X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFileHelper.cxx;h=c12ae7b9e7a1a76fb17a230277430f44f00330f6;hb=721d134c6e594b9a23bf1ce002ed87bfbc1576a7;hp=4c6595a3eaee3fa1b08a1ba2e8a3f75f303ac35e;hpb=0ad9dae4659b21bfd5c834c1af724eab4dcdf4f6;p=gdcm.git diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx index 4c6595a3..c12ae7b9 100644 --- a/src/gdcmFileHelper.cxx +++ b/src/gdcmFileHelper.cxx @@ -3,8 +3,9 @@ Program: gdcm Module: $RCSfile: gdcmFileHelper.cxx,v $ Language: C++ - Date: $Date: 2005/01/23 10:12:34 $ - Version: $Revision: 1.3 $ + + Date: $Date: 2007/10/25 07:52:59 $ + Version: $Revision: 1.136 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -22,18 +23,149 @@ #include "gdcmDocument.h" #include "gdcmDebug.h" #include "gdcmUtil.h" -#include "gdcmBinEntry.h" +#include "gdcmSeqEntry.h" +#include "gdcmSQItem.h" +#include "gdcmDataEntry.h" +#include "gdcmDocEntry.h" #include "gdcmFile.h" #include "gdcmPixelReadConvert.h" #include "gdcmPixelWriteConvert.h" #include "gdcmDocEntryArchive.h" +#include "gdcmDictSet.h" +#include "gdcmOrientation.h" + + + +#include // for transform? + +#if defined(__BORLANDC__) + #include // for memset + #include //for toupper + #include +#endif #include -namespace gdcm -{ -typedef std::pair IterHT; +/* +// ----------------------------- 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(); + +// To decide whether it's an 'image of interest for him, or not, +// 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 (if any) 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 +gdcm::File *fh = new gdcm::FileHelper(); + +fh->SetTypeToRaw(); // Even if it was possible to convert Palette to RGB + // (WriteMode is set) + +// If user wants to write the file as MONOCHROME1 (0=white) +fh->SetPhotometricInterpretationToMonochrome1(); + +fh->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation + // Little Endian is the default, + // bigendian not supported for writting + (-->SetWriteType(ExplicitVR);) + -->WriteType = ExplicitVR; +fh->SetWriteTypeToJPEG(); // lossless compression +fh->SetWriteTypeToJPEG2000(); // lossless compression + +fh->SetImageData( userPixels, userPixelsLength); +or +fh->SetUserData( userPixels, userPixelsLength); // this one performs compression, when required + +fh->Write(newFileName); // overwrites the file, if any + + + +These lines will be moved to the document-to-be 'Developer's Guide' + +WriteMode : WMODE_RAW / WMODE_RGB +WriteType : ImplicitVR, ExplicitVR, ACR, ACR_LIBIDO +PhotometricInterpretation : MONOCHROME2 (0=black), MONOCHROME2 (0=white) + +fh->SetImageData( userPixels, userPixelsLength); +or +fh->SetUserData( userPixels, userPixelsLength); + PixelWriteConverter->SetUserData(inData, expectedSize); + + +fh->SetWriteMode(WMODE_RAW / WMODE_RGB) + +fh->SetWriteType( ImplicitVR/ExplicitVR/ACR/ACR_LIBIDO/JPEG/JPEG2000) + +fh->Write(newFileName); + CheckMandatoryElements(); // Checks existing ones / Add missing ones + Fix VR if unknown elements + SetWriteFileTypeToImplicitVR() / SetWriteFileTypeToExplicitVR(); / + SetWriteFileTypeToACR() / SetWriteFileTypeToJPEG() / SetWriteFileTypeToJ2K() + (Modifies TransferSyntax if any; Pushes to the Archives old one) + SetWriteToRaw(); / SetWriteToRGB(); + (Modifies and pushes to the Archive, when necessary : photochr. interp., + samples per pixel, Planar configuration, + bits allocated, bits stored, high bit -ACR 24 bits- + Pixels element VR, pushes out the LUT ) + SetWriteToRaw() + Sets Photometric Interpretation + DataEntry *pixel =CopyDataEntry(7fe0,0010,VR) + Sets VR, BinArea, Length for PixelData + if MONOCHROME1 + ConvertFixGreyLevels + Archive->Push(photInt); + Archive->Push(pixel); + photInt->Delete(); + pixel->Delete(); + SetWriteToRGB() + if NumberOfScalarComponents==1 + SetWriteToRaw(); return; + PixelReadConverter->BuildRGBImage() + DataEntry *pixel =CopyDataEntry(7fe0,0010,VR) + Archives spp, planConfig,photInt, pixel + Pushes out any LUT + CheckWriteIntegrity(); + (checks user given pixels length) + FileInternal->Write(fileName,WriteType) + fp = opens file(fileName); // out|binary + ComputeGroup0002Length( ); + Document::WriteContent(fp, writetype); + writes Dicom File Preamble not ACR-NEMA + ElementSet::WriteContent(fp, writetype); + writes recursively all DataElements + RestoreWrite(); + (moves back to the gdcm::File all the archived elements) +*/ + + + + +namespace GDCM_NAME_SPACE +{ +typedef std::map GroupHT; // Hash Table //------------------------------------------------------------------------- // Constructor / Destructor /** @@ -42,6 +174,7 @@ 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 @@ -49,9 +182,8 @@ typedef std::pair IterHT; * seen as a side effect). */ FileHelper::FileHelper( ) -{ - FileInternal = new File( ); - SelfHeader = true; +{ + FileInternal = File::New( ); Initialize(); } @@ -61,6 +193,7 @@ 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 @@ -70,29 +203,15 @@ 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, this ); + } } /** @@ -102,39 +221,139 @@ 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 ) - { - delete FileInternal; - } - FileInternal = 0; + FileInternal->Unregister(); } //----------------------------------------------------------------------------- -// 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 ); +} + +/** + * \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->SetPrintLevel(PrintLevel); - PixelReadConverter->Print(os); + PixelReadConverter->GrabInformationsFromFile( FileInternal, this ); + return true; +} + +/** + * \brief Accesses an existing DataEntry through its (group, element) + * and modifies its 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 DataEntry 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 DataEntry through its (group, element) + * and modifies its 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 DataEntry 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 DataEntry 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 + * @param vr Value Representation of the DataElement to be inserted + * \return pointer to the modified/created DataEntry (NULL when creation + * failed). + */ +DataEntry *FileHelper::InsertEntryString(std::string const &content, + uint16_t group, uint16_t elem, + VRKey const &vr ) +{ + return FileInternal->InsertEntryString(content, group, elem, vr); +} + +/** + * \brief Modifies the value of a given DataEntry 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 + * @param vr Value Representation of the DataElement to be inserted + * \return pointer to the modified/created DataEntry (NULL when creation + * failed). + */ +DataEntry *FileHelper::InsertEntryBinArea(uint8_t *binArea, int lgth, + uint16_t group, uint16_t elem, + VRKey const &vr ) +{ + return FileInternal->InsertEntryBinArea(binArea, lgth, group, elem, vr); +} + +/** + * \brief Adds an empty SeqEntry + * (remove any existing entry with same group,elem) + * @param group Group number of the Entry + * @param elem Element number of the Entry + * \return pointer to the created SeqEntry (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 @@ -149,12 +368,11 @@ size_t FileHelper::GetImageDataSize() { return PixelWriteConverter->GetUserDataSize(); } - return PixelReadConverter->GetRGBSize(); } /** - * \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) @@ -166,18 +384,19 @@ size_t FileHelper::GetImageDataRawSize() { return PixelWriteConverter->GetUserDataSize(); } - return PixelReadConverter->GetRawSize(); } /** - * \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 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() @@ -205,22 +424,26 @@ 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. - * \ NULL if alloc fails + * (uint8_t is just for prototyping. feel free to cast) + * NULL if alloc fails */ 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 @@ -243,6 +466,7 @@ uint8_t *FileHelper::GetImageDataRaw () * @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) { if ( ! GetRaw() ) @@ -255,7 +479,7 @@ 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, @@ -267,14 +491,16 @@ 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 @@ -282,30 +508,52 @@ size_t FileHelper::GetImageDataIntoVector (void *destination, size_t maxSize) * '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 it's 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 + * 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) + * @param expectedSize total image size, *in Bytes* */ void FileHelper::SetImageData(uint8_t *inData, size_t expectedSize) { - SetUserData(inData,expectedSize); + PixelWriteConverter->SetUserData(inData, expectedSize); + /// \todo : shouldn't we call SetCompressJPEGUserData/SetCompressJPEG2000UserData + /// here, too? } /** - * \brief Set the image datas defined by the user - * \warning When writting the file, this datas are get as default datas to write + * \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); + // Shouldn't we move theese lines to FileHelper::Write()? +/* + if( WriteType == JPEG2000 ) + { + PixelWriteConverter->SetCompressJPEG2000UserData(inData, expectedSize, FileInternal); + } + else if( WriteType == JPEG ) + { + PixelWriteConverter->SetCompressJPEGUserData(inData, expectedSize, FileInternal); + } + else + { + PixelWriteConverter->SetUserData(inData, expectedSize); + } + */ + // Just try! + PixelWriteConverter->SetUserData(inData, expectedSize); } /** - * \brief Get the image datas defined by the user - * \warning When writting the file, this datas are get as default data to write + * \brief Get the image data defined by the user + * \warning When writting the file, this data are get as default data to write */ uint8_t *FileHelper::GetUserData() { @@ -314,7 +562,7 @@ uint8_t *FileHelper::GetUserData() /** * \brief Get the image data size defined by the user - * \warning When writting the file, this datas are get as default data to write + * \warning When writting the file, this data are get as default data to write */ size_t FileHelper::GetUserDataSize() { @@ -322,7 +570,7 @@ size_t FileHelper::GetUserDataSize() } /** - * \brief Get the image datas from the file. + * \brief Get the image data from the file. * If a LUT is found, the data are expanded to be RGB */ uint8_t *FileHelper::GetRGBData() @@ -340,8 +588,8 @@ size_t FileHelper::GetRGBDataSize() } /** - * \brief Get the image datas from the file. - * If a LUT is found, the datas are not expanded ! + * \brief Get the image data from the file. + * Even when a LUT is found, the data are not expanded to RGB! */ uint8_t *FileHelper::GetRawData() { @@ -350,13 +598,39 @@ 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 PixelReadConverter RGBA LUT + */ +uint8_t* FileHelper::GetLutRGBA() +{ + if ( PixelReadConverter->GetLutRGBA() ==0 ) + PixelReadConverter->BuildLUTRGBA(); + return PixelReadConverter->GetLutRGBA(); +} + +/** + * \brief Access to the underlying PixelReadConverter RGBA LUT Item Number + */ +int FileHelper::GetLutItemNumber() +{ + return PixelReadConverter->GetLutItemNumber(); +} + +/** + * \brief Access to the underlying 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". @@ -365,29 +639,28 @@ 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 @@ -403,7 +676,7 @@ 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 @@ -457,21 +730,58 @@ bool FileHelper::WriteAcr (std::string const &fileName) * @return false if write fails */ bool FileHelper::Write(std::string const &fileName) -{ +{ + CheckMandatoryElements(); //called once, here ! + switch(WriteType) { case ImplicitVR: SetWriteFileTypeToImplicitVR(); break; + + case Unknown: // should never happen; ExplicitVR is the default value case ExplicitVR: + + // We let DocEntry::WriteContent to put vr=UN for undocumented Shadow Groups ! SetWriteFileTypeToExplicitVR(); - break; + + 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, "LO"); SetWriteFileTypeToACR(); + // SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR ! + break; + + /// \todo FIXME : JPEG/JPEG2000 may be either ExplicitVR or ImplicitVR + case JPEG: + SetWriteFileTypeToJPEG(); + // was : + //PixelWriteConverter->SetCompressJPEGUserData( + // inData, expectedSize, FileInternal); + PixelWriteConverter->SetCompressJPEGUserData( + PixelWriteConverter->GetUserData(), + PixelWriteConverter->GetUserDataSize(),FileInternal); + break; + + case JPEG2000: + /// \todo Maybe we should consider doing the compression here ! + // PixelWriteConverter->SetCompressJPEG2000UserData(inData, expectedSize, FileInternal); + + SetWriteFileTypeToJPEG2000(); + PixelWriteConverter->SetCompressJPEG2000UserData( + PixelWriteConverter->GetUserData(), + PixelWriteConverter->GetUserDataSize(), + FileInternal); break; - default: - SetWriteFileTypeToExplicitVR(); } // -------------------------------------------------------------- @@ -482,7 +792,8 @@ 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(); } @@ -495,21 +806,27 @@ 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; + if (WriteType == JPEG || WriteType == JPEG2000) + check = true; + else + check = CheckWriteIntegrity(); // verifies length + + if (check) { check = FileInternal->Write(fileName,WriteType); } RestoreWrite(); - RestoreWriteFileType(); + // RestoreWriteFileType(); + // RestoreWriteMandatory(); // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images @@ -522,184 +839,148 @@ 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::SetEntry(std::string const &content, - uint16_t group, uint16_t elem) -{ - return FileInternal->SetEntry(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::SetEntry(uint8_t *content, int lgth, - uint16_t group, uint16_t elem) -{ - return FileInternal->SetEntry(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). - */ -bool FileHelper::ReplaceOrCreate(std::string const &content, - uint16_t group, uint16_t elem) -{ - return FileInternal->ReplaceOrCreate(content,group,elem) != NULL; -} - -/* - * \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). - */ -bool FileHelper::ReplaceOrCreate(uint8_t *binArea, int lgth, - uint16_t group, uint16_t elem) -{ - return FileInternal->ReplaceOrCreate(binArea,lgth,group,elem) != NULL; -} - -/** - * \brief Access to the underlying \ref PixelReadConverter RGBA LUT - */ -uint8_t* FileHelper::GetLutRGBA() -{ - return PixelReadConverter->GetLutRGBA(); -} - //----------------------------------------------------------------------------- // Protected - /** - * \brief Check the write integrity - * - * The tests made are : - * - verify the size of the image to write with the possible write - * when the user set an image data - * @return true if the check successfulls + * \brief Verifies the size of the user given PixelData + * @return true if check is successfull */ 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->GetTSize() + * FileInternal->GetSamplesPerPixel() + * ( numberBitsAllocated / 8 ); size_t rgbSize = decSize; - if( FileInternal->HasLUT() ) + if ( FileInternal->HasLUT() ) rgbSize = decSize * 3; + size_t userDataSize = PixelWriteConverter->GetUserDataSize(); switch(WriteMode) { case WMODE_RAW : - if( decSize!=PixelWriteConverter->GetUserDataSize() ) + if ( abs((long)(decSize-userDataSize))>1) // ignore padding zero { - gdcmVerboseMacro( "Data size is incorrect (Raw)" << decSize - << " / " << PixelWriteConverter->GetUserDataSize() ); + gdcmWarningMacro( "Data size (Raw) is incorrect. Should be " + << decSize << " / Found :" + << userDataSize ); return false; } break; case WMODE_RGB : - if( rgbSize!=PixelWriteConverter->GetUserDataSize() ) + if ( abs((long)(rgbSize-userDataSize))>1) // ignore padding zero { - gdcmVerboseMacro( "Data size is incorrect (RGB)" << decSize - << " / " << PixelWriteConverter->GetUserDataSize() ); + gdcmWarningMacro( "Data size (RGB) is incorrect. Should be " + << rgbSize << " / Found " + << userDataSize ); return false; } 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) + * WARNING : if SetPhotometricInterpretationToMonochrome1() was called + * before Pixel Elements is modified :-( */ 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()) + // 0x0028,0x0004 : Photometric Interpretation + DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS"); + if (FileInternal->HasLUT() ) { - photInt->SetValue("PALETTE COLOR "); + photInt->SetString("PALETTE COLOR "); } else { - photInt->SetValue("MONOCHROME1 "); + if (GetPhotometricInterpretation() == 2) + photInt->SetString("MONOCHROME2 "); // 0 = Black + else + photInt->SetString("MONOCHROME1 "); // 0 = White ! } 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"; + // For non RAW data. Mainly JPEG/JPEG2000 + if( WriteType == JPEG || WriteType == JPEG2000) + { + vr = "OW"; + } + + DataEntry *pixel = + CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr); + pixel->SetFlag(DataEntry::FLAG_PIXELDATA); pixel->SetBinArea(PixelWriteConverter->GetData(),false); - pixel->SetLength(PixelWriteConverter->GetDataSize()); + pixel->SetLength( + static_cast< uint32_t >(PixelWriteConverter->GetDataSize()) ); + + if (!FileInternal->HasLUT() && GetPhotometricInterpretation() == 1) + { + ConvertFixGreyLevels( pixel->GetBinArea(), pixel->GetLength() ); + } Archive->Push(photInt); Archive->Push(pixel); + + photInt->Delete(); + pixel->Delete(); } } /** - * \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,"US"); + spp->SetString("3 "); // Don't drop trailing space - ValEntry *planConfig = CopyValEntry(0x0028,0x0006); - planConfig->SetValue("0 "); + DataEntry *planConfig = CopyDataEntry(0x0028,0x0006,"US"); + planConfig->SetString("0 "); // Don't drop trailing space - ValEntry *photInt = CopyValEntry(0x0028,0x0004); - photInt->SetValue("RGB "); + DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS"); + photInt->SetString("RGB "); // Don't drop trailing space - if(PixelReadConverter->GetRGB()) + if ( PixelReadConverter->GetRGB() ) { PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(), PixelReadConverter->GetRGBSize()); @@ -710,9 +991,14 @@ 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()); @@ -721,6 +1007,11 @@ 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); @@ -729,23 +1020,30 @@ 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,"US"); + bitsAlloc->SetString("8 "); - ValEntry *bitsStored = CopyValEntry(0x0028,0x0101); - bitsStored->SetValue("8 "); + DataEntry *bitsStored = CopyDataEntry(0x0028,0x0101,"US"); + bitsStored->SetString("8 "); - ValEntry *highBit = CopyValEntry(0x0028,0x0102); - highBit->SetValue("7 "); + DataEntry *highBit = CopyDataEntry(0x0028,0x0102,"US"); + highBit->SetString("7 "); Archive->Push(bitsAlloc); Archive->Push(bitsStored); Archive->Push(highBit); + + bitsAlloc->Delete(); + bitsStored->Delete(); + highBit->Delete(); } } else @@ -755,12 +1053,13 @@ void FileHelper::SetWriteToRGB() } /** - * \brief + * \brief Restore the File write mode */ void FileHelper::RestoreWrite() { Archive->Restore(0x0028,0x0002); Archive->Restore(0x0028,0x0004); + Archive->Restore(0x0028,0x0006); Archive->Restore(GetFile()->GetGrPixel(),GetFile()->GetNumPixel()); @@ -776,202 +1075,1227 @@ 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 Sets in the File the TransferSyntax to 'JPEG2000' + */ +void FileHelper::SetWriteFileTypeToJPEG2000() +{ + std::string ts = Util::DicomString( + Global::GetTS()->GetSpecialTransferSyntax(TS::JPEG2000Lossless) ); + + DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI"); + tss->SetString(ts); + + Archive->Push(tss); + tss->Delete(); +} + +/** + * \brief Sets in the File the TransferSyntax to 'JPEG' + */ +void FileHelper::SetWriteFileTypeToJPEG() +{ + std::string ts = Util::DicomString( + Global::GetTS()->GetSpecialTransferSyntax(TS::JPEGLosslessProcess14_1) ); + + DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI"); + tss->SetString(ts); + + Archive->Push(tss); + tss->Delete(); } /** - * \brief + * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian" */ 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,"UI"); + tss->SetString(ts); Archive->Push(tss); + tss->Delete(); } /** - * \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,"UI"); + tss->SetString(ts); Archive->Push(tss); + tss->Delete(); } - /** - * \brief + * \brief Set the Write not to Libido format */ -void FileHelper::RestoreWriteFileType() -{ - Archive->Restore(0x0002,0x0010); -} - 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=DataEntry::New(0x0028, 0x0010, "US"); + DataEntry *newCol=DataEntry::New(0x0028, 0x0011, "US"); 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,"LO"); + libidoCode->SetString("ACRNEMA_LIBIDO_1.1"); Archive->Push(libidoCode); + libidoCode->Delete(); } /** - * \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,"LO"); + libidoCode->SetString(""); Archive->Push(libidoCode); + libidoCode->Delete(); } } } /** - * \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 + * \return pointer to the new Bin Entry (NULL when creation failed). + */ +DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem, + const VRKey &vr) { DocEntry *oldE = FileInternal->GetDocEntry(group, elem); - ValEntry *newE; + DataEntry *newE; + + if ( oldE && vr != GDCM_VRUNKNOWN ) + if ( oldE->GetVR() != vr ) + oldE = NULL; - if(oldE) + if ( oldE ) { - newE = new ValEntry(oldE->GetDictEntry()); + newE = DataEntry::New(group, elem, vr); 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 they were before he decided to write. + * + * \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 + * (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) + +/* ------------------------------------------------------------------------------------- +To be moved to User's guide / WIKI ? + +We have to deal with 4 *very* different cases : +-1) user created ex nihilo his own image and wants to write it as a Dicom image. + USER_OWN_IMAGE +-2) user modified the pixels of an existing image. + FILTERED_IMAGE +-3) user created a new image, using a set of existing images (eg MIP, MPR, cartography image) + CREATED_IMAGE +-4) user modified/added some tags *without processing* the pixels (anonymization...) + UNMODIFIED_PIXELS_IMAGE +-Probabely some more to be added. + --> Set it with FileHelper::SetContentType(int); + +gdcm::FileHelper::CheckMandatoryElements() deals automatically with these cases. + +1)2)3)4) +0008 0012 Instance Creation Date +0008 0013 Instance Creation Time +0008 0018 SOP Instance UID +are *always* created with the current values; user has *no* possible intervention on +them. + +'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 allow him to do that + + None of the 'shadow elements' are droped out. + + +1) +'Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image). + +1)3) +'Media Storage SOP Class UID' (0x0002,0x0002) +'SOP Class UID' (0x0008,0x0016) are set to + [Secondary Capture Image Storage] +'Image Type' (0x0008,0x0008) is forced to "DERIVED\PRIMARY" +Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image) + +2)4) +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' + +3) TO DO : find a trick to allow user to pass to the writter the list of the Dicom images + or the Series, (or the Study ?) he used to created his image + (MIP, MPR, cartography image, ...) + These info should be stored (?) + 0008 1110 SQ 1 Referenced Study Sequence + 0008 1115 SQ 1 Referenced Series Sequence + 0008 1140 SQ 1 Referenced Image Sequence + +4) When user *knows* he didn't modified the pixels, we keep some informations unchanged : +'Media Storage SOP Class UID' (0x0002,0x0002) +'SOP Class UID' (0x0008,0x0016) +'Image Type' (0x0008,0x0008) +'Conversion Type' (0x0008,0x0064) + + +Bellow follows the full description (hope so !) of the consistency checks performed +by gdcm::FileHelper::CheckMandatoryElements() + + +-->'Media Storage SOP Class UID' (0x0002,0x0002) +-->'SOP Class UID' (0x0008,0x0016) are defaulted to + [Secondary Capture Image Storage] +--> 'Image Type' (0x0008,0x0008) + is forced to "DERIVED\PRIMARY" + (The written image is no longer an 'ORIGINAL' one) + Except if user knows he didn't modify the image (e.g. : he just anonymized the file) + + --> Conversion Type (0x0008,0x0064) + is defaulted to 'SYN' (Synthetic Image) + when *he* knows he created his own image ex nihilo + +--> '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) + +--> Imager Pixel Spacing (0x0018,0x1164) : defaulted to Pixel Spacing value + +--> Instance Creation Date, Instance Creation Time are forced to current Date and Time + +--> Study Date, Study Time are defaulted to current Date and Time + (they remain unchanged if they exist) + +--> Patient Orientation : (0x0020,0x0020), if not present, is deduced from + Image Orientation (Patient) : (0020|0037) or from + Image Orientation (RET) : (0020 0035) + +--> 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() { - DocEntry *oldE = FileInternal->GetDocEntry(group, elem); - BinEntry *newE; + std::string sop = Util::CreateUniqueUID(); - if(oldE) + // --------------------- For Meta Elements --------------------- + // just to remember : 'official' 0002 group + if ( WriteType != ACR && WriteType != ACR_LIBIDO ) { - newE = new BinEntry(oldE->GetDictEntry()); - newE->Copy(oldE); + // 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 Storage SOP Class UID + //0002 0003 UI 1 Media Storage 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 + + // Push out 'ACR-NEMA-special' entries, if any + Archive->Push(0x0008,0x0001); // Length to End + Archive->Push(0x0008,0x0010); // Recognition Code + Archive->Push(0x0028,0x0005); // Image Dimension + + // Create them if not found + // Always modify the value + // Push the entries to the archive. + CopyMandatoryEntry(0x0002,0x0000,"0","UL"); + + 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(); + + if ( ContentType == FILTERED_IMAGE || ContentType == UNMODIFIED_PIXELS_IMAGE) + { + // we keep the original 'Media Storage SOP Class UID', we default it if missing + CheckMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7","UI"); + } + else + { + // It's *not* an image comming straight from a source. We force + // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage] + CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7","UI"); + } + + // 'Media Storage SOP Instance UID' + CopyMandatoryEntry(0x0002,0x0003,sop,"UI"); + + // 'Implementation Class UID' + // FIXME : in all examples we have, 0x0002,0x0012 is not so long : + // seems to be Root UID + 4 digits (?) + CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID(),"UI"); + + // 'Implementation Version Name' + std::string version = "GDCM "; + version += Util::GetVersion(); + CopyMandatoryEntry(0x0002,0x0013,version,"SH"); + } + + // --------------------- For DataSet --------------------- + + // check whether 0018|0015 [CS] [Body Part Examined] value is UPPER CASE + // (avoid dciodvfy to complain!) + DataEntry *e_0018_0015 = FileInternal->GetDataEntry(0x0018, 0x0015); + if ( e_0018_0015) + { + std::string bodyPartExamined = e_0018_0015->GetString(); + std::transform(bodyPartExamined.begin(), bodyPartExamined.end(), bodyPartExamined.begin(), + (int(*)(int)) toupper); + CopyMandatoryEntry(0x0018,0x0015,bodyPartExamined,"CS"); + } + + if ( ContentType != USER_OWN_IMAGE) // when it's not a user made image + { + // If 'SOP Class UID' and 'SOP Instance UID' exist ('true DICOM' image) + // we create the 'Source Image Sequence' SeqEntry + // to hold informations about the Source Image + + // 'SOP Instance UID' + DataEntry *e_0008_0016 = FileInternal->GetDataEntry(0x0008, 0x0016); + // + DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018); + if ( e_0008_0016 && e_0008_0018) + { + // Create 'Source Image Sequence' SeqEntry + SeqEntry *sis = SeqEntry::New (0x0008, 0x2112); + SQItem *sqi = SQItem::New(1); + + // create 'Referenced SOP Class UID' from 'SOP Class UID' + + DataEntry *e_0008_1150 = DataEntry::New(0x0008, 0x1150, "UI"); + e_0008_1150->SetString( e_0008_0016->GetString()); + sqi->AddEntry(e_0008_1150); + e_0008_1150->Delete(); + + // create 'Referenced SOP Instance UID' from 'SOP Instance UID' + // DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018); + + DataEntry *e_0008_1155 = DataEntry::New(0x0008, 0x1155, "UI"); + e_0008_1155->SetString( e_0008_0018->GetString()); + sqi->AddEntry(e_0008_1155); + e_0008_1155->Delete(); + + sis->AddSQItem(sqi,1); + sqi->Delete(); + + // 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'? + + if ( ContentType == FILTERED_IMAGE) // the user *knows* he just modified the pixels + { + DataEntry *e_0008_0008 = FileInternal->GetDataEntry(0x0008, 0x0008); + if ( e_0008_0008) + { + std::string imageType = e_0008_0008->GetString(); + std::string::size_type p = imageType.find("ORIGINAL"); + if (p == 0) // image is ORIGINAL one + { + // the image is no longer an 'Original' one + CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY","CS"); + } + // if Image Type was not ORIGINAL\..., we keep it. + } + else // 0008_0008 was missing, wee add it. + { + CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY","CS"); + } + } + } + } + + if ( ContentType == FILTERED_IMAGE || ContentType == UNMODIFIED_PIXELS_IMAGE) + { + // we keep the original 'Media Storage SOP Class UID', we default it if missing (it should be present !) + CheckMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7","UI"); } else { - newE = GetFile()->NewBinEntry(group,elem); + // It's *not* an image comming straight from a source. We force + // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage] + CopyMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7", "UI"); + } + + Archive->Push(0x0028,0x005); // [Image Dimensions (RET) + // Push out 'LibIDO-special' entries, if any + Archive->Push(0x0028,0x0015); + Archive->Push(0x0028,0x0016); + Archive->Push(0x0028,0x0017); + Archive->Push(0x0028,0x0198); // very old versions + Archive->Push(0x0028,0x0199); + + // Replace deprecated 0028 0012 US Planes + // by new 0028 0008 IS Number of Frames + + ///\todo : find if there is a rule! + DataEntry *e_0028_0012 = FileInternal->GetDataEntry(0x0028, 0x0012); + if ( e_0028_0012 ) + { + CopyMandatoryEntry(0x0028, 0x0008,e_0028_0012->GetString(),"IS"); + Archive->Push(0x0028,0x0012); } - return newE; + // Deal with the pb of (Bits Stored = 12) + // - we're gonna write the image as Bits Stored = 16 + if ( FileInternal->GetEntryString(0x0028,0x0100) == "12") + { + CopyMandatoryEntry(0x0028,0x0100,"16","US"); + } + + // Check if user wasn't drunk ;-) + + std::ostringstream s; + // check 'Bits Allocated' vs decent values + int nbBitsAllocated = FileInternal->GetBitsAllocated(); + if ( (nbBitsAllocated == 0 || nbBitsAllocated > 32) + || ( nbBitsAllocated > 8 && nbBitsAllocated <16) ) + { + CopyMandatoryEntry(0x0028,0x0100,"16","US"); + 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(),"US"); + 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(),"US"); + gdcmWarningMacro("(0028,0102) changed from " + << highBitPosition << " to " << nbBitsAllocated-1 + << " for consistency purpose"); + } + + // check Pixel Representation (default it as 0 -unsigned-) + + DataEntry *e_0028_0103 = FileInternal->GetDataEntry(0x0028, 0x0103); + if ( !e_0028_0103 ) + { + gdcmWarningMacro("PixelRepresentation (0028,0103) is supposed to be mandatory"); + CopyMandatoryEntry(0x0028, 0x0103,"0","US"); + } + else + { + int sign = (int)e_0028_0103->GetValue(0); + if (sign !=1 && sign !=0) + { + gdcmWarningMacro("PixelRepresentation (0028,0103) is supposed to be =1 or =0"); + CopyMandatoryEntry(0x0028, 0x0103,"0","US"); + } + } + + std::string pixelAspectRatio = FileInternal->GetEntryString(0x0028,0x0034); + if ( pixelAspectRatio == GDCM_UNFOUND ) // avoid conflict with pixelSpacing ! + { + std::string pixelSpacing = FileInternal->GetEntryString(0x0028,0x0030); + if ( pixelSpacing == GDCM_UNFOUND ) + { + pixelSpacing = "1.0\\1.0"; + // if missing, Pixel Spacing forced to "1.0\1.0" + CopyMandatoryEntry(0x0028,0x0030,pixelSpacing,"DS"); + } + + // 'Imager Pixel Spacing' : defaulted to 'Pixel Spacing' + // --> This one is the *legal* one ! + if ( ContentType != USER_OWN_IMAGE) + // we write it only when we are *sure* the image comes from + // an imager (see also 0008,0x0064) + CheckMandatoryEntry(0x0018,0x1164,pixelSpacing,"DS"); + } +/* +///Exact meaning of RETired fields + +// See page 73 of ACR-NEMA_300-1988.pdf ! + +// 0020,0020 : Patient Orientation : +Patient direction of the first row and +column of the images. The first entry id the direction of the raws, given by the +direction of the last pixel in the first row from the first pixel in tha row. +the second entry is the direction of the columns, given by the direction of the +last pixel in the first column from the first pixel in that column. +L : Left, F : Feet, A : Anterior, P : Posterior. +Up to 3 letters can be used in combination to indicate oblique planes. + +//0020,0030 Image Position (RET) +x,y,z coordinates im mm of the first pixel in the image + +// 0020,0035 Image Orientation (RET) +Direction cosines of the R axis of the image system with respect to the +equipment coordinate axes x,y,z, followed by direction cosines of the C axis of +the image system with respect to the same axes + +//0020,0050 Location +An image location reference, standard for the modality (such as CT bed position), +used to indicate position. Calculation of position for other purposes +is only from (0020,0030) and (0020,0035) +*/ + +/* +// if imagePositionPatient not found, default it with imagePositionRet, if any +// if imageOrientationPatient not found, default it with imageOrientationRet, if any + + std::string imagePositionRet = FileInternal->GetEntryString(0x0020,0x0030); + std::string imageOrientationRet = FileInternal->GetEntryString(0x0020,0x0035); + std::string imagePositionPatient = FileInternal->GetEntryString(0x0020,0x0032); + std::string imageOrientationPatient = FileInternal->GetEntryString(0x0020,0x0037); + + if( imagePositionPatient == GDCM_UNFOUND && imageOrientationPatient == GDCM_UNFOUND + && imagePositionRet != GDCM_UNFOUND && imageOrientationRet != GDCM_UNFOUND) + { + CopyMandatoryEntry(0x0020, 0x0032,imagePositionRet,"DS"); + Archive->Push(0x0020,0x0030); + CopyMandatoryEntry(0x0020, 0x0037,imageOrientationRet,"DS"); + Archive->Push(0x0020,0x0035); + } +*/ + + // Samples Per Pixel (type 1) : default to grayscale + CheckMandatoryEntry(0x0028,0x0002,"1","US"); + + // --- Check UID-related Entries --- + + // 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,"UI"); + + if ( ContentType == USER_OWN_IMAGE) + { + gdcmDebugMacro( "USER_OWN_IMAGE (2)"); + // 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 + + CheckMandatoryEntry(0x0008,0x0064,"SYN","CS"); // Why not? + } +/* + if ( ContentType == CREATED_IMAGE) + { + /// \todo : find a trick to pass the Media Storage SOP Instance UID of the images used to create the current image + + } +*/ + + // ---- 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 + const std::string &date = Util::GetCurrentDate(); + CopyMandatoryEntry(0x0008,0x0012,date,"DA"); + + // Instance Creation Time + const std::string &time = Util::GetCurrentTime(); + CopyMandatoryEntry(0x0008,0x0013,time,"TM"); + + // Study Date + CheckMandatoryEntry(0x0008,0x0020,date,"DA"); + // Study Time + CheckMandatoryEntry(0x0008,0x0030,time,"TM"); + + // Accession Number + //CopyMandatoryEntry(0x0008,0x0050,""); + CheckMandatoryEntry(0x0008,0x0050,"","SH"); + + + // ----- 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 + + // '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(),"UI"); + + // '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 prevent him for doing that + CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID(),"UI"); + + // Study ID + CheckMandatoryEntry(0x0020,0x0010,"","SH"); + + // Series Number + CheckMandatoryEntry(0x0020,0x0011,"","IS"); + + // Instance Number + CheckMandatoryEntry(0x0020,0x0013,"","IS"); + + // Patient Orientation + // Can be computed from (0020|0037) : Image Orientation (Patient) + GDCM_NAME_SPACE::Orientation *o = GDCM_NAME_SPACE::Orientation::New(); + std::string ori = o->GetOrientation ( FileInternal ); + o->Delete(); + if (ori != "\\" && ori != GDCM_UNFOUND) + CheckMandatoryEntry(0x0020,0x0020,ori,"CS"); + else + CheckMandatoryEntry(0x0020,0x0020,"","CS"); + + // Default Patient Position to HFS + CheckMandatoryEntry(0x0018,0x5100,"HFS","CS"); + + // Modality : if missing we set it to 'OTher' + CheckMandatoryEntry(0x0008,0x0060,"OT","CS"); + + // Manufacturer : if missing we set it to 'GDCM Factory' + CheckMandatoryEntry(0x0008,0x0070,"GDCM Factory","LO"); + + // Institution Name : if missing we set it to 'GDCM Hospital' + CheckMandatoryEntry(0x0008,0x0080,"GDCM Hospital","LO"); + + // Patient's Name : if missing, we set it to 'GDCM^Patient' + CheckMandatoryEntry(0x0010,0x0010,"GDCM^Patient","PN"); + + // Patient ID : some clinical softwares *demand* it although it's a 'type 2' entry. + CheckMandatoryEntry(0x0010,0x0020,"gdcm ID","LO"); + + // Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory + CheckMandatoryEntry(0x0010,0x0030,"","DA"); + + // Patient's Sex :'type 2' entry -> must exist, value not mandatory + CheckMandatoryEntry(0x0010,0x0040,"","CS"); + + // Referring Physician's Name :'type 2' entry -> must exist, value not mandatory + CheckMandatoryEntry(0x0008,0x0090,"","PN"); + + /* + // Deal with element 0x0000 (group length) of each group. + // First stage : get all the different Groups + + GroupHT grHT; + DocEntry *d = FileInternal->GetFirstEntry(); + while(d) + { + grHT[d->GetGroup()] = 0; + d=FileInternal->GetNextEntry(); + } + // Second stage : add the missing ones (if any) + for (GroupHT::iterator it = grHT.begin(); it != grHT.end(); ++it) + { + CheckMandatoryEntry(it->first, 0x0000, "0"); + } + // Third stage : update all 'zero level' groups length +*/ + + + if (PhotometricInterpretation == 1) + { + } +} + +void FileHelper::CheckMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr ) +{ + DataEntry *entry = FileInternal->GetDataEntry(group,elem); + if ( !entry ) + { + //entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); + entry = DataEntry::New(group,elem,vr); + entry->SetString(value); + Archive->Push(entry); + entry->Delete(); + } +} + +/// \todo : what is it used for ? (FileHelper::SetMandatoryEntry) +void FileHelper::SetMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr) +{ + //DataEntry *entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); + DataEntry *entry = DataEntry::New(group,elem,vr); + entry->SetString(value); + Archive->Push(entry); + entry->Delete(); +} + +void FileHelper::CopyMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr) +{ + DataEntry *entry = CopyDataEntry(group,elem,vr); + entry->SetString(value); + Archive->Push(entry); + entry->Delete(); +} + +/** + * \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); + + // FIXME : Check if none is missing ! + + 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); +} + +/** + * \brief CallStartMethod + */ +void FileHelper::CallStartMethod() +{ + Progress = 0.0f; + Abort = false; + CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS); +} + +/** + * \brief CallProgressMethod + */ +void FileHelper::CallProgressMethod() +{ + CommandManager::ExecuteCommand(this,CMD_PROGRESS); +} + +/** + * \brief CallEndMethod + */ +void FileHelper::CallEndMethod() +{ + Progress = 1.0f; + CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS); } //----------------------------------------------------------------------------- -// Protected +// Private /** * \brief Factorization for various forms of constructors. */ void FileHelper::Initialize() { + UserFunction = 0; + ContentType = USER_OWN_IMAGE; + WriteMode = WMODE_RAW; WriteType = ExplicitVR; + + PhotometricInterpretation = 2; // Black = 0 - PixelReadConverter = new PixelReadConvert; + PixelReadConverter = new PixelReadConvert; PixelWriteConverter = new PixelWriteConvert; Archive = new DocEntryArchive( FileInternal ); - - if ( FileInternal->IsReadable() ) - { - PixelReadConverter->GrabInformationsFromHeader( FileInternal ); - } + + KeepOverlays = false; } /** - * \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; } +/** + * \brief Deal with Grey levels i.e. re-arange them + * to have low values = dark, high values = bright + */ +void FileHelper::ConvertFixGreyLevels(uint8_t *raw, size_t rawSize) +{ + uint32_t i; // to please M$VC6 + int16_t j; + + // Number of Bits Allocated for storing a Pixel is defaulted to 16 + // when absent from the file. + int bitsAllocated = FileInternal->GetBitsAllocated(); + if ( bitsAllocated == 0 ) + { + bitsAllocated = 16; + } + + else if (bitsAllocated > 8 && bitsAllocated < 16 && bitsAllocated != 12) + { + bitsAllocated = 16; + } + // Number of "Bits Stored", defaulted to number of "Bits Allocated" + // when absent from the file. + int bitsStored = FileInternal->GetBitsStored(); + if ( bitsStored == 0 ) + { + bitsStored = bitsAllocated; + } + + if (!FileInternal->IsSignedPixelData()) + { + if ( bitsAllocated == 8 ) + { + uint8_t *deb = (uint8_t *)raw; + for (i=0; iSetPrintLevel(PrintLevel); + FileInternal->Print(os); + + if ( FileInternal->IsReadable() ) + { + PixelReadConverter->SetPrintLevel(PrintLevel); + PixelReadConverter->Print(os); + } +} //----------------------------------------------------------------------------- } // end namespace gdcm + +/* Probabely something to be added to use Rescale Slope/Intercept +Have a look at ITK code ! + +// Internal function to rescale pixel according to Rescale Slope/Intercept +template +void RescaleFunction(TBuffer* buffer, TSource *source, + double slope, double intercept, size_t size) +{ + size /= sizeof(TSource); + + if (slope != 1.0 && intercept != 0.0) + { + // Duff's device. Instead of this code: + // + // for(unsigned int i=0; i 0); + } + } + else if (slope == 1.0 && intercept != 0.0) + { + // Duff's device. Instead of this code: + // + // for(unsigned int i=0; i 0); + } + } + else if (slope != 1.0 && intercept == 0.0) + { + // Duff's device. Instead of this code: + // + // for(unsigned int i=0; i 0); + } + } + else + { + // Duff's device. Instead of this code: + // + // for(unsigned int i=0; i 0); + } + } +} + + +template +void RescaleFunction(ImageIOBase::IOComponentType bufferType, + void* buffer, TSource *source, + double slope, double intercept, size_t size) +{ + switch (bufferType) + { + case ImageIOBase::UCHAR: + RescaleFunction( (unsigned char *)buffer, source, slope, intercept, size); + break; + case ImageIOBase::CHAR: + RescaleFunction( (char *)buffer, source, slope, intercept, size); + break; + case ImageIOBase::USHORT: + RescaleFunction( (unsigned short *)buffer, source, slope, intercept,size); + break; + case ImageIOBase::SHORT: + RescaleFunction( (short *)buffer, source, slope, intercept, size); + break; + case ImageIOBase::UINT: + RescaleFunction( (unsigned int *)buffer, source, slope, intercept, size); + break; + case ImageIOBase::INT: + RescaleFunction( (int *)buffer, source, slope, intercept, size); + break; + case ImageIOBase::FLOAT: + RescaleFunction( (float *)buffer, source, slope, intercept, size); + break; + case ImageIOBase::DOUBLE: + RescaleFunction( (double *)buffer, source, slope, intercept, size); + break; + default: + ::itk::OStringStream message; + message << "itk::ERROR: GDCMImageIO: Unknown component type : " << bufferType; + ::itk::ExceptionObject e(__FILE__, __LINE__, message.str().c_str(),ITK_LOCATION); + throw e; + } +} +*/