1 /*=========================================================================
4 Module: $RCSfile: gdcmFileHelper.cxx,v $
7 Date: $Date: 2007/09/17 12:16:02 $
8 Version: $Revision: 1.129 $
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 !
735 SetWriteFileTypeToImplicitVR();
738 case Unknown: // should never happen; ExplicitVR is the default value
741 // We let DocEntry::WriteContent to put vr=UN for undocumented Shadow Groups !
742 SetWriteFileTypeToExplicitVR();
747 // NOTHING is done here just for LibIDO.
748 // Just to avoid further trouble if user creates a file ex-nihilo,
749 // wants to write it as an ACR-NEMA file,
750 // and forgets to create any Entry belonging to group 0008
752 // We add Recognition Code (RET)
753 if ( ! FileInternal->GetDataEntry(0x0008, 0x0010) )
754 FileInternal->InsertEntryString("ACR-NEMA V1.0 ",
755 0x0008, 0x0010, "LO");
756 SetWriteFileTypeToACR();
757 // SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR !
760 /// \todo FIXME : JPEG/JPEG2000 may be either ExplicitVR or ImplicitVR
762 SetWriteFileTypeToJPEG();
764 //PixelWriteConverter->SetCompressJPEGUserData(
765 // inData, expectedSize, FileInternal);
766 PixelWriteConverter->SetCompressJPEGUserData(
767 PixelWriteConverter->GetUserData(),
768 PixelWriteConverter->GetUserDataSize(),FileInternal);
772 /// \todo Maybe we should consider doing the compression here !
773 // PixelWriteConverter->SetCompressJPEG2000UserData(inData, expectedSize, FileInternal);
775 SetWriteFileTypeToJPEG2000();
776 PixelWriteConverter->SetCompressJPEG2000UserData(
777 PixelWriteConverter->GetUserData(),
778 PixelWriteConverter->GetUserDataSize(),
783 // --------------------------------------------------------------
784 // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
786 // if recognition code tells us we dealt with a LibIDO image
787 // we reproduce on disk the switch between lineNumber and columnNumber
788 // just before writting ...
789 /// \todo the best trick would be *change* the recognition code
790 /// but pb expected if user deals with, e.g. COMPLEX images
792 if ( WriteType == ACR_LIBIDO )
798 SetWriteToNoLibido();
800 // ----------------- End of Special Patch ----------------
805 SetWriteToRaw(); // modifies and pushes to the archive, when necessary
808 SetWriteToRGB(); // modifies and pushes to the archive, when necessary
813 if (WriteType == JPEG || WriteType == JPEG2000)
816 check = CheckWriteIntegrity(); // verifies length
820 check = FileInternal->Write(fileName,WriteType);
824 // RestoreWriteFileType();
825 // RestoreWriteMandatory();
827 // --------------------------------------------------------------
828 // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
830 // ...and we restore the header to be Dicom Compliant again
831 // just after writting
832 RestoreWriteOfLibido();
833 // ----------------- End of Special Patch ----------------
838 //-----------------------------------------------------------------------------
841 * \brief Verifies the size of the user given PixelData
842 * @return true if check is successfull
844 bool FileHelper::CheckWriteIntegrity()
846 if ( PixelWriteConverter->GetUserData() )
848 int numberBitsAllocated = FileInternal->GetBitsAllocated();
849 if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
851 gdcmWarningMacro( "numberBitsAllocated changed from "
852 << numberBitsAllocated << " to 16 "
853 << " for consistency purpose" );
854 numberBitsAllocated = 16;
857 size_t decSize = FileInternal->GetXSize()
858 * FileInternal->GetYSize()
859 * FileInternal->GetZSize()
860 * FileInternal->GetTSize()
861 * FileInternal->GetSamplesPerPixel()
862 * ( numberBitsAllocated / 8 );
863 size_t rgbSize = decSize;
864 if ( FileInternal->HasLUT() )
865 rgbSize = decSize * 3;
867 size_t userDataSize = PixelWriteConverter->GetUserDataSize();
871 if ( abs((long)(decSize-userDataSize))>1) // ignore padding zero
873 gdcmWarningMacro( "Data size (Raw) is incorrect. Should be "
874 << decSize << " / Found :"
880 if ( abs((long)(rgbSize-userDataSize))>1) // ignore padding zero
882 gdcmWarningMacro( "Data size (RGB) is incorrect. Should be "
883 << rgbSize << " / Found "
894 * \brief Updates the File to write RAW data (as opposed to RGB data)
895 * (modifies, when necessary, photochromatic interpretation,
896 * bits allocated, Pixels element VR)
897 * WARNING : if SetPhotometricInterpretationToMonochrome1() was called
898 * before Pixel Elements is modified :-(
900 void FileHelper::SetWriteToRaw()
902 if ( FileInternal->GetNumberOfScalarComponents() == 3
903 && !FileInternal->HasLUT() )
909 // 0x0028,0x0004 : Photometric Interpretation
910 DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS");
911 if (FileInternal->HasLUT() )
913 photInt->SetString("PALETTE COLOR ");
917 if (GetPhotometricInterpretation() == 2)
918 photInt->SetString("MONOCHROME2 "); // 0 = Black
920 photInt->SetString("MONOCHROME1 "); // 0 = White !
923 PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
924 PixelReadConverter->GetRawSize());
926 std::string vr = "OB";
927 if ( FileInternal->GetBitsAllocated()>8 )
929 if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files
931 // For non RAW data. Mainly JPEG/JPEG2000
932 if( WriteType == JPEG || WriteType == JPEG2000)
938 CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr);
939 pixel->SetFlag(DataEntry::FLAG_PIXELDATA);
940 pixel->SetBinArea(PixelWriteConverter->GetData(),false);
942 static_cast< uint32_t >(PixelWriteConverter->GetDataSize()) );
944 if (!FileInternal->HasLUT() && GetPhotometricInterpretation() == 1)
946 ConvertFixGreyLevels( pixel->GetBinArea(), pixel->GetLength() );
949 Archive->Push(photInt);
950 Archive->Push(pixel);
958 * \brief Updates the File to write RGB data (as opposed to RAW data)
959 * (modifies, when necessary, photochromatic interpretation,
960 * samples per pixel, Planar configuration,
961 * bits allocated, bits stored, high bit -ACR 24 bits-
962 * Pixels element VR, pushes out the LUT, )
964 void FileHelper::SetWriteToRGB()
966 if ( FileInternal->GetNumberOfScalarComponents()==3 )
968 PixelReadConverter->BuildRGBImage();
970 DataEntry *spp = CopyDataEntry(0x0028,0x0002,"US");
971 spp->SetString("3 "); // Don't drop trailing space
973 DataEntry *planConfig = CopyDataEntry(0x0028,0x0006,"US");
974 planConfig->SetString("0 "); // Don't drop trailing space
976 DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS");
977 photInt->SetString("RGB "); // Don't drop trailing space
979 if ( PixelReadConverter->GetRGB() )
981 PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(),
982 PixelReadConverter->GetRGBSize());
986 PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
987 PixelReadConverter->GetRawSize());
990 std::string vr = "OB";
991 if ( FileInternal->GetBitsAllocated()>8 )
993 if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files
996 CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr);
997 pixel->SetFlag(DataEntry::FLAG_PIXELDATA);
998 pixel->SetBinArea(PixelWriteConverter->GetData(),false);
999 pixel->SetLength(PixelWriteConverter->GetDataSize());
1002 Archive->Push(planConfig);
1003 Archive->Push(photInt);
1004 Archive->Push(pixel);
1007 planConfig->Delete();
1012 Archive->Push(0x0028,0x1101);
1013 Archive->Push(0x0028,0x1102);
1014 Archive->Push(0x0028,0x1103);
1015 Archive->Push(0x0028,0x1201);
1016 Archive->Push(0x0028,0x1202);
1017 Archive->Push(0x0028,0x1203);
1019 // push out Palette Color Lookup Table UID, if any
1020 Archive->Push(0x0028,0x1199);
1022 // For old '24 Bits' ACR-NEMA
1023 // Thus, we have a RGB image and the bits allocated = 24 and
1024 // samples per pixels = 1 (in the read file)
1025 if ( FileInternal->GetBitsAllocated()==24 )
1027 DataEntry *bitsAlloc = CopyDataEntry(0x0028,0x0100,"US");
1028 bitsAlloc->SetString("8 ");
1030 DataEntry *bitsStored = CopyDataEntry(0x0028,0x0101,"US");
1031 bitsStored->SetString("8 ");
1033 DataEntry *highBit = CopyDataEntry(0x0028,0x0102,"US");
1034 highBit->SetString("7 ");
1036 Archive->Push(bitsAlloc);
1037 Archive->Push(bitsStored);
1038 Archive->Push(highBit);
1040 bitsAlloc->Delete();
1041 bitsStored->Delete();
1052 * \brief Restore the File write mode
1054 void FileHelper::RestoreWrite()
1056 Archive->Restore(0x0028,0x0002);
1057 Archive->Restore(0x0028,0x0004);
1059 Archive->Restore(0x0028,0x0006);
1060 Archive->Restore(GetFile()->GetGrPixel(),GetFile()->GetNumPixel());
1062 // For old ACR-NEMA (24 bits problem)
1063 Archive->Restore(0x0028,0x0100);
1064 Archive->Restore(0x0028,0x0101);
1065 Archive->Restore(0x0028,0x0102);
1068 Archive->Restore(0x0028,0x1101);
1069 Archive->Restore(0x0028,0x1102);
1070 Archive->Restore(0x0028,0x1103);
1071 Archive->Restore(0x0028,0x1201);
1072 Archive->Restore(0x0028,0x1202);
1073 Archive->Restore(0x0028,0x1203);
1075 // For the Palette Color Lookup Table UID
1076 Archive->Restore(0x0028,0x1203);
1078 // group 0002 may be pushed out for ACR-NEMA writting purposes
1079 Archive->Restore(0x0002,0x0000);
1080 Archive->Restore(0x0002,0x0001);
1081 Archive->Restore(0x0002,0x0002);
1082 Archive->Restore(0x0002,0x0003);
1083 Archive->Restore(0x0002,0x0010);
1084 Archive->Restore(0x0002,0x0012);
1085 Archive->Restore(0x0002,0x0013);
1086 Archive->Restore(0x0002,0x0016);
1087 Archive->Restore(0x0002,0x0100);
1088 Archive->Restore(0x0002,0x0102);
1093 * \brief Pushes out the whole group 0002
1094 * FIXME : better, set a flag to tell the writer not to write it ...
1095 * FIXME : method should probably have an other name !
1096 * SetWriteFileTypeToACR is NOT opposed to
1097 * SetWriteFileTypeToExplicitVR and SetWriteFileTypeToImplicitVR
1099 void FileHelper::SetWriteFileTypeToACR()
1101 Archive->Push(0x0002,0x0000);
1102 Archive->Push(0x0002,0x0001);
1103 Archive->Push(0x0002,0x0002);
1104 Archive->Push(0x0002,0x0003);
1105 Archive->Push(0x0002,0x0010);
1106 Archive->Push(0x0002,0x0012);
1107 Archive->Push(0x0002,0x0013);
1108 Archive->Push(0x0002,0x0016);
1109 Archive->Push(0x0002,0x0100);
1110 Archive->Push(0x0002,0x0102);
1114 * \brief Sets in the File the TransferSyntax to 'JPEG2000'
1116 void FileHelper::SetWriteFileTypeToJPEG2000()
1118 std::string ts = Util::DicomString(
1119 Global::GetTS()->GetSpecialTransferSyntax(TS::JPEG2000Lossless) );
1121 DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
1129 * \brief Sets in the File the TransferSyntax to 'JPEG'
1131 void FileHelper::SetWriteFileTypeToJPEG()
1133 std::string ts = Util::DicomString(
1134 Global::GetTS()->GetSpecialTransferSyntax(TS::JPEGLosslessProcess14_1) );
1136 DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
1144 * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian"
1146 void FileHelper::SetWriteFileTypeToExplicitVR()
1148 std::string ts = Util::DicomString(
1149 Global::GetTS()->GetSpecialTransferSyntax(TS::ExplicitVRLittleEndian) );
1151 DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
1158 * \brief Sets in the File the TransferSyntax to 'Implicit VR Little Endian"
1160 void FileHelper::SetWriteFileTypeToImplicitVR()
1162 std::string ts = Util::DicomString(
1163 Global::GetTS()->GetSpecialTransferSyntax(TS::ImplicitVRLittleEndian) );
1165 DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
1172 * \brief Set the Write not to Libido format
1174 void FileHelper::SetWriteToLibido()
1176 DataEntry *oldRow = FileInternal->GetDataEntry(0x0028, 0x0010);
1177 DataEntry *oldCol = FileInternal->GetDataEntry(0x0028, 0x0011);
1179 if ( oldRow && oldCol )
1181 std::string rows, columns;
1183 DataEntry *newRow=DataEntry::New(0x0028, 0x0010, "US");
1184 DataEntry *newCol=DataEntry::New(0x0028, 0x0011, "US");
1186 newRow->Copy(oldCol);
1187 newCol->Copy(oldRow);
1189 newRow->SetString(oldCol->GetString());
1190 newCol->SetString(oldRow->GetString());
1192 Archive->Push(newRow);
1193 Archive->Push(newCol);
1199 DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010,"LO");
1200 libidoCode->SetString("ACRNEMA_LIBIDO_1.1");
1201 Archive->Push(libidoCode);
1202 libidoCode->Delete();
1206 * \brief Set the Write not to No Libido format
1208 void FileHelper::SetWriteToNoLibido()
1210 DataEntry *recCode = FileInternal->GetDataEntry(0x0008,0x0010);
1213 if ( recCode->GetString() == "ACRNEMA_LIBIDO_1.1" )
1215 DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010,"LO");
1216 libidoCode->SetString("");
1217 Archive->Push(libidoCode);
1218 libidoCode->Delete();
1224 * \brief Restore the Write format
1226 void FileHelper::RestoreWriteOfLibido()
1228 Archive->Restore(0x0028,0x0010);
1229 Archive->Restore(0x0028,0x0011);
1230 Archive->Restore(0x0008,0x0010);
1232 // Restore 'LibIDO-special' entries, if any
1233 Archive->Restore(0x0028,0x0015);
1234 Archive->Restore(0x0028,0x0016);
1235 Archive->Restore(0x0028,0x0017);
1236 Archive->Restore(0x0028,0x00199);
1240 * \brief Duplicates a DataEntry or creates it.
1241 * @param group Group number of the Entry
1242 * @param elem Element number of the Entry
1243 * @param vr Value Representation of the Entry
1244 * \return pointer to the new Bin Entry (NULL when creation failed).
1246 DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem,
1249 DocEntry *oldE = FileInternal->GetDocEntry(group, elem);
1252 if ( oldE && vr != GDCM_VRUNKNOWN )
1253 if ( oldE->GetVR() != vr )
1258 newE = DataEntry::New(group, elem, vr);
1263 newE = GetFile()->NewDataEntry(group, elem, vr);
1270 * \brief This method is called automatically, just before writting
1271 * in order to produce a 'True Dicom V3' image.
1273 * We cannot know *how* the user made the File :
1274 * (reading an old ACR-NEMA file or a not very clean DICOM file ...)
1275 * Just before writting :
1276 * - we check the Entries
1277 * - we create the mandatory entries if they are missing
1278 * - we modify the values if necessary
1279 * - we push the sensitive entries to the Archive
1280 * The writing process will restore the entries as they where before
1281 * entering FileHelper::CheckMandatoryElements, so the user will always
1282 * see the entries just as they were before he decided to write.
1285 * - Entries whose type is 1 are mandatory, with a mandatory value
1286 * - Entries whose type is 1c are mandatory-inside-a-Sequence,
1287 * with a mandatory value
1288 * - Entries whose type is 2 are mandatory, with an optional value
1289 * - Entries whose type is 2c are mandatory-inside-a-Sequence,
1290 * with an optional value
1291 * - Entries whose type is 3 are optional
1294 * - warn the user if we had to add some entries :
1295 * even if a mandatory entry is missing, we add it, with a default value
1296 * (we don't want to give up the writting process if user forgot to
1297 * specify Lena's Patient ID, for instance ...)
1298 * - read the whole PS 3.3 Part of DICOM (890 pages)
1299 * and write a *full* checker (probably one method per Modality ...)
1300 * Any contribution is welcome.
1301 * - write a user callable full checker, to allow post reading
1302 * and/or pre writting image consistency check.
1305 /* -------------------------------------------------------------------------------------
1306 To be moved to User's guide / WIKI ?
1308 We have to deal with 4 *very* different cases :
1309 -1) user created ex nihilo his own image and wants to write it as a Dicom image.
1311 -2) user modified the pixels of an existing image.
1313 -3) user created a new image, using a set of existing images (eg MIP, MPR, cartography image)
1315 -4) user modified/added some tags *without processing* the pixels (anonymization...)
1316 UNMODIFIED_PIXELS_IMAGE
1317 -Probabely some more to be added.
1318 --> Set it with FileHelper::SetContentType(int);
1320 gdcm::FileHelper::CheckMandatoryElements() deals automatically with these cases.
1323 0008 0012 Instance Creation Date
1324 0008 0013 Instance Creation Time
1325 0008 0018 SOP Instance UID
1326 are *always* created with the current values; user has *no* possible intervention on
1329 'Serie Instance UID'(0x0020,0x000e)
1330 'Study Instance UID'(0x0020,0x000d) are kept as is if already exist,
1331 created if it doesn't.
1332 The user is allowed to create his own Series/Studies,
1333 keeping the same 'Serie Instance UID' / 'Study Instance UID' for various images
1335 The user shouldn't add any image to a 'Manufacturer Serie'
1336 but there is no way no to allow him to do that
1338 None of the 'shadow elements' are droped out.
1342 'Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image).
1345 'Media Storage SOP Class UID' (0x0002,0x0002)
1346 'SOP Class UID' (0x0008,0x0016) are set to
1347 [Secondary Capture Image Storage]
1348 'Image Type' (0x0008,0x0008) is forced to "DERIVED\PRIMARY"
1349 Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image)
1352 If 'SOP Class UID' exists in the native image ('true DICOM' image)
1353 we create the 'Source Image Sequence' SeqEntry (0x0008, 0x2112)
1354 --> 'Referenced SOP Class UID' (0x0008, 0x1150)
1355 whose value is the original 'SOP Class UID'
1356 --> 'Referenced SOP Instance UID' (0x0008, 0x1155)
1357 whose value is the original 'SOP Class UID'
1359 3) TO DO : find a trick to allow user to pass to the writter the list of the Dicom images
1360 or the Series, (or the Study ?) he used to created his image
1361 (MIP, MPR, cartography image, ...)
1362 These info should be stored (?)
1363 0008 1110 SQ 1 Referenced Study Sequence
1364 0008 1115 SQ 1 Referenced Series Sequence
1365 0008 1140 SQ 1 Referenced Image Sequence
1367 4) When user *knows* he didn't modified the pixels, we keep some informations unchanged :
1368 'Media Storage SOP Class UID' (0x0002,0x0002)
1369 'SOP Class UID' (0x0008,0x0016)
1370 'Image Type' (0x0008,0x0008)
1371 'Conversion Type' (0x0008,0x0064)
1374 Bellow follows the full description (hope so !) of the consistency checks performed
1375 by gdcm::FileHelper::CheckMandatoryElements()
1378 -->'Media Storage SOP Class UID' (0x0002,0x0002)
1379 -->'SOP Class UID' (0x0008,0x0016) are defaulted to
1380 [Secondary Capture Image Storage]
1381 --> 'Image Type' (0x0008,0x0008)
1382 is forced to "DERIVED\PRIMARY"
1383 (The written image is no longer an 'ORIGINAL' one)
1384 Except if user knows he didn't modify the image (e.g. : he just anonymized the file)
1386 --> Conversion Type (0x0008,0x0064)
1387 is defaulted to 'SYN' (Synthetic Image)
1388 when *he* knows he created his own image ex nihilo
1390 --> 'Modality' (0x0008,0x0060)
1391 is defaulted to "OT" (other) if missing.
1392 (a fully user created image belongs to *no* modality)
1394 --> 'Media Storage SOP Instance UID' (0x0002,0x0003)
1395 --> 'Implementation Class UID' (0x0002,0x0012)
1396 are automatically generated; no user intervention possible
1398 --> 'Serie Instance UID'(0x0020,0x000e)
1399 --> 'Study Instance UID'(0x0020,0x000d) are kept as is if already exist
1400 created if it doesn't.
1401 The user is allowed to create his own Series/Studies,
1402 keeping the same 'Serie Instance UID' / 'Study Instance UID'
1405 The user shouldn't add any image to a 'Manufacturer Serie'
1406 but there is no way no to allowed him to do that
1408 --> If 'SOP Class UID' exists in the native image ('true DICOM' image)
1409 we create the 'Source Image Sequence' SeqEntry (0x0008, 0x2112)
1411 --> 'Referenced SOP Class UID' (0x0008, 0x1150)
1412 whose value is the original 'SOP Class UID'
1413 --> 'Referenced SOP Instance UID' (0x0008, 0x1155)
1414 whose value is the original 'SOP Class UID'
1416 --> Bits Stored, Bits Allocated, Hight Bit Position are checked for consistency
1417 --> Pixel Spacing (0x0028,0x0030) is defaulted to "1.0\1.0"
1418 --> Samples Per Pixel (0x0028,0x0002) is defaulted to 1 (grayscale)
1420 --> Imager Pixel Spacing (0x0018,0x1164) : defaulted to Pixel Spacing value
1422 --> Instance Creation Date, Instance Creation Time are forced to current Date and Time
1424 --> Study Date, Study Time are defaulted to current Date and Time
1425 (they remain unchanged if they exist)
1427 --> Patient Orientation : (0x0020,0x0020), if not present, is deduced from
1428 Image Orientation (Patient) : (0020|0037) or from
1429 Image Orientation (RET) : (0020 0035)
1431 --> Study ID, Series Number, Instance Number, Patient Orientation (Type 2)
1432 are created, with empty value if there are missing.
1434 --> Manufacturer, Institution Name, Patient's Name, (Type 2)
1435 are defaulted with a 'gdcm' value.
1437 --> Patient ID, Patient's Birth Date, Patient's Sex, (Type 2)
1438 --> Referring Physician's Name (Type 2)
1439 are created, with empty value if there are missing.
1441 -------------------------------------------------------------------------------------*/
1443 void FileHelper::CheckMandatoryElements()
1445 std::string sop = Util::CreateUniqueUID();
1447 // --------------------- For Meta Elements ---------------------
1448 // just to remember : 'official' 0002 group
1449 if ( WriteType != ACR && WriteType != ACR_LIBIDO )
1451 // Group 000002 (Meta Elements) already pushed out
1453 //0002 0000 UL 1 Meta Group Length
1454 //0002 0001 OB 1 File Meta Information Version
1455 //0002 0002 UI 1 Media Storage SOP Class UID
1456 //0002 0003 UI 1 Media Storage SOP Instance UID
1457 //0002 0010 UI 1 Transfer Syntax UID
1458 //0002 0012 UI 1 Implementation Class UID
1459 //0002 0013 SH 1 Implementation Version Name
1460 //0002 0016 AE 1 Source Application Entity Title
1461 //0002 0100 UI 1 Private Information Creator
1462 //0002 0102 OB 1 Private Information
1464 // Push out 'ACR-NEMA-special' entries, if any
1465 Archive->Push(0x0008,0x0001); // Length to End
1466 Archive->Push(0x0008,0x0010); // Recognition Code
1467 Archive->Push(0x0028,0x0005); // Image Dimension
1469 // Create them if not found
1470 // Always modify the value
1471 // Push the entries to the archive.
1472 CopyMandatoryEntry(0x0002,0x0000,"0","UL");
1474 DataEntry *e_0002_0001 = CopyDataEntry(0x0002,0x0001, "OB");
1475 e_0002_0001->SetBinArea((uint8_t*)Util::GetFileMetaInformationVersion(),
1477 e_0002_0001->SetLength(2);
1478 Archive->Push(e_0002_0001);
1479 e_0002_0001->Delete();
1481 if ( ContentType == FILTERED_IMAGE || ContentType == UNMODIFIED_PIXELS_IMAGE)
1483 // we keep the original 'Media Storage SOP Class UID', we default it if missing
1484 CheckMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7","UI");
1488 // It's *not* an image comming straight from a source. We force
1489 // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage]
1490 CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7","UI");
1493 // 'Media Storage SOP Instance UID'
1494 CopyMandatoryEntry(0x0002,0x0003,sop,"UI");
1496 // 'Implementation Class UID'
1497 // FIXME : in all examples we have, 0x0002,0x0012 is not so long :
1498 // seems to be Root UID + 4 digits (?)
1499 CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID(),"UI");
1501 // 'Implementation Version Name'
1502 std::string version = "GDCM ";
1503 version += Util::GetVersion();
1504 CopyMandatoryEntry(0x0002,0x0013,version,"SH");
1507 // --------------------- For DataSet ---------------------
1509 if ( ContentType != USER_OWN_IMAGE) // when it's not a user made image
1511 // If 'SOP Class UID' and 'SOP Instance UID' exist ('true DICOM' image)
1512 // we create the 'Source Image Sequence' SeqEntry
1513 // to hold informations about the Source Image
1515 DataEntry *e_0008_0016 = FileInternal->GetDataEntry(0x0008, 0x0016);
1516 DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018);
1517 if ( e_0008_0016 && e_0008_0018)
1519 // Create 'Source Image Sequence' SeqEntry
1520 SeqEntry *sis = SeqEntry::New (0x0008, 0x2112);
1521 SQItem *sqi = SQItem::New(1);
1523 // create 'Referenced SOP Class UID' from 'SOP Class UID'
1525 DataEntry *e_0008_1150 = DataEntry::New(0x0008, 0x1150, "UI");
1526 e_0008_1150->SetString( e_0008_0016->GetString());
1527 sqi->AddEntry(e_0008_1150);
1528 e_0008_1150->Delete();
1530 // create 'Referenced SOP Instance UID' from 'SOP Instance UID'
1531 DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018);
1533 DataEntry *e_0008_1155 = DataEntry::New(0x0008, 0x1155, "UI");
1534 e_0008_1155->SetString( e_0008_0018->GetString());
1535 sqi->AddEntry(e_0008_1155);
1536 e_0008_1155->Delete();
1538 sis->AddSQItem(sqi,1);
1541 // temporarily replaces any previous 'Source Image Sequence'
1544 // FIXME : is 'Image Type' *really* depending on the presence of 'SOP Class UID'?
1545 if ( ContentType == FILTERED_IMAGE)
1546 // the user *knows* he just modified the pixels
1547 // the image is no longer an 'Original' one
1548 CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY","CS");
1552 if ( ContentType == FILTERED_IMAGE || ContentType == UNMODIFIED_PIXELS_IMAGE)
1554 // we keep the original 'Media Storage SOP Class UID', we default it if missing (it should be present !)
1555 CheckMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7","UI");
1559 // It's *not* an image comming straight from a source. We force
1560 // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage]
1561 CopyMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7", "UI");
1564 Archive->Push(0x0028,0x005); // [Image Dimensions (RET)
1565 // Push out 'LibIDO-special' entries, if any
1566 Archive->Push(0x0028,0x0015);
1567 Archive->Push(0x0028,0x0016);
1568 Archive->Push(0x0028,0x0017);
1569 Archive->Push(0x0028,0x0198); // very old versions
1570 Archive->Push(0x0028,0x0199);
1572 // Replace deprecated 0028 0012 US Planes
1573 // by new 0028 0008 IS Number of Frames
1575 ///\todo : find if there is a rule!
1576 DataEntry *e_0028_0012 = FileInternal->GetDataEntry(0x0028, 0x0012);
1579 CopyMandatoryEntry(0x0028, 0x0008,e_0028_0012->GetString(),"IS");
1580 Archive->Push(0x0028,0x0012);
1583 // Deal with the pb of (Bits Stored = 12)
1584 // - we're gonna write the image as Bits Stored = 16
1585 if ( FileInternal->GetEntryString(0x0028,0x0100) == "12")
1587 CopyMandatoryEntry(0x0028,0x0100,"16","US");
1590 // Check if user wasn't drunk ;-)
1592 std::ostringstream s;
1593 // check 'Bits Allocated' vs decent values
1594 int nbBitsAllocated = FileInternal->GetBitsAllocated();
1595 if ( (nbBitsAllocated == 0 || nbBitsAllocated > 32)
1596 || ( nbBitsAllocated > 8 && nbBitsAllocated <16) )
1598 CopyMandatoryEntry(0x0028,0x0100,"16","US");
1599 gdcmWarningMacro("(0028,0100) changed from "
1600 << nbBitsAllocated << " to 16 for consistency purpose");
1601 nbBitsAllocated = 16;
1603 // check 'Bits Stored' vs 'Bits Allocated'
1604 int nbBitsStored = FileInternal->GetBitsStored();
1605 if ( nbBitsStored == 0 || nbBitsStored > nbBitsAllocated )
1608 s << nbBitsAllocated;
1609 CopyMandatoryEntry(0x0028,0x0101,s.str(),"US");
1610 gdcmWarningMacro("(0028,0101) changed from "
1611 << nbBitsStored << " to " << nbBitsAllocated
1612 << " for consistency purpose" );
1613 nbBitsStored = nbBitsAllocated;
1615 // check 'Hight Bit Position' vs 'Bits Allocated' and 'Bits Stored'
1616 int highBitPosition = FileInternal->GetHighBitPosition();
1617 if ( highBitPosition == 0 ||
1618 highBitPosition > nbBitsAllocated-1 ||
1619 highBitPosition < nbBitsStored-1 )
1622 s << nbBitsStored - 1;
1623 CopyMandatoryEntry(0x0028,0x0102,s.str(),"US");
1624 gdcmWarningMacro("(0028,0102) changed from "
1625 << highBitPosition << " to " << nbBitsAllocated-1
1626 << " for consistency purpose");
1629 // check Pixel Representation (default it as 0 -unsigned-)
1631 DataEntry *e_0028_0103 = FileInternal->GetDataEntry(0x0028, 0x0103);
1634 gdcmWarningMacro("PixelRepresentation (0028,0103) is supposed to be mandatory");
1635 CopyMandatoryEntry(0x0028, 0x0103,"0","US");
1639 int sign = (int)e_0028_0103->GetValue(0);
1640 if (sign !=1 && sign !=0)
1642 gdcmWarningMacro("PixelRepresentation (0028,0103) is supposed to be =1 or =0");
1643 CopyMandatoryEntry(0x0028, 0x0103,"0","US");
1647 std::string pixelAspectRatio = FileInternal->GetEntryString(0x0028,0x0034);
1648 if ( pixelAspectRatio == GDCM_UNFOUND ) // avoid conflict with pixelSpacing !
1650 std::string pixelSpacing = FileInternal->GetEntryString(0x0028,0x0030);
1651 if ( pixelSpacing == GDCM_UNFOUND )
1653 pixelSpacing = "1.0\\1.0";
1654 // if missing, Pixel Spacing forced to "1.0\1.0"
1655 CopyMandatoryEntry(0x0028,0x0030,pixelSpacing,"DS");
1658 // 'Imager Pixel Spacing' : defaulted to 'Pixel Spacing'
1659 // --> This one is the *legal* one !
1660 if ( ContentType != USER_OWN_IMAGE)
1661 // we write it only when we are *sure* the image comes from
1662 // an imager (see also 0008,0x0064)
1663 CheckMandatoryEntry(0x0018,0x1164,pixelSpacing,"DS");
1666 ///Exact meaning of RETired fields
1668 // See page 73 of ACR-NEMA_300-1988.pdf !
1670 // 0020,0020 : Patient Orientation :
1671 Patient direction of the first row and
1672 column of the images. The first entry id the direction of the raws, given by the
1673 direction of the last pixel in the first row from the first pixel in tha row.
1674 the second entry is the direction of the columns, given by the direction of the
1675 last pixel in the first column from the first pixel in that column.
1676 L : Left, F : Feet, A : Anterior, P : Posterior.
1677 Up to 3 letters can be used in combination to indicate oblique planes.
1679 //0020,0030 Image Position (RET)
1680 x,y,z coordinates im mm of the first pixel in the image
1682 // 0020,0035 Image Orientation (RET)
1683 Direction cosines of the R axis of the image system with respect to the
1684 equipment coordinate axes x,y,z, followed by direction cosines of the C axis of
1685 the image system with respect to the same axes
1687 //0020,0050 Location
1688 An image location reference, standard for the modality (such as CT bed position),
1689 used to indicate position. Calculation of position for other purposes
1690 is only from (0020,0030) and (0020,0035)
1694 // if imagePositionPatient not found, default it with imagePositionRet, if any
1695 // if imageOrientationPatient not found, default it with imageOrientationRet, if any
1697 std::string imagePositionRet = FileInternal->GetEntryString(0x0020,0x0030);
1698 std::string imageOrientationRet = FileInternal->GetEntryString(0x0020,0x0035);
1699 std::string imagePositionPatient = FileInternal->GetEntryString(0x0020,0x0032);
1700 std::string imageOrientationPatient = FileInternal->GetEntryString(0x0020,0x0037);
1702 if( imagePositionPatient == GDCM_UNFOUND && imageOrientationPatient == GDCM_UNFOUND
1703 && imagePositionRet != GDCM_UNFOUND && imageOrientationRet != GDCM_UNFOUND)
1705 CopyMandatoryEntry(0x0020, 0x0032,imagePositionRet,"DS");
1706 Archive->Push(0x0020,0x0030);
1707 CopyMandatoryEntry(0x0020, 0x0037,imageOrientationRet,"DS");
1708 Archive->Push(0x0020,0x0035);
1712 // Samples Per Pixel (type 1) : default to grayscale
1713 CheckMandatoryEntry(0x0028,0x0002,"1","US");
1715 // --- Check UID-related Entries ---
1717 // At the end, not to overwrite the original ones,
1718 // needed by 'Referenced SOP Instance UID', 'Referenced SOP Class UID'
1719 // 'SOP Instance UID'
1720 CopyMandatoryEntry(0x0008,0x0018,sop,"UI");
1722 if ( ContentType == USER_OWN_IMAGE)
1724 gdcmDebugMacro( "USER_OWN_IMAGE (2)");
1726 // Other possible values are :
1727 // See PS 3.3, Page 408
1729 // DV = Digitized Video
1730 // DI = Digital Interface
1731 // DF = Digitized Film
1732 // WSD = Workstation
1733 // SD = Scanned Document
1734 // SI = Scanned Image
1736 // SYN = Synthetic Image
1738 CheckMandatoryEntry(0x0008,0x0064,"SYN","CS"); // Why not?
1741 if ( ContentType == CREATED_IMAGE)
1743 /// \todo : find a trick to pass the Media Storage SOP Instance UID of the images used to create the current image
1748 // ---- The user will never have to take any action on the following ----
1750 // new value for 'SOP Instance UID'
1751 //SetMandatoryEntry(0x0008,0x0018,Util::CreateUniqueUID());
1753 // Instance Creation Date
1754 const std::string &date = Util::GetCurrentDate();
1755 CopyMandatoryEntry(0x0008,0x0012,date,"DA");
1757 // Instance Creation Time
1758 const std::string &time = Util::GetCurrentTime();
1759 CopyMandatoryEntry(0x0008,0x0013,time,"TM");
1762 CheckMandatoryEntry(0x0008,0x0020,date,"DA");
1764 CheckMandatoryEntry(0x0008,0x0030,time,"TM");
1767 //CopyMandatoryEntry(0x0008,0x0050,"");
1768 CheckMandatoryEntry(0x0008,0x0050,"","SH");
1771 // ----- Add Mandatory Entries if missing ---
1772 // Entries whose type is 1 are mandatory, with a mandatory value
1773 // Entries whose type is 1c are mandatory-inside-a-Sequence,
1774 // with a mandatory value
1775 // Entries whose type is 2 are mandatory, with an optional value
1776 // Entries whose type is 2c are mandatory-inside-a-Sequence,
1777 // with an optional value
1778 // Entries whose type is 3 are optional
1780 // 'Study Instance UID'
1781 // Keep the value if exists
1782 // The user is allowed to create his own Study,
1783 // keeping the same 'Study Instance UID' for various images
1784 // The user may add images to a 'Manufacturer Study',
1785 // adding new Series to an already existing Study
1786 CheckMandatoryEntry(0x0020,0x000d,Util::CreateUniqueUID(),"UI");
1788 // 'Serie Instance UID'
1789 // Keep the value if exists
1790 // The user is allowed to create his own Series,
1791 // keeping the same 'Serie Instance UID' for various images
1792 // The user shouldn't add any image to a 'Manufacturer Serie'
1793 // but there is no way no to prevent him for doing that
1794 CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID(),"UI");
1797 CheckMandatoryEntry(0x0020,0x0010,"","SH");
1800 CheckMandatoryEntry(0x0020,0x0011,"","IS");
1803 CheckMandatoryEntry(0x0020,0x0013,"","IS");
1805 // Patient Orientation
1806 // Can be computed from (0020|0037) : Image Orientation (Patient)
1807 GDCM_NAME_SPACE::Orientation *o = GDCM_NAME_SPACE::Orientation::New();
1808 std::string ori = o->GetOrientation ( FileInternal );
1810 if (ori != "\\" && ori != GDCM_UNFOUND)
1811 CheckMandatoryEntry(0x0020,0x0020,ori,"CS");
1813 CheckMandatoryEntry(0x0020,0x0020,"","CS");
1815 // Default Patient Position to HFS
1816 CheckMandatoryEntry(0x0018,0x5100,"HFS","CS");
1818 // Modality : if missing we set it to 'OTher'
1819 CheckMandatoryEntry(0x0008,0x0060,"OT","CS");
1821 // Manufacturer : if missing we set it to 'GDCM Factory'
1822 CheckMandatoryEntry(0x0008,0x0070,"GDCM Factory","LO");
1824 // Institution Name : if missing we set it to 'GDCM Hospital'
1825 CheckMandatoryEntry(0x0008,0x0080,"GDCM Hospital","LO");
1827 // Patient's Name : if missing, we set it to 'GDCM^Patient'
1828 CheckMandatoryEntry(0x0010,0x0010,"GDCM^Patient","PN");
1830 // Patient ID : some clinical softwares *demand* it although it's a 'type 2' entry.
1831 CheckMandatoryEntry(0x0010,0x0020,"gdcm ID","LO");
1833 // Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory
1834 CheckMandatoryEntry(0x0010,0x0030,"","DA");
1836 // Patient's Sex :'type 2' entry -> must exist, value not mandatory
1837 CheckMandatoryEntry(0x0010,0x0040,"","CS");
1839 // Referring Physician's Name :'type 2' entry -> must exist, value not mandatory
1840 CheckMandatoryEntry(0x0008,0x0090,"","PN");
1843 // Deal with element 0x0000 (group length) of each group.
1844 // First stage : get all the different Groups
1847 DocEntry *d = FileInternal->GetFirstEntry();
1850 grHT[d->GetGroup()] = 0;
1851 d=FileInternal->GetNextEntry();
1853 // Second stage : add the missing ones (if any)
1854 for (GroupHT::iterator it = grHT.begin(); it != grHT.end(); ++it)
1856 CheckMandatoryEntry(it->first, 0x0000, "0");
1858 // Third stage : update all 'zero level' groups length
1862 if (PhotometricInterpretation == 1)
1867 void FileHelper::CheckMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr )
1869 DataEntry *entry = FileInternal->GetDataEntry(group,elem);
1872 //entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
1873 entry = DataEntry::New(group,elem,vr);
1874 entry->SetString(value);
1875 Archive->Push(entry);
1880 /// \todo : what is it used for ? (FileHelper::SetMandatoryEntry)
1881 void FileHelper::SetMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr)
1883 //DataEntry *entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
1884 DataEntry *entry = DataEntry::New(group,elem,vr);
1885 entry->SetString(value);
1886 Archive->Push(entry);
1890 void FileHelper::CopyMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr)
1892 DataEntry *entry = CopyDataEntry(group,elem,vr);
1893 entry->SetString(value);
1894 Archive->Push(entry);
1899 * \brief Restore in the File the initial group 0002
1901 void FileHelper::RestoreWriteMandatory()
1903 // group 0002 may be pushed out for ACR-NEMA writting purposes
1904 Archive->Restore(0x0002,0x0000);
1905 Archive->Restore(0x0002,0x0001);
1906 Archive->Restore(0x0002,0x0002);
1907 Archive->Restore(0x0002,0x0003);
1908 Archive->Restore(0x0002,0x0010);
1909 Archive->Restore(0x0002,0x0012);
1910 Archive->Restore(0x0002,0x0013);
1911 Archive->Restore(0x0002,0x0016);
1912 Archive->Restore(0x0002,0x0100);
1913 Archive->Restore(0x0002,0x0102);
1915 // FIXME : Check if none is missing !
1917 Archive->Restore(0x0008,0x0012);
1918 Archive->Restore(0x0008,0x0013);
1919 Archive->Restore(0x0008,0x0016);
1920 Archive->Restore(0x0008,0x0018);
1921 Archive->Restore(0x0008,0x0060);
1922 Archive->Restore(0x0008,0x0070);
1923 Archive->Restore(0x0008,0x0080);
1924 Archive->Restore(0x0008,0x0090);
1925 Archive->Restore(0x0008,0x2112);
1927 Archive->Restore(0x0010,0x0010);
1928 Archive->Restore(0x0010,0x0030);
1929 Archive->Restore(0x0010,0x0040);
1931 Archive->Restore(0x0020,0x000d);
1932 Archive->Restore(0x0020,0x000e);
1936 * \brief CallStartMethod
1938 void FileHelper::CallStartMethod()
1942 CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS);
1946 * \brief CallProgressMethod
1948 void FileHelper::CallProgressMethod()
1950 CommandManager::ExecuteCommand(this,CMD_PROGRESS);
1954 * \brief CallEndMethod
1956 void FileHelper::CallEndMethod()
1959 CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS);
1962 //-----------------------------------------------------------------------------
1965 * \brief Factorization for various forms of constructors.
1967 void FileHelper::Initialize()
1970 ContentType = USER_OWN_IMAGE;
1972 WriteMode = WMODE_RAW;
1973 WriteType = ExplicitVR;
1975 PhotometricInterpretation = 2; // Black = 0
1977 PixelReadConverter = new PixelReadConvert;
1978 PixelWriteConverter = new PixelWriteConvert;
1979 Archive = new DocEntryArchive( FileInternal );
1981 KeepOverlays = false;
1985 * \brief Reads/[decompresses] the pixels,
1986 * *without* making RGB from Palette Colors
1987 * @return the pixels area, whatever its type
1988 * (uint8_t is just for prototyping : feel free to Cast it)
1990 uint8_t *FileHelper::GetRaw()
1992 PixelReadConverter->SetUserFunction( UserFunction );
1994 uint8_t *raw = PixelReadConverter->GetRaw();
1997 // The Raw image migth not be loaded yet:
1998 std::ifstream *fp = FileInternal->OpenFile();
1999 PixelReadConverter->ReadAndDecompressPixelData( fp );
2001 FileInternal->CloseFile();
2003 raw = PixelReadConverter->GetRaw();
2006 gdcmWarningMacro( "Read/decompress of pixel data apparently went wrong.");
2014 * \brief Deal with Grey levels i.e. re-arange them
2015 * to have low values = dark, high values = bright
2017 void FileHelper::ConvertFixGreyLevels(uint8_t *raw, size_t rawSize)
2019 uint32_t i; // to please M$VC6
2022 // Number of Bits Allocated for storing a Pixel is defaulted to 16
2023 // when absent from the file.
2024 int bitsAllocated = FileInternal->GetBitsAllocated();
2025 if ( bitsAllocated == 0 )
2030 else if (bitsAllocated > 8 && bitsAllocated < 16 && bitsAllocated != 12)
2034 // Number of "Bits Stored", defaulted to number of "Bits Allocated"
2035 // when absent from the file.
2036 int bitsStored = FileInternal->GetBitsStored();
2037 if ( bitsStored == 0 )
2039 bitsStored = bitsAllocated;
2042 if (!FileInternal->IsSignedPixelData())
2044 if ( bitsAllocated == 8 )
2046 uint8_t *deb = (uint8_t *)raw;
2047 for (i=0; i<rawSize; i++)
2055 if ( bitsAllocated == 16 )
2058 for (j=0; j<bitsStored-1; j++)
2060 mask = (mask << 1) +1; // will be fff when BitsStored=12
2063 uint16_t *deb = (uint16_t *)raw;
2064 for (i=0; i<rawSize/2; i++)
2074 if ( bitsAllocated == 8 )
2076 uint8_t smask8 = 255;
2077 uint8_t *deb = (uint8_t *)raw;
2078 for (i=0; i<rawSize; i++)
2080 *deb = smask8 - *deb;
2085 if ( bitsAllocated == 16 )
2087 uint16_t smask16 = 65535;
2088 uint16_t *deb = (uint16_t *)raw;
2089 for (i=0; i<rawSize/2; i++)
2091 *deb = smask16 - *deb;
2099 //-----------------------------------------------------------------------------
2101 * \brief Prints the FileInternal + info on PixelReadConvertor
2102 * @param os ostream we want to print in
2103 * @param indent (unused)
2105 void FileHelper::Print(std::ostream &os, std::string const &)
2107 FileInternal->SetPrintLevel(PrintLevel);
2108 FileInternal->Print(os);
2110 if ( FileInternal->IsReadable() )
2112 PixelReadConverter->SetPrintLevel(PrintLevel);
2113 PixelReadConverter->Print(os);
2117 //-----------------------------------------------------------------------------
2118 } // end namespace gdcm
2121 /* Probabely something to be added to use Rescale Slope/Intercept
2122 Have a look ,at ITK code !
2124 // Internal function to rescale pixel according to Rescale Slope/Intercept
2125 template<class TBuffer, class TSource>
2126 void RescaleFunction(TBuffer* buffer, TSource *source,
2127 double slope, double intercept, size_t size)
2129 size /= sizeof(TSource);
2131 if (slope != 1.0 && intercept != 0.0)
2133 // Duff's device. Instead of this code:
2135 // for(unsigned int i=0; i<size; i++)
2137 // buffer[i] = (TBuffer)(source[i]*slope + intercept);
2140 // use Duff's device which exploits "fall through"
2141 register size_t n = (size + 7) / 8;
2144 case 0: do { *buffer++ = (TBuffer)((*source++)*slope + intercept);
2145 case 7: *buffer++ = (TBuffer)((*source++)*slope + intercept);
2146 case 6: *buffer++ = (TBuffer)((*source++)*slope + intercept);
2147 case 5: *buffer++ = (TBuffer)((*source++)*slope + intercept);
2148 case 4: *buffer++ = (TBuffer)((*source++)*slope + intercept);
2149 case 3: *buffer++ = (TBuffer)((*source++)*slope + intercept);
2150 case 2: *buffer++ = (TBuffer)((*source++)*slope + intercept);
2151 case 1: *buffer++ = (TBuffer)((*source++)*slope + intercept);
2155 else if (slope == 1.0 && intercept != 0.0)
2157 // Duff's device. Instead of this code:
2159 // for(unsigned int i=0; i<size; i++)
2161 // buffer[i] = (TBuffer)(source[i] + intercept);
2164 // use Duff's device which exploits "fall through"
2165 register size_t n = (size + 7) / 8;
2168 case 0: do { *buffer++ = (TBuffer)(*source++ + intercept);
2169 case 7: *buffer++ = (TBuffer)(*source++ + intercept);
2170 case 6: *buffer++ = (TBuffer)(*source++ + intercept);
2171 case 5: *buffer++ = (TBuffer)(*source++ + intercept);
2172 case 4: *buffer++ = (TBuffer)(*source++ + intercept);
2173 case 3: *buffer++ = (TBuffer)(*source++ + intercept);
2174 case 2: *buffer++ = (TBuffer)(*source++ + intercept);
2175 case 1: *buffer++ = (TBuffer)(*source++ + intercept);
2179 else if (slope != 1.0 && intercept == 0.0)
2181 // Duff's device. Instead of this code:
2183 // for(unsigned int i=0; i<size; i++)
2185 // buffer[i] = (TBuffer)(source[i]*slope);
2188 // use Duff's device which exploits "fall through"
2189 register size_t n = (size + 7) / 8;
2192 case 0: do { *buffer++ = (TBuffer)((*source++)*slope);
2193 case 7: *buffer++ = (TBuffer)((*source++)*slope);
2194 case 6: *buffer++ = (TBuffer)((*source++)*slope);
2195 case 5: *buffer++ = (TBuffer)((*source++)*slope);
2196 case 4: *buffer++ = (TBuffer)((*source++)*slope);
2197 case 3: *buffer++ = (TBuffer)((*source++)*slope);
2198 case 2: *buffer++ = (TBuffer)((*source++)*slope);
2199 case 1: *buffer++ = (TBuffer)((*source++)*slope);
2205 // Duff's device. Instead of this code:
2207 // for(unsigned int i=0; i<size; i++)
2209 // buffer[i] = (TBuffer)(source[i]);
2212 // use Duff's device which exploits "fall through"
2213 register size_t n = (size + 7) / 8;
2216 case 0: do { *buffer++ = (TBuffer)(*source++);
2217 case 7: *buffer++ = (TBuffer)(*source++);
2218 case 6: *buffer++ = (TBuffer)(*source++);
2219 case 5: *buffer++ = (TBuffer)(*source++);
2220 case 4: *buffer++ = (TBuffer)(*source++);
2221 case 3: *buffer++ = (TBuffer)(*source++);
2222 case 2: *buffer++ = (TBuffer)(*source++);
2223 case 1: *buffer++ = (TBuffer)(*source++);
2230 template<class TSource>
2231 void RescaleFunction(ImageIOBase::IOComponentType bufferType,
2232 void* buffer, TSource *source,
2233 double slope, double intercept, size_t size)
2237 case ImageIOBase::UCHAR:
2238 RescaleFunction( (unsigned char *)buffer, source, slope, intercept, size);
2240 case ImageIOBase::CHAR:
2241 RescaleFunction( (char *)buffer, source, slope, intercept, size);
2243 case ImageIOBase::USHORT:
2244 RescaleFunction( (unsigned short *)buffer, source, slope, intercept,size);
2246 case ImageIOBase::SHORT:
2247 RescaleFunction( (short *)buffer, source, slope, intercept, size);
2249 case ImageIOBase::UINT:
2250 RescaleFunction( (unsigned int *)buffer, source, slope, intercept, size);
2252 case ImageIOBase::INT:
2253 RescaleFunction( (int *)buffer, source, slope, intercept, size);
2255 case ImageIOBase::FLOAT:
2256 RescaleFunction( (float *)buffer, source, slope, intercept, size);
2258 case ImageIOBase::DOUBLE:
2259 RescaleFunction( (double *)buffer, source, slope, intercept, size);
2262 ::itk::OStringStream message;
2263 message << "itk::ERROR: GDCMImageIO: Unknown component type : " << bufferType;
2264 ::itk::ExceptionObject e(__FILE__, __LINE__, message.str().c_str(),ITK_LOCATION);