X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFileHelper.cxx;h=0aeffd71d5ad91a34246d8ccd7b6e4ddfbffcf74;hb=c36a3a368b73cd8755907d9b94706cad7176dfa2;hp=9e2ad9bba34af51f0946ef9b1d7121fe1ad090a2;hpb=4f1339cf2b02a0b5dbad52de043ec93f86956982;p=gdcm.git diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx index 9e2ad9bb..0aeffd71 100644 --- a/src/gdcmFileHelper.cxx +++ b/src/gdcmFileHelper.cxx @@ -4,8 +4,8 @@ Module: $RCSfile: gdcmFileHelper.cxx,v $ Language: C++ - Date: $Date: 2005/04/29 15:11:56 $ - Version: $Revision: 1.36 $ + Date: $Date: 2005/06/24 10:55:59 $ + Version: $Revision: 1.46 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -172,20 +172,20 @@ 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; } @@ -238,7 +238,7 @@ bool FileHelper::SetBinEntry(uint8_t *content, int lgth, ValEntry *FileHelper::InsertValEntry(std::string const &content, uint16_t group, uint16_t elem) { - return FileInternal->InsertValEntry(content,group,elem); + return FileInternal->InsertValEntry(content, group, elem); } /** @@ -500,9 +500,27 @@ 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". @@ -520,7 +538,7 @@ bool FileHelper::WriteRawData(std::string const &fileName) return false; } - if( PixelWriteConverter->GetUserData() ) + if ( PixelWriteConverter->GetUserData() ) { fp1.write( (char *)PixelWriteConverter->GetUserData(), PixelWriteConverter->GetUserDataSize() ); @@ -623,7 +641,7 @@ bool FileHelper::Write(std::string const &fileName) if ( ! FileInternal->GetValEntry(0x0008, 0x0010) ) FileInternal->InsertValEntry("", 0x0008, 0x0010); SetWriteFileTypeToACR(); - SetWriteFileTypeToImplicitVR(); + // SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR ! break; } CheckMandatoryElements(); @@ -637,7 +655,7 @@ 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(); } @@ -658,7 +676,7 @@ bool FileHelper::Write(std::string const &fileName) } bool check = CheckWriteIntegrity(); // verifies length - if(check) + if (check) { check = FileInternal->Write(fileName,WriteType); } @@ -690,11 +708,14 @@ 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; } @@ -704,13 +725,13 @@ bool FileHelper::CheckWriteIntegrity() * 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 :" @@ -719,7 +740,7 @@ 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 " @@ -739,15 +760,15 @@ 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()) + if (FileInternal->HasLUT() ) { photInt->SetValue("PALETTE COLOR "); } @@ -760,9 +781,9 @@ void FileHelper::SetWriteToRaw() 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); @@ -784,7 +805,7 @@ void FileHelper::SetWriteToRaw() */ void FileHelper::SetWriteToRGB() { - if(FileInternal->GetNumberOfScalarComponents()==3) + if ( FileInternal->GetNumberOfScalarComponents()==3 ) { PixelReadConverter->BuildRGBImage(); @@ -797,7 +818,7 @@ void FileHelper::SetWriteToRGB() ValEntry *photInt = CopyValEntry(0x0028,0x0004); photInt->SetValue("RGB "); - if(PixelReadConverter->GetRGB()) + if ( PixelReadConverter->GetRGB() ) { PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(), PixelReadConverter->GetRGBSize()); @@ -809,9 +830,9 @@ 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); @@ -832,10 +853,13 @@ 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 "); @@ -880,6 +904,10 @@ 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); @@ -960,7 +988,7 @@ void FileHelper::SetWriteToLibido() ValEntry *oldCol = dynamic_cast (FileInternal->GetDocEntry(0x0028, 0x0011)); - if( oldRow && oldCol ) + if ( oldRow && oldCol ) { std::string rows, columns; @@ -989,9 +1017,9 @@ void FileHelper::SetWriteToNoLibido() { ValEntry *recCode = dynamic_cast (FileInternal->GetDocEntry(0x0008,0x0010)); - if( recCode ) + if ( recCode ) { - if( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" ) + if ( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" ) { ValEntry *libidoCode = CopyValEntry(0x0008,0x0010); libidoCode->SetValue(""); @@ -1027,7 +1055,7 @@ ValEntry *FileHelper::CopyValEntry(uint16_t group, uint16_t elem) DocEntry *oldE = FileInternal->GetDocEntry(group, elem); ValEntry *newE; - if( oldE ) + if ( oldE ) { newE = new ValEntry(oldE->GetDictEntry()); newE->Copy(oldE); @@ -1054,11 +1082,11 @@ BinEntry *FileHelper::CopyBinEntry(uint16_t group, uint16_t elem, DocEntry *oldE = FileInternal->GetDocEntry(group, elem); BinEntry *newE; - if( oldE ) - if( oldE->GetVR()!=vr ) + if ( oldE ) + if ( oldE->GetVR()!=vr ) oldE = NULL; - if( oldE ) + if ( oldE ) { newE = new BinEntry(oldE->GetDictEntry()); newE->Copy(oldE); @@ -1100,7 +1128,10 @@ BinEntry *FileHelper::CopyBinEntry(uint16_t group, uint16_t elem, void FileHelper::CheckMandatoryElements() { // 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 @@ -1115,41 +1146,42 @@ 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); + ValEntry *e_0002_0000 = CopyValEntry(0x0002,0x0000); e_0002_0000->SetValue("0"); // for the moment Archive->Push(e_0002_0000); - BinEntry *e_0002_0001 = CopyBinEntry(0x0002,0x0001, "OB"); + BinEntry *e_0002_0001 = CopyBinEntry(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); + 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); // 'Media Stored SOP Instance UID' - ValEntry *e_0002_0003 = CopyValEntry(0x0002,0x0003); + ValEntry *e_0002_0003 = CopyValEntry(0x0002,0x0003); e_0002_0003->SetValue(Util::CreateUniqueUID()); Archive->Push(e_0002_0003); // 'Implementation Class UID' - ValEntry *e_0002_0012 = CopyValEntry(0x0002,0x0012); + ValEntry *e_0002_0012 = CopyValEntry(0x0002,0x0012); e_0002_0012->SetValue(Util::CreateUniqueUID()); Archive->Push(e_0002_0012); // 'Implementation Version Name' - ValEntry *e_0002_0013 = CopyValEntry(0x0002,0x0013); - e_0002_0013->SetValue("GDCM 1.0"); + ValEntry *e_0002_0013 = CopyValEntry(0x0002,0x0013); + e_0002_0013->SetValue("GDCM 1.1"); 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); + } // Push out 'LibIDO-special' entries, if any Archive->Push(0x0028,0x0015); @@ -1166,7 +1198,49 @@ void FileHelper::CheckMandatoryElements() Archive->Push(e_0028_0100); } - // --- Check UID-related Entries --- + // Check if user wasn't drunk ;-) + + std::ostringstream s; + // check 'Bits Allocated' vs decent values + int nbBitsAllocated = FileInternal->GetBitsAllocated(); + if ( nbBitsAllocated == 0 || nbBitsAllocated > 32) + { + ValEntry *e_0028_0100 = CopyValEntry(0x0028,0x0100); + e_0028_0100->SetValue("16"); + Archive->Push(e_0028_0100); + 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 << nbBitsAllocated; + ValEntry *e_0028_0101 = CopyValEntry(0x0028,0x0101); + e_0028_0101->SetValue( s.str() ); + Archive->Push(e_0028_0101); + 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 ) + { + ValEntry *e_0028_0102 = CopyValEntry(0x0028,0x0102); + + s << nbBitsStored - 1; + e_0028_0102->SetValue( s.str() ); + Archive->Push(e_0028_0102); + 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 @@ -1176,7 +1250,7 @@ void FileHelper::CheckMandatoryElements() if ( e_0008_0016 != 0 ) { // 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) @@ -1193,9 +1267,9 @@ void FileHelper::CheckMandatoryElements() e_0008_1155->SetValue( e_0008_0018->GetValue()); 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); @@ -1365,11 +1439,30 @@ 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); + } //----------------------------------------------------------------------------- @@ -1406,7 +1499,7 @@ uint8_t *FileHelper::GetRaw() // 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();