X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFileHelper.cxx;h=3357faa8f85dde82ad697a17ba18de0a89c7d912;hb=928d3c30e40ab7f3d12bfd038ce8a48befcddce8;hp=583a619297edf04e7c93673f42596f9ae82416d3;hpb=408fab710453f393e745037b04ae8aec68509b87;p=gdcm.git diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx index 583a6192..3357faa8 100644 --- a/src/gdcmFileHelper.cxx +++ b/src/gdcmFileHelper.cxx @@ -4,8 +4,8 @@ Module: $RCSfile: gdcmFileHelper.cxx,v $ Language: C++ - Date: $Date: 2005/04/19 12:31:56 $ - Version: $Revision: 1.34 $ + Date: $Date: 2005/10/21 10:29:51 $ + Version: $Revision: 1.66 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -23,11 +23,9 @@ #include "gdcmDocument.h" #include "gdcmDebug.h" #include "gdcmUtil.h" -#include "gdcmBinEntry.h" -#include "gdcmValEntry.h" #include "gdcmSeqEntry.h" #include "gdcmSQItem.h" -#include "gdcmContentEntry.h" +#include "gdcmDataEntry.h" #include "gdcmFile.h" #include "gdcmPixelReadConvert.h" #include "gdcmPixelWriteConvert.h" @@ -42,32 +40,43 @@ These lines will be moved to the document-to-be 'User's Guide' // To read an image, user needs a gdcm::File -gdcm::File *f1 = new gdcm::File(fileName); +gdcm::File *f = new gdcm::File(fileName); +// or (advanced) : +// user may also decide he doesn't want to load some parts of the header +gdcm::File *f = new gdcm::File(); +f->SetFileName(fileName); + f->SetLoadMode(LD_NOSEQ); // or + f->SetLoadMode(LD_NOSHADOW); // or + f->SetLoadMode(LD_NOSEQ | LD_NOSHADOW); // or + f->SetLoadMode(LD_NOSHADOWSEQ); +f->Load(); + // user can now check some values -std::string v = f1->GetEntryValue(groupNb,ElementNb); +std::string v = f->GetEntryValue(groupNb,ElementNb); + // to get the pixels, user needs a gdcm::FileHelper -gdcm::FileHelper *fh1 = new gdcm::FileHelper(f1); +gdcm::FileHelper *fh = new gdcm::FileHelper(f); // user may ask not to convert Palette to RGB -uint8_t *pixels = fh1->GetImageDataRaw(); -int imageLength = fh1->GetImageDataRawSize(); +uint8_t *pixels = fh->GetImageDataRaw(); +int imageLength = fh->GetImageDataRawSize(); // He can now use the pixels, create a new image, ... uint8_t *userPixels = ... To re-write the image, user re-uses the gdcm::FileHelper -fh1->SetImageData( userPixels, userPixelsLength); -fh1->SetTypeToRaw(); // Even if it was possible to convert Palette to RGB +fh->SetImageData( userPixels, userPixelsLength); +fh->SetTypeToRaw(); // Even if it was possible to convert Palette to RGB // (WriteMode is set) -fh1->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation +fh->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation // Little Endian is the default // no other value is allowed (-->SetWriteType(ExplicitVR);) -->WriteType = ExplicitVR; -fh1->Write(newFileName); // overwrites the file, if any +fh->Write(newFileName); // overwrites the file, if any // or : -fh1->WriteDcmExplVR(newFileName); +fh->WriteDcmExplVR(newFileName); // ----------------------------- WARNING ------------------------- @@ -89,7 +98,7 @@ fh1->Write(newFileName); (checks user given pixels length) FileInternal->Write(fileName,WriteType) fp = opens file(fileName); - ComputeGroup0002Length(writetype); + ComputeGroup0002Length( ); BitsAllocated 12->16 RemoveEntryNoDestroy(palettes, etc) Document::WriteContent(fp, writetype); @@ -112,6 +121,7 @@ namespace gdcm * Opens (in read only and when possible) an existing file and checks * for DICOM compliance. Returns NULL on failure. * It will be up to the user to load the pixels into memory + * ( GetImageDataSize() + GetImageData() methods) * \note the in-memory representation of all available tags found in * the DICOM header is post-poned to first header information access. * This avoid a double parsing of public part of the header when @@ -119,7 +129,7 @@ namespace gdcm * seen as a side effect). */ FileHelper::FileHelper( ) -{ +{ FileInternal = new File( ); SelfHeader = true; Initialize(); @@ -131,6 +141,7 @@ FileHelper::FileHelper( ) * Opens (in read only and when possible) an existing file and checks * for DICOM compliance. Returns NULL on failure. * It will be up to the user to load the pixels into memory + * ( GetImageDataSize() + GetImageData() methods) * \note the in-memory representation of all available tags found in * the DICOM header is post-poned to first header information access. * This avoid a double parsing of public part of the header when @@ -143,10 +154,16 @@ FileHelper::FileHelper(File *header) FileInternal = header; SelfHeader = false; Initialize(); + if ( FileInternal->IsReadable() ) + { + PixelReadConverter->GrabInformationsFromFile( FileInternal ); + } } +#ifndef GDCM_LEGACY_REMOVE /** - * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 + * \brief DEPRECATED : use SetFilename() + SetLoadMode() + Load() methods + * Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 * file (gdcm::File only deals with the ... header) * Opens (in read only and when possible) an existing file and checks * for DICOM compliance. Returns NULL on failure. @@ -157,13 +174,21 @@ FileHelper::FileHelper(File *header) * one sets an a posteriori shadow dictionary (efficiency can be * seen as a side effect). * @param filename file to be opened for parsing + * @deprecated use SetFilename() + Load() methods */ FileHelper::FileHelper(std::string const &filename ) { - FileInternal = new File( filename ); + FileInternal = new File( ); + FileInternal->SetFileName( filename ); + FileInternal->Load(); SelfHeader = true; Initialize(); + if ( FileInternal->IsReadable() ) + { + PixelReadConverter->GrabInformationsFromFile( FileInternal ); + } } +#endif /** * \brief canonical destructor @@ -172,20 +197,20 @@ FileHelper::FileHelper(std::string const &filename ) */ FileHelper::~FileHelper() { - if( PixelReadConverter ) + if ( PixelReadConverter ) { delete PixelReadConverter; } - if( PixelWriteConverter ) + if ( PixelWriteConverter ) { delete PixelWriteConverter; } - if( Archive ) + if ( Archive ) { delete Archive; } - if( SelfHeader ) + if ( SelfHeader ) { delete FileInternal; } @@ -194,6 +219,43 @@ FileHelper::~FileHelper() //----------------------------------------------------------------------------- // Public + +/** + * \brief Sets the LoadMode of the internal gdcm::File as a boolean string. + * NO_SEQ, NO_SHADOW, NO_SHADOWSEQ + *... (nothing more, right now) + * WARNING : before using NO_SHADOW, be sure *all* your files + * contain accurate values in the 0x0000 element (if any) + * of *each* Shadow Group. The parser will fail if the size is wrong ! + * @param loadMode Load mode to be used + */ +void FileHelper::SetLoadMode(int loadMode) +{ + GetFile()->SetLoadMode( loadMode ); +} +/** + * \brief Sets the LoadMode of the internal gdcm::File + * @param fileName name of the file to be open + */ +void FileHelper::SetFileName(std::string const &fileName) +{ + FileInternal->SetFileName( fileName ); +} + +/** + * \brief Loader + * @return false if file cannot be open or no swap info was found, + * or no tag was found. + */ +bool FileHelper::Load() +{ + if ( !FileInternal->Load() ) + return false; + + PixelReadConverter->GrabInformationsFromFile( FileInternal ); + return true; +} + /** * \brief Accesses an existing DocEntry (i.e. a Dicom Element) * through it's (group, element) and modifies it's content with @@ -203,10 +265,10 @@ FileHelper::~FileHelper() * @param elem element number of the Dicom Element to modify * \return false if DocEntry not found */ -bool FileHelper::SetValEntry(std::string const &content, - uint16_t group, uint16_t elem) +bool FileHelper::SetEntryString(std::string const &content, + uint16_t group, uint16_t elem) { - return FileInternal->SetValEntry(content, group, elem); + return FileInternal->SetEntryString(content, group, elem); } @@ -220,10 +282,10 @@ bool FileHelper::SetValEntry(std::string const &content, * @param elem element number of the Dicom Element to modify * \return false if DocEntry not found */ -bool FileHelper::SetBinEntry(uint8_t *content, int lgth, - uint16_t group, uint16_t elem) +bool FileHelper::SetEntryBinArea(uint8_t *content, int lgth, + uint16_t group, uint16_t elem) { - return FileInternal->SetBinEntry(content, lgth, group, elem); + return FileInternal->SetEntryBinArea(content, lgth, group, elem); } /** @@ -235,10 +297,10 @@ bool FileHelper::SetBinEntry(uint8_t *content, int lgth, * \return pointer to the modified/created Dicom entry (NULL when creation * failed). */ -ValEntry *FileHelper::InsertValEntry(std::string const &content, - uint16_t group, uint16_t elem) +DataEntry *FileHelper::InsertEntryString(std::string const &content, + uint16_t group, uint16_t elem) { - return FileInternal->InsertValEntry(content,group,elem); + return FileInternal->InsertEntryString(content, group, elem); } /** @@ -252,10 +314,10 @@ ValEntry *FileHelper::InsertValEntry(std::string const &content, * \return pointer to the modified/created Dicom entry (NULL when creation * failed). */ -BinEntry *FileHelper::InsertBinEntry(uint8_t *binArea, int lgth, - uint16_t group, uint16_t elem) +DataEntry *FileHelper::InsertEntryBinArea(uint8_t *binArea, int lgth, + uint16_t group, uint16_t elem) { - return FileInternal->InsertBinEntry(binArea, lgth, group, elem); + return FileInternal->InsertEntryBinArea(binArea, lgth, group, elem); } /** @@ -285,7 +347,6 @@ size_t FileHelper::GetImageDataSize() { return PixelWriteConverter->GetUserDataSize(); } - return PixelReadConverter->GetRGBSize(); } @@ -302,7 +363,6 @@ size_t FileHelper::GetImageDataRawSize() { return PixelWriteConverter->GetUserDataSize(); } - return PixelReadConverter->GetRawSize(); } @@ -354,9 +414,11 @@ uint8_t *FileHelper::GetImageDataRaw () return GetRaw(); } +#ifndef GDCM_LEGACY_REMOVE /** - * \brief - * Read the pixels from disk (uncompress if necessary), + * \brief Useless function, since PixelReadConverter forces us + * copy the Pixels anyway. + * Reads the pixels from disk (uncompress if necessary), * Transforms YBR pixels, if any, into RGB pixels * Transforms 3 planes R, G, B, if any, into a single RGB Plane * Transforms single Grey plane + 3 Palettes into a RGB Plane @@ -407,10 +469,11 @@ size_t FileHelper::GetImageDataIntoVector (void *destination, size_t maxSize) return 0; } memcpy( destination, - (void*)PixelReadConverter->GetRaw(), + (void *)PixelReadConverter->GetRaw(), PixelReadConverter->GetRawSize() ); return PixelReadConverter->GetRawSize(); } +#endif /** * \brief Points the internal pointer to the callers inData @@ -502,9 +565,27 @@ size_t FileHelper::GetRawDataSize() */ uint8_t* FileHelper::GetLutRGBA() { + if ( PixelReadConverter->GetLutRGBA() ==0 ) + PixelReadConverter->BuildLUTRGBA(); return PixelReadConverter->GetLutRGBA(); } +/** + * \brief Access to the underlying \ref PixelReadConverter RGBA LUT Item Number + */ +int FileHelper::GetLutItemNumber() +{ + return PixelReadConverter->GetLutItemNumber(); +} + +/** + * \brief Access to the underlying \ref PixelReadConverter RGBA LUT Item Size + */ +int FileHelper::GetLutItemSize() +{ + return PixelReadConverter->GetLutItemSize(); +} + /** * \brief Writes on disk A SINGLE Dicom file * NO test is performed on processor "Endiannity". @@ -522,19 +603,19 @@ bool FileHelper::WriteRawData(std::string const &fileName) return false; } - if( PixelWriteConverter->GetUserData() ) + if ( PixelWriteConverter->GetUserData() ) { - fp1.write( (char*)PixelWriteConverter->GetUserData(), + fp1.write( (char *)PixelWriteConverter->GetUserData(), PixelWriteConverter->GetUserDataSize() ); } else if ( PixelReadConverter->GetRGB() ) { - fp1.write( (char*)PixelReadConverter->GetRGB(), + fp1.write( (char *)PixelReadConverter->GetRGB(), PixelReadConverter->GetRGBSize()); } else if ( PixelReadConverter->GetRaw() ) { - fp1.write( (char*)PixelReadConverter->GetRaw(), + fp1.write( (char *)PixelReadConverter->GetRaw(), PixelReadConverter->GetRawSize()); } else @@ -550,7 +631,7 @@ bool FileHelper::WriteRawData(std::string const &fileName) /** * \brief Writes on disk A SINGLE Dicom file, * using the Implicit Value Representation convention - * NO test is performed on processor "Endiannity". + * NO test is performed on processor "Endianity". * @param fileName name of the file to be created * (any already existing file is overwritten) * @return false if write fails @@ -609,28 +690,30 @@ bool FileHelper::Write(std::string const &fileName) { case ImplicitVR: SetWriteFileTypeToImplicitVR(); - CheckMandatoryElements(); break; case Unknown: // should never happen; ExplicitVR is the default value case ExplicitVR: SetWriteFileTypeToExplicitVR(); - CheckMandatoryElements(); break; case ACR: case ACR_LIBIDO: - // Just to avoid further trouble if user create a file ex-nihilo, + // NOTHING is done here just for LibIDO. + // Just to avoid further trouble if user creates a file ex-nihilo, // wants to write it as an ACR-NEMA file, - // and forget to create any Entry belonging to group 0008 + // and forgets to create any Entry belonging to group 0008 // (shame on him !) // We add Recognition Code (RET) - if ( ! FileInternal->GetValEntry(0x0008, 0x0010) ) - FileInternal->InsertValEntry("", 0x0008, 0x0010); + if ( ! FileInternal->GetDataEntry(0x0008, 0x0010) ) + FileInternal->InsertEntryString("ACR-NEMA V1.0 ", 0x0008, 0x0010); SetWriteFileTypeToACR(); - SetWriteFileTypeToImplicitVR(); - CheckMandatoryElements(); + // SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR ! + break; + case JPEG: + SetWriteFileTypeToJPEG(); + std::cerr << "Writting as JPEG" << std::endl; break; - } + CheckMandatoryElements(); // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images @@ -641,7 +724,7 @@ bool FileHelper::Write(std::string const &fileName) /// \todo the best trick would be *change* the recognition code /// but pb expected if user deals with, e.g. COMPLEX images - if( WriteType == ACR_LIBIDO ) + if ( WriteType == ACR_LIBIDO ) { SetWriteToLibido(); } @@ -662,7 +745,8 @@ bool FileHelper::Write(std::string const &fileName) } bool check = CheckWriteIntegrity(); // verifies length - if(check) + if (WriteType == JPEG ) check = true; + if (check) { check = FileInternal->Write(fileName,WriteType); } @@ -694,27 +778,30 @@ bool FileHelper::Write(std::string const &fileName) */ bool FileHelper::CheckWriteIntegrity() { - if(PixelWriteConverter->GetUserData()) + if ( PixelWriteConverter->GetUserData() ) { int numberBitsAllocated = FileInternal->GetBitsAllocated(); if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 ) { + gdcmWarningMacro( "numberBitsAllocated changed from " + << numberBitsAllocated << " to 16 " + << " for consistency purpose" ); numberBitsAllocated = 16; } size_t decSize = FileInternal->GetXSize() - * FileInternal->GetYSize() - * FileInternal->GetZSize() - * ( numberBitsAllocated / 8 ) - * FileInternal->GetSamplesPerPixel(); + * FileInternal->GetYSize() + * FileInternal->GetZSize() + * FileInternal->GetSamplesPerPixel() + * ( numberBitsAllocated / 8 ); size_t rgbSize = decSize; - if( FileInternal->HasLUT() ) + if ( FileInternal->HasLUT() ) rgbSize = decSize * 3; switch(WriteMode) { case WMODE_RAW : - if( decSize!=PixelWriteConverter->GetUserDataSize() ) + if ( decSize!=PixelWriteConverter->GetUserDataSize() ) { gdcmWarningMacro( "Data size (Raw) is incorrect. Should be " << decSize << " / Found :" @@ -723,7 +810,7 @@ bool FileHelper::CheckWriteIntegrity() } break; case WMODE_RGB : - if( rgbSize!=PixelWriteConverter->GetUserDataSize() ) + if ( rgbSize!=PixelWriteConverter->GetUserDataSize() ) { gdcmWarningMacro( "Data size (RGB) is incorrect. Should be " << decSize << " / Found " @@ -733,7 +820,7 @@ bool FileHelper::CheckWriteIntegrity() break; } } - + return true; } @@ -744,34 +831,34 @@ bool FileHelper::CheckWriteIntegrity() */ void FileHelper::SetWriteToRaw() { - if( FileInternal->GetNumberOfScalarComponents() == 3 - && !FileInternal->HasLUT()) + if ( FileInternal->GetNumberOfScalarComponents() == 3 + && !FileInternal->HasLUT() ) { SetWriteToRGB(); } else { - ValEntry *photInt = CopyValEntry(0x0028,0x0004); - if(FileInternal->HasLUT()) + DataEntry *photInt = CopyDataEntry(0x0028,0x0004); + if (FileInternal->HasLUT() ) { - photInt->SetValue("PALETTE COLOR "); + photInt->SetString("PALETTE COLOR "); } else { - photInt->SetValue("MONOCHROME2 "); + photInt->SetString("MONOCHROME2 "); } PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(), PixelReadConverter->GetRawSize()); std::string vr = "OB"; - if( FileInternal->GetBitsAllocated()>8 ) + if ( FileInternal->GetBitsAllocated()>8 ) vr = "OW"; - if( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files + if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files vr = "OB"; - BinEntry *pixel = - CopyBinEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr); - pixel->SetValue(GDCM_BINLOADED); + DataEntry *pixel = + CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr); + pixel->SetFlag(DataEntry::FLAG_PIXELDATA); pixel->SetBinArea(PixelWriteConverter->GetData(),false); pixel->SetLength(PixelWriteConverter->GetDataSize()); @@ -789,20 +876,20 @@ void FileHelper::SetWriteToRaw() */ void FileHelper::SetWriteToRGB() { - if(FileInternal->GetNumberOfScalarComponents()==3) + if ( FileInternal->GetNumberOfScalarComponents()==3 ) { PixelReadConverter->BuildRGBImage(); - ValEntry *spp = CopyValEntry(0x0028,0x0002); - spp->SetValue("3 "); + DataEntry *spp = CopyDataEntry(0x0028,0x0002); + spp->SetString("3 "); - ValEntry *planConfig = CopyValEntry(0x0028,0x0006); - planConfig->SetValue("0 "); + DataEntry *planConfig = CopyDataEntry(0x0028,0x0006); + planConfig->SetString("0 "); - ValEntry *photInt = CopyValEntry(0x0028,0x0004); - photInt->SetValue("RGB "); + DataEntry *photInt = CopyDataEntry(0x0028,0x0004); + photInt->SetString("RGB "); - if(PixelReadConverter->GetRGB()) + if ( PixelReadConverter->GetRGB() ) { PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(), PixelReadConverter->GetRGBSize()); @@ -814,13 +901,13 @@ void FileHelper::SetWriteToRGB() } std::string vr = "OB"; - if( FileInternal->GetBitsAllocated()>8 ) + if ( FileInternal->GetBitsAllocated()>8 ) vr = "OW"; - if( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files + if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files vr = "OB"; - BinEntry *pixel = - CopyBinEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr); - pixel->SetValue(GDCM_BINLOADED); + DataEntry *pixel = + CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr); + pixel->SetFlag(DataEntry::FLAG_PIXELDATA); pixel->SetBinArea(PixelWriteConverter->GetData(),false); pixel->SetLength(PixelWriteConverter->GetDataSize()); @@ -837,19 +924,22 @@ void FileHelper::SetWriteToRGB() Archive->Push(0x0028,0x1202); Archive->Push(0x0028,0x1203); + // push out Palette Color Lookup Table UID, if any + Archive->Push(0x0028,0x1199); + // For old '24 Bits' ACR-NEMA // Thus, we have a RGB image and the bits allocated = 24 and // samples per pixels = 1 (in the read file) - if(FileInternal->GetBitsAllocated()==24) + if ( FileInternal->GetBitsAllocated()==24 ) { - ValEntry *bitsAlloc = CopyValEntry(0x0028,0x0100); - bitsAlloc->SetValue("8 "); + DataEntry *bitsAlloc = CopyDataEntry(0x0028,0x0100); + bitsAlloc->SetString("8 "); - ValEntry *bitsStored = CopyValEntry(0x0028,0x0101); - bitsStored->SetValue("8 "); + DataEntry *bitsStored = CopyDataEntry(0x0028,0x0101); + bitsStored->SetString("8 "); - ValEntry *highBit = CopyValEntry(0x0028,0x0102); - highBit->SetValue("7 "); + DataEntry *highBit = CopyDataEntry(0x0028,0x0102); + highBit->SetString("7 "); Archive->Push(bitsAlloc); Archive->Push(bitsStored); @@ -885,6 +975,10 @@ void FileHelper::RestoreWrite() Archive->Restore(0x0028,0x1202); Archive->Restore(0x0028,0x1203); + // For the Palette Color Lookup Table UID + Archive->Restore(0x0028,0x1203); + + // group 0002 may be pushed out for ACR-NEMA writting purposes Archive->Restore(0x0002,0x0000); Archive->Restore(0x0002,0x0001); @@ -922,13 +1016,24 @@ void FileHelper::SetWriteFileTypeToACR() /** * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian" */ +void FileHelper::SetWriteFileTypeToJPEG() +{ + std::string ts = Util::DicomString( + Global::GetTS()->GetSpecialTransferSyntax(TS::JPEGBaselineProcess1) ); + + DataEntry *tss = CopyDataEntry(0x0002,0x0010); + tss->SetString(ts); + + Archive->Push(tss); +} + void FileHelper::SetWriteFileTypeToExplicitVR() { std::string ts = Util::DicomString( Global::GetTS()->GetSpecialTransferSyntax(TS::ExplicitVRLittleEndian) ); - ValEntry *tss = CopyValEntry(0x0002,0x0010); - tss->SetValue(ts); + DataEntry *tss = CopyDataEntry(0x0002,0x0010); + tss->SetString(ts); Archive->Push(tss); } @@ -941,8 +1046,8 @@ void FileHelper::SetWriteFileTypeToImplicitVR() std::string ts = Util::DicomString( Global::GetTS()->GetSpecialTransferSyntax(TS::ImplicitVRLittleEndian) ); - ValEntry *tss = CopyValEntry(0x0002,0x0010); - tss->SetValue(ts); + DataEntry *tss = CopyDataEntry(0x0002,0x0010); + tss->SetString(ts); Archive->Push(tss); } @@ -960,30 +1065,28 @@ void FileHelper::RestoreWriteFileType() */ void FileHelper::SetWriteToLibido() { - ValEntry *oldRow = dynamic_cast - (FileInternal->GetDocEntry(0x0028, 0x0010)); - ValEntry *oldCol = dynamic_cast - (FileInternal->GetDocEntry(0x0028, 0x0011)); + DataEntry *oldRow = FileInternal->GetDataEntry(0x0028, 0x0010); + DataEntry *oldCol = FileInternal->GetDataEntry(0x0028, 0x0011); - if( oldRow && oldCol ) + if ( oldRow && oldCol ) { std::string rows, columns; - ValEntry *newRow=new ValEntry(oldRow->GetDictEntry()); - ValEntry *newCol=new ValEntry(oldCol->GetDictEntry()); + DataEntry *newRow=new DataEntry(oldRow->GetDictEntry()); + DataEntry *newCol=new DataEntry(oldCol->GetDictEntry()); newRow->Copy(oldCol); newCol->Copy(oldRow); - newRow->SetValue(oldCol->GetValue()); - newCol->SetValue(oldRow->GetValue()); + newRow->SetString(oldCol->GetString()); + newCol->SetString(oldRow->GetString()); Archive->Push(newRow); Archive->Push(newCol); } - ValEntry *libidoCode = CopyValEntry(0x0008,0x0010); - libidoCode->SetValue("ACRNEMA_LIBIDO_1.1"); + DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010); + libidoCode->SetString("ACRNEMA_LIBIDO_1.1"); Archive->Push(libidoCode); } @@ -992,14 +1095,13 @@ void FileHelper::SetWriteToLibido() */ void FileHelper::SetWriteToNoLibido() { - ValEntry *recCode = dynamic_cast - (FileInternal->GetDocEntry(0x0008,0x0010)); - if( recCode ) + DataEntry *recCode = FileInternal->GetDataEntry(0x0008,0x0010); + if ( recCode ) { - if( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" ) + if ( recCode->GetString() == "ACRNEMA_LIBIDO_1.1" ) { - ValEntry *libidoCode = CopyValEntry(0x0008,0x0010); - libidoCode->SetValue(""); + DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010); + libidoCode->SetString(""); Archive->Push(libidoCode); } } @@ -1022,55 +1124,31 @@ void FileHelper::RestoreWriteOfLibido() } /** - * \brief Duplicates a ValEntry or creates it. - * @param group Group number of the Entry - * @param elem Element number of the Entry - * \return pointer to the new Val Entry (NULL when creation failed). - */ -ValEntry *FileHelper::CopyValEntry(uint16_t group, uint16_t elem) -{ - DocEntry *oldE = FileInternal->GetDocEntry(group, elem); - ValEntry *newE; - - if( oldE ) - { - newE = new ValEntry(oldE->GetDictEntry()); - newE->Copy(oldE); - } - else - { - newE = GetFile()->NewValEntry(group, elem); - } - - return newE; -} - -/** - * \brief Duplicates a BinEntry or creates it. + * \brief Duplicates a DataEntry or creates it. * @param group Group number of the Entry * @param elem Element number of the Entry * @param vr Value Representation of the Entry * FIXME : what is it used for? * \return pointer to the new Bin Entry (NULL when creation failed). */ -BinEntry *FileHelper::CopyBinEntry(uint16_t group, uint16_t elem, - const std::string &vr) +DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem, + const TagName &vr) { DocEntry *oldE = FileInternal->GetDocEntry(group, elem); - BinEntry *newE; + DataEntry *newE; - if( oldE ) - if( oldE->GetVR()!=vr ) + if ( oldE && vr != GDCM_VRUNKNOWN ) + if ( oldE->GetVR() != vr ) oldE = NULL; - if( oldE ) + if ( oldE ) { - newE = new BinEntry(oldE->GetDictEntry()); + newE = new DataEntry(oldE->GetDictEntry()); newE->Copy(oldE); } else { - newE = GetFile()->NewBinEntry(group, elem, vr); + newE = GetFile()->NewDataEntry(group, elem, vr); } return newE; @@ -1104,8 +1182,13 @@ BinEntry *FileHelper::CopyBinEntry(uint16_t group, uint16_t elem, void FileHelper::CheckMandatoryElements() { + std::string sop = Util::CreateUniqueUID(); + // just to remember : 'official' 0002 group - + if ( WriteType != ACR && WriteType != ACR_LIBIDO ) + { + // Group 000002 (Meta Elements) already pushed out + //0002 0000 UL 1 Meta Group Length //0002 0001 OB 1 File Meta Information Version //0002 0002 UI 1 Media Stored SOP Class UID @@ -1120,41 +1203,29 @@ void FileHelper::CheckMandatoryElements() // Create them if not found // Always modify the value // Push the entries to the archive. - ValEntry *e_0002_0000 = CopyValEntry(0x0002,0x0000); - e_0002_0000->SetValue("0"); // for the moment - Archive->Push(e_0002_0000); + CopyMandatoryEntry(0x0002,0x0000,"0"); - BinEntry *e_0002_0001 = CopyBinEntry(0x0002,0x0001, "OB"); + DataEntry *e_0002_0001 = CopyDataEntry(0x0002,0x0001, "OB"); e_0002_0001->SetBinArea((uint8_t*)Util::GetFileMetaInformationVersion(), false); e_0002_0001->SetLength(2); Archive->Push(e_0002_0001); - // 'Media Stored SOP Class UID' - ValEntry *e_0002_0002 = CopyValEntry(0x0002,0x0002); - // [Secondary Capture Image Storage] - e_0002_0002->SetValue("1.2.840.10008.5.1.4.1.1.7"); - Archive->Push(e_0002_0002); + // Potentialy post-processed image --> [Secondary Capture Image Storage] + // 'Media Storage SOP Class UID' + CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7"); - // 'Media Stored SOP Instance UID' - ValEntry *e_0002_0003 = CopyValEntry(0x0002,0x0003); - e_0002_0003->SetValue(Util::CreateUniqueUID()); - Archive->Push(e_0002_0003); - + // 'Media Storage SOP Instance UID' + CopyMandatoryEntry(0x0002,0x0003,sop); + // 'Implementation Class UID' - ValEntry *e_0002_0012 = CopyValEntry(0x0002,0x0012); - e_0002_0012->SetValue(Util::CreateUniqueUID()); - Archive->Push(e_0002_0012); + CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID()); // 'Implementation Version Name' - ValEntry *e_0002_0013 = CopyValEntry(0x0002,0x0013); - e_0002_0013->SetValue("GDCM 1.0"); - Archive->Push(e_0002_0013); - - //'Source Application Entity Title' Not Mandatory - //ValEntry *e_0002_0016 = CopyValEntry(0x0002,0x0016); - // e_0002_0016->SetValue("1.2.840.10008.5.1.4.1.1.7"); - // Archive->Push(e_0002_0016); + std::string version = "GDCM "; + version += Util::GetVersion(); + CopyMandatoryEntry(0x0002,0x0013,version); + } // Push out 'LibIDO-special' entries, if any Archive->Push(0x0028,0x0015); @@ -1162,41 +1233,83 @@ void FileHelper::CheckMandatoryElements() Archive->Push(0x0028,0x0017); Archive->Push(0x0028,0x00199); - // --- Check UID-related Entries --- + // Deal with the pb of (Bits Stored = 12) + // - we're gonna write the image as Bits Stored = 16 + if ( FileInternal->GetEntryString(0x0028,0x0100) == "12") + { + CopyMandatoryEntry(0x0028,0x0100,"16"); + } + + // Check if user wasn't drunk ;-) + + std::ostringstream s; + // check 'Bits Allocated' vs decent values + int nbBitsAllocated = FileInternal->GetBitsAllocated(); + if ( nbBitsAllocated == 0 || nbBitsAllocated > 32) + { + CopyMandatoryEntry(0x0028,0x0100,"16"); + gdcmWarningMacro("(0028,0100) changed from " + << nbBitsAllocated << " to 16 for consistency purpose"); + nbBitsAllocated = 16; + } + // check 'Bits Stored' vs 'Bits Allocated' + int nbBitsStored = FileInternal->GetBitsStored(); + if ( nbBitsStored == 0 || nbBitsStored > nbBitsAllocated ) + { + s.str(""); + s << nbBitsAllocated; + CopyMandatoryEntry(0x0028,0x0101,s.str()); + gdcmWarningMacro("(0028,0101) changed from " + << nbBitsStored << " to " << nbBitsAllocated + << " for consistency purpose" ); + nbBitsStored = nbBitsAllocated; + } + // check 'Hight Bit Position' vs 'Bits Allocated' and 'Bits Stored' + int highBitPosition = FileInternal->GetHighBitPosition(); + if ( highBitPosition == 0 || + highBitPosition > nbBitsAllocated-1 || + highBitPosition < nbBitsStored-1 ) + { + s.str(""); + s << nbBitsStored - 1; + CopyMandatoryEntry(0x0028,0x0102,s.str()); + gdcmWarningMacro("(0028,0102) changed from " + << highBitPosition << " to " << nbBitsAllocated-1 + << " for consistency purpose"); + } + // --- Check UID-related Entries --- // If 'SOP Class UID' exists ('true DICOM' image) // we create the 'Source Image Sequence' SeqEntry // to hold informations about the Source Image - ValEntry *e_0008_0016 = FileInternal->GetValEntry(0x0008, 0x0016); - if ( e_0008_0016 != 0 ) + DataEntry *e_0008_0016 = FileInternal->GetDataEntry(0x0008, 0x0016); + if ( e_0008_0016 ) { // Create 'Source Image Sequence' SeqEntry - SeqEntry *s = new SeqEntry ( + SeqEntry *sis = new SeqEntry ( Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x2112) ); SQItem *sqi = new SQItem(1); // (we assume 'SOP Instance UID' exists too) // create 'Referenced SOP Class UID' - ValEntry *e_0008_1150 = new ValEntry( + DataEntry *e_0008_1150 = new DataEntry( Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) ); - e_0008_1150->SetValue( e_0008_0016->GetValue()); + e_0008_1150->SetString( e_0008_0016->GetString()); sqi->AddEntry(e_0008_1150); // create 'Referenced SOP Instance UID' - ValEntry *e_0008_0018 = FileInternal->GetValEntry(0x0008, 0x0018); - ValEntry *e_0008_1155 = new ValEntry( + DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018); + DataEntry *e_0008_1155 = new DataEntry( Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1155) ); - e_0008_1155->SetValue( e_0008_0018->GetValue()); + e_0008_1155->SetString( e_0008_0018->GetString()); sqi->AddEntry(e_0008_1155); - s->AddSQItem(sqi,1); + sis->AddSQItem(sqi,1); // temporarily replaces any previous 'Source Image Sequence' - Archive->Push(s); + Archive->Push(sis); // 'Image Type' (The written image is no longer an 'ORIGINAL' one) - ValEntry *e_0008_0008 = CopyValEntry(0x0008,0x0008); - e_0008_0008->SetValue("DERIVED\\PRIMARY"); - Archive->Push(e_0008_0008); + CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY"); } else { @@ -1204,153 +1317,111 @@ void FileHelper::CheckMandatoryElements() // the source image was NOT a true Dicom one. // We consider the image is a 'Secondary Capture' one // SOP Class UID - e_0008_0016 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0016) ); // [Secondary Capture Image Storage] - e_0008_0016 ->SetValue("1.2.840.10008.5.1.4.1.1.7"); - Archive->Push(e_0008_0016); + SetMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7"); } + // At the end, not to overwrite the original ones, + // needed by 'Referenced SOP Instance UID', 'Referenced SOP Class UID' + // 'SOP Instance UID' + CopyMandatoryEntry(0x0008,0x0018,sop); + // 'SOP Class UID' + CopyMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7"); + // ---- The user will never have to take any action on the following ----. - // new value for 'SOP Instance UID' - ValEntry *e_0008_0018 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0018) ); - e_0008_0018->SetValue( Util::CreateUniqueUID() ); - Archive->Push(e_0008_0018); + //SetMandatoryEntry(0x0008,0x0018,Util::CreateUniqueUID()); // Instance Creation Date - ValEntry *e_0008_0012 = CopyValEntry(0x0008,0x0012); - std::string date = Util::GetCurrentDate(); - e_0008_0012->SetValue(date.c_str()); - Archive->Push(e_0008_0012); + CopyMandatoryEntry(0x0008,0x0012,Util::GetCurrentDate().c_str()); // Instance Creation Time - ValEntry *e_0008_0013 = CopyValEntry(0x0008,0x0013); - std::string time = Util::GetCurrentTime(); - e_0008_0013->SetValue(time.c_str()); - Archive->Push(e_0008_0013); + CopyMandatoryEntry(0x0008,0x0013,Util::GetCurrentTime().c_str()); // ----- Add Mandatory Entries if missing --- - // Entries whose type is 1 are mandatory, with a mandatory value // Entries whose type is 1c are mandatory-inside-a-Sequence // Entries whose type is 2 are mandatory, with a optional value // Entries whose type is 2c are mandatory-inside-a-Sequence // Entries whose type is 3 are optional - // 'Serie Instance UID' - // Keep the value if exists - // The user is allowed to create his own Series, - // keeping the same 'Serie Instance UID' for various images - // The user shouldn't add any image to a 'Manufacturer Serie' - // but there is no way no to allowed him to do that - ValEntry *e_0020_000e = FileInternal->GetValEntry(0x0020, 0x000e); - if ( !e_0020_000e ) - { - e_0020_000e = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0020, 0x000e) ); - e_0020_000e->SetValue(Util::CreateUniqueUID() ); - Archive->Push(e_0020_000e); - } - // 'Study Instance UID' // Keep the value if exists // The user is allowed to create his own Study, // keeping the same 'Study Instance UID' for various images // The user may add images to a 'Manufacturer Study', // adding new series to an already existing Study - ValEntry *e_0020_000d = FileInternal->GetValEntry(0x0020, 0x000d); - if ( !e_0020_000d ) - { - e_0020_000d = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0020, 0x000d) ); - e_0020_000d->SetValue(Util::CreateUniqueUID() ); - Archive->Push(e_0020_000d); - } + CheckMandatoryEntry(0x0020,0x000d,Util::CreateUniqueUID()); + // 'Serie Instance UID' + // Keep the value if exists + // The user is allowed to create his own Series, + // keeping the same 'Serie Instance UID' for various images + // The user shouldn't add any image to a 'Manufacturer Serie' + // but there is no way no to allowed him to do that + CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID()); + // Modality : if missing we set it to 'OTher' - ValEntry *e_0008_0060 = FileInternal->GetValEntry(0x0008, 0x0060); - if ( !e_0008_0060 ) - { - e_0008_0060 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0060) ); - e_0008_0060->SetValue("OT"); - Archive->Push(e_0008_0060); - } + CheckMandatoryEntry(0x0008,0x0060,"OT"); // Manufacturer : if missing we set it to 'GDCM Factory' - ValEntry *e_0008_0070 = FileInternal->GetValEntry(0x0008, 0x0070); - if ( !e_0008_0070 ) - { - e_0008_0070 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0070) ); - e_0008_0070->SetValue("GDCM Factory"); - Archive->Push(e_0008_0070); - } + CheckMandatoryEntry(0x0008,0x0070,"GDCM Factory"); // Institution Name : if missing we set it to 'GDCM Hospital' - ValEntry *e_0008_0080 = FileInternal->GetValEntry(0x0008, 0x0080); - if ( !e_0008_0080 ) - { - e_0008_0080 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0080) ); - e_0008_0080->SetValue("GDCM Hospital"); - Archive->Push(e_0008_0080); - } + CheckMandatoryEntry(0x0008,0x0080,"GDCM Hospital"); // Patient's Name : if missing, we set it to 'GDCM^Patient' - ValEntry *e_0010_0010 = FileInternal->GetValEntry(0x0010, 0x0010); - if ( !e_0010_0010 ) - { - e_0010_0010 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0010) ); - e_0010_0010->SetValue("GDCM^Patient"); - Archive->Push(e_0010_0010); - } + CheckMandatoryEntry(0x0010,0x0010,"GDCM^Patient"); // Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory - ValEntry *e_0010_0030 = FileInternal->GetValEntry(0x0010, 0x0030); - if ( !e_0010_0030 ) - { - e_0010_0030 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0030) ); - e_0010_0030->SetValue(""); - Archive->Push(e_0010_0030); - } + CheckMandatoryEntry(0x0010,0x0030,""); // Patient's Sex :'type 2' entry -> must exist, value not mandatory - ValEntry *e_0010_0040 = FileInternal->GetValEntry(0x0010, 0x0040); - if ( !e_0010_0040 ) - { - e_0010_0040 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0040) ); - e_0010_0040->SetValue(""); - Archive->Push(e_0010_0040); - } + CheckMandatoryEntry(0x0010,0x0040,""); // Referring Physician's Name :'type 2' entry -> must exist, value not mandatory - ValEntry *e_0008_0090 = FileInternal->GetValEntry(0x0008, 0x0090); - if ( !e_0008_0090 ) - { - e_0008_0090 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0090) ); - e_0008_0090->SetValue(""); - Archive->Push(e_0008_0090); - } - + CheckMandatoryEntry(0x0008,0x0090,""); + + // Pixel Spacing : defaulted to 1.0\1.0 + CheckMandatoryEntry(0x0028,0x0030,"1.0\\1.0"); + // Remove some inconstencies (probably some more will be added) // if (0028 0008)Number of Frames exists // Push out (0020 0052),Frame of Reference UID // (only meaningfull within a Serie) - ValEntry *e_0028_0008 = FileInternal->GetValEntry(0x0028, 0x0008); + DataEntry *e_0028_0008 = FileInternal->GetDataEntry(0x0028, 0x0008); if ( !e_0028_0008 ) { Archive->Push(0x0020, 0X0052); } } - + +void FileHelper::CheckMandatoryEntry(uint16_t group,uint16_t elem,std::string value) +{ + DataEntry *entry = FileInternal->GetDataEntry(group,elem); + if ( !entry ) + { + entry = new DataEntry(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); + entry->SetString(value); + Archive->Push(entry); + } +} + +void FileHelper::SetMandatoryEntry(uint16_t group,uint16_t elem,std::string value) +{ + DataEntry *entry = new DataEntry(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); + entry->SetString(value); + Archive->Push(entry); +} + +void FileHelper::CopyMandatoryEntry(uint16_t group,uint16_t elem,std::string value) +{ + DataEntry *entry = CopyDataEntry(group,elem); + entry->SetString(value); + Archive->Push(entry); +} + /** * \brief Restore in the File the initial group 0002 */ @@ -1361,11 +1432,30 @@ void FileHelper::RestoreWriteMandatory() Archive->Restore(0x0002,0x0001); Archive->Restore(0x0002,0x0002); Archive->Restore(0x0002,0x0003); + Archive->Restore(0x0002,0x0010); Archive->Restore(0x0002,0x0012); Archive->Restore(0x0002,0x0013); Archive->Restore(0x0002,0x0016); Archive->Restore(0x0002,0x0100); Archive->Restore(0x0002,0x0102); + + Archive->Restore(0x0008,0x0012); + Archive->Restore(0x0008,0x0013); + Archive->Restore(0x0008,0x0016); + Archive->Restore(0x0008,0x0018); + Archive->Restore(0x0008,0x0060); + Archive->Restore(0x0008,0x0070); + Archive->Restore(0x0008,0x0080); + Archive->Restore(0x0008,0x0090); + Archive->Restore(0x0008,0x2112); + + Archive->Restore(0x0010,0x0010); + Archive->Restore(0x0010,0x0030); + Archive->Restore(0x0010,0x0040); + + Archive->Restore(0x0020,0x000d); + Archive->Restore(0x0020,0x000e); + } //----------------------------------------------------------------------------- @@ -1375,17 +1465,14 @@ void FileHelper::RestoreWriteMandatory() */ void FileHelper::Initialize() { + UserFunction = 0; + WriteMode = WMODE_RAW; WriteType = ExplicitVR; PixelReadConverter = new PixelReadConvert; PixelWriteConverter = new PixelWriteConvert; Archive = new DocEntryArchive( FileInternal ); - - if ( FileInternal->IsReadable() ) - { - PixelReadConverter->GrabInformationsFromFile( FileInternal ); - } } /** @@ -1396,13 +1483,15 @@ void FileHelper::Initialize() */ uint8_t *FileHelper::GetRaw() { + PixelReadConverter->SetUserFunction( UserFunction ); + uint8_t *raw = PixelReadConverter->GetRaw(); if ( ! raw ) { // The Raw image migth not be loaded yet: std::ifstream *fp = FileInternal->OpenFile(); PixelReadConverter->ReadAndDecompressPixelData( fp ); - if(fp) + if ( fp ) FileInternal->CloseFile(); raw = PixelReadConverter->GetRaw(); @@ -1412,13 +1501,12 @@ uint8_t *FileHelper::GetRaw() return 0; } } - return raw; } //----------------------------------------------------------------------------- /** - * \brief Prints the common part of ValEntry, BinEntry, SeqEntry + * \brief Prints the common part of DataEntry, SeqEntry * @param os ostream we want to print in * @param indent (unused) */ @@ -1427,8 +1515,11 @@ void FileHelper::Print(std::ostream &os, std::string const &) FileInternal->SetPrintLevel(PrintLevel); FileInternal->Print(os); - PixelReadConverter->SetPrintLevel(PrintLevel); - PixelReadConverter->Print(os); + if ( FileInternal->IsReadable() ) + { + PixelReadConverter->SetPrintLevel(PrintLevel); + PixelReadConverter->Print(os); + } } //-----------------------------------------------------------------------------