X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFileHelper.cxx;h=3357faa8f85dde82ad697a17ba18de0a89c7d912;hb=928d3c30e40ab7f3d12bfd038ce8a48befcddce8;hp=9d8e8f440499036f1e16f7e360de94c91641962a;hpb=ce8913daafe02955368fd2f07e777e86824467cc;p=gdcm.git diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx index 9d8e8f44..3357faa8 100644 --- a/src/gdcmFileHelper.cxx +++ b/src/gdcmFileHelper.cxx @@ -3,8 +3,9 @@ Program: gdcm Module: $RCSfile: gdcmFileHelper.cxx,v $ Language: C++ - Date: $Date: 2005/01/25 15:44:24 $ - Version: $Revision: 1.7 $ + + Date: $Date: 2005/10/21 10:29:51 $ + Version: $Revision: 1.66 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -22,20 +23,96 @@ #include "gdcmDocument.h" #include "gdcmDebug.h" #include "gdcmUtil.h" -#include "gdcmBinEntry.h" -#include "gdcmValEntry.h" -#include "gdcmContentEntry.h" +#include "gdcmSeqEntry.h" +#include "gdcmSQItem.h" +#include "gdcmDataEntry.h" #include "gdcmFile.h" #include "gdcmPixelReadConvert.h" #include "gdcmPixelWriteConvert.h" #include "gdcmDocEntryArchive.h" +#include "gdcmDictSet.h" #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 { -typedef std::pair IterHT; - //------------------------------------------------------------------------- // Constructor / Destructor /** @@ -44,6 +121,7 @@ typedef std::pair IterHT; * 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 @@ -51,7 +129,7 @@ typedef std::pair IterHT; * seen as a side effect). */ FileHelper::FileHelper( ) -{ +{ FileInternal = new File( ); SelfHeader = true; Initialize(); @@ -63,6 +141,7 @@ 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 @@ -75,10 +154,16 @@ 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. @@ -89,13 +174,21 @@ 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 ) +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 @@ -104,20 +197,20 @@ 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; } @@ -125,18 +218,121 @@ FileHelper::~FileHelper() } //----------------------------------------------------------------------------- -// Print -void FileHelper::Print(std::ostream &os, std::string const &) +// 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->SetPrintLevel(PrintLevel); - FileInternal->Print(os); + FileInternal->SetFileName( fileName ); +} - PixelReadConverter->SetPrintLevel(PrintLevel); - PixelReadConverter->Print(os); +/** + * \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 + * the given value. + * @param content new value (string) to substitute with + * @param group group number of the Dicom Element to modify + * @param elem element number of the Dicom Element to modify + * \return false if DocEntry not found + */ +bool FileHelper::SetEntryString(std::string const &content, + uint16_t group, uint16_t elem) +{ + return FileInternal->SetEntryString(content, group, elem); +} + + +/** + * \brief Accesses an existing DocEntry (i.e. a Dicom Element) + * through it's (group, element) and modifies it's content with + * the given value. + * @param content new value (void* -> uint8_t*) to substitute with + * @param lgth new value length + * @param group group number of the Dicom Element to modify + * @param elem element number of the Dicom Element to modify + * \return false if DocEntry not found + */ +bool FileHelper::SetEntryBinArea(uint8_t *content, int lgth, + uint16_t group, uint16_t elem) +{ + return FileInternal->SetEntryBinArea(content, lgth, group, elem); +} + +/** + * \brief Modifies the value of a given DocEntry (Dicom entry) + * when it exists. Creates it with the given value when unexistant. + * @param content (string)value to be set + * @param group Group number of the Entry + * @param elem Element number of the Entry + * \return pointer to the modified/created Dicom entry (NULL when creation + * failed). + */ +DataEntry *FileHelper::InsertEntryString(std::string const &content, + uint16_t group, uint16_t elem) +{ + return FileInternal->InsertEntryString(content, group, elem); +} + +/** + * \brief Modifies the value of a given DocEntry (Dicom entry) + * when it exists. Creates it with the given value when unexistant. + * A copy of the binArea is made to be kept in the Document. + * @param binArea (binary)value to be set + * @param lgth new value length + * @param group Group number of the Entry + * @param elem Element number of the Entry + * \return pointer to the modified/created Dicom entry (NULL when creation + * failed). + */ +DataEntry *FileHelper::InsertEntryBinArea(uint8_t *binArea, int lgth, + uint16_t group, uint16_t elem) +{ + return FileInternal->InsertEntryBinArea(binArea, lgth, group, elem); +} + +/** + * \brief Modifies the value of a given DocEntry (Dicom entry) + * when it exists. Creates it, empty (?!) when unexistant. + * @param group Group number of the Entry + * @param elem Element number of the Entry + * \return pointer to the modified/created Dicom entry (NULL when creation + * failed). + */ +SeqEntry *FileHelper::InsertSeqEntry(uint16_t group, uint16_t elem) +{ + return FileInternal->InsertSeqEntry(group, elem); } -//----------------------------------------------------------------------------- -// Public /** * \brief Get the size of the image data * If the image can be RGB (with a lut or by default), the size @@ -151,7 +347,6 @@ size_t FileHelper::GetImageDataSize() { return PixelWriteConverter->GetUserDataSize(); } - return PixelReadConverter->GetRGBSize(); } @@ -168,14 +363,13 @@ size_t FileHelper::GetImageDataRawSize() { return PixelWriteConverter->GetUserDataSize(); } - return PixelReadConverter->GetRawSize(); } /** - * \brief - Allocates necessary memory, + * \brief - Allocates necessary memory, * - Reads the pixels from disk (uncompress if necessary), - * - Transforms YBR pixels, if any, into RGB pixels + * - 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. @@ -213,16 +407,18 @@ uint8_t *FileHelper::GetImageData() * 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. - * \ NULL if alloc fails + * NULL if alloc fails */ 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 @@ -257,7 +453,7 @@ size_t FileHelper::GetImageDataIntoVector (void *destination, size_t maxSize) { if ( PixelReadConverter->GetRGBSize() > maxSize ) { - gdcmVerboseMacro( "Pixel data bigger than caller's expected MaxSize"); + gdcmWarningMacro( "Pixel data bigger than caller's expected MaxSize"); return 0; } memcpy( destination, @@ -269,14 +465,15 @@ size_t FileHelper::GetImageDataIntoVector (void *destination, size_t maxSize) // Either no LUT conversion necessary or LUT conversion failed if ( PixelReadConverter->GetRawSize() > maxSize ) { - gdcmVerboseMacro( "Pixel data bigger than caller's expected MaxSize"); + gdcmWarningMacro( "Pixel data bigger than caller's expected 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 @@ -285,24 +482,28 @@ size_t FileHelper::GetImageDataIntoVector (void *destination, size_t maxSize) * '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. - * @param inData user supplied pixel area - * @param expectedSize total image size, in Bytes - * - * @return boolean + * the Write() method ) + * @param inData user supplied pixel area (uint8_t* is just for the compiler. + * user is allowed to pass any kind of pixelsn since the size is + * given in bytes) + * @param expectedSize total image size, *in Bytes* */ void FileHelper::SetImageData(uint8_t *inData, size_t expectedSize) { - SetUserData(inData,expectedSize); + SetUserData(inData, expectedSize); } /** * \brief Set the image data defined by the user * \warning When writting the file, this data are get as default data to write + * @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) + * @param expectedSize total image size, *in Bytes* */ -void FileHelper::SetUserData(uint8_t *data, size_t expectedSize) +void FileHelper::SetUserData(uint8_t *inData, size_t expectedSize) { - PixelWriteConverter->SetUserData(data,expectedSize); + PixelWriteConverter->SetUserData(inData, expectedSize); } /** @@ -343,7 +544,7 @@ size_t FileHelper::GetRGBDataSize() /** * \brief Get the image data from the file. - * If a LUT is found, the data are not expanded ! + * Even when a LUT is found, the data are not expanded to RGB! */ uint8_t *FileHelper::GetRawData() { @@ -352,13 +553,39 @@ uint8_t *FileHelper::GetRawData() /** * \brief Get the image data size from the file. - * If a LUT is found, the data are not expanded ! + * Even when a LUT is found, the data are not expanded to RGB! */ size_t FileHelper::GetRawDataSize() { return PixelReadConverter->GetRawSize(); } +/** + * \brief Access to the underlying \ref PixelReadConverter RGBA LUT + */ +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". @@ -367,29 +594,28 @@ size_t FileHelper::GetRawDataSize() * (any already existing file is over written) * @return false if write fails */ - 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) { - gdcmVerboseMacro( "Fail to open (write) file:" << fileName.c_str()); + 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 @@ -405,7 +631,7 @@ 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 @@ -465,16 +691,29 @@ bool FileHelper::Write(std::string const &fileName) case ImplicitVR: SetWriteFileTypeToImplicitVR(); break; + case Unknown: // should never happen; ExplicitVR is the default value case ExplicitVR: SetWriteFileTypeToExplicitVR(); 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->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; - default: - SetWriteFileTypeToExplicitVR(); } + CheckMandatoryElements(); // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images @@ -484,7 +723,8 @@ 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(); } @@ -497,21 +737,23 @@ bool FileHelper::Write(std::string const &fileName) switch(WriteMode) { case WMODE_RAW : - SetWriteToRaw(); + SetWriteToRaw(); // modifies and pushes to the archive, when necessary break; case WMODE_RGB : - SetWriteToRGB(); + SetWriteToRGB(); // modifies and pushes to the archive, when necessary break; } - bool check = CheckWriteIntegrity(); - if(check) + bool check = CheckWriteIntegrity(); // verifies length + if (WriteType == JPEG ) check = true; + if (check) { check = FileInternal->Write(fileName,WriteType); } RestoreWrite(); RestoreWriteFileType(); + RestoreWriteMandatory(); // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images @@ -524,94 +766,10 @@ bool FileHelper::Write(std::string const &fileName) return check; } -/** - * \brief Accesses an existing DocEntry (i.e. a Dicom Element) - * through it's (group, element) and modifies it's content with - * the given value. - * @param content new value (string) to substitute with - * @param group group number of the Dicom Element to modify - * @param elem element number of the Dicom Element to modify - */ -bool FileHelper::SetValEntry(std::string const &content, - uint16_t group, uint16_t elem) -{ - return FileInternal->SetValEntry(content,group,elem); -} - - -/** - * \brief Accesses an existing DocEntry (i.e. a Dicom Element) - * through it's (group, element) and modifies it's content with - * the given value. - * @param content new value (void* -> uint8_t*) to substitute with - * @param lgth new value length - * @param group group number of the Dicom Element to modify - * @param elem element number of the Dicom Element to modify - */ -bool FileHelper::SetBinEntry(uint8_t *content, int lgth, - uint16_t group, uint16_t elem) -{ - return FileInternal->SetBinEntry(content,lgth,group,elem); -} - -/** - * \brief Modifies the value of a given DocEntry (Dicom entry) - * when it exists. Create it with the given value when unexistant. - * @param content (string) Value to be set - * @param group Group number of the Entry - * @param elem Element number of the Entry - * \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) -{ - return FileInternal->InsertValEntry(content,group,elem); -} - -/* - * \brief Modifies the value of a given DocEntry (Dicom entry) - * when it exists. Create it with the given value when unexistant. - * A copy of the binArea is made to be kept in the Document. - * @param binArea (binary) value to be set - * @param group Group number of the Entry - * @param elem Element number of the Entry - * \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) -{ - return FileInternal->InsertBinEntry(binArea,lgth,group,elem); -} - -/* - * \brief Modifies the value of a given DocEntry (Dicom entry) - * when it exists. Create it with the given value when unexistant. - * A copy of the binArea is made to be kept in the Document. - * @param group Group number of the Entry - * @param elem Element number of the Entry - * \return pointer to the modified/created Dicom entry (NULL when creation - * failed). - */ -SeqEntry *FileHelper::InsertSeqEntry(uint16_t group, uint16_t elem) -{ - return FileInternal->InsertSeqEntry(group,elem); -} - -/** - * \brief Access to the underlying \ref PixelReadConverter RGBA LUT - */ -uint8_t* FileHelper::GetLutRGBA() -{ - return PixelReadConverter->GetLutRGBA(); -} - //----------------------------------------------------------------------------- // Protected - /** - * \brief Check the write integrity + * \brief Checks the write integrity * * The tests made are : * - verify the size of the image to write with the possible write @@ -620,38 +778,41 @@ uint8_t* FileHelper::GetLutRGBA() */ 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() ) { - gdcmVerboseMacro( "Data size (Raw) is incorrect. Should be " + gdcmWarningMacro( "Data size (Raw) is incorrect. Should be " << decSize << " / Found :" << PixelWriteConverter->GetUserDataSize() ); return false; } break; case WMODE_RGB : - if( rgbSize!=PixelWriteConverter->GetUserDataSize() ) + if ( rgbSize!=PixelWriteConverter->GetUserDataSize() ) { - gdcmVerboseMacro( "Data size (RGB) is incorrect. Should be " + gdcmWarningMacro( "Data size (RGB) is incorrect. Should be " << decSize << " / Found " << PixelWriteConverter->GetUserDataSize() ); return false; @@ -659,38 +820,45 @@ bool FileHelper::CheckWriteIntegrity() break; } } - + return true; } /** - * \brief + * \brief Updates the File to write RAW data (as opposed to RGB data) + * (modifies, when necessary, photochromatic interpretation, + * bits allocated, Pixels element VR) */ 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()) + DataEntry *photInt = CopyDataEntry(0x0028,0x0004); + if (FileInternal->HasLUT() ) { - photInt->SetValue("PALETTE COLOR "); + photInt->SetString("PALETTE COLOR "); } else { - photInt->SetValue("MONOCHROME1 "); + photInt->SetString("MONOCHROME2 "); } PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(), PixelReadConverter->GetRawSize()); - BinEntry *pixel = - CopyBinEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel()); - pixel->SetValue(GDCM_BINLOADED); + std::string vr = "OB"; + if ( FileInternal->GetBitsAllocated()>8 ) + vr = "OW"; + if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files + vr = "OB"; + DataEntry *pixel = + CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr); + pixel->SetFlag(DataEntry::FLAG_PIXELDATA); pixel->SetBinArea(PixelWriteConverter->GetData(),false); pixel->SetLength(PixelWriteConverter->GetDataSize()); @@ -700,24 +868,28 @@ void FileHelper::SetWriteToRaw() } /** - * \brief + * \brief Updates the File to write RGB data (as opposed to RAW data) + * (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, ) */ void FileHelper::SetWriteToRGB() { - if(FileInternal->GetNumberOfScalarComponents()==3) + if ( FileInternal->GetNumberOfScalarComponents()==3 ) { 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()) + if ( PixelReadConverter->GetRGB() ) { PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(), PixelReadConverter->GetRGBSize()); @@ -728,9 +900,14 @@ void FileHelper::SetWriteToRGB() PixelReadConverter->GetRawSize()); } - BinEntry *pixel = - CopyBinEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel()); - pixel->SetValue(GDCM_BINLOADED); + std::string vr = "OB"; + if ( FileInternal->GetBitsAllocated()>8 ) + vr = "OW"; + if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files + vr = "OB"; + DataEntry *pixel = + CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr); + pixel->SetFlag(DataEntry::FLAG_PIXELDATA); pixel->SetBinArea(PixelWriteConverter->GetData(),false); pixel->SetLength(PixelWriteConverter->GetDataSize()); @@ -747,19 +924,22 @@ void FileHelper::SetWriteToRGB() Archive->Push(0x0028,0x1202); Archive->Push(0x0028,0x1203); - // For old ACR-NEMA + // 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 "); + 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); @@ -773,7 +953,7 @@ void FileHelper::SetWriteToRGB() } /** - * \brief + * \brief Restore the File write mode */ void FileHelper::RestoreWrite() { @@ -794,202 +974,553 @@ void FileHelper::RestoreWrite() Archive->Restore(0x0028,0x1201); 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); + 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); } /** - * \brief + * \brief Pushes out the whole group 0002 + * FIXME : better, set a flag to tell the writer not to write it ... + * FIXME : method should probably have an other name ! + * SetWriteFileTypeToACR is NOT opposed to + * SetWriteFileTypeToExplicitVR and SetWriteFileTypeToImplicitVR */ void FileHelper::SetWriteFileTypeToACR() { + Archive->Push(0x0002,0x0000); + Archive->Push(0x0002,0x0001); + Archive->Push(0x0002,0x0002); + Archive->Push(0x0002,0x0003); Archive->Push(0x0002,0x0010); + Archive->Push(0x0002,0x0012); + Archive->Push(0x0002,0x0013); + Archive->Push(0x0002,0x0016); + Archive->Push(0x0002,0x0100); + Archive->Push(0x0002,0x0102); } /** - * \brief + * \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); +} + 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); } /** - * \brief + * \brief Sets in the File the TransferSyntax to 'Implicit VR Little Endian" */ 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); } /** - * \brief + * \brief Restore in the File the initial group 0002 */ void FileHelper::RestoreWriteFileType() { - Archive->Restore(0x0002,0x0010); } +/** + * \brief Set the Write not to Libido format + */ 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 ) + if ( oldRow && oldCol ) { std::string rows, columns; - ValEntry *newRow=new ValEntry(oldRow->GetDictEntry()); - ValEntry *newCol=new ValEntry(oldCol->GetDictEntry()); + DataEntry *newRow=new DataEntry(oldRow->GetDictEntry()); + DataEntry *newCol=new DataEntry(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); } - 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); } /** - * \brief + * \brief Set the Write not to No Libido format */ void FileHelper::SetWriteToNoLibido() { - ValEntry *recCode = dynamic_cast - (FileInternal->GetDocEntry(0x0008,0x0010)); - if( recCode ) + 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); } } } /** - * \brief + * \brief Restore the Write format */ 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); } -ValEntry *FileHelper::CopyValEntry(uint16_t group,uint16_t elem) +/** + * \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). + */ +DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem, + const TagName &vr) { DocEntry *oldE = FileInternal->GetDocEntry(group, elem); - ValEntry *newE; + DataEntry *newE; - if(oldE) + if ( oldE && vr != GDCM_VRUNKNOWN ) + if ( oldE->GetVR() != vr ) + oldE = NULL; + + if ( oldE ) { - newE = new ValEntry(oldE->GetDictEntry()); + newE = new DataEntry(oldE->GetDictEntry()); newE->Copy(oldE); } else { - newE = GetFile()->NewValEntry(group,elem); + newE = GetFile()->NewDataEntry(group, elem, vr); } return newE; } /** - * \brief Modifies the value of a given Bin Entry (Dicom Element) - * when it exists. Create it with the given value when unexistant. - * @param group Group number of the Entry - * @param elem Element number of the Entry - * \return pointer to the modified/created Bin Entry (NULL when creation - * failed). + * \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. */ -BinEntry *FileHelper::CopyBinEntry(uint16_t group,uint16_t elem) + +void FileHelper::CheckMandatoryElements() { - DocEntry *oldE = FileInternal->GetDocEntry(group, elem); - BinEntry *newE; + std::string sop = Util::CreateUniqueUID(); + + // 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 + //0002 0003 UI 1 Media Stored SOP Instance UID + //0002 0010 UI 1 Transfer Syntax UID + //0002 0012 UI 1 Implementation Class UID + //0002 0013 SH 1 Implementation Version Name + //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 + // Always modify the value + // Push the entries to the archive. + CopyMandatoryEntry(0x0002,0x0000,"0"); + + 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); + + // 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 Storage SOP Instance UID' + CopyMandatoryEntry(0x0002,0x0003,sop); + + // 'Implementation Class UID' + CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID()); - if(oldE) + // 'Implementation Version Name' + std::string version = "GDCM "; + version += Util::GetVersion(); + CopyMandatoryEntry(0x0002,0x0013,version); + } + + // Push out 'LibIDO-special' entries, if any + Archive->Push(0x0028,0x0015); + Archive->Push(0x0028,0x0016); + Archive->Push(0x0028,0x0017); + Archive->Push(0x0028,0x00199); + + // Deal with the pb of (Bits Stored = 12) + // - we're gonna write the image as Bits Stored = 16 + if ( FileInternal->GetEntryString(0x0028,0x0100) == "12") { - newE = new BinEntry(oldE->GetDictEntry()); - newE->Copy(oldE); + CopyMandatoryEntry(0x0028,0x0100,"16"); } + + // Check if user wasn't drunk ;-) + + std::ostringstream s; + // check 'Bits Allocated' vs decent values + int nbBitsAllocated = FileInternal->GetBitsAllocated(); + if ( nbBitsAllocated == 0 || nbBitsAllocated > 32) + { + CopyMandatoryEntry(0x0028,0x0100,"16"); + 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.str(""); + s << nbBitsAllocated; + CopyMandatoryEntry(0x0028,0x0101,s.str()); + 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 ) + { + s.str(""); + s << nbBitsStored - 1; + CopyMandatoryEntry(0x0028,0x0102,s.str()); + 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 + // to hold informations about the Source Image + + DataEntry *e_0008_0016 = FileInternal->GetDataEntry(0x0008, 0x0016); + if ( e_0008_0016 ) + { + // 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' + DataEntry *e_0008_1150 = new DataEntry( + Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) ); + e_0008_1150->SetString( e_0008_0016->GetString()); + sqi->AddEntry(e_0008_1150); + + // create 'Referenced SOP Instance UID' + DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018); + DataEntry *e_0008_1155 = new DataEntry( + Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1155) ); + e_0008_1155->SetString( e_0008_0018->GetString()); + sqi->AddEntry(e_0008_1155); + + sis->AddSQItem(sqi,1); + // temporarily replaces any previous 'Source Image Sequence' + Archive->Push(sis); + + // 'Image Type' (The written image is no longer an 'ORIGINAL' one) + CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY"); + } else { - newE = GetFile()->NewBinEntry(group,elem); + // 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 + // [Secondary Capture Image Storage] + SetMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7"); } - return newE; + // 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); + // 'SOP Class UID' + 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' + //SetMandatoryEntry(0x0008,0x0018,Util::CreateUniqueUID()); + + // Instance Creation Date + CopyMandatoryEntry(0x0008,0x0012,Util::GetCurrentDate().c_str()); + + // Instance Creation Time + CopyMandatoryEntry(0x0008,0x0013,Util::GetCurrentTime().c_str()); + +// ----- 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 +// 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 + // 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 + CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID()); + + // Modality : if missing we set it to 'OTher' + CheckMandatoryEntry(0x0008,0x0060,"OT"); + + // Manufacturer : if missing we set it to 'GDCM Factory' + CheckMandatoryEntry(0x0008,0x0070,"GDCM Factory"); + + // Institution Name : if missing we set it to 'GDCM Hospital' + CheckMandatoryEntry(0x0008,0x0080,"GDCM Hospital"); + + // Patient's Name : if missing, we set it to 'GDCM^Patient' + CheckMandatoryEntry(0x0010,0x0010,"GDCM^Patient"); + + // Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory + CheckMandatoryEntry(0x0010,0x0030,""); + + // Patient's Sex :'type 2' entry -> must exist, value not mandatory + CheckMandatoryEntry(0x0010,0x0040,""); + + // Referring Physician's Name :'type 2' entry -> must exist, value not mandatory + CheckMandatoryEntry(0x0008,0x0090,""); + + // Pixel Spacing : defaulted to 1.0\1.0 + CheckMandatoryEntry(0x0028,0x0030,"1.0\\1.0"); + + // 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) + DataEntry *e_0028_0008 = FileInternal->GetDataEntry(0x0028, 0x0008); + if ( !e_0028_0008 ) + { + 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 = new DataEntry(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); + entry->SetString(value); + Archive->Push(entry); + } +} + +void FileHelper::SetMandatoryEntry(uint16_t group,uint16_t elem,std::string value) +{ + DataEntry *entry = new DataEntry(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); + entry->SetString(value); + Archive->Push(entry); +} + +void FileHelper::CopyMandatoryEntry(uint16_t group,uint16_t elem,std::string value) +{ + DataEntry *entry = CopyDataEntry(group,elem); + entry->SetString(value); + Archive->Push(entry); +} + +/** + * \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); + } //----------------------------------------------------------------------------- -// Protected +// Private /** * \brief Factorization for various forms of constructors. */ 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->GrabInformationsFromHeader( 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(); if ( ! raw ) { - gdcmVerboseMacro( "Read/decompress of pixel data apparently went wrong."); + gdcmWarningMacro( "Read/decompress of pixel data apparently went wrong."); return 0; } } - return raw; } //----------------------------------------------------------------------------- -// Private +/** + * \brief Prints the common part of DataEntry, 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); + + if ( FileInternal->IsReadable() ) + { + PixelReadConverter->SetPrintLevel(PrintLevel); + PixelReadConverter->Print(os); + } +} //----------------------------------------------------------------------------- } // end namespace gdcm -