the pixels from disk (uncompress if necessary),
441 * Transforms YBR pixels, if any, into RGB pixels
442 * Transforms 3 planes R, G, B, if any, into a single RGB Plane
443 * Transforms single Grey plane + 3 Palettes into a RGB Plane
444 * Copies at most MaxSize bytes of pixel data to caller allocated
446 * \warning This function allows people that want to build a volume
447 * from an image stack *not to* have, first to get the image pixels,
448 * and then move them to the volume area.
449 * It's absolutely useless for any VTK user since vtk chooses
450 * to invert the lines of an image, that is the last line comes first
451 * (for some axis related reasons?). Hence he will have
452 * to load the image line by line, starting from the end.
453 * VTK users have to call GetImageData
455 * @param destination Address (in caller's memory space) at which the
456 * pixel data should be copied
457 * @param maxSize Maximum number of bytes to be copied. When MaxSize
458 * is not sufficient to hold the pixel data the copy is not
459 * executed (i.e. no partial copy).
460 * @return On success, the number of bytes actually copied. Zero on
461 * failure e.g. MaxSize is lower than necessary.
464 size_t FileHelper::GetImageDataIntoVector (void *destination, size_t maxSize)
468 // If the decompression failed nothing can be done.
472 if ( FileInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
474 if ( PixelReadConverter->GetRGBSize() > maxSize )
476 gdcmWarningMacro( "Pixel data bigger than caller's expected MaxSize");
480 (void*)PixelReadConverter->GetRGB(),
481 PixelReadConverter->GetRGBSize() );
482 return PixelReadConverter->GetRGBSize();
485 // Either no LUT conversion necessary or LUT conversion failed
486 if ( PixelReadConverter->GetRawSize() > maxSize )
488 gdcmWarningMacro( "Pixel data bigger than caller's expected MaxSize");
492 (void *)PixelReadConverter->GetRaw(),
493 PixelReadConverter->GetRawSize() );
494 return PixelReadConverter->GetRawSize();
500 * \brief Points the internal pointer to the callers inData
501 * image representation, BUT WITHOUT COPYING THE DATA.
502 * 'image' Pixels are presented as C-like 2D arrays : line per line.
503 * 'volume'Pixels are presented as C-like 3D arrays : plane per plane
504 * \warning Since the pixels are not copied, it is the caller's responsability
505 * not to deallocate its data before gdcm uses them (e.g. with
506 * the Write() method )
507 * @param inData user supplied pixel area (uint8_t* is just for the compiler.
508 * user is allowed to pass any kind of pixels since the size is
510 * @param expectedSize total image size, *in Bytes*
512 void FileHelper::SetImageData(uint8_t *inData, size_t expectedSize)
514 PixelWriteConverter->SetUserData(inData, expectedSize);
515 /// \todo : shouldn't we call SetCompressJPEGUserData/SetCompressJPEG2000UserData
520 * \brief Set the image data defined by the user
521 * \warning When writting the file, this data are get as default data to write
522 * @param inData user supplied pixel area (uint8_t* is just for the compiler.
523 * user is allowed to pass any kind of pixels since the size is
525 * @param expectedSize total image size, *in Bytes*
527 void FileHelper::SetUserData(uint8_t *inData, size_t expectedSize)
529 // Shouldn't we move theese lines to FileHelper::Write()?
531 if( WriteType == JPEG2000 )
533 PixelWriteConverter->SetCompressJPEG2000UserData(inData, expectedSize, FileInternal);
535 else if( WriteType == JPEG )
537 PixelWriteConverter->SetCompressJPEGUserData(inData, expectedSize, FileInternal);
541 PixelWriteConverter->SetUserData(inData, expectedSize);
545 PixelWriteConverter->SetUserData(inData, expectedSize);
549 * \brief Get the image data defined by the user
550 * \warning When writting the file, this data are get as default data to write
552 uint8_t *FileHelper::GetUserData()
554 return PixelWriteConverter->GetUserData();
558 * \brief Get the image data size defined by the user
559 * \warning When writting the file, this data are get as default data to write
561 size_t FileHelper::GetUserDataSize()
563 return PixelWriteConverter->GetUserDataSize();
567 * \brief Get the image data from the file.
568 * If a LUT is found, the data are expanded to be RGB
570 uint8_t *FileHelper::GetRGBData()
572 return PixelReadConverter->GetRGB();
576 * \brief Get the image data size from the file.
577 * If a LUT is found, the data are expanded to be RGB
579 size_t FileHelper::GetRGBDataSize()
581 return PixelReadConverter->GetRGBSize();
585 * \brief Get the image data from the file.
586 * Even when a LUT is found, the data are not expanded to RGB!
588 uint8_t *FileHelper::GetRawData()
590 return PixelReadConverter->GetRaw();
594 * \brief Get the image data size from the file.
595 * Even when a LUT is found, the data are not expanded to RGB!
597 size_t FileHelper::GetRawDataSize()
599 return PixelReadConverter->GetRawSize();
603 * \brief Access to the underlying PixelReadConverter RGBA LUT
605 uint8_t* FileHelper::GetLutRGBA()
607 if ( PixelReadConverter->GetLutRGBA() ==0 )
608 PixelReadConverter->BuildLUTRGBA();
609 return PixelReadConverter->GetLutRGBA();
613 * \brief Access to the underlying PixelReadConverter RGBA LUT Item Number
615 int FileHelper::GetLutItemNumber()
617 return PixelReadConverter->GetLutItemNumber();
621 * \brief Access to the underlying PixelReadConverter RGBA LUT Item Size
623 int FileHelper::GetLutItemSize()
625 return PixelReadConverter->GetLutItemSize();
629 * \brief Writes on disk A SINGLE Dicom file
630 * NO test is performed on processor "Endiannity".
631 * It's up to the user to call his Reader properly
632 * @param fileName name of the file to be created
633 * (any already existing file is over written)
634 * @return false if write fails
636 bool FileHelper::WriteRawData(std::string const &fileName)
638 std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary );
641 gdcmWarningMacro( "Fail to open (write) file:" << fileName.c_str());
645 if ( PixelWriteConverter->GetUserData() )
647 fp1.write( (char *)PixelWriteConverter->GetUserData(),
648 PixelWriteConverter->GetUserDataSize() );
650 else if ( PixelReadConverter->GetRGB() )
652 fp1.write( (char *)PixelReadConverter->GetRGB(),
653 PixelReadConverter->GetRGBSize());
655 else if ( PixelReadConverter->GetRaw() )
657 fp1.write( (char *)PixelReadConverter->GetRaw(),
658 PixelReadConverter->GetRawSize());
662 gdcmErrorMacro( "Nothing written." );
671 * \brief Writes on disk A SINGLE Dicom file,
672 * using the Implicit Value Representation convention
673 * NO test is performed on processor "Endianity".
674 * @param fileName name of the file to be created
675 * (any already existing file is overwritten)
676 * @return false if write fails
679 bool FileHelper::WriteDcmImplVR (std::string const &fileName)
681 SetWriteTypeToDcmImplVR();
682 return Write(fileName);
686 * \brief Writes on disk A SINGLE Dicom file,
687 * using the Explicit Value Representation convention
688 * NO test is performed on processor "Endiannity".
689 * @param fileName name of the file to be created
690 * (any already existing file is overwritten)
691 * @return false if write fails
694 bool FileHelper::WriteDcmExplVR (std::string const &fileName)
696 SetWriteTypeToDcmExplVR();
697 return Write(fileName);
701 * \brief Writes on disk A SINGLE Dicom file,
702 * using the ACR-NEMA convention
703 * NO test is performed on processor "Endiannity".
704 * (a l'attention des logiciels cliniques
705 * qui ne prennent en entrée QUE des images ACR ...
706 * \warning if a DICOM_V3 header is supplied,
707 * groups < 0x0008 and shadow groups are ignored
708 * \warning NO TEST is performed on processor "Endiannity".
709 * @param fileName name of the file to be created
710 * (any already existing file is overwritten)
711 * @return false if write fails
714 bool FileHelper::WriteAcr (std::string const &fileName)
717 return Write(fileName);
721 * \brief Writes on disk A SINGLE Dicom file,
722 * @param fileName name of the file to be created
723 * (any already existing file is overwritten)
724 * @return false if write fails
726 bool FileHelper::Write(std::string const &fileName)
728 CheckMandatoryElements(); //called once, here !
734 SetWriteFileTypeToImplicitVR();
737 case Unknown: // should never happen; ExplicitVR is the default value
740 // We let DocEntry::WriteContent to put vr=UN for undocumented Shadow Groups !
741 SetWriteFileTypeToExplicitVR();
746 // NOTHING is done here just for LibIDO.
747 // Just to avoid further trouble if user creates a file ex-nihilo,
748 // wants to write it as an ACR-NEMA file,
749 // and forgets to create any Entry belonging to group 0008
751 // We add Recognition Code (RET)
752 if ( ! FileInternal->GetDataEntry(0x0008, 0x0010) )
753 FileInternal->InsertEntryString("ACR-NEMA V1.0 ",
754 0x0008, 0x0010, "LO");
755 SetWriteFileTypeToACR();
756 // SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR !
759 /// \todo FIXME : JPEG/JPEG2000 may be either ExplicitVR or ImplicitVR
761 SetWriteFileTypeToJPEG();
763 //PixelWriteConverter->SetCompressJPEGUserData(
764 // inData, expectedSize, FileInternal);
765 PixelWriteConverter->SetCompressJPEGUserData(
766 PixelWriteConverter->GetUserData(),
767 PixelWriteConverter->GetUserDataSize(),FileInternal);
771 /// \todo Maybe we should consider doing the compression here !
772 // PixelWriteConverter->SetCompressJPEG2000UserData(inData, expectedSize, FileInternal);
774 SetWriteFileTypeToJPEG2000();
775 PixelWriteConverter->SetCompressJPEG2000UserData(
776 PixelWriteConverter->GetUserData(),
777 PixelWriteConverter->GetUserDataSize(),
782 // --------------------------------------------------------------
783 // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
785 // if recognition code tells us we dealt with a LibIDO image
786 // we reproduce on disk the switch between lineNumber and columnNumber
787 // just before writting ...
788 /// \todo the best trick would be *change* the recognition code
789 /// but pb expected if user deals with, e.g. COMPLEX images
791 if ( WriteType == ACR_LIBIDO )
797 SetWriteToNoLibido();
799 // ----------------- End of Special Patch ----------------
804 SetWriteToRaw(); // modifies and pushes to the archive, when necessary
807 SetWriteToRGB(); // modifies and pushes to the archive, when necessary
812 if (WriteType == JPEG || WriteType == JPEG2000)
815 check = CheckWriteIntegrity(); // verifies length
819 check = FileInternal->Write(fileName,WriteType);
823 // RestoreWriteFileType();
824 // RestoreWriteMandatory();
826 // --------------------------------------------------------------
827 // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
829 // ...and we restore the header to be Dicom Compliant again
830 // just after writting
831 RestoreWriteOfLibido();
832 // ----------------- End of Special Patch ----------------
837 //-----------------------------------------------------------------------------
840 * \brief Verifies the size of the user given PixelData
841 * @return true if check is successfull
843 bool FileHelper::CheckWriteIntegrity()
845 if ( PixelWriteConverter->GetUserData() )
847 int numberBitsAllocated = FileInternal->GetBitsAllocated();
848 if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
850 gdcmWarningMacro( "numberBitsAllocated changed from "
851 << numberBitsAllocated << " to 16 "
852 << " for consistency purpose" );
853 numberBitsAllocated = 16;
856 size_t decSize = FileInternal->GetXSize()
857 * FileInternal->GetYSize()
858 * FileInternal->GetZSize()
859 * FileInternal->GetTSize()
860 * FileInternal->GetSamplesPerPixel()
861 * ( numberBitsAllocated / 8 );
862 size_t rgbSize = decSize;
863 if ( FileInternal->HasLUT() )
864 rgbSize = decSize * 3;
866 size_t userDataSize = PixelWriteConverter->GetUserDataSize();
870 if ( abs((long)(decSize-userDataSize))>1) // ignore padding zero
872 gdcmWarningMacro( "Data size (Raw) is incorrect. Should be "
873 << decSize << " / Found :"
879 if ( abs((long)(rgbSize-userDataSize))>1) // ignore padding zero
881 gdcmWarningMacro( "Data size (RGB) is incorrect. Should be "
882 << rgbSize << " / Found "
893 * \brief Updates the File to write RAW data (as opposed to RGB data)
894 * (modifies, when necessary, photochromatic interpretation,
895 * bits allocated, Pixels element VR)
896 * WARNING : if SetPhotometricInterpretationToMonochrome1() was called
897 * before Pixel Elements is modified :-(
899 void FileHelper::SetWriteToRaw()
901 if ( FileInternal->GetNumberOfScalarComponents() == 3
902 && !FileInternal->HasLUT() )
908 // 0x0028,0x0004 : Photometric Interpretation
909 DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS");
910 if (FileInternal->HasLUT() )
912 photInt->SetString("PALETTE COLOR ");
916 if (GetPhotometricInterpretation() == 2)
917 photInt->SetString("MONOCHROME2 "); // 0 = Black
919 photInt->SetString("MONOCHROME1 "); // 0 = White !
922 PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
923 PixelReadConverter->GetRawSize());
925 std::string vr = "OB";
926 if ( FileInternal->GetBitsAllocated()>8 )
928 if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files
930 // For non RAW data. Mainly JPEG/JPEG2000
931 if( WriteType == JPEG || WriteType == JPEG2000)
937 CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr);
938 pixel->SetFlag(DataEntry::FLAG_PIXELDATA);
939 pixel->SetBinArea(PixelWriteConverter->GetData(),false);
941 static_cast< uint32_t >(PixelWriteConverter->GetDataSize()) );
943 if (!FileInternal->HasLUT() && GetPhotometricInterpretation() == 1)
945 ConvertFixGreyLevels( pixel->GetBinArea(), pixel->GetLength() );
948 Archive->Push(photInt);
949 Archive->Push(pixel);
957 * \brief Updates the File to write RGB data (as opposed to RAW data)
958 * (modifies, when necessary, photochromatic interpretation,
959 * samples per pixel, Planar configuration,
960 * bits allocated, bits stored, high bit -ACR 24 bits-
961 * Pixels element VR, pushes out the LUT, )
963 void FileHelper::SetWriteToRGB()
965 if ( FileInternal->GetNumberOfScalarComponents()==3 )
967 PixelReadConverter->BuildRGBImage();
969 DataEntry *spp = CopyDataEntry(0x0028,0x0002,"US");
970 spp->SetString("3 "); // Don't drop trailing space
972 DataEntry *planConfig = CopyDataEntry(0x0028,0x0006,"US");
973 planConfig->SetString("0 "); // Don't drop trailing space
975 DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS");
976 photInt->SetString("RGB "); // Don't drop trailing space
978 if ( PixelReadConverter->GetRGB() )
980 PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(),
981 PixelReadConverter->GetRGBSize());
985 PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
986 PixelReadConverter->GetRawSize());
989 std::string vr = "OB";
990 if ( FileInternal->GetBitsAllocated()>8 )
992 if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files
995 CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr);
996 pixel->SetFlag(DataEntry::FLAG_PIXELDATA);
997 pixel->SetBinArea(PixelWriteConverter->GetData(),false);
998 pixel->SetLength(PixelWriteConverter->GetDataSize());
1001 Archive->Push(planConfig);
1002 Archive->Push(photInt);
1003 Archive->Push(pixel);
1006 planConfig->Delete();
1011 Archive->Push(0x0028,0x1101);
1012 Archive->Push(0x0028,0x1102);
1013 Archive->Push(0x0028,0x1103);
1014 Archive->Push(0x0028,0x1201);
1015 Archive->Push(0x0028,0x1202);
1016 Archive->Push(0x0028,0x1203);
1018 // push out Palette Color Lookup Table UID, if any
1019 Archive->Push(0x0028,0x1199);
1021 // For old '24 Bits' ACR-NEMA
1022 // Thus, we have a RGB image and the bits allocated = 24 and
1023 // samples per pixels = 1 (in the read file)
1024 if ( FileInternal->GetBitsAllocated()==24 )
1026 DataEntry *bitsAlloc = CopyDataEntry(0x0028,0x0100,"US");
1027 bitsAlloc->SetString("8 ");
1029 DataEntry *bitsStored = CopyDataEntry(0x0028,0x0101,"US");
1030 bitsStored->SetString("8 ");
1032 DataEntry *highBit = CopyDataEntry(0x0028,0x0102,"US");
1033 highBit->SetString("7 ");
1035 Archive->Push(bitsAlloc);
1036 Archive->Push(bitsStored);
1037 Archive->Push(highBit);
1039 bitsAlloc->Delete();
1040 bitsStored->Delete();
1051 * \brief Restore the File write mode
1053 void FileHelper::RestoreWrite()
1055 Archive->Restore(0x0028,0x0002);
1056 Archive->Restore(0x0028,0x0004);
1058 Archive->Restore(0x0028,0x0006);
1059 Archive->Restore(GetFile()->GetGrPixel(),GetFile()->GetNumPixel());
1061 // For old ACR-NEMA (24 bits problem)
1062 Archive->Restore(0x0028,0x0100);
1063 Archive->Restore(0x0028,0x0101);
1064 Archive->Restore(0x0028,0x0102);
1067 Archive->Restore(0x0028,0x1101);
1068 Archive->Restore(0x0028,0x1102);
1069 Archive->Restore(0x0028,0x1103);
1070 Archive->Restore(0x0028,0x1201);
1071 Archive->Restore(0x0028,0x1202);
1072 Archive->Restore(0x0028,0x1203);
1074 // For the Palette Color Lookup Table UID
1075 Archive->Restore(0x0028,0x1203);
1077 // group 0002 may be pushed out for ACR-NEMA writting purposes
1078 Archive->Restore(0x0002,0x0000);
1079 Archive->Restore(0x0002,0x0001);
1080 Archive->Restore(0x0002,0x0002);
1081 Archive->Restore(0x0002,0x0003);
1082 Archive->Restore(0x0002,0x0010);
1083 Archive->Restore(0x0002,0x0012);
1084 Archive->Restore(0x0002,0x0013);
1085 Archive->Restore(0x0002,0x0016);
1086 Archive->Restore(0x0002,0x0100);
1087 Archive->Restore(0x0002,0x0102);
1092 * \brief Pushes out the whole group 0002
1093 * FIXME : better, set a flag to tell the writer not to write it ...
1094 * FIXME : method should probably have an other name !
1095 * SetWriteFileTypeToACR is NOT opposed to
1096 * SetWriteFileTypeToExplicitVR and SetWriteFileTypeToImplicitVR
1098 void FileHelper::SetWriteFileTypeToACR()
1100 Archive->Push(0x0002,0x0000);
1101 Archive->Push(0x0002,0x0001);
1102 Archive->Push(0x0002,0x0002);
1103 Archive->Push(0x0002,0x0003);
1104 Archive->Push(0x0002,0x0010);
1105 Archive->Push(0x0002,0x0012);
1106 Archive->Push(0x0002,0x0013);
1107 Archive->Push(0x0002,0x0016);
1108 Archive->Push(0x0002,0x0100);
1109 Archive->Push(0x0002,0x0102);
1113 * \brief Sets in the File the TransferSyntax to 'JPEG2000'
1115 void FileHelper::SetWriteFileTypeToJPEG2000()
1117 std::string ts = Util::DicomString(
1118 Global::GetTS()->GetSpecialTransferSyntax(TS::JPEG2000Lossless) );
1120 DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
1128 * \brief Sets in the File the TransferSyntax to 'JPEG'
1130 void FileHelper::SetWriteFileTypeToJPEG()
1132 std::string ts = Util::DicomString(
1133 Global::GetTS()->GetSpecialTransferSyntax(TS::JPEGLosslessProcess14_1) );
1135 DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
1143 * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian"
1145 void FileHelper::SetWriteFileTypeToExplicitVR()
1147 std::string ts = Util::DicomString(
1148 Global::GetTS()->GetSpecialTransferSyntax(TS::ExplicitVRLittleEndian) );
1150 DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
1157 * \brief Sets in the File the TransferSyntax to 'Implicit VR Little Endian"
1159 void FileHelper::SetWriteFileTypeToImplicitVR()
1161 std::string ts = Util::DicomString(
1162 Global::GetTS()->GetSpecialTransferSyntax(TS::ImplicitVRLittleEndian) );
1164 DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
1171 * \brief Set the Write not to Libido format
1173 void FileHelper::SetWriteToLibido()
1175 DataEntry *oldRow = FileInternal->GetDataEntry(0x0028, 0x0010);
1176 DataEntry *oldCol = FileInternal->GetDataEntry(0x0028, 0x0011);
1178 if ( oldRow && oldCol )
1180 std::string rows, columns;
1182 DataEntry *newRow=DataEntry::New(0x0028, 0x0010, "US");
1183 DataEntry *newCol=DataEntry::New(0x0028, 0x0011, "US");
1185 newRow->Copy(oldCol);
1186 newCol->Copy(oldRow);
1188 newRow->SetString(oldCol->GetString());
1189 newCol->SetString(oldRow->GetString());
1191 Archive->Push(newRow);
1192 Archive->Push(newCol);
1198 DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010,"LO");
1199 libidoCode->SetString("ACRNEMA_LIBIDO_1.1");
1200 Archive->Push(libidoCode);
1201 libidoCode->Delete();
1205 * \brief Set the Write not to No Libido format
1207 void FileHelper::SetWriteToNoLibido()
1209 DataEntry *recCode = FileInternal->GetDataEntry(0x0008,0x0010);
1212 if ( recCode->GetString() == "ACRNEMA_LIBIDO_1.1" )
1214 DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010,"LO");
1215 libidoCode->SetString("");
1216 Archive->Push(libidoCode);
1217 libidoCode->Delete();
1223 * \brief Restore the Write format
1225 void FileHelper::RestoreWriteOfLibido()
1227 Archive->Restore(0x0028,0x0010);
1228 Archive->Restore(0x0028,0x0011);
1229 Archive->Restore(0x0008,0x0010);
1231 // Restore 'LibIDO-special' entries, if any
1232 Archive->Restore(0x0028,0x0015);
1233 Archive->Restore(0x0028,0x0016);
1234 Archive->Restore(0x0028,0x0017);
1235 Archive->Restore(0x0028,0x00199);
1239 * \brief Duplicates a DataEntry or creates it.
1240 * @param group Group number of the Entry
1241 * @param elem Element number of the Entry
1242 * @param vr Value Representation of the Entry
1243 * \return pointer to the new Bin Entry (NULL when creation failed).
1245 DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem,
1248 DocEntry *oldE = FileInternal->GetDocEntry(group, elem);
1251 if ( oldE && vr != GDCM_VRUNKNOWN )
1252 if ( oldE->GetVR() != vr )
1257 newE = DataEntry::New(group, elem, vr);
1262 newE = GetFile()->NewDataEntry(group, elem, vr);
1269 * \brief This method is called automatically, just before writting
1270 * in order to produce a 'True Dicom V3' image.
1272 * We cannot know *how* the user made the File :
1273 * (reading an old ACR-NEMA file or a not very clean DICOM file ...)
1274 * Just before writting :
1275 * - we check the Entries
1276 * - we create the mandatory entries if they are missing
1277 * - we modify the values if necessary
1278 * - we push the sensitive entries to the Archive
1279 * The writing process will restore the entries as they where before
1280 * entering FileHelper::CheckMandatoryElements, so the user will always
1281 * see the entries just as they were before he decided to write.
1284 * - Entries whose type is 1 are mandatory, with a mandatory value
1285 * - Entries whose type is 1c are mandatory-inside-a-Sequence,
1286 * with a mandatory value
1287 * - Entries whose type is 2 are mandatory, with an optional value
1288 * - Entries whose type is 2c are mandatory-inside-a-Sequence,
1289 * with an optional value
1290 * - Entries whose type is 3 are optional
1293 * - warn the user if we had to add some entries :
1294 * even if a mandatory entry is missing, we add it, with a default value
1295 * (we don't want to give up the writting process if user forgot to
1296 * specify Lena's Patient ID, for instance ...)
1297 * - read the whole PS 3.3 Part of DICOM (890 pages)
1298 * and write a *full* checker (probably one method per Modality ...)
1299 * Any contribution is welcome.
1300 * - write a user callable full checker, to allow post reading
1301 * and/or pre writting image consistency check.
1304 /* -------------------------------------------------------------------------------------
1305 To be moved to User's guide / WIKI ?
1307 We have to deal with 4 *very* different cases :
1308 -1) user created ex nihilo his own image and wants to write it as a Dicom image.
1310 -2) user modified the pixels of an existing image.
1312 -3) user created a new image, using a set of existing images (eg MIP, MPR, cartography image)
1314 -4) user modified/added some tags *without processing* the pixels (anonymization...)
1315 UNMODIFIED_PIXELS_IMAGE
1316 -Probabely some more to be added.
1317 --> Set it with FileHelper::SetContentType(int);
1319 gdcm::FileHelper::CheckMandatoryElements() deals automatically with these cases.
1322 0008 0012 Instance Creation Date
1323 0008 0013 Instance Creation Time
1324 0008 0018 SOP Instance UID
1325 are *always* created with the current values; user has *no* possible intervention on
1328 'Serie Instance UID'(0x0020,0x000e)
1329 'Study Instance UID'(0x0020,0x000d) are kept as is if already exist,
1330 created if it doesn't.
1331 The user is allowed to create his own Series/Studies,
1332 keeping the same 'Serie Instance UID' / 'Study Instance UID' for various images
1334 The user shouldn't add any image to a 'Manufacturer Serie'
1335 but there is no way no to allow him to do that
1337 None of the 'shadow elements' are droped out.
1341 'Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image).
1344 'Media Storage SOP Class UID' (0x0002,0x0002)
1345 'SOP Class UID' (0x0008,0x0016) are set to
1346 [Secondary Capture Image Storage]
1347 'Image Type' (0x0008,0x0008) is forced to "DERIVED\PRIMARY"
1348 Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image)
1351 If 'SOP Class UID' exists in the native image ('true DICOM' image)
1352 we create the 'Source Image Sequence' SeqEntry (0x0008, 0x2112)
1353 --> 'Referenced SOP Class UID' (0x0008, 0x1150)
1354 whose value is the original 'SOP Class UID'
1355 --> 'Referenced SOP Instance UID' (0x0008, 0x1155)
1356 whose value is the original 'SOP Class UID'
1358 3) TO DO : find a trick to allow user to pass to the writter the list of the Dicom images
1359 or the Series, (or the Study ?) he used to created his image
1360 (MIP, MPR, cartography image, ...)
1361 These info should be stored (?)
1362 0008 1110 SQ 1 Referenced Study Sequence
1363 0008 1115 SQ 1 Referenced Series Sequence
1364 0008 1140 SQ 1 Referenced Image Sequence
1366 4) When user *knows* he didn't modified the pixels, we keep some informations unchanged :
1367 'Media Storage SOP Class UID' (0x0002,0x0002)
1368 'SOP Class UID' (0x0008,0x0016)
1369 'Image Type' (0x0008,0x0008)
1370 'Conversion Type' (0x0008,0x0064)
1373 Bellow follows the full description (hope so !) of the consistency checks performed
1374 by gdcm::FileHelper::CheckMandatoryElements()
1377 -->'Media Storage SOP Class UID' (0x0002,0x0002)
1378 -->'SOP Class UID' (0x0008,0x0016) are defaulted to
1379 [Secondary Capture Image Storage]
1380 --> 'Image Type' (0x0008,0x0008)
1381 is forced to "DERIVED\PRIMARY"
1382 (The written image is no longer an 'ORIGINAL' one)
1383 Except if user knows he didn't modify the image (e.g. : he just anonymized the file)
1385 --> Conversion Type (0x0008,0x0064)
1386 is defaulted to 'SYN' (Synthetic Image)
1387 when *he* knows he created his own image ex nihilo
1389 --> 'Modality' (0x0008,0x0060)
1390 is defaulted to "OT" (other) if missing.
1391 (a fully user created image belongs to *no* modality)
1393 --> 'Media Storage SOP Instance UID' (0x0002,0x0003)
1394 --> 'Implementation Class UID' (0x0002,0x0012)
1395 are automatically generated; no user intervention possible
1397 --> 'Serie Instance UID'(0x0020,0x000e)
1398 --> 'Study Instance UID'(0x0020,0x000d) are kept as is if already exist
1399 created if it doesn't.
1400 The user is allowed to create his own Series/Studies,
1401 keeping the same 'Serie Instance UID' / 'Study Instance UID'
1404 The user shouldn't add any image to a 'Manufacturer Serie'
1405 but there is no way no to allowed him to do that
1407 --> If 'SOP Class UID' exists in the native image ('true DICOM' image)
1408 we create the 'Source Image Sequence' SeqEntry (0x0008, 0x2112)
1410 --> 'Referenced SOP Class UID' (0x0008, 0x1150)
1411 whose value is the original 'SOP Class UID'
1412 --> 'Referenced SOP Instance UID' (0x0008, 0x1155)
1413 whose value is the original 'SOP Class UID'
1415 --> Bits Stored, Bits Allocated, Hight Bit Position are checked for consistency
1416 --> Pixel Spacing (0x0028,0x0030) is defaulted to "1.0\1.0"
1417 --> Samples Per Pixel (0x0028,0x0002) is defaulted to 1 (grayscale)
1419 --> Imager Pixel Spacing (0x0018,0x1164) : defaulted to Pixel Spacing value
1421 --> Instance Creation Date, Instance Creation Time are forced to current Date and Time
1423 --> Study Date, Study Time are defaulted to current Date and Time
1424 (they remain unchanged if they exist)
1426 --> Patient Orientation : (0x0020,0x0020), if not present, is deduced from
1427 Image Orientation (Patient) : (0020|0037) or from
1428 Image Orientation (RET) : (0020 0035)
1430 --> Study ID, Series Number, Instance Number, Patient Orientation (Type 2)
1431 are created, with empty value if there are missing.
1433 --> Manufacturer, Institution Name, Patient's Name, (Type 2)
1434 are defaulted with a 'gdcm' value.
1436 --> Patient ID, Patient's Birth Date, Patient's Sex, (Type 2)
1437 --> Referring Physician's Name (Type 2)
1438 are created, with empty value if there are missing.
1440 -------------------------------------------------------------------------------------*/
1442 void FileHelper::CheckMandatoryElements()
1444 std::string sop = Util::CreateUniqueUID();
1446 // --------------------- For Meta Elements ---------------------
1447 // just to remember : 'official' 0002 group
1448 if ( WriteType != ACR && WriteType != ACR_LIBIDO )
1450 // Group 000002 (Meta Elements) already pushed out
1452 //0002 0000 UL 1 Meta Group Length
1453 //0002 0001 OB 1 File Meta Information Version
1454 //0002 0002 UI 1 Media Storage SOP Class UID
1455 //0002 0003 UI 1 Media Storage SOP Instance UID
1456 //0002 0010 UI 1 Transfer Syntax UID
1457 //0002 0012 UI 1 Implementation Class UID
1458 //0002 0013 SH 1 Implementation Version Name
1459 //0002 0016 AE 1 Source Application Entity Title
1460 //0002 0100 UI 1 Private Information Creator
1461 //0002 0102 OB 1 Private Information
1463 // Push out 'ACR-NEMA-special' entries, if any
1464 Archive->Push(0x0008,0x0001); // Length to End
1465 Archive->Push(0x0008,0x0010); // Recognition Code
1466 Archive->Push(0x0028,0x0005); // Image Dimension
1468 // Create them if not found
1469 // Always modify the value
1470 // Push the entries to the archive.
1471 CopyMandatoryEntry(0x0002,0x0000,"0","UL");
1473 DataEntry *e_0002_0001 = CopyDataEntry(0x0002,0x0001, "OB");
1474 e_0002_0001->SetBinArea((uint8_t*)Util::GetFileMetaInformationVersion(),
1476 e_0002_0001->SetLength(2);
1477 Archive->Push(e_0002_0001);
1478 e_0002_0001->Delete();
1480 if ( ContentType == FILTERED_IMAGE || ContentType == UNMODIFIED_PIXELS_IMAGE)
1482 // we keep the original 'Media Storage SOP Class UID', we default it if missing
1483 CheckMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7","UI");
1487 // It's *not* an image comming straight from a source. We force
1488 // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage]
1489 CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7","UI");
1492 // 'Media Storage SOP Instance UID'
1493 CopyMandatoryEntry(0x0002,0x0003,sop,"UI");
1495 // 'Implementation Class UID'
1496 // FIXME : in all examples we have, 0x0002,0x0012 is not so long :
1497 // seems to be Root UID + 4 digits (?)
1498 CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID(),"UI");
1500 // 'Implementation Version Name'
1501 std::string version = "GDCM ";
1502 version += Util::GetVersion();
1503 CopyMandatoryEntry(0x0002,0x0013,version,"SH");
1506 // --------------------- For DataSet ---------------------
1508 if ( ContentType != USER_OWN_IMAGE) // when it's not a user made image
1510 // If 'SOP Class UID' and 'SOP Instance UID' exist ('true DICOM' image)
1511 // we create the 'Source Image Sequence' SeqEntry
1512 // to hold informations about the Source Image
1514 DataEntry *e_0008_0016 = FileInternal->GetDataEntry(0x0008, 0x0016);
1515 DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018);
1516 if ( e_0008_0016 && e_0008_0018)
1518 // Create 'Source Image Sequence' SeqEntry
1519 SeqEntry *sis = SeqEntry::New (0x0008, 0x2112);
1520 SQItem *sqi = SQItem::New(1);
1522 // create 'Referenced SOP Class UID' from 'SOP Class UID'
1524 DataEntry *e_0008_1150 = DataEntry::New(0x0008, 0x1150, "UI");
1525 e_0008_1150->SetString( e_0008_0016->GetString());
1526 sqi->AddEntry(e_0008_1150);
1527 e_0008_1150->Delete();
1529 // create 'Referenced SOP Instance UID' from 'SOP Instance UID'
1530 DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018);
1532 DataEntry *e_0008_1155 = DataEntry::New(0x0008, 0x1155, "UI");
1533 e_0008_1155->SetString( e_0008_0018->GetString());
1534 sqi->AddEntry(e_0008_1155);
1535 e_0008_1155->Delete();
1537 sis->AddSQItem(sqi,1);
1540 // temporarily replaces any previous 'Source Image Sequence'
1543 // FIXME : is 'Image Type' *really* depending on the presence of 'SOP Class UID'?
1544 if ( ContentType == FILTERED_IMAGE)
1545 // the user *knows* he just modified the pixels
1546 // the image is no longer an 'Original' one
1547 CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY","CS");
1551 if ( ContentType == FILTERED_IMAGE || ContentType == UNMODIFIED_PIXELS_IMAGE)
1553 // we keep the original 'Media Storage SOP Class UID', we default it if missing (it should be present !)
1554 CheckMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7","UI");
1558 // It's *not* an image comming straight from a source. We force
1559 // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage]
1560 CopyMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7", "UI");
1563 Archive->Push(0x0028,0x005); // [Image Dimensions (RET)
1564 // Push out 'LibIDO-special' entries, if any
1565 Archive->Push(0x0028,0x0015);
1566 Archive->Push(0x0028,0x0016);
1567 Archive->Push(0x0028,0x0017);
1568 Archive->Push(0x0028,0x0198); // very old versions
1569 Archive->Push(0x0028,0x0199);
1571 // Replace deprecated 0028 0012 US Planes
1572 // by new 0028 0008 IS Number of Frames
1574 ///\todo : find if there is a rule!
1575 DataEntry *e_0028_0012 = FileInternal->GetDataEntry(0x0028, 0x0012);
1578 CopyMandatoryEntry(0x0028, 0x0008,e_0028_0012->GetString(),"IS");
1579 Archive->Push(0x0028,0x0012);
1582 // Deal with the pb of (Bits Stored = 12)
1583 // - we're gonna write the image as Bits Stored = 16
1584 if ( FileInternal->GetEntryString(0x0028,0x0100) == "12")
1586 CopyMandatoryEntry(0x0028,0x0100,"16","US");
1589 // Check if user wasn't drunk ;-)
1591 std::ostringstream s;
1592 // check 'Bits Allocated' vs decent values
1593 int nbBitsAllocated = FileInternal->GetBitsAllocated();
1594 if ( (nbBitsAllocated == 0 || nbBitsAllocated > 32)
1595 || ( nbBitsAllocated > 8 && nbBitsAllocated <16) )
1597 CopyMandatoryEntry(0x0028,0x0100,"16","US");
1598 gdcmWarningMacro("(0028,0100) changed from "
1599 << nbBitsAllocated << " to 16 for consistency purpose");
1600 nbBitsAllocated = 16;
1602 // check 'Bits Stored' vs 'Bits Allocated'
1603 int nbBitsStored = FileInternal->GetBitsStored();
1604 if ( nbBitsStored == 0 || nbBitsStored > nbBitsAllocated )
1607 s << nbBitsAllocated;
1608 CopyMandatoryEntry(0x0028,0x0101,s.str(),"US");
1609 gdcmWarningMacro("(0028,0101) changed from "
1610 << nbBitsStored << " to " << nbBitsAllocated
1611 << " for consistency purpose" );
1612 nbBitsStored = nbBitsAllocated;
1614 // check 'Hight Bit Position' vs 'Bits Allocated' and 'Bits Stored'
1615 int highBitPosition = FileInternal->GetHighBitPosition();
1616 if ( highBitPosition == 0 ||
1617 highBitPosition > nbBitsAllocated-1 ||
1618 highBitPosition < nbBitsStored-1 )
1621 s << nbBitsStored - 1;
1622 CopyMandatoryEntry(0x0028,0x0102,s.str(),"US");
1623 gdcmWarningMacro("(0028,0102) changed from "
1624 << highBitPosition << " to " << nbBitsAllocated-1
1625 << " for consistency purpose");
1628 // check Pixel Representation (default it as 0 -unsigned-)
1630 DataEntry *e_0028_0103 = FileInternal->GetDataEntry(0x0028, 0x0103);
1633 gdcmWarningMacro("PixelRepresentation (0028,0103) is supposed to be mandatory");
1634 CopyMandatoryEntry(0x0028, 0x0103,"0","US");
1638 int sign = (int)e_0028_0103->GetValue(0);
1639 if (sign !=1 && sign !=0)
1641 gdcmWarningMacro("PixelRepresentation (0028,0103) is supposed to be =1 or =0");
1642 CopyMandatoryEntry(0x0028, 0x0103,"0","US");
1646 std::string pixelAspectRatio = FileInternal->GetEntryString(0x0028,0x0034);
1647 if ( pixelAspectRatio == GDCM_UNFOUND ) // avoid conflict with pixelSpacing !
1649 std::string pixelSpacing = FileInternal->GetEntryString(0x0028,0x0030);
1650 if ( pixelSpacing == GDCM_UNFOUND )
1652 pixelSpacing = "1.0\\1.0";
1653 // if missing, Pixel Spacing forced to "1.0\1.0"
1654 CopyMandatoryEntry(0x0028,0x0030,pixelSpacing,"DS");
1657 // 'Imager Pixel Spacing' : defaulted to 'Pixel Spacing'
1658 // --> This one is the *legal* one !
1659 if ( ContentType != USER_OWN_IMAGE)
1660 // we write it only when we are *sure* the image comes from
1661 // an imager (see also 0008,0x0064)
1662 CheckMandatoryEntry(0x0018,0x1164,pixelSpacing,"DS");
1665 ///Exact meaning of RETired fields
1667 // See page 73 of ACR-NEMA_300-1988.pdf !
1669 // 0020,0020 : Patient Orientation :
1670 Patient direction of the first row and
1671 column of the images. The first entry id the direction of the raws, given by the
1672 direction of the last pixel in the first row from the first pixel in tha row.
1673 the second entry is the direction of the columns, given by the direction of the
1674 last pixel in the first column from the first pixel in that column.
1675 L : Left, F : Feet, A : Anterior, P : Posterior.
1676 Up to 3 letters can be used in combination to indicate oblique planes.
1678 //0020,0030 Image Position (RET)
1679 x,y,z coordinates im mm of the first pixel in the image
1681 // 0020,0035 Image Orientation (RET)
1682 Direction cosines of the R axis of the image system with respect to the
1683 equipment coordinate axes x,y,z, followed by direction cosines of the C axis of
1684 the image system with respect to the same axes
1686 //0020,0050 Location
1687 An image location reference, standard for the modality (such as CT bed position),
1688 used to indicate position. Calculation of position for other purposes
1689 is only from (0020,0030) and (0020,0035)
1693 // if imagePositionPatient not found, default it with imagePositionRet, if any
1694 // if imageOrientationPatient not found, default it with imageOrientationRet, if any
1696 std::string imagePositionRet = FileInternal->GetEntryString(0x0020,0x0030);
1697 std::string imageOrientationRet = FileInternal->GetEntryString(0x0020,0x0035);
1698 std::string imagePositionPatient = FileInternal->GetEntryString(0x0020,0x0032);
1699 std::string imageOrientationPatient = FileInternal->GetEntryString(0x0020,0x0037);
1701 if( imagePositionPatient == GDCM_UNFOUND && imageOrientationPatient == GDCM_UNFOUND
1702 && imagePositionRet != GDCM_UNFOUND && imageOrientationRet != GDCM_UNFOUND)
1704 CopyMandatoryEntry(0x0020, 0x0032,imagePositionRet,"DS");
1705 Archive->Push(0x0020,0x0030);
1706 CopyMandatoryEntry(0x0020, 0x0037,imageOrientationRet,"DS");
1707 Archive->Push(0x0020,0x0035);
1711 // Samples Per Pixel (type 1) : default to grayscale
1712 CheckMandatoryEntry(0x0028,0x0002,"1","US");
1714 // --- Check UID-related Entries ---
1716 // At the end, not to overwrite the original ones,
1717 // needed by 'Referenced SOP Instance UID', 'Referenced SOP Class UID'
1718 // 'SOP Instance UID'
1719 CopyMandatoryEntry(0x0008,0x0018,sop,"UI");
1721 if ( ContentType == USER_OWN_IMAGE)
1723 gdcmDebugMacro( "USER_OWN_IMAGE (2)");
1725 // Other possible values are :
1726 // See PS 3.3, Page 408
1728 // DV = Digitized Video
1729 // DI = Digital Interface
1730 // DF = Digitized Film
1731 // WSD = Workstation
1732 // SD = Scanned Document
1733 // SI = Scanned Image
1735 // SYN = Synthetic Image
1737 CheckMandatoryEntry(0x0008,0x0064,"SYN","CS"); // Why not?
1740 if ( ContentType == CREATED_IMAGE)
1742 /// \todo : find a trick to pass the Media Storage SOP Instance UID of the images used to create the current image
1747 // ---- The user will never have to take any action on the following ----
1749 // new value for 'SOP Instance UID'
1750 //SetMandatoryEntry(0x0008,0x0018,Util::CreateUniqueUID());
1752 // Instance Creation Date
1753 const std::string &date = Util::GetCurrentDate();
1754 CopyMandatoryEntry(0x0008,0x0012,date,"DA");
1756 // Instance Creation Time
1757 const std::string &time = Util::GetCurrentTime();
1758 CopyMandatoryEntry(0x0008,0x0013,time,"TM");
1761 CheckMandatoryEntry(0x0008,0x0020,date,"DA");
1763 CheckMandatoryEntry(0x0008,0x0030,time,"TM");
1766 //CopyMandatoryEntry(0x0008,0x0050,"");
1767 CheckMandatoryEntry(0x0008,0x0050,"","SH");
1770 // ----- Add Mandatory Entries if missing ---
1771 // Entries whose type is 1 are mandatory, with a mandatory value
1772 // Entries whose type is 1c are mandatory-inside-a-Sequence,
1773 // with a mandatory value
1774 // Entries whose type is 2 are mandatory, with an optional value
1775 // Entries whose type is 2c are mandatory-inside-a-Sequence,
1776 // with an optional value
1777 // Entries whose type is 3 are optional
1779 // 'Study Instance UID'
1780 // Keep the value if exists
1781 // The user is allowed to create his own Study,
1782 // keeping the same 'Study Instance UID' for various images
1783 // The user may add images to a 'Manufacturer Study',
1784 // adding new Series to an already existing Study
1785 CheckMandatoryEntry(0x0020,0x000d,Util::CreateUniqueUID(),"UI");
1787 // 'Serie Instance UID'
1788 // Keep the value if exists
1789 // The user is allowed to create his own Series,
1790 // keeping the same 'Serie Instance UID' for various images
1791 // The user shouldn't add any image to a 'Manufacturer Serie'
1792 // but there is no way no to prevent him for doing that
1793 CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID(),"UI");
1796 CheckMandatoryEntry(0x0020,0x0010,"","SH");
1799 CheckMandatoryEntry(0x0020,0x0011,"","IS");
1802 CheckMandatoryEntry(0x0020,0x0013,"","IS");
1804 // Patient Orientation
1805 // Can be computed from (0020|0037) : Image Orientation (Patient)
1806 GDCM_NAME_SPACE::Orientation *o = GDCM_NAME_SPACE::Orientation::New();
1807 std::string ori = o->GetOrientation ( FileInternal );
1809 if (ori != "\\" && ori != GDCM_UNFOUND)
1810 CheckMandatoryEntry(0x0020,0x0020,ori,"CS");
1812 CheckMandatoryEntry(0x0020,0x0020,"","CS");
1814 // Default Patient Position to HFS
1815 CheckMandatoryEntry(0x0018,0x5100,"HFS","CS");
1817 // Modality : if missing we set it to 'OTher'
1818 CheckMandatoryEntry(0x0008,0x0060,"OT","CS");
1820 // Manufacturer : if missing we set it to 'GDCM Factory'
1821 CheckMandatoryEntry(0x0008,0x0070,"GDCM Factory","LO");
1823 // Institution Name : if missing we set it to 'GDCM Hospital'
1824 CheckMandatoryEntry(0x0008,0x0080,"GDCM Hospital","LO");
1826 // Patient's Name : if missing, we set it to 'GDCM^Patient'
1827 CheckMandatoryEntry(0x0010,0x0010,"GDCM^Patient","PN");
1829 // Patient ID : some clinical softwares *demand* it although it's a 'type 2' entry.
1830 CheckMandatoryEntry(0x0010,0x0020,"gdcm ID","LO");
1832 // Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory
1833 CheckMandatoryEntry(0x0010,0x0030,"","DA");
1835 // Patient's Sex :'type 2' entry -> must exist, value not mandatory
1836 CheckMandatoryEntry(0x0010,0x0040,"","CS");
1838 // Referring Physician's Name :'type 2' entry -> must exist, value not mandatory
1839 CheckMandatoryEntry(0x0008,0x0090,"","PN");
1842 // Deal with element 0x0000 (group length) of each group.
1843 // First stage : get all the different Groups
1846 DocEntry *d = FileInternal->GetFirstEntry();
1849 grHT[d->GetGroup()] = 0;
1850 d=FileInternal->GetNextEntry();
1852 // Second stage : add the missing ones (if any)
1853 for (GroupHT::iterator it = grHT.begin(); it != grHT.end(); ++it)
1855 CheckMandatoryEntry(it->first, 0x0000, "0");
1857 // Third stage : update all 'zero level' groups length
1861 if (PhotometricInterpretation == 1)
1866 void FileHelper::CheckMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr )
1868 DataEntry *entry = FileInternal->GetDataEntry(group,elem);
1871 //entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
1872 entry = DataEntry::New(group,elem,vr);
1873 entry->SetString(value);
1874 Archive->Push(entry);
1879 /// \todo : what is it used for ? (FileHelper::SetMandatoryEntry)
1880 void FileHelper::SetMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr)
1882 //DataEntry *entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
1883 DataEntry *entry = DataEntry::New(group,elem,vr);
1884 entry->SetString(value);
1885 Archive->Push(entry);
1889 void FileHelper::CopyMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr)
1891 DataEntry *entry = CopyDataEntry(group,elem,vr);
1892 entry->SetString(value);
1893 Archive->Push(entry);
1898 * \brief Restore in the File the initial group 0002
1900 void FileHelper::RestoreWriteMandatory()
1902 // group 0002 may be pushed out for ACR-NEMA writting purposes
1903 Archive->Restore(0x0002,0x0000);
1904 Archive->Restore(0x0002,0x0001);
1905 Archive->Restore(0x0002,0x0002);
1906 Archive->Restore(0x0002,0x0003);
1907 Archive->Restore(0x0002,0x0010);
1908 Archive->Restore(0x0002,0x0012);
1909 Archive->Restore(0x0002,0x0013);
1910 Archive->Restore(0x0002,0x0016);
1911 Archive->Restore(0x0002,0x0100);
1912 Archive->Restore(0x0002,0x0102);
1914 // FIXME : Check if none is missing !
1916 Archive->Restore(0x0008,0x0012);
1917 Archive->Restore(0x0008,0x0013);
1918 Archive->Restore(0x0008,0x0016);
1919 Archive->Restore(0x0008,0x0018);
1920 Archive->Restore(0x0008,0x0060);
1921 Archive->Restore(0x0008,0x0070);
1922 Archive->Restore(0x0008,0x0080);
1923 Archive->Restore(0x0008,0x0090);
1924 Archive->Restore(0x0008,0x2112);
1926 Archive->Restore(0x0010,0x0010);
1927 Archive->Restore(0x0010,0x0030);
1928 Archive->Restore(0x0010,0x0040);
1930 Archive->Restore(0x0020,0x000d);
1931 Archive->Restore(0x0020,0x000e);
1935 * \brief CallStartMethod
1937 void FileHelper::CallStartMethod()
1941 CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS);
1945 * \brief CallProgressMethod
1947 void FileHelper::CallProgressMethod()
1949 CommandManager::ExecuteCommand(this,CMD_PROGRESS);
1953 * \brief CallEndMethod
1955 void FileHelper::CallEndMethod()
1958 CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS);
1961 //-----------------------------------------------------------------------------
1964 * \brief Factorization for various forms of constructors.
1966 void FileHelper::Initialize()
1969 ContentType = USER_OWN_IMAGE;
1971 WriteMode = WMODE_RAW;
1972 WriteType = ExplicitVR;
1974 PhotometricInterpretation = 2; // Black = 0
1976 PixelReadConverter = new PixelReadConvert;
1977 PixelWriteConverter = new PixelWriteConvert;
1978 Archive = new DocEntryArchive( FileInternal );
1980 KeepOverlays = false;
1984 * \brief Reads/[decompresses] the pixels,
1985 * *without* making RGB from Palette Colors
1986 * @return the pixels area, whatever its type
1987 * (uint8_t is just for prototyping : feel free to Cast it)
1989 uint8_t *FileHelper::GetRaw()
1991 PixelReadConverter->SetUserFunction( UserFunction );
1993 uint8_t *raw = PixelReadConverter->GetRaw();
1996 // The Raw image migth not be loaded yet:
1997 std::ifstream *fp = FileInternal->OpenFile();
1998 PixelReadConverter->ReadAndDecompressPixelData( fp );
2000 FileInternal->CloseFile();
2002 raw = PixelReadConverter->GetRaw();
2005 gdcmWarningMacro( "Read/decompress of pixel data apparently went wrong.");
2013 * \brief Deal with Grey levels i.e. re-arange them
2014 * to have low values = dark, high values = bright
2016 void FileHelper::ConvertFixGreyLevels(uint8_t *raw, size_t rawSize)
2018 uint32_t i; // to please M$VC6
2021 // Number of Bits Allocated for storing a Pixel is defaulted to 16
2022 // when absent from the file.
2023 int bitsAllocated = FileInternal->GetBitsAllocated();
2024 if ( bitsAllocated == 0 )
2029 else if (bitsAllocated > 8 && bitsAllocated < 16 && bitsAllocated != 12)
2033 // Number of "Bits Stored", defaulted to number of "Bits Allocated"
2034 // when absent from the file.
2035 int bitsStored = FileInternal->GetBitsStored();
2036 if ( bitsStored == 0 )
2038 bitsStored = bitsAllocated;
2041 if (!FileInternal->IsSignedPixelData())
2043 if ( bitsAllocated == 8 )
2045 uint8_t *deb = (uint8_t *)raw;
2046 for (i=0; i<rawSize; i++)
2054 if ( bitsAllocated == 16 )
2057 for (j=0; j<bitsStored-1; j++)
2059 mask = (mask << 1) +1; // will be fff when BitsStored=12
2062 uint16_t *deb = (uint16_t *)raw;
2063 for (i=0; i<rawSize/2; i++)
2073 if ( bitsAllocated == 8 )
2075 uint8_t smask8 = 255;
2076 uint8_t *deb = (uint8_t *)raw;
2077 for (i=0; i<rawSize; i++)
2079 *deb = smask8 - *deb;
2084 if ( bitsAllocated == 16 )
2086 uint16_t smask16 = 65535;
2087 uint16_t *deb = (uint16_t *)raw;
2088 for (i=0; i<rawSize/2; i++)
2090 *deb = smask16 - *deb;
2098 //-----------------------------------------------------------------------------
2100 * \brief Prints the FileInternal + info on PixelReadConvertor
2101 * @param os ostream we want to print in
2102 * @param indent (unused)
2104 void FileHelper::Print(std::ostream &os, std::string const &)
2106 FileInternal->SetPrintLevel(PrintLevel);
2107 FileInternal->Print(os);
2109 if ( FileInternal->IsReadable() )
2111 PixelReadConverter->SetPrintLevel(PrintLevel);
2112 PixelReadConverter->Print(os);
2116 //-----------------------------------------------------------------------------
2117 } // end namespace gdcm
2120 /* Probabely something to be added to use Rescale Slope/Intercept
2121 Have a look at ITK code !
2123 // Internal function to rescale pixel according to Rescale Slope/Intercept
2124 template<class TBuffer, class TSource>
2125 void RescaleFunction(TBuffer* buffer, TSource *source,
2126 double slope, double intercept, size_t size)
2128 size /= sizeof(TSource);
2130 if (slope != 1.0 && intercept != 0.0)
2132 // Duff's device. Instead of this code:
2134 // for(unsigned int i=0; i<size; i++)
2136 // buffer[i] = (TBuffer)(source[i]*slope + intercept);
2139 // use Duff's device which exploits "fall through"
2140 register size_t n = (size + 7) / 8;
2143 case 0: do { *buffer++ = (TBuffer)((*source++)*slope + intercept);
2144 case 7: *buffer++ = (TBuffer)((*source++)*slope + intercept);
2145 case 6: *buffer++ = (TBuffer)((*source++)*slope + intercept);
2146 case 5: *buffer++ = (TBuffer)((*source++)*slope + intercept);
2147 case 4: *buffer++ = (TBuffer)((*source++)*slope + intercept);
2148 case 3: *buffer++ = (TBuffer)((*source++)*slope + intercept);
2149 case 2: *buffer++ = (TBuffer)((*source++)*slope + intercept);
2150 case 1: *buffer++ = (TBuffer)((*source++)*slope + intercept);
2154 else if (slope == 1.0 && intercept != 0.0)
2156 // Duff's device. Instead of this code:
2158 // for(unsigned int i=0; i<size; i++)
2160 // buffer[i] = (TBuffer)(source[i] + intercept);
2163 // use Duff's device which exploits "fall through"
2164 register size_t n = (size + 7) / 8;
2167 case 0: do { *buffer++ = (TBuffer)(*source++ + intercept);
2168 case 7: *buffer++ = (TBuffer)(*source++ + intercept);
2169 case 6: *buffer++ = (TBuffer)(*source++ + intercept);
2170 case 5: *buffer++ = (TBuffer)(*source++ + intercept);
2171 case 4: *buffer++ = (TBuffer)(*source++ + intercept);
2172 case 3: *buffer++ = (TBuffer)(*source++ + intercept);
2173 case 2: *buffer++ = (TBuffer)(*source++ + intercept);
2174 case 1: *buffer++ = (TBuffer)(*source++ + intercept);
2178 else if (slope != 1.0 && intercept == 0.0)
2180 // Duff's device. Instead of this code:
2182 // for(unsigned int i=0; i<size; i++)
2184 // buffer[i] = (TBuffer)(source[i]*slope);
2187 // use Duff's device which exploits "fall through"
2188 register size_t n = (size + 7) / 8;
2191 case 0: do { *buffer++ = (TBuffer)((*source++)*slope);
2192 case 7: *buffer++ = (TBuffer)((*source++)*slope);
2193 case 6: *buffer++ = (TBuffer)((*source++)*slope);
2194 case 5: *buffer++ = (TBuffer)((*source++)*slope);
2195 case 4: *buffer++ = (TBuffer)((*source++)*slope);
2196 case 3: *buffer++ = (TBuffer)((*source++)*slope);
2197 case 2: *buffer++ = (TBuffer)((*source++)*slope);
2198 case 1: *buffer++ = (TBuffer)((*source++)*slope);
2204 // Duff's device. Instead of this code:
2206 // for(unsigned int i=0; i<size; i++)
2208 // buffer[i] = (TBuffer)(source[i]);
2211 // use Duff's device which exploits "fall through"
2212 register size_t n = (size + 7) / 8;
2215 case 0: do { *buffer++ = (TBuffer)(*source++);
2216 case 7: *buffer++ = (TBuffer)(*source++);
2217 case 6: *buffer++ = (TBuffer)(*source++);
2218 case 5: *buffer++ = (TBuffer)(*source++);
2219 case 4: *buffer++ = (TBuffer)(*source++);
2220 case 3: *buffer++ = (TBuffer)(*source++);
2221 case 2: *buffer++ = (TBuffer)(*source++);
2222 case 1: *buffer++ = (TBuffer)(*source++);
2229 template<class TSource>
2230 void RescaleFunction(ImageIOBase::IOComponentType bufferType,
2231 void* buffer, TSource *source,
2232 double slope, double intercept, size_t size)
2236 case ImageIOBase::UCHAR:
2237 RescaleFunction( (unsigned char *)buffer, source, slope, intercept, size);
2239 case ImageIOBase::CHAR:
2240 RescaleFunction( (char *)buffer, source, slope, intercept, size);
2242 case ImageIOBase::USHORT:
2243 RescaleFunction( (unsigned short *)buffer, source, slope, intercept,size);
2245 case ImageIOBase::SHORT:
2246 RescaleFunction( (short *)buffer, source, slope, intercept, size);
2248 case ImageIOBase::UINT:
2249 RescaleFunction( (unsigned int *)buffer, source, slope, intercept, size);
2251 case ImageIOBase::INT:
2252 RescaleFunction( (int *)buffer, source, slope, intercept, size);
2254 case ImageIOBase::FLOAT:
2255 RescaleFunction( (float *)buffer, source, slope, intercept, size);
2257 case ImageIOBase::DOUBLE:
2258 RescaleFunction( (double *)buffer, source, slope, intercept, size);
2261 ::itk::OStringStream message;
2262 message << "itk::ERROR: GDCMImageIO: Unknown component type : " << bufferType;
2263 ::itk::ExceptionObject e(__FILE__, __LINE__, message.str().c_str(),ITK_LOCATION);