X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFileHelper.cxx;h=bc56a312b4f7872fa1d8a66aa70553171ac8558e;hb=87d658ea3d71cf417c73a9b109ae6e7ba8b3881f;hp=0a35393d8d55f234dbfc8b14c6bdcae6ca4721bd;hpb=72cb0d598d43f8da30e2167e5ab5413fce8d9bb8;p=gdcm.git diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx index 0a35393d..bc56a312 100644 --- a/src/gdcmFileHelper.cxx +++ b/src/gdcmFileHelper.cxx @@ -4,8 +4,8 @@ Module: $RCSfile: gdcmFileHelper.cxx,v $ Language: C++ - Date: $Date: 2005/03/04 16:24:19 $ - Version: $Revision: 1.27 $ + Date: $Date: 2005/05/20 08:27:55 $ + Version: $Revision: 1.40 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -285,7 +285,6 @@ size_t FileHelper::GetImageDataSize() { return PixelWriteConverter->GetUserDataSize(); } - return PixelReadConverter->GetRGBSize(); } @@ -302,7 +301,6 @@ size_t FileHelper::GetImageDataRawSize() { return PixelWriteConverter->GetUserDataSize(); } - return PixelReadConverter->GetRawSize(); } @@ -407,7 +405,7 @@ size_t FileHelper::GetImageDataIntoVector (void *destination, size_t maxSize) return 0; } memcpy( destination, - (void*)PixelReadConverter->GetRaw(), + (void *)PixelReadConverter->GetRaw(), PixelReadConverter->GetRawSize() ); return PixelReadConverter->GetRawSize(); } @@ -524,17 +522,17 @@ bool FileHelper::WriteRawData(std::string const &fileName) 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 +548,7 @@ 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 @@ -609,20 +607,26 @@ 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: + // 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 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); SetWriteFileTypeToACR(); + SetWriteFileTypeToImplicitVR(); break; - default: - SetWriteFileTypeToExplicitVR(); - CheckMandatoryElements(); } + CheckMandatoryElements(); // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images @@ -632,6 +636,7 @@ bool FileHelper::Write(std::string const &fileName) // just before writting ... /// \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 ) { SetWriteToLibido(); @@ -660,6 +665,7 @@ bool FileHelper::Write(std::string const &fileName) RestoreWrite(); RestoreWriteFileType(); + RestoreWriteMandatory(); // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images @@ -689,14 +695,17 @@ bool FileHelper::CheckWriteIntegrity() 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() ) rgbSize = decSize * 3; @@ -722,8 +731,7 @@ bool FileHelper::CheckWriteIntegrity() } break; } - } - + } return true; } @@ -943,17 +951,6 @@ void FileHelper::SetWriteFileTypeToImplicitVR() */ void FileHelper::RestoreWriteFileType() { - // group 0002 may be pushed out for ACR-NEMA writting purposes - Archive->Restore(0x0002,0x0000); - 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); } /** @@ -1014,6 +1011,12 @@ void FileHelper::RestoreWriteOfLibido() Archive->Restore(0x0028,0x0010); Archive->Restore(0x0028,0x0011); Archive->Restore(0x0008,0x0010); + + // Restore 'LibIDO-special' entries, if any + Archive->Restore(0x0028,0x0015); + Archive->Restore(0x0028,0x0016); + Archive->Restore(0x0028,0x0017); + Archive->Restore(0x0028,0x00199); } /** @@ -1054,16 +1057,10 @@ BinEntry *FileHelper::CopyBinEntry(uint16_t group, uint16_t elem, DocEntry *oldE = FileInternal->GetDocEntry(group, elem); BinEntry *newE; - if( oldE ) // Is this really usefull? + if( oldE ) if( oldE->GetVR()!=vr ) - { - gdcmWarningMacro( " Unconsistent VR for Bin Entry : [" << oldE->GetVR() - << "] vs [" << vr << "] for " << - std::hex << group << "|" << elem); - //delete oldE; - oldE = NULL; // Revert temporary to old code to avoid Seg Fault - /// \ todo fixme - } + oldE = NULL; + if( oldE ) { newE = new BinEntry(oldE->GetDictEntry()); @@ -1105,6 +1102,7 @@ BinEntry *FileHelper::CopyBinEntry(uint16_t group, uint16_t elem, void FileHelper::CheckMandatoryElements() { + // just to remember : 'official' 0002 group //0002 0000 UL 1 Meta Group Length @@ -1121,7 +1119,6 @@ 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); @@ -1130,7 +1127,9 @@ void FileHelper::CheckMandatoryElements() 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"); @@ -1141,11 +1140,6 @@ void FileHelper::CheckMandatoryElements() e_0002_0003->SetValue(Util::CreateUniqueUID()); Archive->Push(e_0002_0003); - ValEntry *e_0002_0010 = CopyValEntry(0x0002,0x0010); - //[Explicit VR - Little Endian] - e_0002_0010->SetValue("1.2.840.10008.1.2.1"); - Archive->Push(e_0002_0010); - // 'Implementation Class UID' ValEntry *e_0002_0012 = CopyValEntry(0x0002,0x0012); e_0002_0012->SetValue(Util::CreateUniqueUID()); @@ -1167,7 +1161,58 @@ 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->GetEntryValue(0x0028,0x0100) == "12") + { + ValEntry *e_0028_0100 = CopyValEntry(0x0028,0x0100); + e_0028_0100->SetValue("16"); + Archive->Push(e_0028_0100); + } + + // 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 @@ -1177,7 +1222,7 @@ 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) @@ -1194,9 +1239,9 @@ 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); @@ -1314,17 +1359,7 @@ void FileHelper::CheckMandatoryElements() Archive->Push(e_0010_0010); } - // Patient's ID : if missing, we set it to 'GDCM_Patient_ID' - ValEntry *e_0010_0020 = FileInternal->GetValEntry(0x0010, 0x0020); - if ( !e_0010_0020 ) - { - e_0010_0020 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0020) ); - e_0010_0020->SetValue("GDCM_Patient_ID"); - Archive->Push(e_0010_0020); - } - - // Patient's Birth Date :'type 2' entry -> must exist, value not mandatory + // Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory ValEntry *e_0010_0030 = FileInternal->GetValEntry(0x0010, 0x0030); if ( !e_0010_0030 ) { @@ -1366,6 +1401,41 @@ void FileHelper::CheckMandatoryElements() } } +/** + * \brief Restore in the File the initial group 0002 + */ +void FileHelper::RestoreWriteMandatory() +{ + // group 0002 may be pushed out for ACR-NEMA writting purposes + Archive->Restore(0x0002,0x0000); + Archive->Restore(0x0002,0x0001); + Archive->Restore(0x0002,0x0002); + Archive->Restore(0x0002,0x0003); + 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); + +} + //----------------------------------------------------------------------------- // Private /** @@ -1387,7 +1457,10 @@ void FileHelper::Initialize() } /** - * \brief + * \brief Reads/[decompresses] the pixels, + * *without* making RGB from Palette Colors + * @return the pixels area, whatever its type + * (uint8_t is just for prototyping : feel free to Cast it) */ uint8_t *FileHelper::GetRaw() { @@ -1407,12 +1480,15 @@ uint8_t *FileHelper::GetRaw() return 0; } } - return raw; } //----------------------------------------------------------------------------- -// Print +/** + * \brief Prints the common part of ValEntry, BinEntry, SeqEntry + * @param os ostream we want to print in + * @param indent (unused) + */ void FileHelper::Print(std::ostream &os, std::string const &) { FileInternal->SetPrintLevel(PrintLevel);