X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFileHelper.cxx;h=e91570e2833ee4a2ee654470002d92259bea5621;hb=c95e0f505e46f71f658c62901c68521ac4afeccb;hp=f6f222fa1efbb292b838ffda5a110085743a3b37;hpb=c139e38830c393a2de12de8c686f36f3c544774e;p=gdcm.git diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx index f6f222fa..e91570e2 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 11:15:56 $ - Version: $Revision: 1.26 $ + Date: $Date: 2005/09/07 08:55:23 $ + Version: $Revision: 1.58 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -42,32 +42,43 @@ 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 +100,7 @@ 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 +123,7 @@ 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 +131,7 @@ namespace gdcm * seen as a side effect). */ FileHelper::FileHelper( ) -{ +{ FileInternal = new File( ); SelfHeader = true; Initialize(); @@ -131,6 +143,7 @@ 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 +156,16 @@ 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 +176,21 @@ 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 +199,20 @@ 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 +221,43 @@ 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 @@ -238,7 +302,7 @@ 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); } /** @@ -285,7 +349,6 @@ size_t FileHelper::GetImageDataSize() { return PixelWriteConverter->GetUserDataSize(); } - return PixelReadConverter->GetRGBSize(); } @@ -302,7 +365,6 @@ size_t FileHelper::GetImageDataRawSize() { return PixelWriteConverter->GetUserDataSize(); } - return PixelReadConverter->GetRawSize(); } @@ -354,9 +416,11 @@ 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 +471,11 @@ 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 +567,27 @@ 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 +605,19 @@ 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 +633,7 @@ 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 +692,26 @@ 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(); // ACR IS implicit VR ! break; - default: - SetWriteFileTypeToExplicitVR(); - CheckMandatoryElements(); } + CheckMandatoryElements(); // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images @@ -632,7 +721,8 @@ 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 ) + + if ( WriteType == ACR_LIBIDO ) { SetWriteToLibido(); } @@ -653,13 +743,14 @@ bool FileHelper::Write(std::string const &fileName) } bool check = CheckWriteIntegrity(); // verifies length - if(check) + if (check) { check = FileInternal->Write(fileName,WriteType); } RestoreWrite(); RestoreWriteFileType(); + RestoreWriteMandatory(); // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images @@ -684,27 +775,30 @@ 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 :" @@ -713,7 +807,7 @@ 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 " @@ -722,8 +816,7 @@ bool FileHelper::CheckWriteIntegrity() } break; } - } - + } return true; } @@ -734,15 +827,15 @@ 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 "); } @@ -755,9 +848,9 @@ 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); @@ -779,7 +872,7 @@ void FileHelper::SetWriteToRaw() */ void FileHelper::SetWriteToRGB() { - if(FileInternal->GetNumberOfScalarComponents()==3) + if ( FileInternal->GetNumberOfScalarComponents()==3 ) { PixelReadConverter->BuildRGBImage(); @@ -792,7 +885,7 @@ void FileHelper::SetWriteToRGB() ValEntry *photInt = CopyValEntry(0x0028,0x0004); photInt->SetValue("RGB "); - if(PixelReadConverter->GetRGB()) + if ( PixelReadConverter->GetRGB() ) { PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(), PixelReadConverter->GetRGBSize()); @@ -804,9 +897,9 @@ 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); @@ -827,10 +920,13 @@ 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 "); @@ -875,6 +971,10 @@ 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); @@ -943,17 +1043,6 @@ 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); } /** @@ -966,7 +1055,7 @@ void FileHelper::SetWriteToLibido() ValEntry *oldCol = dynamic_cast (FileInternal->GetDocEntry(0x0028, 0x0011)); - if( oldRow && oldCol ) + if ( oldRow && oldCol ) { std::string rows, columns; @@ -995,9 +1084,9 @@ 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(""); @@ -1014,6 +1103,12 @@ 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); } /** @@ -1027,7 +1122,7 @@ 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); @@ -1054,17 +1149,11 @@ BinEntry *FileHelper::CopyBinEntry(uint16_t group, uint16_t elem, DocEntry *oldE = FileInternal->GetDocEntry(group, elem); BinEntry *newE; + if ( oldE ) + if ( oldE->GetVR()!=vr ) + oldE = NULL; - if( oldE ) // Is this really usefull? - if( oldE->GetVR()!=vr ) - { - //oldE = NULL; - gdcmWarningMacro( " Unconsistent VR for Bin Entry : [" << oldE->GetVR() - << "] vs [" << vr << "] for " << - std::hex << group << "|" << elem); - delete oldE; - } - if( oldE ) + if ( oldE ) { newE = new BinEntry(oldE->GetDictEntry()); newE->Copy(oldE); @@ -1106,7 +1195,10 @@ 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 @@ -1121,45 +1213,44 @@ 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); - ValEntry *e_0002_0002 = CopyValEntry(0x0002,0x0002); + // '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); // '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); - 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); + 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); + std::string version = "GDCM "; + version += Util::GetVersion(); + e_0002_0013->SetValue(version); 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); @@ -1167,7 +1258,58 @@ 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 +1319,7 @@ 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 +1336,9 @@ 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 +1456,7 @@ 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 +1498,42 @@ 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(0x0002,0x0010); + 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); + +} + //----------------------------------------------------------------------------- // Private /** @@ -1373,31 +1541,33 @@ void FileHelper::CheckMandatoryElements() */ 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 ); - } } /** - * \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() { + 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(); @@ -1407,19 +1577,25 @@ 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); FileInternal->Print(os); - PixelReadConverter->SetPrintLevel(PrintLevel); - PixelReadConverter->Print(os); + if ( FileInternal->IsReadable() ) + { + PixelReadConverter->SetPrintLevel(PrintLevel); + PixelReadConverter->Print(os); + } } //-----------------------------------------------------------------------------