X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFileHelper.cxx;h=e91570e2833ee4a2ee654470002d92259bea5621;hb=c95e0f505e46f71f658c62901c68521ac4afeccb;hp=1e31cd1ca71d20b5058799defa0924a162bc8127;hpb=f12e51a575034ba832a0ff3b9f9c5ba219fc8562;p=gdcm.git diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx index 1e31cd1c..e91570e2 100644 --- a/src/gdcmFileHelper.cxx +++ b/src/gdcmFileHelper.cxx @@ -3,8 +3,9 @@ Program: gdcm Module: $RCSfile: gdcmFileHelper.cxx,v $ Language: C++ - Date: $Date: 2005/02/23 09:54:59 $ - Version: $Revision: 1.20 $ + + 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 @@ -35,6 +36,83 @@ #include +/* +// ----------------------------- WARNING ------------------------- + +These lines will be moved to the document-to-be 'User's Guide' + +// To read an image, user needs a gdcm::File +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 = f->GetEntryValue(groupNb,ElementNb); + +// to get the pixels, user needs a gdcm::FileHelper +gdcm::FileHelper *fh = new gdcm::FileHelper(f); +// user may ask not to convert Palette to RGB +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 + +fh->SetImageData( userPixels, userPixelsLength); +fh->SetTypeToRaw(); // Even if it was possible to convert Palette to RGB + // (WriteMode is set) + +fh->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation + // Little Endian is the default + // no other value is allowed + (-->SetWriteType(ExplicitVR);) + -->WriteType = ExplicitVR; +fh->Write(newFileName); // overwrites the file, if any + +// or : +fh->WriteDcmExplVR(newFileName); + + +// ----------------------------- WARNING ------------------------- + +These lines will be moved to the document-to-be 'Developer's Guide' + +WriteMode : WMODE_RAW / WMODE_RGB +WriteType : ImplicitVR, ExplicitVR, ACR, ACR_LIBIDO + +fh1->Write(newFileName); + SetWriteFileTypeToImplicitVR() / SetWriteFileTypeToExplicitVR(); + (modifies TransferSyntax) + SetWriteToRaw(); / SetWriteToRGB(); + (modifies, when necessary : photochromatic interpretation, + samples per pixel, Planar configuration, + bits allocated, bits stored, high bit -ACR 24 bits- + Pixels element VR, pushes out the LUT ) + CheckWriteIntegrity(); + (checks user given pixels length) + FileInternal->Write(fileName,WriteType) + fp = opens file(fileName); + ComputeGroup0002Length( ); + BitsAllocated 12->16 + RemoveEntryNoDestroy(palettes, etc) + Document::WriteContent(fp, writetype); + RestoreWrite(); + (moves back to the File all the archived elements) + RestoreWriteFileType(); + (pushes back group 0002, with TransferSyntax) +*/ + + + + namespace gdcm { //------------------------------------------------------------------------- @@ -45,6 +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 @@ -52,7 +131,7 @@ namespace gdcm * seen as a side effect). */ FileHelper::FileHelper( ) -{ +{ FileInternal = new File( ); SelfHeader = true; Initialize(); @@ -64,6 +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 @@ -76,10 +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. @@ -90,13 +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 @@ -105,20 +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; } @@ -127,6 +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 @@ -171,7 +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); } /** @@ -218,7 +349,6 @@ size_t FileHelper::GetImageDataSize() { return PixelWriteConverter->GetUserDataSize(); } - return PixelReadConverter->GetRGBSize(); } @@ -235,7 +365,6 @@ size_t FileHelper::GetImageDataRawSize() { return PixelWriteConverter->GetUserDataSize(); } - return PixelReadConverter->GetRawSize(); } @@ -287,9 +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 @@ -340,13 +471,17 @@ 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 Set the image data defined by the user, BUT WITHOUT COPYING THE DATA. + * \brief Points the internal pointer to the callers inData + * image representation, BUT WITHOUT COPYING THE DATA. + * 'image' Pixels are presented as C-like 2D arrays : line per line. + * 'volume'Pixels are presented as C-like 3D arrays : plane per plane * \warning Since the pixels are not copied, it is the caller's responsability * not to deallocate its data before gdcm uses them (e.g. with * the Write() method ) @@ -361,11 +496,8 @@ void FileHelper::SetImageData(uint8_t *inData, size_t expectedSize) } /** - * \brief Set the image data defined by the user, BUT WITHOUT COPYING THE DATA. + * \brief Set the image data defined by the user * \warning When writting the file, this data are get as default data to write - * \warning Since the pixels are not copied, it is the caller's responsability - * not to deallocate its data before gdcm uses them (e.g. with - * the Write() method ) * @param inData user supplied pixel area (uint8_t* is just for the compiler. * user is allowed to pass any kind of pixels since the size is * given in bytes) @@ -435,9 +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". @@ -448,26 +598,26 @@ uint8_t* FileHelper::GetLutRGBA() */ bool FileHelper::WriteRawData(std::string const &fileName) { - std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary ); + std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary ); if (!fp1) { gdcmWarningMacro( "Fail to open (write) file:" << fileName.c_str()); 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 @@ -483,7 +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 @@ -542,20 +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 @@ -565,7 +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(); } @@ -586,13 +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 @@ -617,27 +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 :" @@ -646,7 +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 " @@ -655,8 +816,7 @@ bool FileHelper::CheckWriteIntegrity() } break; } - } - + } return true; } @@ -667,15 +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 "); } @@ -688,9 +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); @@ -712,7 +872,7 @@ void FileHelper::SetWriteToRaw() */ void FileHelper::SetWriteToRGB() { - if(FileInternal->GetNumberOfScalarComponents()==3) + if ( FileInternal->GetNumberOfScalarComponents()==3 ) { PixelReadConverter->BuildRGBImage(); @@ -725,7 +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()); @@ -737,9 +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); @@ -760,10 +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 "); @@ -808,6 +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); @@ -834,7 +1001,7 @@ void FileHelper::SetWriteFileTypeToACR() Archive->Push(0x0002,0x0001); Archive->Push(0x0002,0x0002); Archive->Push(0x0002,0x0003); - Archive->Push(0x0002,0x0010);// Only TransferSyntax was pushed out ! + Archive->Push(0x0002,0x0010); Archive->Push(0x0002,0x0012); Archive->Push(0x0002,0x0013); Archive->Push(0x0002,0x0016); @@ -876,17 +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);//only TransferSyntax was pushed out/restored - Archive->Restore(0x0002,0x0012); - Archive->Restore(0x0002,0x0013); - Archive->Restore(0x0002,0x0016); - Archive->Restore(0x0002,0x0100); - Archive->Restore(0x0002,0x0102); } /** @@ -899,7 +1055,7 @@ void FileHelper::SetWriteToLibido() ValEntry *oldCol = dynamic_cast (FileInternal->GetDocEntry(0x0028, 0x0011)); - if( oldRow && oldCol ) + if ( oldRow && oldCol ) { std::string rows, columns; @@ -928,9 +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(""); @@ -947,6 +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); } /** @@ -960,7 +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); @@ -987,11 +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 ) + if ( oldE ) + if ( oldE->GetVR()!=vr ) oldE = NULL; - if( oldE ) + if ( oldE ) { newE = new BinEntry(oldE->GetDictEntry()); newE->Copy(oldE); @@ -1005,15 +1167,38 @@ BinEntry *FileHelper::CopyBinEntry(uint16_t group, uint16_t elem, } /** - * \brief Checks the Mandatory Elements - * adds the mandatory Entries if not found - * (when user asks to write as a DICOM file, an ACR-NEMA file - * he read before) + * \brief This method is called automatically, just before writting + * in order to produce a 'True Dicom V3' image + * We cannot know *how* the user made the File (reading an old ACR-NEMA + * file or a not very clean DICOM file ...) + * + * Just before writting : + * - we check the Entries + * - we create the mandatory entries if they are missing + * - we modify the values if necessary + * - we push the sensitive entries to the Archive + * The writing process will restore the entries as they where before + * entering FileHelper::CheckMandatoryElements, so the user will always + * see the entries just as he left them. + * + * \todo : - warn the user if we had to add some entries : + * even if a mandatory entry is missing, we add it, with a default value + * (we don't want to give up the writting process if user forgot to + * specify Lena's Patient ID, for instance ...) + * - read the whole PS 3.3 Part of DICOM (890 pages) + * and write a *full* checker (probably one method per Modality ...) + * Any contribution is welcome. + * - write a user callable full checker, to allow post reading + * and/or pre writting image consistency check. */ + 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 @@ -1024,46 +1209,48 @@ void FileHelper::CheckMandatoryElements() //0002 0016 AE 1 Source Application Entity Title //0002 0100 UI 1 Private Information Creator //0002 0102 OB 1 Private Information - - + // Create them if not found - ValEntry *e0002_0000 = CopyValEntry(0x0002,0x0000); - e0002_0000->SetValue("0"); // for the moment - Archive->Push(e0002_0000); + // 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); -/* BinEntry *e0002_0001 = CopyBinEntry(0x0002,0x0001, "OB"); - e0002_0001->SetBinArea((uint8_t*)Util::GetFileMetaInformationVersion(),false); - e0002_0001->SetLength(2);*/ - -/* ValEntry *e0002_0002 = CopyValEntry(0x0002,0x0002); - // [Secondary Capture Image Storage] - e0002_0002->SetValue("1.2.840.10008.5.1.4.1.1.7"); - Archive->Push(e0002_0002);*/ + 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); + // [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 *e0002_0003 = CopyValEntry(0x0002,0x0003); - e0002_0003->SetValue(Util::CreateUniqueUID()); - Archive->Push(e0002_0003); */ - -/* ValEntry *e0002_0010 = CopyValEntry(0x0002,0x0010); - //[Explicit VR - Little Endian] - e0002_0010->SetValue("1.2.840.10008.1.2.1"); - Archive->Push(e0002_0010);*/ - + ValEntry *e_0002_0003 = CopyValEntry(0x0002,0x0003); + e_0002_0003->SetValue(Util::CreateUniqueUID()); + Archive->Push(e_0002_0003); + // 'Implementation Class UID' -/* ValEntry *e0002_0012 = CopyValEntry(0x0002,0x0012); - e0002_0012->SetValue(Util::CreateUniqueUID()); - Archive->Push(e0002_0012); */ + ValEntry *e_0002_0012 = CopyValEntry(0x0002,0x0012); + e_0002_0012->SetValue(Util::CreateUniqueUID()); + Archive->Push(e_0002_0012); // 'Implementation Version Name' - ValEntry *e0002_0013 = CopyValEntry(0x0002,0x0013); - e0002_0013->SetValue("GDCM 1.0"); - Archive->Push(e0002_0013); + 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 *e0002_0016 = CopyValEntry(0x0002,0x0016); - // e0002_0016->SetValue("1.2.840.10008.5.1.4.1.1.7"); - // Archive->Push(e0002_0016); + //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); @@ -1071,148 +1258,205 @@ 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) - ValEntry *e0008_0016 = FileInternal->GetValEntry(0x0008, 0x0016); - if ( e0008_0016 != 0 ) + // 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 ) { -/* // Create 'Source Image Sequence' SeqEntry - SeqEntry *s = new SeqEntry ( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x2112) ); + // Create 'Source Image Sequence' 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 *e0008_1150 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) ); - e0008_1150->SetValue( e0008_0016->GetValue()); - sqi->AddEntry(e0008_1150); + ValEntry *e_0008_1150 = new ValEntry( + Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) ); + e_0008_1150->SetValue( e_0008_0016->GetValue()); + sqi->AddEntry(e_0008_1150); // create 'Referenced SOP Instance UID' - ValEntry *e0008_0018 = FileInternal->GetValEntry(0x0008, 0x0018); - ValEntry *e0008_1155 = new ValEntry( + ValEntry *e_0008_0018 = FileInternal->GetValEntry(0x0008, 0x0018); + ValEntry *e_0008_1155 = new ValEntry( Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1155) ); - e0008_1155->SetValue( e0008_0018->GetValue()); - sqi->AddEntry(e0008_1155); + 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' - ValEntry *e0008_0008 = CopyValEntry(0x0008,0x0008); - e0008_0008->SetValue("DERIVED\\PRIMARY"); - Archive->Push(e0008_0008);*/ + // '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); } else { - // SOP Class UID -/* e0008_0016 = new ValEntry( + // There was no 'SOP Class UID'. + // 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] - e0008_0016 ->SetValue("1.2.840.10008.5.1.4.1.1.7"); - Archive->Push(e0008_0016); */ + e_0008_0016 ->SetValue("1.2.840.10008.5.1.4.1.1.7"); + Archive->Push(e_0008_0016); } +// ---- The user will never have to take any action on the following ----. + // new value for 'SOP Instance UID' - ValEntry *e0008_0018 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0018) ); - e0008_0018->SetValue( Util::CreateUniqueUID() ); - Archive->Push(e0008_0018); + ValEntry *e_0008_0018 = new ValEntry( + Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0018) ); + e_0008_0018->SetValue( Util::CreateUniqueUID() ); + Archive->Push(e_0008_0018); // Instance Creation Date - ValEntry *e0008_0012 = CopyValEntry(0x0008,0x0012); + ValEntry *e_0008_0012 = CopyValEntry(0x0008,0x0012); std::string date = Util::GetCurrentDate(); - e0008_0012->SetValue(date.c_str()); - Archive->Push(e0008_0012); + e_0008_0012->SetValue(date.c_str()); + Archive->Push(e_0008_0012); // Instance Creation Time - ValEntry *e0008_0013 = CopyValEntry(0x0008,0x0013); + ValEntry *e_0008_0013 = CopyValEntry(0x0008,0x0013); std::string time = Util::GetCurrentTime(); - e0008_0013->SetValue(time.c_str()); - Archive->Push(e0008_0013); - -/* // new value for 'Serie Instance UID' - // TODO prevoir booleen pour figer la valeur d'un appel a l'autre - // calculer nouvelle valeur a chaque fois - - ValEntry *e0020_000e = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0020, 0x000e) ); - e0020_000e->SetValue( Util::CreateUniqueUID() ); - Archive->Push(e0020_000e); - - // new value for 'Study Instance UID' - // TODO prevoir flag pour figer la valeur d'un appel a l'autre - // calculer nouvelle valeur a chaque fois - // reutiliser la valeur image origine - - ValEntry *e0020_000d = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0020, 0x000d) ); - e0020_000d->SetValue( Util::CreateUniqueUID() ); - Archive->Push(e0020_000d); -*/ + e_0008_0013->SetValue(time.c_str()); + Archive->Push(e_0008_0013); // ----- Add Mandatory Entries if missing --- // Entries whose type is 1 are mandatory, with a mandatory value -// Entries whose type is 1c are ? +// 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 ? +// Entries whose type is 2c are mandatory-inside-a-Sequence // Entries whose type is 3 are optional -// ValEntry *e; + // '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); + } - // Modality -/* ValEntry *e0008_0060 = FileInternal->GetValEntry(0x0008, 0x0060); - if ( !e0008_0060 ) + // Modality : if missing we set it to 'OTher' + ValEntry *e_0008_0060 = FileInternal->GetValEntry(0x0008, 0x0060); + if ( !e_0008_0060 ) { - e0008_0060 = new ValEntry( + e_0008_0060 = new ValEntry( Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0060) ); - e0008_0060->SetValue("OT"); - Archive->Push(e0008_0060); + e_0008_0060->SetValue("OT"); + Archive->Push(e_0008_0060); } - // Manufacturer - ValEntry *e0008_0070 = FileInternal->GetValEntry(0x0008, 0x0070); - if ( !e0008_0070 ) + // Manufacturer : if missing we set it to 'GDCM Factory' + ValEntry *e_0008_0070 = FileInternal->GetValEntry(0x0008, 0x0070); + if ( !e_0008_0070 ) { - e0008_0070 = new ValEntry( + e_0008_0070 = new ValEntry( Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0070) ); - e0008_0070->SetValue("GDCM Factory"); - Archive->Push(e0008_0070); - } + e_0008_0070->SetValue("GDCM Factory"); + Archive->Push(e_0008_0070); + } - // Institution Name - ValEntry *e0008_0080 = FileInternal->GetValEntry(0x0008, 0x0080); - if ( !e0008_0080 ) + // Institution Name : if missing we set it to 'GDCM Hospital' + ValEntry *e_0008_0080 = FileInternal->GetValEntry(0x0008, 0x0080); + if ( !e_0008_0080 ) { - e0008_0080 = new ValEntry( + e_0008_0080 = new ValEntry( Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0080) ); - e0008_0080->SetValue("GDCM Hospital"); - Archive->Push(e0008_0080); - } + e_0008_0080->SetValue("GDCM Hospital"); + Archive->Push(e_0008_0080); + } - // Patient's Name - ValEntry *e0010_0010 = FileInternal->GetValEntry(0x0010, 0x0010); - if ( !e0010_0010 ) + // Patient's Name : if missing, we set it to 'GDCM^Patient' + ValEntry *e_0010_0010 = FileInternal->GetValEntry(0x0010, 0x0010); + if ( !e_0010_0010 ) { - e0010_0010 = new ValEntry( + e_0010_0010 = new ValEntry( Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0010) ); - e0010_0010->SetValue("GDCM_Patient"); - Archive->Push(e0010_0010); - } - - // Patient's ID - ValEntry *e_0010_0020 = FileInternal->GetValEntry(0x0010, 0x0020); - if ( !e ) - { - e_0010_0020 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0020) ); - e_0010_0020->SetValue("GDCM_Patient_ID"); - Archive->Push(e_0010_0020); - } + e_0010_0010->SetValue("GDCM^Patient"); + Archive->Push(e_0010_0010); + } - // Patient's Birth Date + // Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory ValEntry *e_0010_0030 = FileInternal->GetValEntry(0x0010, 0x0030); if ( !e_0010_0030 ) { @@ -1222,7 +1466,7 @@ void FileHelper::CheckMandatoryElements() Archive->Push(e_0010_0030); } - // Patient's Sex + // Patient's Sex :'type 2' entry -> must exist, value not mandatory ValEntry *e_0010_0040 = FileInternal->GetValEntry(0x0010, 0x0040); if ( !e_0010_0040 ) { @@ -1232,7 +1476,7 @@ void FileHelper::CheckMandatoryElements() Archive->Push(e_0010_0040); } - // Referring Physician's Name + // Referring Physician's Name :'type 2' entry -> must exist, value not mandatory ValEntry *e_0008_0090 = FileInternal->GetValEntry(0x0008, 0x0090); if ( !e_0008_0090 ) { @@ -1240,9 +1484,56 @@ void FileHelper::CheckMandatoryElements() Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0090) ); e_0008_0090->SetValue(""); Archive->Push(e_0008_0090); - }*/ + } + + // 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); + if ( !e_0028_0008 ) + { + Archive->Push(0x0020, 0X0052); + } } +/** + * \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 /** @@ -1250,31 +1541,33 @@ void FileHelper::CheckMandatoryElements() */ void FileHelper::Initialize() { + UserFunction = 0; + WriteMode = WMODE_RAW; WriteType = ExplicitVR; - PixelReadConverter = new PixelReadConvert; + 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(); @@ -1284,19 +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); + } } //-----------------------------------------------------------------------------