X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFileHelper.cxx;h=e2326b53faf0abf8d6af3649d64fcfa207fd5c36;hb=f14e091ab076314a54459f1b2b0efeaa03a2bc56;hp=0aeffd71d5ad91a34246d8ccd7b6e4ddfbffcf74;hpb=9ca0e4bb2208be93bebf21d0c5d75c8018e7605a;p=gdcm.git diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx index 0aeffd71..e2326b53 100644 --- a/src/gdcmFileHelper.cxx +++ b/src/gdcmFileHelper.cxx @@ -4,8 +4,8 @@ Module: $RCSfile: gdcmFileHelper.cxx,v $ Language: C++ - Date: $Date: 2005/06/24 10:55:59 $ - Version: $Revision: 1.46 $ + Date: $Date: 2005/10/26 08:28:58 $ + Version: $Revision: 1.76 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -23,11 +23,9 @@ #include "gdcmDocument.h" #include "gdcmDebug.h" #include "gdcmUtil.h" -#include "gdcmBinEntry.h" -#include "gdcmValEntry.h" #include "gdcmSeqEntry.h" #include "gdcmSQItem.h" -#include "gdcmContentEntry.h" +#include "gdcmDataEntry.h" #include "gdcmFile.h" #include "gdcmPixelReadConvert.h" #include "gdcmPixelWriteConvert.h" @@ -42,32 +40,43 @@ These lines will be moved to the document-to-be 'User's Guide' // To read an image, user needs a gdcm::File -gdcm::File *f1 = new gdcm::File(fileName); +gdcm::File *f = new gdcm::File(fileName); +// or (advanced) : +// user may also decide he doesn't want to load some parts of the header +gdcm::File *f = new gdcm::File(); +f->SetFileName(fileName); + f->SetLoadMode(LD_NOSEQ); // or + f->SetLoadMode(LD_NOSHADOW); // or + f->SetLoadMode(LD_NOSEQ | LD_NOSHADOW); // or + f->SetLoadMode(LD_NOSHADOWSEQ); +f->Load(); + // user can now check some values -std::string v = f1->GetEntryValue(groupNb,ElementNb); +std::string v = f->GetEntryValue(groupNb,ElementNb); + // to get the pixels, user needs a gdcm::FileHelper -gdcm::FileHelper *fh1 = new gdcm::FileHelper(f1); +gdcm::FileHelper *fh = new gdcm::FileHelper(f); // user may ask not to convert Palette to RGB -uint8_t *pixels = fh1->GetImageDataRaw(); -int imageLength = fh1->GetImageDataRawSize(); +uint8_t *pixels = fh->GetImageDataRaw(); +int imageLength = fh->GetImageDataRawSize(); // He can now use the pixels, create a new image, ... uint8_t *userPixels = ... To re-write the image, user re-uses the gdcm::FileHelper -fh1->SetImageData( userPixels, userPixelsLength); -fh1->SetTypeToRaw(); // Even if it was possible to convert Palette to RGB +fh->SetImageData( userPixels, userPixelsLength); +fh->SetTypeToRaw(); // Even if it was possible to convert Palette to RGB // (WriteMode is set) -fh1->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation +fh->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation // Little Endian is the default // no other value is allowed (-->SetWriteType(ExplicitVR);) -->WriteType = ExplicitVR; -fh1->Write(newFileName); // overwrites the file, if any +fh->Write(newFileName); // overwrites the file, if any // or : -fh1->WriteDcmExplVR(newFileName); +fh->WriteDcmExplVR(newFileName); // ----------------------------- WARNING ------------------------- @@ -89,9 +98,9 @@ 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) + RemoveEntry(palettes, etc) Document::WriteContent(fp, writetype); RestoreWrite(); (moves back to the File all the archived elements) @@ -112,6 +121,7 @@ namespace gdcm * Opens (in read only and when possible) an existing file and checks * for DICOM compliance. Returns NULL on failure. * It will be up to the user to load the pixels into memory + * ( GetImageDataSize() + GetImageData() methods) * \note the in-memory representation of all available tags found in * the DICOM header is post-poned to first header information access. * This avoid a double parsing of public part of the header when @@ -119,9 +129,8 @@ namespace gdcm * seen as a side effect). */ FileHelper::FileHelper( ) -{ - FileInternal = new File( ); - SelfHeader = true; +{ + FileInternal = File::New( ); Initialize(); } @@ -131,6 +140,7 @@ 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 @@ -140,29 +150,15 @@ FileHelper::FileHelper( ) */ FileHelper::FileHelper(File *header) { - FileInternal = header; - SelfHeader = false; - Initialize(); -} + gdcmAssertMacro(header); -/** - * \brief 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. - * It will be up to the user to load the pixels into memory - * \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 - * one sets an a posteriori shadow dictionary (efficiency can be - * seen as a side effect). - * @param filename file to be opened for parsing - */ -FileHelper::FileHelper(std::string const &filename ) -{ - FileInternal = new File( filename ); - SelfHeader = true; + FileInternal = header; + FileInternal->Register(); Initialize(); + if ( FileInternal->IsReadable() ) + { + PixelReadConverter->GrabInformationsFromFile( FileInternal ); + } } /** @@ -185,15 +181,47 @@ FileHelper::~FileHelper() delete Archive; } - if ( SelfHeader ) - { - delete FileInternal; - } - FileInternal = 0; + FileInternal->Unregister(); } //----------------------------------------------------------------------------- // Public + +/** + * \brief Sets the LoadMode of the internal gdcm::File as a boolean string. + * NO_SEQ, NO_SHADOW, NO_SHADOWSEQ ... (nothing more, right now) + * WARNING : before using NO_SHADOW, be sure *all* your files + * contain accurate values in the 0x0000 element (if any) + * of *each* Shadow Group. The parser will fail if the size is wrong ! + * @param loadMode Load mode to be used + */ +void FileHelper::SetLoadMode(int loadMode) +{ + GetFile()->SetLoadMode( loadMode ); +} +/** + * \brief Sets the LoadMode of the internal gdcm::File + * @param fileName name of the file to be open + */ +void FileHelper::SetFileName(std::string const &fileName) +{ + FileInternal->SetFileName( fileName ); +} + +/** + * \brief Loader + * @return false if file cannot be open or no swap info was found, + * or no tag was found. + */ +bool FileHelper::Load() +{ + if ( !FileInternal->Load() ) + return false; + + PixelReadConverter->GrabInformationsFromFile( FileInternal ); + return true; +} + /** * \brief Accesses an existing DocEntry (i.e. a Dicom Element) * through it's (group, element) and modifies it's content with @@ -203,10 +231,10 @@ FileHelper::~FileHelper() * @param elem element number of the Dicom Element to modify * \return false if DocEntry not found */ -bool FileHelper::SetValEntry(std::string const &content, - uint16_t group, uint16_t elem) +bool FileHelper::SetEntryString(std::string const &content, + uint16_t group, uint16_t elem) { - return FileInternal->SetValEntry(content, group, elem); + return FileInternal->SetEntryString(content, group, elem); } @@ -220,10 +248,10 @@ bool FileHelper::SetValEntry(std::string const &content, * @param elem element number of the Dicom Element to modify * \return false if DocEntry not found */ -bool FileHelper::SetBinEntry(uint8_t *content, int lgth, - uint16_t group, uint16_t elem) +bool FileHelper::SetEntryBinArea(uint8_t *content, int lgth, + uint16_t group, uint16_t elem) { - return FileInternal->SetBinEntry(content, lgth, group, elem); + return FileInternal->SetEntryBinArea(content, lgth, group, elem); } /** @@ -235,10 +263,10 @@ bool FileHelper::SetBinEntry(uint8_t *content, int lgth, * \return pointer to the modified/created Dicom entry (NULL when creation * failed). */ -ValEntry *FileHelper::InsertValEntry(std::string const &content, - uint16_t group, uint16_t elem) +DataEntry *FileHelper::InsertEntryString(std::string const &content, + uint16_t group, uint16_t elem) { - return FileInternal->InsertValEntry(content, group, elem); + return FileInternal->InsertEntryString(content, group, elem); } /** @@ -252,10 +280,10 @@ ValEntry *FileHelper::InsertValEntry(std::string const &content, * \return pointer to the modified/created Dicom entry (NULL when creation * failed). */ -BinEntry *FileHelper::InsertBinEntry(uint8_t *binArea, int lgth, - uint16_t group, uint16_t elem) +DataEntry *FileHelper::InsertEntryBinArea(uint8_t *binArea, int lgth, + uint16_t group, uint16_t elem) { - return FileInternal->InsertBinEntry(binArea, lgth, group, elem); + return FileInternal->InsertEntryBinArea(binArea, lgth, group, elem); } /** @@ -289,7 +317,7 @@ size_t FileHelper::GetImageDataSize() } /** - * \brief Get the size of the image data + * \brief Get the size of the image data. * If the image could be converted to RGB using a LUT, * this transformation is not taken into account by GetImageDataRawSize * (use GetImageDataSize if you wish) @@ -305,13 +333,15 @@ size_t FileHelper::GetImageDataRawSize() } /** - * \brief - Allocates necessary memory, + * \brief brings pixels into memory : + * - Allocates necessary memory, * - 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 * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone. * @return Pointer to newly allocated pixel data. + * (uint8_t is just for prototyping. feel free to cast) * NULL if alloc fails */ uint8_t *FileHelper::GetImageData() @@ -339,12 +369,14 @@ uint8_t *FileHelper::GetImageData() } /** - * \brief Allocates necessary memory, - * Transforms YBR pixels (if any) into RGB pixels - * Transforms 3 planes R, G, B (if any) into a single RGB Plane - * Copies the pixel data (image[s]/volume[s]) to newly allocated zone. - * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane + * \brief brings pixels into memory : + * - Allocates necessary memory, + * - Transforms YBR pixels (if any) into RGB pixels + * - Transforms 3 planes R, G, B (if any) into a single RGB Plane + * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone. + * - DOES NOT transform Grey plane + 3 Palettes into a RGB Plane * @return Pointer to newly allocated pixel data. + * (uint8_t is just for prototyping. feel free to cast) * NULL if alloc fails */ uint8_t *FileHelper::GetImageDataRaw () @@ -352,15 +384,17 @@ uint8_t *FileHelper::GetImageDataRaw () return GetRaw(); } -/** - * \brief - * Read the pixels from disk (uncompress if necessary), +#ifndef GDCM_LEGACY_REMOVE +/* + * \ 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 * Copies at most MaxSize bytes of pixel data to caller allocated * memory space. - * \warning This function allows people that want to build a volume + * \ warning This function allows people that want to build a volume * from an image stack *not to* have, first to get the image pixels, * and then move them to the volume area. * It's absolutely useless for any VTK user since vtk chooses @@ -369,12 +403,12 @@ uint8_t *FileHelper::GetImageDataRaw () * to load the image line by line, starting from the end. * VTK users have to call GetImageData * - * @param destination Address (in caller's memory space) at which the + * @ param destination Address (in caller's memory space) at which the * pixel data should be copied - * @param maxSize Maximum number of bytes to be copied. When MaxSize + * @ param maxSize Maximum number of bytes to be copied. When MaxSize * is not sufficient to hold the pixel data the copy is not * executed (i.e. no partial copy). - * @return On success, the number of bytes actually copied. Zero on + * @ return On success, the number of bytes actually copied. Zero on * failure e.g. MaxSize is lower than necessary. */ size_t FileHelper::GetImageDataIntoVector (void *destination, size_t maxSize) @@ -409,6 +443,7 @@ size_t FileHelper::GetImageDataIntoVector (void *destination, size_t maxSize) PixelReadConverter->GetRawSize() ); return PixelReadConverter->GetRawSize(); } +#endif /** * \brief Points the internal pointer to the callers inData @@ -638,11 +673,15 @@ bool FileHelper::Write(std::string const &fileName) // and forgets to create any Entry belonging to group 0008 // (shame on him !) // We add Recognition Code (RET) - if ( ! FileInternal->GetValEntry(0x0008, 0x0010) ) - FileInternal->InsertValEntry("", 0x0008, 0x0010); + if ( ! FileInternal->GetDataEntry(0x0008, 0x0010) ) + FileInternal->InsertEntryString("ACR-NEMA V1.0 ", 0x0008, 0x0010); SetWriteFileTypeToACR(); // SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR ! break; + case JPEG: + SetWriteFileTypeToJPEG(); + std::cerr << "Writting as JPEG" << std::endl; + break; } CheckMandatoryElements(); @@ -676,6 +715,7 @@ bool FileHelper::Write(std::string const &fileName) } bool check = CheckWriteIntegrity(); // verifies length + if (WriteType == JPEG ) check = true; if (check) { check = FileInternal->Write(fileName,WriteType); @@ -749,7 +789,8 @@ bool FileHelper::CheckWriteIntegrity() } break; } - } + } + return true; } @@ -767,14 +808,14 @@ void FileHelper::SetWriteToRaw() } else { - ValEntry *photInt = CopyValEntry(0x0028,0x0004); + DataEntry *photInt = CopyDataEntry(0x0028,0x0004); if (FileInternal->HasLUT() ) { - photInt->SetValue("PALETTE COLOR "); + photInt->SetString("PALETTE COLOR "); } else { - photInt->SetValue("MONOCHROME2 "); + photInt->SetString("MONOCHROME2 "); } PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(), @@ -785,14 +826,17 @@ void FileHelper::SetWriteToRaw() vr = "OW"; if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files vr = "OB"; - BinEntry *pixel = - CopyBinEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr); - pixel->SetValue(GDCM_BINLOADED); + DataEntry *pixel = + CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr); + pixel->SetFlag(DataEntry::FLAG_PIXELDATA); pixel->SetBinArea(PixelWriteConverter->GetData(),false); pixel->SetLength(PixelWriteConverter->GetDataSize()); Archive->Push(photInt); Archive->Push(pixel); + + photInt->Delete(); + pixel->Delete(); } } @@ -809,14 +853,14 @@ void FileHelper::SetWriteToRGB() { PixelReadConverter->BuildRGBImage(); - ValEntry *spp = CopyValEntry(0x0028,0x0002); - spp->SetValue("3 "); + DataEntry *spp = CopyDataEntry(0x0028,0x0002); + spp->SetString("3 "); - ValEntry *planConfig = CopyValEntry(0x0028,0x0006); - planConfig->SetValue("0 "); + DataEntry *planConfig = CopyDataEntry(0x0028,0x0006); + planConfig->SetString("0 "); - ValEntry *photInt = CopyValEntry(0x0028,0x0004); - photInt->SetValue("RGB "); + DataEntry *photInt = CopyDataEntry(0x0028,0x0004); + photInt->SetString("RGB "); if ( PixelReadConverter->GetRGB() ) { @@ -834,9 +878,9 @@ void FileHelper::SetWriteToRGB() vr = "OW"; if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files vr = "OB"; - BinEntry *pixel = - CopyBinEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr); - pixel->SetValue(GDCM_BINLOADED); + DataEntry *pixel = + CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr); + pixel->SetFlag(DataEntry::FLAG_PIXELDATA); pixel->SetBinArea(PixelWriteConverter->GetData(),false); pixel->SetLength(PixelWriteConverter->GetDataSize()); @@ -845,6 +889,11 @@ void FileHelper::SetWriteToRGB() Archive->Push(photInt); Archive->Push(pixel); + spp->Delete(); + planConfig->Delete(); + photInt->Delete(); + pixel->Delete(); + // Remove any LUT Archive->Push(0x0028,0x1101); Archive->Push(0x0028,0x1102); @@ -861,18 +910,22 @@ void FileHelper::SetWriteToRGB() // samples per pixels = 1 (in the read file) if ( FileInternal->GetBitsAllocated()==24 ) { - ValEntry *bitsAlloc = CopyValEntry(0x0028,0x0100); - bitsAlloc->SetValue("8 "); + DataEntry *bitsAlloc = CopyDataEntry(0x0028,0x0100); + bitsAlloc->SetString("8 "); - ValEntry *bitsStored = CopyValEntry(0x0028,0x0101); - bitsStored->SetValue("8 "); + DataEntry *bitsStored = CopyDataEntry(0x0028,0x0101); + bitsStored->SetString("8 "); - ValEntry *highBit = CopyValEntry(0x0028,0x0102); - highBit->SetValue("7 "); + DataEntry *highBit = CopyDataEntry(0x0028,0x0102); + highBit->SetString("7 "); Archive->Push(bitsAlloc); Archive->Push(bitsStored); Archive->Push(highBit); + + bitsAlloc->Delete(); + bitsStored->Delete(); + highBit->Delete(); } } else @@ -945,15 +998,28 @@ void FileHelper::SetWriteFileTypeToACR() /** * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian" */ +void FileHelper::SetWriteFileTypeToJPEG() +{ + std::string ts = Util::DicomString( + Global::GetTS()->GetSpecialTransferSyntax(TS::JPEGBaselineProcess1) ); + + DataEntry *tss = CopyDataEntry(0x0002,0x0010); + tss->SetString(ts); + + Archive->Push(tss); + tss->Delete(); +} + void FileHelper::SetWriteFileTypeToExplicitVR() { std::string ts = Util::DicomString( Global::GetTS()->GetSpecialTransferSyntax(TS::ExplicitVRLittleEndian) ); - ValEntry *tss = CopyValEntry(0x0002,0x0010); - tss->SetValue(ts); + DataEntry *tss = CopyDataEntry(0x0002,0x0010); + tss->SetString(ts); Archive->Push(tss); + tss->Delete(); } /** @@ -964,10 +1030,11 @@ void FileHelper::SetWriteFileTypeToImplicitVR() std::string ts = Util::DicomString( Global::GetTS()->GetSpecialTransferSyntax(TS::ImplicitVRLittleEndian) ); - ValEntry *tss = CopyValEntry(0x0002,0x0010); - tss->SetValue(ts); + DataEntry *tss = CopyDataEntry(0x0002,0x0010); + tss->SetString(ts); Archive->Push(tss); + tss->Delete(); } @@ -983,31 +1050,33 @@ void FileHelper::RestoreWriteFileType() */ void FileHelper::SetWriteToLibido() { - ValEntry *oldRow = dynamic_cast - (FileInternal->GetDocEntry(0x0028, 0x0010)); - ValEntry *oldCol = dynamic_cast - (FileInternal->GetDocEntry(0x0028, 0x0011)); + DataEntry *oldRow = FileInternal->GetDataEntry(0x0028, 0x0010); + DataEntry *oldCol = FileInternal->GetDataEntry(0x0028, 0x0011); if ( oldRow && oldCol ) { std::string rows, columns; - ValEntry *newRow=new ValEntry(oldRow->GetDictEntry()); - ValEntry *newCol=new ValEntry(oldCol->GetDictEntry()); + DataEntry *newRow=DataEntry::New(oldRow->GetDictEntry()); + DataEntry *newCol=DataEntry::New(oldCol->GetDictEntry()); newRow->Copy(oldCol); newCol->Copy(oldRow); - newRow->SetValue(oldCol->GetValue()); - newCol->SetValue(oldRow->GetValue()); + newRow->SetString(oldCol->GetString()); + newCol->SetString(oldRow->GetString()); Archive->Push(newRow); Archive->Push(newCol); + + newRow->Delete(); + newCol->Delete(); } - ValEntry *libidoCode = CopyValEntry(0x0008,0x0010); - libidoCode->SetValue("ACRNEMA_LIBIDO_1.1"); + DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010); + libidoCode->SetString("ACRNEMA_LIBIDO_1.1"); Archive->Push(libidoCode); + libidoCode->Delete(); } /** @@ -1015,15 +1084,15 @@ void FileHelper::SetWriteToLibido() */ void FileHelper::SetWriteToNoLibido() { - ValEntry *recCode = dynamic_cast - (FileInternal->GetDocEntry(0x0008,0x0010)); + DataEntry *recCode = FileInternal->GetDataEntry(0x0008,0x0010); if ( recCode ) { - if ( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" ) + if ( recCode->GetString() == "ACRNEMA_LIBIDO_1.1" ) { - ValEntry *libidoCode = CopyValEntry(0x0008,0x0010); - libidoCode->SetValue(""); + DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010); + libidoCode->SetString(""); Archive->Push(libidoCode); + libidoCode->Delete(); } } } @@ -1045,55 +1114,31 @@ void FileHelper::RestoreWriteOfLibido() } /** - * \brief Duplicates a ValEntry or creates it. - * @param group Group number of the Entry - * @param elem Element number of the Entry - * \return pointer to the new Val Entry (NULL when creation failed). - */ -ValEntry *FileHelper::CopyValEntry(uint16_t group, uint16_t elem) -{ - DocEntry *oldE = FileInternal->GetDocEntry(group, elem); - ValEntry *newE; - - if ( oldE ) - { - newE = new ValEntry(oldE->GetDictEntry()); - newE->Copy(oldE); - } - else - { - newE = GetFile()->NewValEntry(group, elem); - } - - return newE; -} - -/** - * \brief Duplicates a BinEntry or creates it. + * \brief Duplicates a DataEntry or creates it. * @param group Group number of the Entry * @param elem Element number of the Entry * @param vr Value Representation of the Entry * FIXME : what is it used for? * \return pointer to the new Bin Entry (NULL when creation failed). */ -BinEntry *FileHelper::CopyBinEntry(uint16_t group, uint16_t elem, - const std::string &vr) +DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem, + const TagName &vr) { DocEntry *oldE = FileInternal->GetDocEntry(group, elem); - BinEntry *newE; + DataEntry *newE; - if ( oldE ) - if ( oldE->GetVR()!=vr ) + if ( oldE && vr != GDCM_VRUNKNOWN ) + if ( oldE->GetVR() != vr ) oldE = NULL; if ( oldE ) { - newE = new BinEntry(oldE->GetDictEntry()); + newE = DataEntry::New(oldE->GetDictEntry()); newE->Copy(oldE); } else { - newE = GetFile()->NewBinEntry(group, elem, vr); + newE = GetFile()->NewDataEntry(group, elem, vr); } return newE; @@ -1113,6 +1158,14 @@ BinEntry *FileHelper::CopyBinEntry(uint16_t group, uint16_t elem, * 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. + * \note + * - Entries whose type is 1 are mandatory, with a mandatory value + * - Entries whose type is 1c are mandatory-inside-a-Sequence, + * with a mandatory value + * - Entries whose type is 2 are mandatory, with an optional value + * - Entries whose type is 2c are mandatory-inside-a-Sequence, + * with an optional value + * - Entries whose type is 3 are optional * * \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 @@ -1124,9 +1177,74 @@ BinEntry *FileHelper::CopyBinEntry(uint16_t group, uint16_t elem, * - write a user callable full checker, to allow post reading * and/or pre writting image consistency check. */ + +/* ------------------------------------------------------------------------------------- +To be moved to User's guide / WIKI ? + + +-->'Media Storage SOP Class UID' (0x0002,0x0002) +-->'SOP Class UID' (0x0008,0x0016) are set to + [Secondary Capture Image Storage] + (Potentialy, the image was modified by user, and post-processed; + it's no longer a 'native' image) + +--> 'Image Type' (0x0008,0x0008) + is forced to "DERIVED\PRIMARY" + (The written image is no longer an 'ORIGINAL' one) + +--> 'Modality' (0x0008,0x0060) + is defaulted to "OT" (other) if missing. + (a fully user created image belongs to *no* modality) + +--> 'Media Storage SOP Instance UID' (0x0002,0x0003) +--> 'Implementation Class UID' (0x0002,0x0012) + are automatically generated; no user intervention possible + +--> 'Serie Instance UID'(0x0020,0x000e) +--> 'Study Instance UID'(0x0020,0x000d) are kept as is if already exist + created if it doesn't. + The user is allowed to create his own Series/Studies, + keeping the same 'Serie Instance UID' / 'Study Instance UID' + for various images + Warning : + The user shouldn't add any image to a 'Manufacturer Serie' + but there is no way no to allowed him to do that + + +--> If 'SOP Class UID' exists in the native image ('true DICOM' image) + we create the 'Source Image Sequence' SeqEntry (0x0008, 0x2112) + + --> 'Referenced SOP Class UID' (0x0008, 0x1150) + whose value is the original 'SOP Class UID' + ---> 'Referenced SOP Instance UID' (0x0008, 0x1155) + whose value is the original 'SOP Class UID' + +--> Bits Stored, Bits Allocated, Hight Bit Position are checked for consistency +--> Pixel Spacing (0x0028,0x0030) is defaulted to "1.0\1.0" +--> Samples Per Pixel (0x0028,0x0002) is defaulted to 1 (grayscale) + +--> Instance Creation Date, Instance Creation Time, Study Date, Study Time + are force to current Date and Time + +--> Conversion Type (0x0008,0x0064) + is forced to 'SYN' (Synthetic Image) + +--> Study ID, Series Number, Instance Number, Patient Orientation (Type 2) + are created, with empty value if there are missing. + +--> Manufacturer, Institution Name, Patient's Name, (Type 2) + are defaulted with a 'gdcm' value. + +--> Patient ID, Patient's Birth Date, Patient's Sex, (Type 2) +--> Referring Physician's Name (Type 2) + are created, with empty value if there are missing. + + -------------------------------------------------------------------------------------*/ void FileHelper::CheckMandatoryElements() { + std::string sop = Util::CreateUniqueUID(); + // just to remember : 'official' 0002 group if ( WriteType != ACR && WriteType != ACR_LIBIDO ) { @@ -1146,41 +1264,29 @@ void FileHelper::CheckMandatoryElements() // Create them if not found // Always modify the value // Push the entries to the archive. - ValEntry *e_0002_0000 = CopyValEntry(0x0002,0x0000); - e_0002_0000->SetValue("0"); // for the moment - Archive->Push(e_0002_0000); + CopyMandatoryEntry(0x0002,0x0000,"0"); - BinEntry *e_0002_0001 = CopyBinEntry(0x0002,0x0001, "OB"); + DataEntry *e_0002_0001 = CopyDataEntry(0x0002,0x0001, "OB"); e_0002_0001->SetBinArea((uint8_t*)Util::GetFileMetaInformationVersion(), false); e_0002_0001->SetLength(2); Archive->Push(e_0002_0001); + e_0002_0001->Delete(); - // 'Media Stored SOP Class UID' - ValEntry *e_0002_0002 = CopyValEntry(0x0002,0x0002); - // [Secondary Capture Image Storage] - e_0002_0002->SetValue("1.2.840.10008.5.1.4.1.1.7"); - Archive->Push(e_0002_0002); + // Potentialy post-processed image --> [Secondary Capture Image Storage] + // 'Media Storage SOP Class UID' + CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7"); - // 'Media Stored SOP Instance UID' - ValEntry *e_0002_0003 = CopyValEntry(0x0002,0x0003); - e_0002_0003->SetValue(Util::CreateUniqueUID()); - Archive->Push(e_0002_0003); - + // 'Media Storage SOP Instance UID' + CopyMandatoryEntry(0x0002,0x0003,sop); + // 'Implementation Class UID' - ValEntry *e_0002_0012 = CopyValEntry(0x0002,0x0012); - e_0002_0012->SetValue(Util::CreateUniqueUID()); - Archive->Push(e_0002_0012); + CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID()); // 'Implementation Version Name' - ValEntry *e_0002_0013 = CopyValEntry(0x0002,0x0013); - e_0002_0013->SetValue("GDCM 1.1"); - 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); + std::string version = "GDCM "; + version += Util::GetVersion(); + CopyMandatoryEntry(0x0002,0x0013,version); } // Push out 'LibIDO-special' entries, if any @@ -1191,11 +1297,9 @@ void FileHelper::CheckMandatoryElements() // Deal with the pb of (Bits Stored = 12) // - we're gonna write the image as Bits Stored = 16 - if ( FileInternal->GetEntryValue(0x0028,0x0100) == "12") + if ( FileInternal->GetEntryString(0x0028,0x0100) == "12") { - ValEntry *e_0028_0100 = CopyValEntry(0x0028,0x0100); - e_0028_0100->SetValue("16"); - Archive->Push(e_0028_0100); + CopyMandatoryEntry(0x0028,0x0100,"16"); } // Check if user wasn't drunk ;-) @@ -1205,9 +1309,7 @@ void FileHelper::CheckMandatoryElements() 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); + CopyMandatoryEntry(0x0028,0x0100,"16"); gdcmWarningMacro("(0028,0100) changed from " << nbBitsAllocated << " to 16 for consistency purpose"); nbBitsAllocated = 16; @@ -1216,10 +1318,9 @@ void FileHelper::CheckMandatoryElements() int nbBitsStored = FileInternal->GetBitsStored(); if ( nbBitsStored == 0 || nbBitsStored > nbBitsAllocated ) { + s.str(""); s << nbBitsAllocated; - ValEntry *e_0028_0101 = CopyValEntry(0x0028,0x0101); - e_0028_0101->SetValue( s.str() ); - Archive->Push(e_0028_0101); + CopyMandatoryEntry(0x0028,0x0101,s.str()); gdcmWarningMacro("(0028,0101) changed from " << nbBitsStored << " to " << nbBitsAllocated << " for consistency purpose" ); @@ -1231,91 +1332,127 @@ void FileHelper::CheckMandatoryElements() highBitPosition > nbBitsAllocated-1 || highBitPosition < nbBitsStored-1 ) { - ValEntry *e_0028_0102 = CopyValEntry(0x0028,0x0102); - + s.str(""); s << nbBitsStored - 1; - e_0028_0102->SetValue( s.str() ); - Archive->Push(e_0028_0102); + CopyMandatoryEntry(0x0028,0x0102,s.str()); gdcmWarningMacro("(0028,0102) changed from " << highBitPosition << " to " << nbBitsAllocated-1 << " for consistency purpose"); } + + // Pixel Spacing : defaulted to 1.0\1.0 + CheckMandatoryEntry(0x0028,0x0030,"1.0\\1.0"); + + // Samples Per Pixel (type 1) : default to grayscale + CheckMandatoryEntry(0x0028,0x0002,"1"); + + // --- Check UID-related Entries --- // If 'SOP Class UID' exists ('true DICOM' image) // we create the 'Source Image Sequence' SeqEntry // to hold informations about the Source Image - ValEntry *e_0008_0016 = FileInternal->GetValEntry(0x0008, 0x0016); - if ( e_0008_0016 != 0 ) + DataEntry *e_0008_0016 = FileInternal->GetDataEntry(0x0008, 0x0016); + if ( e_0008_0016 ) { // Create 'Source Image Sequence' SeqEntry - SeqEntry *sis = new SeqEntry ( + SeqEntry *sis = SeqEntry::New ( Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x2112) ); - SQItem *sqi = new SQItem(1); + SQItem *sqi = SQItem::New(1); // (we assume 'SOP Instance UID' exists too) // create 'Referenced SOP Class UID' - ValEntry *e_0008_1150 = new ValEntry( + DataEntry *e_0008_1150 = DataEntry::New( Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) ); - e_0008_1150->SetValue( e_0008_0016->GetValue()); + e_0008_1150->SetString( e_0008_0016->GetString()); sqi->AddEntry(e_0008_1150); + e_0008_1150->Delete(); // create 'Referenced SOP Instance UID' - ValEntry *e_0008_0018 = FileInternal->GetValEntry(0x0008, 0x0018); - ValEntry *e_0008_1155 = new ValEntry( + DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018); + DataEntry *e_0008_1155 = DataEntry::New( Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1155) ); - e_0008_1155->SetValue( e_0008_0018->GetValue()); + e_0008_1155->SetString( e_0008_0018->GetString()); sqi->AddEntry(e_0008_1155); + e_0008_1155->Delete(); + + sis->AddSQItem(sqi,1); + sqi->Delete(); - sis->AddSQItem(sqi,1); // temporarily replaces any previous 'Source Image Sequence' Archive->Push(sis); + sis->Delete(); + // FIXME : is 'Image Type' *really* depending on the presence of'SOP Class UID'? + // '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 - { - // 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] - e_0008_0016 ->SetValue("1.2.840.10008.5.1.4.1.1.7"); - Archive->Push(e_0008_0016); + CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY"); } + // At the end, not to overwrite the original ones, + // needed by 'Referenced SOP Instance UID', 'Referenced SOP Class UID' + // 'SOP Instance UID' + CopyMandatoryEntry(0x0008,0x0018,sop); + + // whether a 'SOP Class UID' already exists or not in the original image + // the gdcm written image *is* a [Secondary Capture Image Storage] ! + // 'SOP Class UID' : [Secondary Capture Image Storage] + CopyMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7"); + // ---- The user will never have to take any action on the following ----. - // new value for 'SOP Instance UID' - ValEntry *e_0008_0018 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0018) ); - e_0008_0018->SetValue( Util::CreateUniqueUID() ); - Archive->Push(e_0008_0018); + //SetMandatoryEntry(0x0008,0x0018,Util::CreateUniqueUID()); // Instance Creation Date - ValEntry *e_0008_0012 = CopyValEntry(0x0008,0x0012); - std::string date = Util::GetCurrentDate(); - e_0008_0012->SetValue(date.c_str()); - Archive->Push(e_0008_0012); + const std::string &date = Util::GetCurrentDate(); + CopyMandatoryEntry(0x0008,0x0012,date); // Instance Creation Time - ValEntry *e_0008_0013 = CopyValEntry(0x0008,0x0013); - std::string time = Util::GetCurrentTime(); - e_0008_0013->SetValue(time.c_str()); - Archive->Push(e_0008_0013); + const std::string &time = Util::GetCurrentTime(); + CopyMandatoryEntry(0x0008,0x0013,time); + + // Study Date + CopyMandatoryEntry(0x0008,0x0020,date); + // Study Time + CopyMandatoryEntry(0x0008,0x0030,time); + + // Accession Number + CopyMandatoryEntry(0x0008,0x0050,""); + + // Conversion Type. + // Other possible values are : + // See PS 3.3, Page 408 + + // DV = Digitized Video + // DI = Digital Interface + // DF = Digitized Film + // WSD = Workstation + // SD = Scanned Document + // SI = Scanned Image + // DRW = Drawing + // SYN = Synthetic Image + + // FIXME : Must we Force Value, or Default value ? + // Is it Type 1 for any Modality ? + // --> Answer seems to be NO :-( + CopyMandatoryEntry(0x0008,0x0064,"SYN"); // ----- Add Mandatory Entries if missing --- + // Entries whose type is 1 are mandatory, with a mandatory value + // Entries whose type is 1c are mandatory-inside-a-Sequence, + // with a mandatory value + // Entries whose type is 2 are mandatory, with an optional value + // Entries whose type is 2c are mandatory-inside-a-Sequence, + // with an optional value + // Entries whose type is 3 are optional -// Entries whose type is 1 are mandatory, with a mandatory value -// Entries whose type is 1c are mandatory-inside-a-Sequence -// Entries whose type is 2 are mandatory, with a optional value -// Entries whose type is 2c are mandatory-inside-a-Sequence -// Entries whose type is 3 are optional + // '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 + CheckMandatoryEntry(0x0020,0x000d,Util::CreateUniqueUID()); // 'Serie Instance UID' // Keep the value if exists @@ -1323,112 +1460,84 @@ void FileHelper::CheckMandatoryElements() // 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); - } + CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID()); - // '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); - } + // Study ID + CheckMandatoryEntry(0x0020,0x0010,""); + + // Series Number + CheckMandatoryEntry(0x0020,0x0011,""); + // Instance Number + CheckMandatoryEntry(0x0020,0x0013,""); + + // Patient Orientation FIXME 1\0\0\0\1\0 or empty ? + CheckMandatoryEntry(0x0020,0x0020,""); + // Modality : if missing we set it to 'OTher' - ValEntry *e_0008_0060 = FileInternal->GetValEntry(0x0008, 0x0060); - if ( !e_0008_0060 ) - { - e_0008_0060 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0060) ); - e_0008_0060->SetValue("OT"); - Archive->Push(e_0008_0060); - } + CheckMandatoryEntry(0x0008,0x0060,"OT"); // Manufacturer : if missing we set it to 'GDCM Factory' - ValEntry *e_0008_0070 = FileInternal->GetValEntry(0x0008, 0x0070); - if ( !e_0008_0070 ) - { - e_0008_0070 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0070) ); - e_0008_0070->SetValue("GDCM Factory"); - Archive->Push(e_0008_0070); - } + CheckMandatoryEntry(0x0008,0x0070,"GDCM Factory"); // Institution Name : if missing we set it to 'GDCM Hospital' - ValEntry *e_0008_0080 = FileInternal->GetValEntry(0x0008, 0x0080); - if ( !e_0008_0080 ) - { - e_0008_0080 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0080) ); - e_0008_0080->SetValue("GDCM Hospital"); - Archive->Push(e_0008_0080); - } + CheckMandatoryEntry(0x0008,0x0080,"GDCM Hospital"); // Patient's Name : if missing, we set it to 'GDCM^Patient' - ValEntry *e_0010_0010 = FileInternal->GetValEntry(0x0010, 0x0010); - if ( !e_0010_0010 ) - { - e_0010_0010 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0010) ); - e_0010_0010->SetValue("GDCM^Patient"); - Archive->Push(e_0010_0010); - } + CheckMandatoryEntry(0x0010,0x0010,"GDCM^Patient"); + + // Patient ID + CheckMandatoryEntry(0x0010,0x0020,""); // Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory - ValEntry *e_0010_0030 = FileInternal->GetValEntry(0x0010, 0x0030); - if ( !e_0010_0030 ) - { - e_0010_0030 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0030) ); - e_0010_0030->SetValue(""); - Archive->Push(e_0010_0030); - } + CheckMandatoryEntry(0x0010,0x0030,""); // Patient's Sex :'type 2' entry -> must exist, value not mandatory - ValEntry *e_0010_0040 = FileInternal->GetValEntry(0x0010, 0x0040); - if ( !e_0010_0040 ) - { - e_0010_0040 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0040) ); - e_0010_0040->SetValue(""); - Archive->Push(e_0010_0040); - } + CheckMandatoryEntry(0x0010,0x0040,""); // Referring Physician's Name :'type 2' entry -> must exist, value not mandatory - ValEntry *e_0008_0090 = FileInternal->GetValEntry(0x0008, 0x0090); - if ( !e_0008_0090 ) - { - e_0008_0090 = new ValEntry( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0090) ); - e_0008_0090->SetValue(""); - Archive->Push(e_0008_0090); - } - + CheckMandatoryEntry(0x0008,0x0090,""); + // Remove some inconstencies (probably some more will be added) // if (0028 0008)Number of Frames exists // Push out (0020 0052),Frame of Reference UID // (only meaningfull within a Serie) - ValEntry *e_0028_0008 = FileInternal->GetValEntry(0x0028, 0x0008); + DataEntry *e_0028_0008 = FileInternal->GetDataEntry(0x0028, 0x0008); if ( !e_0028_0008 ) { - Archive->Push(0x0020, 0X0052); + Archive->Push(0x0020, 0x0052); } } - + +void FileHelper::CheckMandatoryEntry(uint16_t group,uint16_t elem,std::string value) +{ + DataEntry *entry = FileInternal->GetDataEntry(group,elem); + if ( !entry ) + { + entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); + entry->SetString(value); + Archive->Push(entry); + entry->Delete(); + } +} + +void FileHelper::SetMandatoryEntry(uint16_t group,uint16_t elem,std::string value) +{ + DataEntry *entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); + entry->SetString(value); + Archive->Push(entry); + entry->Delete(); +} + +void FileHelper::CopyMandatoryEntry(uint16_t group,uint16_t elem,std::string value) +{ + DataEntry *entry = CopyDataEntry(group,elem); + entry->SetString(value); + Archive->Push(entry); + entry->Delete(); +} + /** * \brief Restore in the File the initial group 0002 */ @@ -1462,7 +1571,6 @@ void FileHelper::RestoreWriteMandatory() Archive->Restore(0x0020,0x000d); Archive->Restore(0x0020,0x000e); - } //----------------------------------------------------------------------------- @@ -1472,17 +1580,14 @@ void FileHelper::RestoreWriteMandatory() */ void FileHelper::Initialize() { + UserFunction = 0; + WriteMode = WMODE_RAW; WriteType = ExplicitVR; PixelReadConverter = new PixelReadConvert; PixelWriteConverter = new PixelWriteConvert; Archive = new DocEntryArchive( FileInternal ); - - if ( FileInternal->IsReadable() ) - { - PixelReadConverter->GrabInformationsFromFile( FileInternal ); - } } /** @@ -1493,6 +1598,8 @@ void FileHelper::Initialize() */ uint8_t *FileHelper::GetRaw() { + PixelReadConverter->SetUserFunction( UserFunction ); + uint8_t *raw = PixelReadConverter->GetRaw(); if ( ! raw ) { @@ -1514,7 +1621,7 @@ uint8_t *FileHelper::GetRaw() //----------------------------------------------------------------------------- /** - * \brief Prints the common part of ValEntry, BinEntry, SeqEntry + * \brief Prints the common part of DataEntry, SeqEntry * @param os ostream we want to print in * @param indent (unused) */ @@ -1523,8 +1630,11 @@ void FileHelper::Print(std::ostream &os, std::string const &) FileInternal->SetPrintLevel(PrintLevel); FileInternal->Print(os); - PixelReadConverter->SetPrintLevel(PrintLevel); - PixelReadConverter->Print(os); + if ( FileInternal->IsReadable() ) + { + PixelReadConverter->SetPrintLevel(PrintLevel); + PixelReadConverter->Print(os); + } } //-----------------------------------------------------------------------------