1 /*=========================================================================
4 Module: $RCSfile: gdcmFileHelper.cxx,v $
7 Date: $Date: 2006/06/29 13:27:28 $
8 Version: $Revision: 1.105 $
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 // user can now check some values
61 std::string v = f->GetEntryValue(groupNb,ElementNb);
63 // to get the pixels, user needs a gdcm::FileHelper
64 gdcm::FileHelper *fh = new gdcm::FileHelper(f);
65 // user may ask not to convert Palette to RGB
66 uint8_t *pixels = fh->GetImageDataRaw();
67 int imageLength = fh->GetImageDataRawSize();
68 // He can now use the pixels, create a new image, ...
69 uint8_t *userPixels = ...
71 To re-write the image, user re-uses the gdcm::FileHelper
73 fh->SetImageData( userPixels, userPixelsLength);
74 fh->SetTypeToRaw(); // Even if it was possible to convert Palette to RGB
77 fh->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation
78 // Little Endian is the default
79 // no other value is allowed
80 (-->SetWriteType(ExplicitVR);)
81 -->WriteType = ExplicitVR;
82 fh->Write(newFileName); // overwrites the file, if any
85 fh->WriteDcmExplVR(newFileName);
88 // ----------------------------- WARNING -------------------------
90 These lines will be moved to the document-to-be 'Developer's Guide'
92 WriteMode : WMODE_RAW / WMODE_RGB
93 WriteType : ImplicitVR, ExplicitVR, ACR, ACR_LIBIDO
95 fh1->Write(newFileName);
96 SetWriteFileTypeToImplicitVR() / SetWriteFileTypeToExplicitVR();
97 (modifies TransferSyntax)
98 SetWriteToRaw(); / SetWriteToRGB();
99 (modifies, when necessary : photochromatic interpretation,
100 samples per pixel, Planar configuration,
101 bits allocated, bits stored, high bit -ACR 24 bits-
102 Pixels element VR, pushes out the LUT )
103 CheckWriteIntegrity();
104 (checks user given pixels length)
105 FileInternal->Write(fileName,WriteType)
106 fp = opens file(fileName);
107 ComputeGroup0002Length( );
109 RemoveEntry(palettes, etc)
110 Document::WriteContent(fp, writetype);
112 (moves back to the File all the archived elements)
113 RestoreWriteFileType();
114 (pushes back group 0002, with TransferSyntax)
122 typedef std::map<uint16_t, int> GroupHT; // Hash Table
123 //-------------------------------------------------------------------------
124 // Constructor / Destructor
126 * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
127 * file (gdcm::File only deals with the ... header)
128 * Opens (in read only and when possible) an existing file and checks
129 * for DICOM compliance. Returns NULL on failure.
130 * It will be up to the user to load the pixels into memory
131 * ( GetImageDataSize() + GetImageData() methods)
132 * \note the in-memory representation of all available tags found in
133 * the DICOM header is post-poned to first header information access.
134 * This avoid a double parsing of public part of the header when
135 * one sets an a posteriori shadow dictionary (efficiency can be
136 * seen as a side effect).
138 FileHelper::FileHelper( )
140 FileInternal = File::New( );
145 * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
146 * file (File only deals with the ... header)
147 * Opens (in read only and when possible) an existing file and checks
148 * for DICOM compliance. Returns NULL on failure.
149 * It will be up to the user to load the pixels into memory
150 * ( GetImageDataSize() + GetImageData() methods)
151 * \note the in-memory representation of all available tags found in
152 * the DICOM header is post-poned to first header information access.
153 * This avoid a double parsing of public part of the header when
154 * user sets an a posteriori shadow dictionary (efficiency can be
155 * seen as a side effect).
156 * @param header already built Header
158 FileHelper::FileHelper(File *header)
160 gdcmAssertMacro(header);
162 FileInternal = header;
163 FileInternal->Register();
165 if ( FileInternal->IsReadable() )
167 PixelReadConverter->GrabInformationsFromFile( FileInternal, this );
172 * \brief canonical destructor
173 * \note If the header (gdcm::File) was created by the FileHelper constructor,
174 * it is destroyed by the FileHelper
176 FileHelper::~FileHelper()
178 if ( PixelReadConverter )
180 delete PixelReadConverter;
182 if ( PixelWriteConverter )
184 delete PixelWriteConverter;
191 FileInternal->Unregister();
194 //-----------------------------------------------------------------------------
198 * \brief Sets the LoadMode of the internal gdcm::File as a boolean string.
199 * NO_SEQ, NO_SHADOW, NO_SHADOWSEQ ... (nothing more, right now)
200 * WARNING : before using NO_SHADOW, be sure *all* your files
201 * contain accurate values in the 0x0000 element (if any)
202 * of *each* Shadow Group. The parser will fail if the size is wrong !
203 * @param loadMode Load mode to be used
205 void FileHelper::SetLoadMode(int loadMode)
207 GetFile()->SetLoadMode( loadMode );
210 * \brief Sets the LoadMode of the internal gdcm::File
211 * @param fileName name of the file to be open
213 void FileHelper::SetFileName(std::string const &fileName)
215 FileInternal->SetFileName( fileName );
220 * @return false if file cannot be open or no swap info was found,
221 * or no tag was found.
223 bool FileHelper::Load()
225 if ( !FileInternal->Load() )
228 PixelReadConverter->GrabInformationsFromFile( FileInternal, this );
233 * \brief Accesses an existing DataEntry through it's (group, element)
234 * and modifies it's content with the given value.
235 * @param content new value (string) to substitute with
236 * @param group group number of the Dicom Element to modify
237 * @param elem element number of the Dicom Element to modify
238 * \return false if DataEntry not found
240 bool FileHelper::SetEntryString(std::string const &content,
241 uint16_t group, uint16_t elem)
243 return FileInternal->SetEntryString(content, group, elem);
248 * \brief Accesses an existing DataEntry through it's (group, element)
249 * and modifies it's content with the given value.
250 * @param content new value (void* -> uint8_t*) to substitute with
251 * @param lgth new value length
252 * @param group group number of the Dicom Element to modify
253 * @param elem element number of the Dicom Element to modify
254 * \return false if DataEntry not found
256 bool FileHelper::SetEntryBinArea(uint8_t *content, int lgth,
257 uint16_t group, uint16_t elem)
259 return FileInternal->SetEntryBinArea(content, lgth, group, elem);
263 * \brief Modifies the value of a given DataEntry when it exists.
264 * Creates it with the given value when unexistant.
265 * @param content (string) value to be set
266 * @param group Group number of the Entry
267 * @param elem Element number of the Entry
268 * \return pointer to the modified/created DataEntry (NULL when creation
271 DataEntry *FileHelper::InsertEntryString(std::string const &content,
272 uint16_t group, uint16_t elem,
275 return FileInternal->InsertEntryString(content, group, elem, vr);
279 * \brief Modifies the value of a given DataEntry when it exists.
280 * Creates it with the given value when unexistant.
281 * A copy of the binArea is made to be kept in the Document.
282 * @param binArea (binary)value to be set
283 * @param lgth new value length
284 * @param group Group number of the Entry
285 * @param elem Element number of the Entry
286 * @param vr Value Represenation of the DataElement to be inserted
287 * \return pointer to the modified/created DataEntry (NULL when creation
290 DataEntry *FileHelper::InsertEntryBinArea(uint8_t *binArea, int lgth,
291 uint16_t group, uint16_t elem,
294 return FileInternal->InsertEntryBinArea(binArea, lgth, group, elem, vr);
298 * \brief Adds an empty SeqEntry
299 * (remove any existing entry with same group,elem)
300 * @param group Group number of the Entry
301 * @param elem Element number of the Entry
302 * \return pointer to the created SeqEntry (NULL when creation
305 SeqEntry *FileHelper::InsertSeqEntry(uint16_t group, uint16_t elem)
307 return FileInternal->InsertSeqEntry(group, elem);
311 * \brief Get the size of the image data
312 * If the image can be RGB (with a lut or by default), the size
313 * corresponds to the RGB image
314 * (use GetImageDataRawSize if you want to be sure to get *only*
315 * the size of the pixels)
316 * @return The image size
318 size_t FileHelper::GetImageDataSize()
320 if ( PixelWriteConverter->GetUserData() )
322 return PixelWriteConverter->GetUserDataSize();
324 return PixelReadConverter->GetRGBSize();
328 * \brief Get the size of the image data.
329 * If the image could be converted to RGB using a LUT,
330 * this transformation is not taken into account by GetImageDataRawSize
331 * (use GetImageDataSize if you wish)
332 * @return The raw image size
334 size_t FileHelper::GetImageDataRawSize()
336 if ( PixelWriteConverter->GetUserData() )
338 return PixelWriteConverter->GetUserDataSize();
340 return PixelReadConverter->GetRawSize();
344 * \brief brings pixels into memory :
345 * - Allocates necessary memory,
346 * - Reads the pixels from disk (uncompress if necessary),
347 * - Transforms YBR pixels, if any, into RGB pixels,
348 * - Transforms 3 planes R, G, B, if any, into a single RGB Plane
349 * - Transforms single Grey plane + 3 Palettes into a RGB Plane
350 * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
351 * @return Pointer to newly allocated pixel data.
352 * (uint8_t is just for prototyping. feel free to cast)
353 * NULL if alloc fails
355 uint8_t *FileHelper::GetImageData()
357 if ( PixelWriteConverter->GetUserData() )
359 return PixelWriteConverter->GetUserData();
364 // If the decompression failed nothing can be done.
368 if ( FileInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
370 return PixelReadConverter->GetRGB();
374 // When no LUT or LUT conversion fails, return the Raw
375 return PixelReadConverter->GetRaw();
380 * \brief brings pixels into memory :
381 * - Allocates necessary memory,
382 * - Transforms YBR pixels (if any) into RGB pixels
383 * - Transforms 3 planes R, G, B (if any) into a single RGB Plane
384 * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
385 * - DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
386 * @return Pointer to newly allocated pixel data.
387 * (uint8_t is just for prototyping. feel free to cast)
388 * NULL if alloc fails
390 uint8_t *FileHelper::GetImageDataRaw ()
395 //#ifndef GDCM_LEGACY_REMOVE
397 * \brief Useless function, since PixelReadConverter forces us
398 * copy the Pixels anyway.
399 * Reads the pixels from disk (uncompress if necessary),
400 * Transforms YBR pixels, if any, into RGB pixels
401 * Transforms 3 planes R, G, B, if any, into a single RGB Plane
402 * Transforms single Grey plane + 3 Palettes into a RGB Plane
403 * Copies at most MaxSize bytes of pixel data to caller allocated
405 * \warning This function allows people that want to build a volume
406 * from an image stack *not to* have, first to get the image pixels,
407 * and then move them to the volume area.
408 * It's absolutely useless for any VTK user since vtk chooses
409 * to invert the lines of an image, that is the last line comes first
410 * (for some axis related reasons?). Hence he will have
411 * to load the image line by line, starting from the end.
412 * VTK users have to call GetImageData
414 * @param destination Address (in caller's memory space) at which the
415 * pixel data should be copied
416 * @param maxSize Maximum number of bytes to be copied. When MaxSize
417 * is not sufficient to hold the pixel data the copy is not
418 * executed (i.e. no partial copy).
419 * @return On success, the number of bytes actually copied. Zero on
420 * failure e.g. MaxSize is lower than necessary.
423 size_t FileHelper::GetImageDataIntoVector (void *destination, size_t maxSize)
427 // If the decompression failed nothing can be done.
431 if ( FileInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
433 if ( PixelReadConverter->GetRGBSize() > maxSize )
435 gdcmWarningMacro( "Pixel data bigger than caller's expected MaxSize");
439 (void*)PixelReadConverter->GetRGB(),
440 PixelReadConverter->GetRGBSize() );
441 return PixelReadConverter->GetRGBSize();
444 // Either no LUT conversion necessary or LUT conversion failed
445 if ( PixelReadConverter->GetRawSize() > maxSize )
447 gdcmWarningMacro( "Pixel data bigger than caller's expected MaxSize");
451 (void *)PixelReadConverter->GetRaw(),
452 PixelReadConverter->GetRawSize() );
453 return PixelReadConverter->GetRawSize();
459 * \brief Points the internal pointer to the callers inData
460 * image representation, BUT WITHOUT COPYING THE DATA.
461 * 'image' Pixels are presented as C-like 2D arrays : line per line.
462 * 'volume'Pixels are presented as C-like 3D arrays : plane per plane
463 * \warning Since the pixels are not copied, it is the caller's responsability
464 * not to deallocate its data before gdcm uses them (e.g. with
465 * the Write() method )
466 * @param inData user supplied pixel area (uint8_t* is just for the compiler.
467 * user is allowed to pass any kind of pixelsn since the size is
469 * @param expectedSize total image size, *in Bytes*
471 void FileHelper::SetImageData(uint8_t *inData, size_t expectedSize)
473 SetUserData(inData, expectedSize);
477 * \brief Set the image data defined by the user
478 * \warning When writting the file, this data are get as default data to write
479 * @param inData user supplied pixel area (uint8_t* is just for the compiler.
480 * user is allowed to pass any kind of pixels since the size is
482 * @param expectedSize total image size, *in Bytes*
484 void FileHelper::SetUserData(uint8_t *inData, size_t expectedSize)
486 PixelWriteConverter->SetUserData(inData, expectedSize);
490 * \brief Get the image data defined by the user
491 * \warning When writting the file, this data are get as default data to write
493 uint8_t *FileHelper::GetUserData()
495 return PixelWriteConverter->GetUserData();
499 * \brief Get the image data size defined by the user
500 * \warning When writting the file, this data are get as default data to write
502 size_t FileHelper::GetUserDataSize()
504 return PixelWriteConverter->GetUserDataSize();
508 * \brief Get the image data from the file.
509 * If a LUT is found, the data are expanded to be RGB
511 uint8_t *FileHelper::GetRGBData()
513 return PixelReadConverter->GetRGB();
517 * \brief Get the image data size from the file.
518 * If a LUT is found, the data are expanded to be RGB
520 size_t FileHelper::GetRGBDataSize()
522 return PixelReadConverter->GetRGBSize();
526 * \brief Get the image data from the file.
527 * Even when a LUT is found, the data are not expanded to RGB!
529 uint8_t *FileHelper::GetRawData()
531 return PixelReadConverter->GetRaw();
535 * \brief Get the image data size from the file.
536 * Even when a LUT is found, the data are not expanded to RGB!
538 size_t FileHelper::GetRawDataSize()
540 return PixelReadConverter->GetRawSize();
544 * \brief Access to the underlying \ref PixelReadConverter RGBA LUT
546 uint8_t* FileHelper::GetLutRGBA()
548 if ( PixelReadConverter->GetLutRGBA() ==0 )
549 PixelReadConverter->BuildLUTRGBA();
550 return PixelReadConverter->GetLutRGBA();
554 * \brief Access to the underlying \ref PixelReadConverter RGBA LUT Item Number
556 int FileHelper::GetLutItemNumber()
558 return PixelReadConverter->GetLutItemNumber();
562 * \brief Access to the underlying \ref PixelReadConverter RGBA LUT Item Size
564 int FileHelper::GetLutItemSize()
566 return PixelReadConverter->GetLutItemSize();
570 * \brief Writes on disk A SINGLE Dicom file
571 * NO test is performed on processor "Endiannity".
572 * It's up to the user to call his Reader properly
573 * @param fileName name of the file to be created
574 * (any already existing file is over written)
575 * @return false if write fails
577 bool FileHelper::WriteRawData(std::string const &fileName)
579 std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary );
582 gdcmWarningMacro( "Fail to open (write) file:" << fileName.c_str());
586 if ( PixelWriteConverter->GetUserData() )
588 fp1.write( (char *)PixelWriteConverter->GetUserData(),
589 PixelWriteConverter->GetUserDataSize() );
591 else if ( PixelReadConverter->GetRGB() )
593 fp1.write( (char *)PixelReadConverter->GetRGB(),
594 PixelReadConverter->GetRGBSize());
596 else if ( PixelReadConverter->GetRaw() )
598 fp1.write( (char *)PixelReadConverter->GetRaw(),
599 PixelReadConverter->GetRawSize());
603 gdcmErrorMacro( "Nothing written." );
612 * \brief Writes on disk A SINGLE Dicom file,
613 * using the Implicit Value Representation convention
614 * NO test is performed on processor "Endianity".
615 * @param fileName name of the file to be created
616 * (any already existing file is overwritten)
617 * @return false if write fails
620 bool FileHelper::WriteDcmImplVR (std::string const &fileName)
622 SetWriteTypeToDcmImplVR();
623 return Write(fileName);
627 * \brief Writes on disk A SINGLE Dicom file,
628 * using the Explicit Value Representation convention
629 * NO test is performed on processor "Endiannity".
630 * @param fileName name of the file to be created
631 * (any already existing file is overwritten)
632 * @return false if write fails
635 bool FileHelper::WriteDcmExplVR (std::string const &fileName)
637 SetWriteTypeToDcmExplVR();
638 return Write(fileName);
642 * \brief Writes on disk A SINGLE Dicom file,
643 * using the ACR-NEMA convention
644 * NO test is performed on processor "Endiannity".
645 * (a l'attention des logiciels cliniques
646 * qui ne prennent en entrée QUE des images ACR ...
647 * \warning if a DICOM_V3 header is supplied,
648 * groups < 0x0008 and shadow groups are ignored
649 * \warning NO TEST is performed on processor "Endiannity".
650 * @param fileName name of the file to be created
651 * (any already existing file is overwritten)
652 * @return false if write fails
655 bool FileHelper::WriteAcr (std::string const &fileName)
658 return Write(fileName);
662 * \brief Writes on disk A SINGLE Dicom file,
663 * @param fileName name of the file to be created
664 * (any already existing file is overwritten)
665 * @return false if write fails
667 bool FileHelper::Write(std::string const &fileName)
670 CheckMandatoryElements(); //called once, here !
677 SetWriteFileTypeToImplicitVR();
680 case Unknown: // should never happen; ExplicitVR is the default value
683 // User should ask gdcm to write an image in Explicit VR mode
684 // only when he is sure *all* the VR of *all* the DataElements is known.
685 // i.e : when there are *only* Public Groups
686 // or *all* the Shadow Groups are fully described in the relevant Shadow
688 // Let's just *dream* about it; *never* trust a user !
689 // We turn to Implicit VR if at least the VR of one element is unknown.
692 e = FileInternal->GetFirstEntry();
695 if (e->GetVR() == " ")
697 SetWriteTypeToDcmImplVR();
698 SetWriteFileTypeToImplicitVR();
702 e = FileInternal->GetNextEntry();
707 SetWriteFileTypeToExplicitVR();
711 SetWriteFileTypeToExplicitVR(); // to see JPRx
715 // NOTHING is done here just for LibIDO.
716 // Just to avoid further trouble if user creates a file ex-nihilo,
717 // wants to write it as an ACR-NEMA file,
718 // and forgets to create any Entry belonging to group 0008
720 // We add Recognition Code (RET)
721 if ( ! FileInternal->GetDataEntry(0x0008, 0x0010) )
722 FileInternal->InsertEntryString("ACR-NEMA V1.0 ",
723 0x0008, 0x0010, "LO");
724 SetWriteFileTypeToACR();
725 // SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR !
728 /// \todo FIXME : JPEG may be either ExplicitVR or ImplicitVR
730 SetWriteFileTypeToJPEG();
734 // --------------------------------------------------------------
735 // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
737 // if recognition code tells us we dealt with a LibIDO image
738 // we reproduce on disk the switch between lineNumber and columnNumber
739 // just before writting ...
740 /// \todo the best trick would be *change* the recognition code
741 /// but pb expected if user deals with, e.g. COMPLEX images
743 if ( WriteType == ACR_LIBIDO )
749 SetWriteToNoLibido();
751 // ----------------- End of Special Patch ----------------
756 SetWriteToRaw(); // modifies and pushes to the archive, when necessary
759 SetWriteToRGB(); // modifies and pushes to the archive, when necessary
763 bool check = CheckWriteIntegrity(); // verifies length
764 if (WriteType == JPEG ) check = true;
767 check = FileInternal->Write(fileName,WriteType);
771 // RestoreWriteFileType();
772 // RestoreWriteMandatory();
775 // --------------------------------------------------------------
776 // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
778 // ...and we restore the header to be Dicom Compliant again
779 // just after writting
780 RestoreWriteOfLibido();
781 // ----------------- End of Special Patch ----------------
786 //-----------------------------------------------------------------------------
789 * \brief Checks the write integrity
791 * The tests made are :
792 * - verify the size of the image to write with the possible write
793 * when the user set an image data
794 * @return true if check is successfull
796 bool FileHelper::CheckWriteIntegrity()
798 if ( PixelWriteConverter->GetUserData() )
800 int numberBitsAllocated = FileInternal->GetBitsAllocated();
801 if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
803 gdcmWarningMacro( "numberBitsAllocated changed from "
804 << numberBitsAllocated << " to 16 "
805 << " for consistency purpose" );
806 numberBitsAllocated = 16;
809 size_t decSize = FileInternal->GetXSize()
810 * FileInternal->GetYSize()
811 * FileInternal->GetZSize()
812 * FileInternal->GetTSize()
813 * FileInternal->GetSamplesPerPixel()
814 * ( numberBitsAllocated / 8 );
815 size_t rgbSize = decSize;
816 if ( FileInternal->HasLUT() )
817 rgbSize = decSize * 3;
822 if ( decSize!=PixelWriteConverter->GetUserDataSize() )
824 gdcmWarningMacro( "Data size (Raw) is incorrect. Should be "
825 << decSize << " / Found :"
826 << PixelWriteConverter->GetUserDataSize() );
831 if ( rgbSize!=PixelWriteConverter->GetUserDataSize() )
833 gdcmWarningMacro( "Data size (RGB) is incorrect. Should be "
834 << decSize << " / Found "
835 << PixelWriteConverter->GetUserDataSize() );
846 * \brief Updates the File to write RAW data (as opposed to RGB data)
847 * (modifies, when necessary, photochromatic interpretation,
848 * bits allocated, Pixels element VR)
850 void FileHelper::SetWriteToRaw()
852 if ( FileInternal->GetNumberOfScalarComponents() == 3
853 && !FileInternal->HasLUT() )
859 DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS");
860 if (FileInternal->HasLUT() )
862 photInt->SetString("PALETTE COLOR ");
866 photInt->SetString("MONOCHROME2 ");
869 PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
870 PixelReadConverter->GetRawSize());
872 std::string vr = "OB";
873 if ( FileInternal->GetBitsAllocated()>8 )
875 if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files
878 CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr);
879 pixel->SetFlag(DataEntry::FLAG_PIXELDATA);
880 pixel->SetBinArea(PixelWriteConverter->GetData(),false);
881 pixel->SetLength(PixelWriteConverter->GetDataSize());
883 Archive->Push(photInt);
884 Archive->Push(pixel);
892 * \brief Updates the File to write RGB data (as opposed to RAW data)
893 * (modifies, when necessary, photochromatic interpretation,
894 * samples per pixel, Planar configuration,
895 * bits allocated, bits stored, high bit -ACR 24 bits-
896 * Pixels element VR, pushes out the LUT, )
898 void FileHelper::SetWriteToRGB()
900 if ( FileInternal->GetNumberOfScalarComponents()==3 )
902 PixelReadConverter->BuildRGBImage();
904 DataEntry *spp = CopyDataEntry(0x0028,0x0002,"US");
905 spp->SetString("3 ");
907 DataEntry *planConfig = CopyDataEntry(0x0028,0x0006,"US");
908 planConfig->SetString("0 ");
910 DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS");
911 photInt->SetString("RGB ");
913 if ( PixelReadConverter->GetRGB() )
915 PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(),
916 PixelReadConverter->GetRGBSize());
920 PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
921 PixelReadConverter->GetRawSize());
924 std::string vr = "OB";
925 if ( FileInternal->GetBitsAllocated()>8 )
927 if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files
930 CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr);
931 pixel->SetFlag(DataEntry::FLAG_PIXELDATA);
932 pixel->SetBinArea(PixelWriteConverter->GetData(),false);
933 pixel->SetLength(PixelWriteConverter->GetDataSize());
936 Archive->Push(planConfig);
937 Archive->Push(photInt);
938 Archive->Push(pixel);
941 planConfig->Delete();
946 Archive->Push(0x0028,0x1101);
947 Archive->Push(0x0028,0x1102);
948 Archive->Push(0x0028,0x1103);
949 Archive->Push(0x0028,0x1201);
950 Archive->Push(0x0028,0x1202);
951 Archive->Push(0x0028,0x1203);
953 // push out Palette Color Lookup Table UID, if any
954 Archive->Push(0x0028,0x1199);
956 // For old '24 Bits' ACR-NEMA
957 // Thus, we have a RGB image and the bits allocated = 24 and
958 // samples per pixels = 1 (in the read file)
959 if ( FileInternal->GetBitsAllocated()==24 )
961 DataEntry *bitsAlloc = CopyDataEntry(0x0028,0x0100,"US");
962 bitsAlloc->SetString("8 ");
964 DataEntry *bitsStored = CopyDataEntry(0x0028,0x0101,"US");
965 bitsStored->SetString("8 ");
967 DataEntry *highBit = CopyDataEntry(0x0028,0x0102,"US");
968 highBit->SetString("7 ");
970 Archive->Push(bitsAlloc);
971 Archive->Push(bitsStored);
972 Archive->Push(highBit);
975 bitsStored->Delete();
986 * \brief Restore the File write mode
988 void FileHelper::RestoreWrite()
991 Archive->Restore(0x0028,0x0002);
992 Archive->Restore(0x0028,0x0004);
994 Archive->Restore(0x0028,0x0006);
995 Archive->Restore(GetFile()->GetGrPixel(),GetFile()->GetNumPixel());
997 // For old ACR-NEMA (24 bits problem)
998 Archive->Restore(0x0028,0x0100);
999 Archive->Restore(0x0028,0x0101);
1000 Archive->Restore(0x0028,0x0102);
1003 Archive->Restore(0x0028,0x1101);
1004 Archive->Restore(0x0028,0x1102);
1005 Archive->Restore(0x0028,0x1103);
1006 Archive->Restore(0x0028,0x1201);
1007 Archive->Restore(0x0028,0x1202);
1008 Archive->Restore(0x0028,0x1203);
1010 // For the Palette Color Lookup Table UID
1011 Archive->Restore(0x0028,0x1203);
1013 // group 0002 may be pushed out for ACR-NEMA writting purposes
1014 Archive->Restore(0x0002,0x0000);
1015 Archive->Restore(0x0002,0x0001);
1016 Archive->Restore(0x0002,0x0002);
1017 Archive->Restore(0x0002,0x0003);
1018 Archive->Restore(0x0002,0x0010);
1019 Archive->Restore(0x0002,0x0012);
1020 Archive->Restore(0x0002,0x0013);
1021 Archive->Restore(0x0002,0x0016);
1022 Archive->Restore(0x0002,0x0100);
1023 Archive->Restore(0x0002,0x0102);
1028 * \brief Pushes out the whole group 0002
1029 * FIXME : better, set a flag to tell the writer not to write it ...
1030 * FIXME : method should probably have an other name !
1031 * SetWriteFileTypeToACR is NOT opposed to
1032 * SetWriteFileTypeToExplicitVR and SetWriteFileTypeToImplicitVR
1034 void FileHelper::SetWriteFileTypeToACR()
1036 Archive->Push(0x0002,0x0000);
1037 Archive->Push(0x0002,0x0001);
1038 Archive->Push(0x0002,0x0002);
1039 Archive->Push(0x0002,0x0003);
1040 Archive->Push(0x0002,0x0010);
1041 Archive->Push(0x0002,0x0012);
1042 Archive->Push(0x0002,0x0013);
1043 Archive->Push(0x0002,0x0016);
1044 Archive->Push(0x0002,0x0100);
1045 Archive->Push(0x0002,0x0102);
1049 * \brief Sets in the File the TransferSyntax to 'JPEG'
1051 void FileHelper::SetWriteFileTypeToJPEG()
1053 std::string ts = Util::DicomString(
1054 Global::GetTS()->GetSpecialTransferSyntax(TS::JPEGBaselineProcess1) );
1056 DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
1064 * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian"
1066 void FileHelper::SetWriteFileTypeToExplicitVR()
1068 std::string ts = Util::DicomString(
1069 Global::GetTS()->GetSpecialTransferSyntax(TS::ExplicitVRLittleEndian) );
1071 DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
1078 * \brief Sets in the File the TransferSyntax to 'Implicit VR Little Endian"
1080 void FileHelper::SetWriteFileTypeToImplicitVR()
1082 std::string ts = Util::DicomString(
1083 Global::GetTS()->GetSpecialTransferSyntax(TS::ImplicitVRLittleEndian) );
1085 DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
1093 * \brief Restore in the File the initial group 0002
1095 void FileHelper::RestoreWriteFileType()
1100 * \brief Set the Write not to Libido format
1102 void FileHelper::SetWriteToLibido()
1104 DataEntry *oldRow = FileInternal->GetDataEntry(0x0028, 0x0010);
1105 DataEntry *oldCol = FileInternal->GetDataEntry(0x0028, 0x0011);
1107 if ( oldRow && oldCol )
1109 std::string rows, columns;
1111 //DataEntry *newRow=DataEntry::New(oldRow->GetDictEntry());
1112 //DataEntry *newCol=DataEntry::New(oldCol->GetDictEntry());
1114 DataEntry *newRow=DataEntry::New(0x0028, 0x0010, "US");
1115 DataEntry *newCol=DataEntry::New(0x0028, 0x0011, "US");
1117 newRow->Copy(oldCol);
1118 newCol->Copy(oldRow);
1120 newRow->SetString(oldCol->GetString());
1121 newCol->SetString(oldRow->GetString());
1123 Archive->Push(newRow);
1124 Archive->Push(newCol);
1130 DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010,"LO");
1131 libidoCode->SetString("ACRNEMA_LIBIDO_1.1");
1132 Archive->Push(libidoCode);
1133 libidoCode->Delete();
1137 * \brief Set the Write not to No Libido format
1139 void FileHelper::SetWriteToNoLibido()
1141 DataEntry *recCode = FileInternal->GetDataEntry(0x0008,0x0010);
1144 if ( recCode->GetString() == "ACRNEMA_LIBIDO_1.1" )
1146 DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010,"LO");
1147 libidoCode->SetString("");
1148 Archive->Push(libidoCode);
1149 libidoCode->Delete();
1155 * \brief Restore the Write format
1157 void FileHelper::RestoreWriteOfLibido()
1159 Archive->Restore(0x0028,0x0010);
1160 Archive->Restore(0x0028,0x0011);
1161 Archive->Restore(0x0008,0x0010);
1163 // Restore 'LibIDO-special' entries, if any
1164 Archive->Restore(0x0028,0x0015);
1165 Archive->Restore(0x0028,0x0016);
1166 Archive->Restore(0x0028,0x0017);
1167 Archive->Restore(0x0028,0x00199);
1171 * \brief Duplicates a DataEntry or creates it.
1172 * @param group Group number of the Entry
1173 * @param elem Element number of the Entry
1174 * @param vr Value Representation of the Entry
1175 * \return pointer to the new Bin Entry (NULL when creation failed).
1177 DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem,
1180 DocEntry *oldE = FileInternal->GetDocEntry(group, elem);
1183 if ( oldE && vr != GDCM_VRUNKNOWN )
1184 if ( oldE->GetVR() != vr )
1189 //newE = DataEntry::New(oldE->GetDictEntry());
1190 newE = DataEntry::New(group, elem, vr);
1195 newE = GetFile()->NewDataEntry(group, elem, vr);
1202 * \brief This method is called automatically, just before writting
1203 * in order to produce a 'True Dicom V3' image.
1205 * We cannot know *how* the user made the File :
1206 * (reading an old ACR-NEMA file or a not very clean DICOM file ...)
1207 * Just before writting :
1208 * - we check the Entries
1209 * - we create the mandatory entries if they are missing
1210 * - we modify the values if necessary
1211 * - we push the sensitive entries to the Archive
1212 * The writing process will restore the entries as they where before
1213 * entering FileHelper::CheckMandatoryElements, so the user will always
1214 * see the entries just as they were before he decided to write.
1217 * - Entries whose type is 1 are mandatory, with a mandatory value
1218 * - Entries whose type is 1c are mandatory-inside-a-Sequence,
1219 * with a mandatory value
1220 * - Entries whose type is 2 are mandatory, with an optional value
1221 * - Entries whose type is 2c are mandatory-inside-a-Sequence,
1222 * with an optional value
1223 * - Entries whose type is 3 are optional
1226 * - warn the user if we had to add some entries :
1227 * even if a mandatory entry is missing, we add it, with a default value
1228 * (we don't want to give up the writting process if user forgot to
1229 * specify Lena's Patient ID, for instance ...)
1230 * - read the whole PS 3.3 Part of DICOM (890 pages)
1231 * and write a *full* checker (probably one method per Modality ...)
1232 * Any contribution is welcome.
1233 * - write a user callable full checker, to allow post reading
1234 * and/or pre writting image consistency check.
1237 /* -------------------------------------------------------------------------------------
1238 To be moved to User's guide / WIKI ?
1240 We have to deal with 4 *very* different cases :
1241 -1) user created ex nihilo his own image and wants to write it as a Dicom image.
1243 -2) user modified the pixels of an existing image.
1245 -3) user created a new image, using a set of existing images (eg MIP, MPR, cartography image)
1247 -4) user modified/added some tags *without processing* the pixels (anonymization..
1248 UNMODIFIED_PIXELS_IMAGE
1249 -Probabely some more to be added
1251 gdcm::FileHelper::CheckMandatoryElements() deals automatically with these cases.
1254 0008 0012 Instance Creation Date
1255 0008 0013 Instance Creation Time
1256 0008 0018 SOP Instance UID
1257 are *always* created with the current values; user has *no* possible intervention on
1260 'Serie Instance UID'(0x0020,0x000e)
1261 'Study Instance UID'(0x0020,0x000d) are kept as is if already exist,
1262 created if it doesn't.
1263 The user is allowed to create his own Series/Studies,
1264 keeping the same 'Serie Instance UID' / 'Study Instance UID' for various images
1266 The user shouldn't add any image to a 'Manufacturer Serie'
1267 but there is no way no to allow him to do that
1269 None of the 'shadow elements' are droped out.
1273 'Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image).
1276 'Media Storage SOP Class UID' (0x0002,0x0002)
1277 'SOP Class UID' (0x0008,0x0016) are set to
1278 [Secondary Capture Image Storage]
1279 'Image Type' (0x0008,0x0008) is forced to "DERIVED\PRIMARY"
1280 Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image)
1283 If 'SOP Class UID' exists in the native image ('true DICOM' image)
1284 we create the 'Source Image Sequence' SeqEntry (0x0008, 0x2112)
1285 --> 'Referenced SOP Class UID' (0x0008, 0x1150)
1286 whose value is the original 'SOP Class UID'
1287 --> 'Referenced SOP Instance UID' (0x0008, 0x1155)
1288 whose value is the original 'SOP Class UID'
1290 3) TODO : find a trick to allow user to pass to the writter the list of the Dicom images
1291 or the Series, (or the Study ?) he used to created his image
1292 (MIP, MPR, cartography image, ...)
1293 These info should be stored (?)
1294 0008 1110 SQ 1 Referenced Study Sequence
1295 0008 1115 SQ 1 Referenced Series Sequence
1296 0008 1140 SQ 1 Referenced Image Sequence
1298 4) When user *knows* he didn't modified the pixels, we keep some informations unchanged :
1299 'Media Storage SOP Class UID' (0x0002,0x0002)
1300 'SOP Class UID' (0x0008,0x0016)
1301 'Image Type' (0x0008,0x0008)
1302 'Conversion Type' (0x0008,0x0064)
1305 Bellow follows the full description (hope so !) of the consistency checks performed
1306 by gdcm::FileHelper::CheckMandatoryElements()
1309 -->'Media Storage SOP Class UID' (0x0002,0x0002)
1310 -->'SOP Class UID' (0x0008,0x0016) are defaulted to
1311 [Secondary Capture Image Storage]
1312 --> 'Image Type' (0x0008,0x0008)
1313 is forced to "DERIVED\PRIMARY"
1314 (The written image is no longer an 'ORIGINAL' one)
1315 Except if user knows he didn't modify the image (e.g. : he just anonymized the file)
1317 --> Conversion Type (0x0008,0x0064)
1318 is defaulted to 'SYN' (Synthetic Image)
1319 when *he* knows he created his own image ex nihilo
1321 --> 'Modality' (0x0008,0x0060)
1322 is defaulted to "OT" (other) if missing.
1323 (a fully user created image belongs to *no* modality)
1325 --> 'Media Storage SOP Instance UID' (0x0002,0x0003)
1326 --> 'Implementation Class UID' (0x0002,0x0012)
1327 are automatically generated; no user intervention possible
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'
1336 The user shouldn't add any image to a 'Manufacturer Serie'
1337 but there is no way no to allowed him to do that
1339 --> If 'SOP Class UID' exists in the native image ('true DICOM' image)
1340 we create the 'Source Image Sequence' SeqEntry (0x0008, 0x2112)
1342 --> 'Referenced SOP Class UID' (0x0008, 0x1150)
1343 whose value is the original 'SOP Class UID'
1344 --> 'Referenced SOP Instance UID' (0x0008, 0x1155)
1345 whose value is the original 'SOP Class UID'
1347 --> Bits Stored, Bits Allocated, Hight Bit Position are checked for consistency
1348 --> Pixel Spacing (0x0028,0x0030) is defaulted to "1.0\1.0"
1349 --> Samples Per Pixel (0x0028,0x0002) is defaulted to 1 (grayscale)
1351 --> Imager Pixel Spacing (0x0018,0x1164) : defaulted to Pixel Spacing value
1353 --> Instance Creation Date, Instance Creation Time are forced to current Date and Time
1355 --> Study Date, Study Time are defaulted to current Date and Time
1356 (they remain unchanged if they exist)
1358 --> Patient Orientation : (0x0020,0x0020), if not present, is deduced from
1359 Image Orientation (Patient) : (0020|0037) or from
1360 Image Orientation (RET) : (0020 0035)
1362 --> Study ID, Series Number, Instance Number, Patient Orientation (Type 2)
1363 are created, with empty value if there are missing.
1365 --> Manufacturer, Institution Name, Patient's Name, (Type 2)
1366 are defaulted with a 'gdcm' value.
1368 --> Patient ID, Patient's Birth Date, Patient's Sex, (Type 2)
1369 --> Referring Physician's Name (Type 2)
1370 are created, with empty value if there are missing.
1372 -------------------------------------------------------------------------------------*/
1374 void FileHelper::CheckMandatoryElements()
1376 std::string sop = Util::CreateUniqueUID();
1378 // --------------------- For Meta Elements ---------------------
1379 // just to remember : 'official' 0002 group
1380 if ( WriteType != ACR && WriteType != ACR_LIBIDO )
1382 // Group 000002 (Meta Elements) already pushed out
1384 //0002 0000 UL 1 Meta Group Length
1385 //0002 0001 OB 1 File Meta Information Version
1386 //0002 0002 UI 1 Media Stored SOP Class UID
1387 //0002 0003 UI 1 Media Stored SOP Instance UID
1388 //0002 0010 UI 1 Transfer Syntax UID
1389 //0002 0012 UI 1 Implementation Class UID
1390 //0002 0013 SH 1 Implementation Version Name
1391 //0002 0016 AE 1 Source Application Entity Title
1392 //0002 0100 UI 1 Private Information Creator
1393 //0002 0102 OB 1 Private Information
1395 // Create them if not found
1396 // Always modify the value
1397 // Push the entries to the archive.
1398 CopyMandatoryEntry(0x0002,0x0000,"0","UL");
1400 DataEntry *e_0002_0001 = CopyDataEntry(0x0002,0x0001, "OB");
1401 e_0002_0001->SetBinArea((uint8_t*)Util::GetFileMetaInformationVersion(),
1403 e_0002_0001->SetLength(2);
1404 Archive->Push(e_0002_0001);
1405 e_0002_0001->Delete();
1407 if ( ContentType == FILTERED_IMAGE || ContentType == UNMODIFIED_PIXELS_IMAGE)
1409 // we keep the original 'Media Storage SOP Class UID', we default it if missing
1410 CheckMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7","UI");
1414 // It's *not* an image comming straight from a source. We force
1415 // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage]
1416 CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7","UI");
1419 // 'Media Storage SOP Instance UID'
1420 CopyMandatoryEntry(0x0002,0x0003,sop,"UI");
1422 // 'Implementation Class UID'
1423 // FIXME : in all examples we have, 0x0002,0x0012 is not so long :
1424 // seems to be Root UID + 4 digits (?)
1425 CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID(),"UI");
1427 // 'Implementation Version Name'
1428 std::string version = "GDCM ";
1429 version += Util::GetVersion();
1430 CopyMandatoryEntry(0x0002,0x0013,version,"SH");
1433 // --------------------- For DataSet ---------------------
1435 if ( ContentType != USER_OWN_IMAGE) // when it's not a user made image
1438 gdcmDebugMacro( "USER_OWN_IMAGE (1)");
1439 // If 'SOP Class UID' exists ('true DICOM' image)
1440 // we create the 'Source Image Sequence' SeqEntry
1441 // to hold informations about the Source Image
1443 DataEntry *e_0008_0016 = FileInternal->GetDataEntry(0x0008, 0x0016);
1446 // Create 'Source Image Sequence' SeqEntry
1447 // SeqEntry *sis = SeqEntry::New (
1448 // Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x2112) );
1449 SeqEntry *sis = SeqEntry::New (0x0008, 0x2112);
1450 SQItem *sqi = SQItem::New(1);
1451 // (we assume 'SOP Instance UID' exists too)
1452 // create 'Referenced SOP Class UID'
1453 // DataEntry *e_0008_1150 = DataEntry::New(
1454 // Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) );
1455 DataEntry *e_0008_1150 = DataEntry::New(0x0008, 0x1150, "UI");
1456 e_0008_1150->SetString( e_0008_0016->GetString());
1457 sqi->AddEntry(e_0008_1150);
1458 e_0008_1150->Delete();
1460 // create 'Referenced SOP Instance UID'
1461 DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018);
1462 // DataEntry *e_0008_1155 = DataEntry::New(
1463 // Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1155) );
1464 DataEntry *e_0008_1155 = DataEntry::New(0x0008, 0x1155, "UI");
1465 e_0008_1155->SetString( e_0008_0018->GetString());
1466 sqi->AddEntry(e_0008_1155);
1467 e_0008_1155->Delete();
1469 sis->AddSQItem(sqi,1);
1472 // temporarily replaces any previous 'Source Image Sequence'
1476 // FIXME : is 'Image Type' *really* depending on the presence of 'SOP Class UID'?
1477 if ( ContentType == FILTERED_IMAGE)
1478 // the user *knows* he just modified the pixels
1479 // the image is no longer an 'Original' one
1480 CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY","CS");
1484 if ( ContentType == FILTERED_IMAGE || ContentType == UNMODIFIED_PIXELS_IMAGE)
1486 // we keep the original 'Media Storage SOP Class UID', we default it if missing (it should be present !)
1487 CheckMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7","UI");
1491 // It's *not* an image comming straight from a source. We force
1492 // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage]
1493 CopyMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7", "UI");
1496 Archive->Push(0x0028,0x005); // [Image Dimensions (RET)
1497 // Push out 'LibIDO-special' entries, if any
1498 Archive->Push(0x0028,0x0015);
1499 Archive->Push(0x0028,0x0016);
1500 Archive->Push(0x0028,0x0017);
1501 Archive->Push(0x0028,0x0198); // very old versions
1502 Archive->Push(0x0028,0x0199);
1504 // Replace deprecated 0028 0012 US Planes
1505 // by new 0028 0008 IS Number of Frames
1507 ///\todo : find if there is a rule!
1508 DataEntry *e_0028_0012 = FileInternal->GetDataEntry(0x0028, 0x0012);
1511 CopyMandatoryEntry(0x0028, 0x0008,e_0028_0012->GetString(),"IS");
1512 Archive->Push(0x0028,0x0012);
1515 // Deal with the pb of (Bits Stored = 12)
1516 // - we're gonna write the image as Bits Stored = 16
1517 if ( FileInternal->GetEntryString(0x0028,0x0100) == "12")
1519 CopyMandatoryEntry(0x0028,0x0100,"16","US");
1522 // Check if user wasn't drunk ;-)
1524 std::ostringstream s;
1525 // check 'Bits Allocated' vs decent values
1526 int nbBitsAllocated = FileInternal->GetBitsAllocated();
1527 if ( nbBitsAllocated == 0 || nbBitsAllocated > 32)
1529 CopyMandatoryEntry(0x0028,0x0100,"16","US");
1530 gdcmWarningMacro("(0028,0100) changed from "
1531 << nbBitsAllocated << " to 16 for consistency purpose");
1532 nbBitsAllocated = 16;
1534 // check 'Bits Stored' vs 'Bits Allocated'
1535 int nbBitsStored = FileInternal->GetBitsStored();
1536 if ( nbBitsStored == 0 || nbBitsStored > nbBitsAllocated )
1539 s << nbBitsAllocated;
1540 CopyMandatoryEntry(0x0028,0x0101,s.str(),"US");
1541 gdcmWarningMacro("(0028,0101) changed from "
1542 << nbBitsStored << " to " << nbBitsAllocated
1543 << " for consistency purpose" );
1544 nbBitsStored = nbBitsAllocated;
1546 // check 'Hight Bit Position' vs 'Bits Allocated' and 'Bits Stored'
1547 int highBitPosition = FileInternal->GetHighBitPosition();
1548 if ( highBitPosition == 0 ||
1549 highBitPosition > nbBitsAllocated-1 ||
1550 highBitPosition < nbBitsStored-1 )
1553 s << nbBitsStored - 1;
1554 CopyMandatoryEntry(0x0028,0x0102,s.str(),"US");
1555 gdcmWarningMacro("(0028,0102) changed from "
1556 << highBitPosition << " to " << nbBitsAllocated-1
1557 << " for consistency purpose");
1560 std::string pixelSpacing = FileInternal->GetEntryString(0x0028,0x0030);
1561 if ( pixelSpacing == GDCM_UNFOUND )
1563 pixelSpacing = "1.0\\1.0";
1564 // if missing, Pixel Spacing forced to "1.0\1.0"
1565 CopyMandatoryEntry(0x0028,0x0030,pixelSpacing,"DS");
1568 // 'Imager Pixel Spacing' : defaulted to 'Pixel Spacing'
1569 // --> This one is the *legal* one !
1570 if ( ContentType != USER_OWN_IMAGE)
1571 // we write it only when we are *sure* the image comes from
1572 // an imager (see also 0008,0x0064)
1573 CheckMandatoryEntry(0x0018,0x1164,pixelSpacing,"DS");
1578 ///Exact meaning of RETired fields
1580 // See page 73 of ACR-NEMA_300-1988.pdf !
1582 // 0020,0020 : Patient Orientation :
1583 Patient direction of the first row and
1584 column of the images. The first entry id the direction of the raws, given by the
1585 direction of the last pixel in the first row from the first pixel in tha row.
1586 the second entry is the direction of the columns, given by the direction of the
1587 last pixel in the first column from the first pixel in that column.
1588 L : Left, F : Feet, A : Anterior, P : Posterior.
1589 Up to 3 letters can be used in combination to indicate oblique planes.
1591 //0020,0030 Image Position (RET)
1592 x,y,z coordinates im mm of the first pixel in the image
1594 // 0020,0035 Image Orientation (RET)
1595 Direction cosines of the R axis of the image system with respect to the
1596 equipment coordinate axes x,y,z, followed by direction cosines of the C axis of
1597 the image system with respect to the same axes
1599 //0020,0050 Location
1600 An image location reference, standard for the modality (such as CT bed
1601 position), used to indicate position. Calculation of position for other purposes
1602 is only from (0020,0030) and (0020,0035)
1606 // if imagePositionPatient not found, default it with imagePositionRet, if any
1607 // if imageOrientationPatient not found, default it with imageOrientationRet, if any
1609 std::string imagePositionRet = FileInternal->GetEntryString(0x0020,0x0030);
1610 std::string imageOrientationRet = FileInternal->GetEntryString(0x0020,0x0035);
1611 std::string imagePositionPatient = FileInternal->GetEntryString(0x0020,0x0032);
1612 std::string imageOrientationPatient = FileInternal->GetEntryString(0x0020,0x0037);
1614 if( imagePositionPatient == GDCM_UNFOUND && imageOrientationPatient == GDCM_UNFOUND
1615 && imagePositionRet != GDCM_UNFOUND && imageOrientationRet != GDCM_UNFOUND)
1617 CopyMandatoryEntry(0x0020, 0x0032,imagePositionRet,"DS");
1618 Archive->Push(0x0020,0x0030);
1619 CopyMandatoryEntry(0x0020, 0x0037,imageOrientationRet,"DS");
1620 Archive->Push(0x0020,0x0035);
1624 // Samples Per Pixel (type 1) : default to grayscale
1625 CheckMandatoryEntry(0x0028,0x0002,"1","US");
1627 // --- Check UID-related Entries ---
1629 // At the end, not to overwrite the original ones,
1630 // needed by 'Referenced SOP Instance UID', 'Referenced SOP Class UID'
1631 // 'SOP Instance UID'
1632 CopyMandatoryEntry(0x0008,0x0018,sop,"UI");
1634 if ( ContentType == USER_OWN_IMAGE)
1636 gdcmDebugMacro( "USER_OWN_IMAGE (2)");
1638 // Other possible values are :
1639 // See PS 3.3, Page 408
1641 // DV = Digitized Video
1642 // DI = Digital Interface
1643 // DF = Digitized Film
1644 // WSD = Workstation
1645 // SD = Scanned Document
1646 // SI = Scanned Image
1648 // SYN = Synthetic Image
1650 CheckMandatoryEntry(0x0008,0x0064,"SYN","CS"); // Why not?
1653 if ( ContentType == CREATED_IMAGE)
1655 /// \todo : find a trick to pass the Media Storage SOP Instance UID of the images used to create the current image
1660 // ---- The user will never have to take any action on the following ----
1662 // new value for 'SOP Instance UID'
1663 //SetMandatoryEntry(0x0008,0x0018,Util::CreateUniqueUID());
1665 // Instance Creation Date
1666 const std::string &date = Util::GetCurrentDate();
1667 CopyMandatoryEntry(0x0008,0x0012,date,"DA");
1669 // Instance Creation Time
1670 const std::string &time = Util::GetCurrentTime();
1671 CopyMandatoryEntry(0x0008,0x0013,time,"TM");
1674 CheckMandatoryEntry(0x0008,0x0020,date,"DA");
1676 CheckMandatoryEntry(0x0008,0x0030,time,"TM");
1679 //CopyMandatoryEntry(0x0008,0x0050,"");
1680 CheckMandatoryEntry(0x0008,0x0050,"","SH");
1683 // ----- Add Mandatory Entries if missing ---
1684 // Entries whose type is 1 are mandatory, with a mandatory value
1685 // Entries whose type is 1c are mandatory-inside-a-Sequence,
1686 // with a mandatory value
1687 // Entries whose type is 2 are mandatory, with an optional value
1688 // Entries whose type is 2c are mandatory-inside-a-Sequence,
1689 // with an optional value
1690 // Entries whose type is 3 are optional
1692 // 'Study Instance UID'
1693 // Keep the value if exists
1694 // The user is allowed to create his own Study,
1695 // keeping the same 'Study Instance UID' for various images
1696 // The user may add images to a 'Manufacturer Study',
1697 // adding new Series to an already existing Study
1698 CheckMandatoryEntry(0x0020,0x000d,Util::CreateUniqueUID(),"UI");
1700 // 'Serie Instance UID'
1701 // Keep the value if exists
1702 // The user is allowed to create his own Series,
1703 // keeping the same 'Serie Instance UID' for various images
1704 // The user shouldn't add any image to a 'Manufacturer Serie'
1705 // but there is no way no to prevent him for doing that
1706 CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID(),"UI");
1709 CheckMandatoryEntry(0x0020,0x0010,"","SH");
1712 CheckMandatoryEntry(0x0020,0x0011,"","IS");
1715 CheckMandatoryEntry(0x0020,0x0013,"","IS");
1717 // Patient Orientation
1718 // Can be computed from (0020|0037) : Image Orientation (Patient)
1719 gdcm::Orientation *o = gdcm::Orientation::New();
1720 std::string ori = o->GetOrientation ( FileInternal );
1722 if (ori != "\\" && ori != GDCM_UNFOUND)
1723 CheckMandatoryEntry(0x0020,0x0020,ori,"CS");
1725 CheckMandatoryEntry(0x0020,0x0020,"","CS");
1727 // Default Patient Position to HFS
1728 CheckMandatoryEntry(0x0018,0x5100,"HFS","CS");
1730 // Modality : if missing we set it to 'OTher'
1731 CheckMandatoryEntry(0x0008,0x0060,"OT","CS");
1733 // Manufacturer : if missing we set it to 'GDCM Factory'
1734 CheckMandatoryEntry(0x0008,0x0070,"GDCM Factory","LO");
1736 // Institution Name : if missing we set it to 'GDCM Hospital'
1737 CheckMandatoryEntry(0x0008,0x0080,"GDCM Hospital","LO");
1739 // Patient's Name : if missing, we set it to 'GDCM^Patient'
1740 CheckMandatoryEntry(0x0010,0x0010,"GDCM^Patient","PN");
1742 // Patient ID : some clinical softwares *demand* it although it's a 'type 2' entry.
1743 CheckMandatoryEntry(0x0010,0x0020,"gdcm ID","LO");
1745 // Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory
1746 CheckMandatoryEntry(0x0010,0x0030,"","DA");
1748 // Patient's Sex :'type 2' entry -> must exist, value not mandatory
1749 CheckMandatoryEntry(0x0010,0x0040,"","CS");
1751 // Referring Physician's Name :'type 2' entry -> must exist, value not mandatory
1752 CheckMandatoryEntry(0x0008,0x0090,"","PN");
1755 // Deal with element 0x0000 (group length) of each group.
1756 // First stage : get all the different Groups
1759 DocEntry *d = FileInternal->GetFirstEntry();
1762 grHT[d->GetGroup()] = 0;
1763 d=FileInternal->GetNextEntry();
1765 // Second stage : add the missing ones (if any)
1766 for (GroupHT::iterator it = grHT.begin(); it != grHT.end(); ++it)
1768 CheckMandatoryEntry(it->first, 0x0000, "0");
1770 // Third stage : update all 'zero level' groups length
1775 void FileHelper::CheckMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr )
1777 DataEntry *entry = FileInternal->GetDataEntry(group,elem);
1780 //entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
1781 entry = DataEntry::New(group,elem,vr);
1782 entry->SetString(value);
1783 Archive->Push(entry);
1788 /// \todo : what is it used for ? (FileHelper::SetMandatoryEntry)
1789 void FileHelper::SetMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr)
1791 //DataEntry *entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
1792 DataEntry *entry = DataEntry::New(group,elem,vr);
1793 entry->SetString(value);
1794 Archive->Push(entry);
1798 void FileHelper::CopyMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr)
1800 DataEntry *entry = CopyDataEntry(group,elem,vr);
1801 entry->SetString(value);
1802 Archive->Push(entry);
1807 * \brief Restore in the File the initial group 0002
1809 void FileHelper::RestoreWriteMandatory()
1811 // group 0002 may be pushed out for ACR-NEMA writting purposes
1812 Archive->Restore(0x0002,0x0000);
1813 Archive->Restore(0x0002,0x0001);
1814 Archive->Restore(0x0002,0x0002);
1815 Archive->Restore(0x0002,0x0003);
1816 Archive->Restore(0x0002,0x0010);
1817 Archive->Restore(0x0002,0x0012);
1818 Archive->Restore(0x0002,0x0013);
1819 Archive->Restore(0x0002,0x0016);
1820 Archive->Restore(0x0002,0x0100);
1821 Archive->Restore(0x0002,0x0102);
1823 // FIXME : Check if none is missing !
1825 Archive->Restore(0x0008,0x0012);
1826 Archive->Restore(0x0008,0x0013);
1827 Archive->Restore(0x0008,0x0016);
1828 Archive->Restore(0x0008,0x0018);
1829 Archive->Restore(0x0008,0x0060);
1830 Archive->Restore(0x0008,0x0070);
1831 Archive->Restore(0x0008,0x0080);
1832 Archive->Restore(0x0008,0x0090);
1833 Archive->Restore(0x0008,0x2112);
1835 Archive->Restore(0x0010,0x0010);
1836 Archive->Restore(0x0010,0x0030);
1837 Archive->Restore(0x0010,0x0040);
1839 Archive->Restore(0x0020,0x000d);
1840 Archive->Restore(0x0020,0x000e);
1845 * \brief CallStartMethod
1847 void FileHelper::CallStartMethod()
1851 CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS);
1855 * \brief CallProgressMethod
1857 void FileHelper::CallProgressMethod()
1859 CommandManager::ExecuteCommand(this,CMD_PROGRESS);
1863 * \brief CallEndMethod
1865 void FileHelper::CallEndMethod()
1868 CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS);
1871 //-----------------------------------------------------------------------------
1874 * \brief Factorization for various forms of constructors.
1876 void FileHelper::Initialize()
1879 ContentType = USER_OWN_IMAGE;
1881 WriteMode = WMODE_RAW;
1882 WriteType = ExplicitVR;
1884 PixelReadConverter = new PixelReadConvert;
1885 PixelWriteConverter = new PixelWriteConvert;
1886 Archive = new DocEntryArchive( FileInternal );
1890 * \brief Reads/[decompresses] the pixels,
1891 * *without* making RGB from Palette Colors
1892 * @return the pixels area, whatever its type
1893 * (uint8_t is just for prototyping : feel free to Cast it)
1895 uint8_t *FileHelper::GetRaw()
1897 PixelReadConverter->SetUserFunction( UserFunction );
1899 uint8_t *raw = PixelReadConverter->GetRaw();
1902 // The Raw image migth not be loaded yet:
1903 std::ifstream *fp = FileInternal->OpenFile();
1904 PixelReadConverter->ReadAndDecompressPixelData( fp );
1906 FileInternal->CloseFile();
1908 raw = PixelReadConverter->GetRaw();
1911 gdcmWarningMacro( "Read/decompress of pixel data apparently went wrong.");
1918 //-----------------------------------------------------------------------------
1920 * \brief Prints the common part of DataEntry, SeqEntry
1921 * @param os ostream we want to print in
1922 * @param indent (unused)
1924 void FileHelper::Print(std::ostream &os, std::string const &)
1926 FileInternal->SetPrintLevel(PrintLevel);
1927 FileInternal->Print(os);
1929 if ( FileInternal->IsReadable() )
1931 PixelReadConverter->SetPrintLevel(PrintLevel);
1932 PixelReadConverter->Print(os);
1936 //-----------------------------------------------------------------------------
1937 } // end namespace gdcm
1940 /* Probabely something to be added to use Rescale Slope/Intercept
1941 Have a look ,at ITK code !
1943 // Internal function to rescale pixel according to Rescale Slope/Intercept
1944 template<class TBuffer, class TSource>
1945 void RescaleFunction(TBuffer* buffer, TSource *source,
1946 double slope, double intercept, size_t size)
1948 size /= sizeof(TSource);
1950 if (slope != 1.0 && intercept != 0.0)
1952 // Duff's device. Instead of this code:
1954 // for(unsigned int i=0; i<size; i++)
1956 // buffer[i] = (TBuffer)(source[i]*slope + intercept);
1959 // use Duff's device which exploits "fall through"
1960 register size_t n = (size + 7) / 8;
1963 case 0: do { *buffer++ = (TBuffer)((*source++)*slope + intercept);
1964 case 7: *buffer++ = (TBuffer)((*source++)*slope + intercept);
1965 case 6: *buffer++ = (TBuffer)((*source++)*slope + intercept);
1966 case 5: *buffer++ = (TBuffer)((*source++)*slope + intercept);
1967 case 4: *buffer++ = (TBuffer)((*source++)*slope + intercept);
1968 case 3: *buffer++ = (TBuffer)((*source++)*slope + intercept);
1969 case 2: *buffer++ = (TBuffer)((*source++)*slope + intercept);
1970 case 1: *buffer++ = (TBuffer)((*source++)*slope + intercept);
1974 else if (slope == 1.0 && intercept != 0.0)
1976 // Duff's device. Instead of this code:
1978 // for(unsigned int i=0; i<size; i++)
1980 // buffer[i] = (TBuffer)(source[i] + intercept);
1983 // use Duff's device which exploits "fall through"
1984 register size_t n = (size + 7) / 8;
1987 case 0: do { *buffer++ = (TBuffer)(*source++ + intercept);
1988 case 7: *buffer++ = (TBuffer)(*source++ + intercept);
1989 case 6: *buffer++ = (TBuffer)(*source++ + intercept);
1990 case 5: *buffer++ = (TBuffer)(*source++ + intercept);
1991 case 4: *buffer++ = (TBuffer)(*source++ + intercept);
1992 case 3: *buffer++ = (TBuffer)(*source++ + intercept);
1993 case 2: *buffer++ = (TBuffer)(*source++ + intercept);
1994 case 1: *buffer++ = (TBuffer)(*source++ + intercept);
1998 else if (slope != 1.0 && intercept == 0.0)
2000 // Duff's device. Instead of this code:
2002 // for(unsigned int i=0; i<size; i++)
2004 // buffer[i] = (TBuffer)(source[i]*slope);
2007 // use Duff's device which exploits "fall through"
2008 register size_t n = (size + 7) / 8;
2011 case 0: do { *buffer++ = (TBuffer)((*source++)*slope);
2012 case 7: *buffer++ = (TBuffer)((*source++)*slope);
2013 case 6: *buffer++ = (TBuffer)((*source++)*slope);
2014 case 5: *buffer++ = (TBuffer)((*source++)*slope);
2015 case 4: *buffer++ = (TBuffer)((*source++)*slope);
2016 case 3: *buffer++ = (TBuffer)((*source++)*slope);
2017 case 2: *buffer++ = (TBuffer)((*source++)*slope);
2018 case 1: *buffer++ = (TBuffer)((*source++)*slope);
2024 // Duff's device. Instead of this code:
2026 // for(unsigned int i=0; i<size; i++)
2028 // buffer[i] = (TBuffer)(source[i]);
2031 // use Duff's device which exploits "fall through"
2032 register size_t n = (size + 7) / 8;
2035 case 0: do { *buffer++ = (TBuffer)(*source++);
2036 case 7: *buffer++ = (TBuffer)(*source++);
2037 case 6: *buffer++ = (TBuffer)(*source++);
2038 case 5: *buffer++ = (TBuffer)(*source++);
2039 case 4: *buffer++ = (TBuffer)(*source++);
2040 case 3: *buffer++ = (TBuffer)(*source++);
2041 case 2: *buffer++ = (TBuffer)(*source++);
2042 case 1: *buffer++ = (TBuffer)(*source++);
2051 template<class TSource>
2052 void RescaleFunction(ImageIOBase::IOComponentType bufferType,
2053 void* buffer, TSource *source,
2054 double slope, double intercept, size_t size)
2058 case ImageIOBase::UCHAR:
2059 RescaleFunction( (unsigned char *)buffer, source, slope, intercept, size);
2061 case ImageIOBase::CHAR:
2062 RescaleFunction( (char *)buffer, source, slope, intercept, size);
2064 case ImageIOBase::USHORT:
2065 RescaleFunction( (unsigned short *)buffer, source, slope, intercept,size);
2067 case ImageIOBase::SHORT:
2068 RescaleFunction( (short *)buffer, source, slope, intercept, size);
2070 case ImageIOBase::UINT:
2071 RescaleFunction( (unsigned int *)buffer, source, slope, intercept, size);
2073 case ImageIOBase::INT:
2074 RescaleFunction( (int *)buffer, source, slope, intercept, size);
2076 case ImageIOBase::FLOAT:
2077 RescaleFunction( (float *)buffer, source, slope, intercept, size);
2079 case ImageIOBase::DOUBLE:
2080 RescaleFunction( (double *)buffer, source, slope, intercept, size);
2083 ::itk::OStringStream message;
2084 message << "itk::ERROR: GDCMImageIO: Unknown component type : " << bufferType;
2085 ::itk::ExceptionObject e(__FILE__, __LINE__, message.str().c_str(),ITK_LOCATION);