X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=94f5ca5b22b4895807937ffae513695655a7fc4c;hb=92967c3564074740715bcfd833bdd9f6a4e2220e;hp=353b7cd6dbc7911b1edbd085aa46269409fd12ab;hpb=2903216d32144f3c716c1dc14fb29a5bc422c3b4;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 353b7cd6..94f5ca5b 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,10 +1,10 @@ - /*========================================================================= +/*========================================================================= Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/12/16 10:51:49 $ - Version: $Revision: 1.177 $ + Date: $Date: 2005/02/10 20:53:23 $ + Version: $Revision: 1.223 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -16,872 +16,1727 @@ =========================================================================*/ +// +// -------------- Remember ! ---------------------------------- +// +// Image Position Patient (0020,0032): +// If not found (ACR_NEMA) we try Image Position (0020,0030) +// If not found (ACR-NEMA), we consider Slice Location (0020,1041) +// or Location (0020,0050) +// as the Z coordinate, +// 0. for all the coordinates if nothing is found +// +// --------------------------------------------------------------- +// #include "gdcmFile.h" -#include "gdcmDocument.h" -#include "gdcmDebug.h" +#include "gdcmGlobal.h" #include "gdcmUtil.h" +#include "gdcmDebug.h" +#include "gdcmTS.h" +#include "gdcmValEntry.h" #include "gdcmBinEntry.h" -#include "gdcmHeader.h" -#include "gdcmPixelReadConvert.h" -#include "gdcmPixelWriteConvert.h" -#include "gdcmDocEntryArchive.h" +#include "gdcmSeqEntry.h" +#include "gdcmRLEFramesInfo.h" +#include "gdcmJPEGFragmentsInfo.h" -#include +#include //sscanf +#include namespace gdcm { -typedef std::pair IterHT; - -//------------------------------------------------------------------------- +//----------------------------------------------------------------------------- // Constructor / Destructor /** - * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 - * file (Header 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 - * (see GetImageData, GetImageDataRaw) - * \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). + * \brief Constructor + * @param filename name of the file whose header we want to analyze */ -File::File( ) -{ - HeaderInternal = new Header( ); - SelfHeader = true; - Initialise(); +File::File( std::string const &filename ) + :Document( filename ) +{ + RLEInfo = new RLEFramesInfo; + JPEGInfo = new JPEGFragmentsInfo; + + // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010 + // We may encounter the 'RETired' (0x0028, 0x0200) tag + // (Image Location") . This entry contains the number of + // the group that contains the pixel data (hence the "Pixel Data" + // is found by indirection through the "Image Location"). + // Inside the group pointed by "Image Location" the searched element + // is conventionally the element 0x0010 (when the norm is respected). + // When the "Image Location" is missing we default to group 0x7fe0. + // Note: this IS the right place for the code + + // Image Location + const std::string &imgLocation = GetEntryValue(0x0028, 0x0200); + if ( imgLocation == GDCM_UNFOUND ) + { + // default value + GrPixel = 0x7fe0; + } + else + { + GrPixel = (uint16_t) atoi( imgLocation.c_str() ); + } + + // sometimes Image Location value doesn't follow + // the supposed processor endianness. + // see gdcmData/cr172241.dcm + if ( GrPixel == 0xe07f ) + { + GrPixel = 0x7fe0; + } + + if ( GrPixel != 0x7fe0 ) + { + // This is a kludge for old dirty Philips imager. + NumPixel = 0x1010; + } + else + { + NumPixel = 0x0010; + } + + // Now, we know GrPixel and NumPixel. + // Let's create a VirtualDictEntry to allow a further VR modification + // and force VR to match with BitsAllocated. + DocEntry *entry = GetDocEntry(GrPixel, NumPixel); + if ( entry != 0 ) + { + // Compute the RLE or JPEG info + OpenFile(); + std::string ts = GetTransferSyntax(); + Fp->seekg( entry->GetOffset(), std::ios::beg ); + if ( Global::GetTS()->IsRLELossless(ts) ) + ComputeRLEInfo(); + else if ( Global::GetTS()->IsJPEG(ts) ) + ComputeJPEGFragmentInfo(); + CloseFile(); + + // Create a new BinEntry to change the the DictEntry + // The changed DictEntry will have + // - a correct PixelVR OB or OW) + // - a VM to "PXL" + // - the name to "Pixel Data" + BinEntry *oldEntry = dynamic_cast(entry); + if(oldEntry) + { + std::string PixelVR; + // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB) + // more than 8 (i.e 12, 16) is a 'O Words' + if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 ) + PixelVR = "OB"; + else + PixelVR = "OW"; + + // Change only made if usefull + if( PixelVR != oldEntry->GetVR() ) + { + DictEntry* newDict = NewVirtualDictEntry(GrPixel,NumPixel, + PixelVR,"1","Pixel Data"); + + BinEntry *newEntry = new BinEntry(newDict); + newEntry->Copy(entry); + newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea()); + oldEntry->SetSelfArea(false); + + RemoveEntry(oldEntry); + AddEntry(newEntry); + } + } + } } /** - * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 - * file (Header 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 - * (see GetImageData, GetImageDataRaw) - * \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 - * user sets an a posteriori shadow dictionary (efficiency can be - * seen as a side effect). - * @param header already built Header + * \brief Constructor used when we want to generate dicom files from scratch */ -File::File(Header *header) +File::File(): + Document() { - HeaderInternal = header; - SelfHeader = false; - Initialise(); + RLEInfo = new RLEFramesInfo; + JPEGInfo = new JPEGFragmentsInfo; + InitializeDefaultFile(); } /** - * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 - * file (Header 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 - * (see GetImageData, GetImageDataRaw) - * \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 + * \brief Canonical destructor. */ -File::File(std::string const & filename ) +File::~File () { - HeaderInternal = new Header( filename ); - SelfHeader = true; - Initialise(); + if( RLEInfo ) + delete RLEInfo; + if( JPEGInfo ) + delete JPEGInfo; } +//----------------------------------------------------------------------------- +// Public /** - * \brief canonical destructor - * \note If the Header was created by the File constructor, - * it is destroyed by the File + * \brief This predicate, based on hopefully reasonable heuristics, + * decides whether or not the current File was properly parsed + * and contains the mandatory information for being considered as + * a well formed and usable Dicom/Acr File. + * @return true when File is the one of a reasonable Dicom/Acr file, + * false otherwise. */ -File::~File() -{ - if( PixelReadConverter ) +bool File::IsReadable() +{ + if( !Document::IsReadable() ) { - delete PixelReadConverter; + return false; } - if( PixelWriteConverter ) + + const std::string &res = GetEntryValue(0x0028, 0x0005); + if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) { - delete PixelWriteConverter; + return false; // Image Dimensions } - if( Archive ) + if ( !GetDocEntry(0x0028, 0x0100) ) { - delete Archive; + return false; // "Bits Allocated" } - - if( SelfHeader ) + if ( !GetDocEntry(0x0028, 0x0101) ) { - delete HeaderInternal; + return false; // "Bits Stored" + } + if ( !GetDocEntry(0x0028, 0x0102) ) + { + return false; // "High Bit" + } + if ( !GetDocEntry(0x0028, 0x0103) ) + { + return false; // "Pixel Representation" i.e. 'Sign' } - HeaderInternal = 0; -} -//----------------------------------------------------------------------------- -// Print + return true; +} -//----------------------------------------------------------------------------- -// Public /** - * \brief Get the size of the image data - * - * If the image can be RGB (with a lut or by default), the size - * corresponds to the RGB image - * @return The image size + * \brief gets the info from 0020,0013 : Image Number else 0. + * @return image number */ -size_t File::GetImageDataSize() +int File::GetImageNumber() { - if ( PixelWriteConverter->GetUserData() ) + // The function i atoi() takes the address of an area of memory as + // parameter and converts the string stored at that location to an integer + // using the external decimal to internal binary conversion rules. This may + // be preferable to sscanf() since atoi() is a much smaller, simpler and + // faster function. sscanf() can do all possible conversions whereas + // atoi() can only do single decimal integer conversions. + //0020 0013 IS REL Image Number + std::string strImNumber = GetEntryValue(0x0020,0x0013); + if ( strImNumber != GDCM_UNFOUND ) { - return PixelWriteConverter->GetUserDataSize(); + return atoi( strImNumber.c_str() ); } - - return PixelReadConverter->GetRGBSize(); + return 0; //Hopeless } /** - * \brief Get the size of the image data - * - * If the image can be RGB by transformation in a LUT, this - * transformation isn't considered - * @return The raw image size + * \brief gets the info from 0008,0060 : Modality + * @return Modality Type */ -size_t File::GetImageDataRawSize() +ModalityType File::GetModality() { - if ( PixelWriteConverter->GetUserData() ) + // 0008 0060 CS ID Modality + std::string strModality = GetEntryValue(0x0008,0x0060); + if ( strModality != GDCM_UNFOUND ) { - return PixelWriteConverter->GetUserDataSize(); + if ( strModality.find("AU") < strModality.length()) return AU; + else if ( strModality.find("AS") < strModality.length()) return AS; + else if ( strModality.find("BI") < strModality.length()) return BI; + else if ( strModality.find("CF") < strModality.length()) return CF; + else if ( strModality.find("CP") < strModality.length()) return CP; + else if ( strModality.find("CR") < strModality.length()) return CR; + else if ( strModality.find("CT") < strModality.length()) return CT; + else if ( strModality.find("CS") < strModality.length()) return CS; + else if ( strModality.find("DD") < strModality.length()) return DD; + else if ( strModality.find("DF") < strModality.length()) return DF; + else if ( strModality.find("DG") < strModality.length()) return DG; + else if ( strModality.find("DM") < strModality.length()) return DM; + else if ( strModality.find("DS") < strModality.length()) return DS; + else if ( strModality.find("DX") < strModality.length()) return DX; + else if ( strModality.find("ECG") < strModality.length()) return ECG; + else if ( strModality.find("EPS") < strModality.length()) return EPS; + else if ( strModality.find("FA") < strModality.length()) return FA; + else if ( strModality.find("FS") < strModality.length()) return FS; + else if ( strModality.find("HC") < strModality.length()) return HC; + else if ( strModality.find("HD") < strModality.length()) return HD; + else if ( strModality.find("LP") < strModality.length()) return LP; + else if ( strModality.find("LS") < strModality.length()) return LS; + else if ( strModality.find("MA") < strModality.length()) return MA; + else if ( strModality.find("MR") < strModality.length()) return MR; + else if ( strModality.find("NM") < strModality.length()) return NM; + else if ( strModality.find("OT") < strModality.length()) return OT; + else if ( strModality.find("PT") < strModality.length()) return PT; + else if ( strModality.find("RF") < strModality.length()) return RF; + else if ( strModality.find("RG") < strModality.length()) return RG; + else if ( strModality.find("RTDOSE") < strModality.length()) return RTDOSE; + else if ( strModality.find("RTIMAGE") < strModality.length()) return RTIMAGE; + else if ( strModality.find("RTPLAN") < strModality.length()) return RTPLAN; + else if ( strModality.find("RTSTRUCT") < strModality.length()) return RTSTRUCT; + else if ( strModality.find("SM") < strModality.length()) return SM; + else if ( strModality.find("ST") < strModality.length()) return ST; + else if ( strModality.find("TG") < strModality.length()) return TG; + else if ( strModality.find("US") < strModality.length()) return US; + else if ( strModality.find("VF") < strModality.length()) return VF; + else if ( strModality.find("XA") < strModality.length()) return XA; + else if ( strModality.find("XC") < strModality.length()) return XC; + + else + { + /// \todo throw error return value ??? + /// specified <> unknown in our database + return Unknow; + } } - return PixelReadConverter->GetRawSize(); + return Unknow; } /** - * \brief - Allocates necessary memory, - * - Reads the pixels from disk (uncompress if necessary), - * - Transforms YBR pixels, if any, into RGB pixels - * - Transforms 3 planes R, G, B, if any, into a single RGB Plane - * - Transforms single Grey plane + 3 Palettes into a RGB Plane - * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone. - * @return Pointer to newly allocated pixel data. - * NULL if alloc fails + * \brief Retrieve the number of columns of image. + * @return The encountered size when found, 0 by default. + * 0 means the file is NOT USABLE. The caller will have to check */ -uint8_t* File::GetImageData() +int File::GetXSize() { - if ( PixelWriteConverter->GetUserData() ) + const std::string &strSize = GetEntryValue(0x0028,0x0011); + if ( strSize == GDCM_UNFOUND ) { - return PixelWriteConverter->GetUserData(); - } - - if ( ! GetRaw() ) - { - // If the decompression failed nothing can be done. return 0; } - if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() ) + return atoi( strSize.c_str() ); +} + +/** + * \brief Retrieve the number of lines of image. + * \warning The defaulted value is 1 as opposed to File::GetXSize() + * @return The encountered size when found, 1 by default + * (The ACR-NEMA file contains a Signal, not an Image). + */ +int File::GetYSize() +{ + const std::string &strSize = GetEntryValue(0x0028,0x0010); + if ( strSize != GDCM_UNFOUND ) { - return PixelReadConverter->GetRGB(); + return atoi( strSize.c_str() ); } - else + if ( IsDicomV3() ) { - // When no LUT or LUT conversion fails, return the Raw - return PixelReadConverter->GetRaw(); + return 0; } + + // The Rows (0028,0010) entry was optional for ACR/NEMA. It might + // hence be a signal (1D image). So we default to 1: + return 1; } /** - * \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 - * @return Pointer to newly allocated pixel data. - * \ NULL if alloc fails + * \brief Retrieve the number of planes of volume or the number + * of frames of a multiframe. + * \warning When present we consider the "Number of Frames" as the third + * dimension. When Missing we consider the third dimension as + * being the ACR-NEMA "Planes" tag content. + * @return The encountered size when found, 1 by default (single image). */ -uint8_t* File::GetImageDataRaw () +int File::GetZSize() { - return GetRaw(); + // Both DicomV3 and ACR/Nema consider the "Number of Frames" + // as the third dimension. + const std::string &strSize = GetEntryValue(0x0028,0x0008); + if ( strSize != GDCM_UNFOUND ) + { + return atoi( strSize.c_str() ); + } + + // We then consider the "Planes" entry as the third dimension + const std::string &strSize2 = GetEntryValue(0x0028,0x0012); + if ( strSize2 != GDCM_UNFOUND ) + { + return atoi( strSize2.c_str() ); + } + + return 1; } /** - * \brief - * Read the pixels from disk (uncompress if necessary), - * Transforms YBR pixels, if any, into RGB pixels - * Transforms 3 planes R, G, B, if any, into a single RGB Plane - * Transforms single Grey plane + 3 Palettes into a RGB Plane - * Copies at most MaxSize bytes of pixel data to caller allocated - * memory space. - * \warning This function allows people that want to build a volume - * from an image stack *not to* have, first to get the image pixels, - * and then move them to the volume area. - * It's absolutely useless for any VTK user since vtk chooses - * to invert the lines of an image, that is the last line comes first - * (for some axis related reasons?). Hence he will have - * to load the image line by line, starting from the end. - * VTK users have to call GetImageData - * - * @param destination Address (in caller's memory space) at which the - * pixel data should be copied - * @param maxSize Maximum number of bytes to be copied. When MaxSize - * is not sufficient to hold the pixel data the copy is not - * executed (i.e. no partial copy). - * @return On success, the number of bytes actually copied. Zero on - * failure e.g. MaxSize is lower than necessary. - */ -size_t File::GetImageDataIntoVector (void* destination, size_t maxSize) + * \brief gets the info from 0028,0030 : Pixel Spacing + * else 1.0 + * @return X dimension of a pixel + */ +float File::GetXSpacing() { - if ( ! GetRaw() ) + float xspacing = 1.0; + float yspacing = 1.0; + const std::string &strSpacing = GetEntryValue(0x0028,0x0030); + + if( strSpacing == GDCM_UNFOUND ) { - // If the decompression failed nothing can be done. - return 0; + gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); + return 1.; } - if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() ) + int nbValues; + if( ( nbValues = sscanf( strSpacing.c_str(), + "%f\\%f", &yspacing, &xspacing)) != 2 ) { - if ( PixelReadConverter->GetRGBSize() > maxSize ) - { - dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" - "than caller's expected MaxSize"); - return 0; - } - memcpy( destination, - (void*)PixelReadConverter->GetRGB(), - PixelReadConverter->GetRGBSize() ); - return PixelReadConverter->GetRGBSize(); + // if no values, xspacing is set to 1.0 + if( nbValues == 0 ) + xspacing = 1.0; + // if single value is found, xspacing is defaulted to yspacing + if( nbValues == 1 ) + xspacing = yspacing; + + if ( xspacing == 0.0 ) + xspacing = 1.0; + + return xspacing; + } - // Either no LUT conversion necessary or LUT conversion failed - if ( PixelReadConverter->GetRawSize() > maxSize ) + // to avoid troubles with David Clunie's-like images + if ( xspacing == 0. && yspacing == 0.) + return 1.; + + if ( xspacing == 0.) { - dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" - "than caller's expected MaxSize"); - return 0; + gdcmWarningMacro("gdcmData/CT-MONO2-8-abdo.dcm problem"); + // seems to be a bug in the header ... + nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing); + gdcmAssertMacro( nbValues == 2 ); } - memcpy( destination, - (void*)PixelReadConverter->GetRaw(), - PixelReadConverter->GetRawSize() ); - return PixelReadConverter->GetRawSize(); + + return xspacing; } /** - * \brief Points the internal pointer to the callers inData - * image representation, BUT WITHOUT COPYING THE DATA. - * 'image' Pixels are presented as C-like 2D arrays : line per line. - * 'volume'Pixels are presented as C-like 3D arrays : plane per plane - * \warning Since the pixels are not copied, it is the caller's responsability - * not to deallocate 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 - */ -void File::SetImageData(uint8_t* inData, size_t expectedSize) + * \brief gets the info from 0028,0030 : Pixel Spacing + * else 1.0 + * @return Y dimension of a pixel + */ +float File::GetYSpacing() { - SetUserData(inData,expectedSize); -} + float yspacing = 1.; + std::string strSpacing = GetEntryValue(0x0028,0x0030); + + if ( strSpacing == GDCM_UNFOUND ) + { + gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)"); + return 1.; + } + + // if sscanf cannot read any float value, it won't affect yspacing + int nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing); + + // if no values, xspacing is set to 1.0 + if( nbValues == 0 ) + yspacing = 1.0; + + if ( yspacing == 0.0 ) + yspacing = 1.0; + + return yspacing; +} /** - * \brief Set the image datas defined by the user - * \warning When writting the file, this datas are get as default datas to write + * \brief gets the info from 0018,0088 : Space Between Slices + * else from 0018,0050 : Slice Thickness + * else 1.0 + * @return Z dimension of a voxel-to be */ -void File::SetUserData(uint8_t* data, size_t expectedSize) +float File::GetZSpacing() { - PixelWriteConverter->SetUserData(data,expectedSize); + // Spacing Between Slices : distance entre le milieu de chaque coupe + // Les coupes peuvent etre : + // jointives (Spacing between Slices = Slice Thickness) + // chevauchantes (Spacing between Slices < Slice Thickness) + // disjointes (Spacing between Slices > Slice Thickness) + // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal + // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ... + // Si le Spacing Between Slices est Missing, + // on suppose que les coupes sont jointives + + const std::string &strSpacingBSlices = GetEntryValue(0x0018,0x0088); + + if ( strSpacingBSlices == GDCM_UNFOUND ) + { + gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)"); + const std::string &strSliceThickness = GetEntryValue(0x0018,0x0050); + if ( strSliceThickness == GDCM_UNFOUND ) + { + gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); + return 1.; + } + else + { + // if no 'Spacing Between Slices' is found, + // we assume slices join together + // (no overlapping, no interslice gap) + // if they don't, we're fucked up + return (float)atof( strSliceThickness.c_str() ); + } + } + //else + return (float)atof( strSpacingBSlices.c_str() ); } /** - * \brief Get the image datas defined by the user - * \warning When writting the file, this datas are get as default datas to write + * \brief gets the info from 0020,0032 : Image Position Patient + * else from 0020,0030 : Image Position (RET) + * else 0. + * @return up-left image corner X position */ -uint8_t* File::GetUserData() +float File::GetXOrigin() { - return PixelWriteConverter->GetUserData(); + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryValue(0x0020,0x0032); + + if ( strImPos == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); + strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); + return 0.; + } + } + + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) + { + return 0.; + } + + return xImPos; } /** - * \brief Get the image data size defined by the user - * \warning When writting the file, this datas are get as default datas to write + * \brief gets the info from 0020,0032 : Image Position Patient + * else from 0020,0030 : Image Position (RET) + * else 0. + * @return up-left image corner Y position */ -size_t File::GetUserDataSize() +float File::GetYOrigin() { - return PixelWriteConverter->GetUserDataSize(); + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryValue(0x0020,0x0032); + + if ( strImPos == GDCM_UNFOUND) + { + gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); + strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); + return 0.; + } + } + + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) + { + return 0.; + } + + return yImPos; } /** - * \brief Get the image datas from the file. - * If a LUT is found, the datas are expanded to be RGB + * \brief gets the info from 0020,0032 : Image Position Patient + * else from 0020,0030 : Image Position (RET) + * else from 0020,1041 : Slice Location + * else from 0020,0050 : Location + * else 0. + * @return up-left image corner Z position */ -uint8_t* File::GetRGBData() +float File::GetZOrigin() { - return PixelReadConverter->GetRGB(); + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryValue(0x0020,0x0032); + + if ( strImPos != GDCM_UNFOUND ) + { + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) + { + gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); + return 0.; // bug in the element 0x0020,0x0032 + } + else + { + return zImPos; + } + } + + strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos != GDCM_UNFOUND ) + { + if( sscanf( strImPos.c_str(), + "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 ) + { + gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); + return 0.; // bug in the element 0x0020,0x0032 + } + else + { + return zImPos; + } + } + + std::string strSliceLocation = GetEntryValue(0x0020,0x1041); // for *very* old ACR-NEMA images + if ( strSliceLocation != GDCM_UNFOUND ) + { + if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1) + { + gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); + return 0.; // bug in the element 0x0020,0x1041 + } + else + { + return zImPos; + } + } + gdcmWarningMacro( "Unfound Slice Location (0020,1041)"); + + std::string strLocation = GetEntryValue(0x0020,0x0050); + if ( strLocation != GDCM_UNFOUND ) + { + if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1) + { + gdcmWarningMacro( "Wrong Location (0020,0050)"); + return 0.; // bug in the element 0x0020,0x0050 + } + else + { + return zImPos; + } + } + gdcmWarningMacro( "Unfound Location (0020,0050)"); + + return 0.; // Hopeless } /** - * \brief Get the image data size from the file. - * If a LUT is found, the datas are expanded to be RGB - */ -size_t File::GetRGBDataSize() + * \brief gets the info from 0020,0037 : Image Orientation Patient + * (needed to organize DICOM files based on their x,y,z position) + * @param iop adress of the (6)float aray to receive values + * @return cosines of image orientation patient + */ +void File::GetImageOrientationPatient( float iop[6] ) { - return PixelReadConverter->GetRGBSize(); + std::string strImOriPat; + //iop is supposed to be float[6] + iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.; + + // 0020 0037 DS REL Image Orientation (Patient) + if ( (strImOriPat = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND ) + { + if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", + &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) + { + gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." ); + } + } + //For ACR-NEMA + // 0020 0035 DS REL Image Orientation (RET) + else if ( (strImOriPat = GetEntryValue(0x0020,0x0035)) != GDCM_UNFOUND ) + { + if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", + &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) + { + gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." ); + } + } } /** - * \brief Get the image datas from the file. - * If a LUT is found, the datas are not expanded ! + * \brief Retrieve the number of Bits Stored (actually used) + * (as opposed to number of Bits Allocated) + * @return The encountered number of Bits Stored, 0 by default. + * 0 means the file is NOT USABLE. The caller has to check it ! */ -uint8_t* File::GetRawData() +int File::GetBitsStored() { - return PixelReadConverter->GetRaw(); + std::string strSize = GetEntryValue( 0x0028, 0x0101 ); + if ( strSize == GDCM_UNFOUND ) + { + gdcmWarningMacro("(0028,0101) is supposed to be mandatory"); + return 0; // It's supposed to be mandatory + // the caller will have to check + } + return atoi( strSize.c_str() ); } /** - * \brief Get the image data size from the file. - * If a LUT is found, the datas are not expanded ! + * \brief Retrieve the number of Bits Allocated + * (8, 12 -compacted ACR-NEMA files, 16, ...) + * @return The encountered number of Bits Allocated, 0 by default. + * 0 means the file is NOT USABLE. The caller has to check it ! */ -size_t File::GetRawDataSize() +int File::GetBitsAllocated() { - return PixelReadConverter->GetRawSize(); + std::string strSize = GetEntryValue(0x0028,0x0100); + if ( strSize == GDCM_UNFOUND ) + { + gdcmWarningMacro( "(0028,0100) is supposed to be mandatory"); + return 0; // It's supposed to be mandatory + // the caller will have to check + } + return atoi( strSize.c_str() ); } /** - * \brief Writes on disk A SINGLE Dicom file - * NO test is performed on processor "Endiannity". - * It's up to the user to call his Reader properly - * @param fileName name of the file to be created - * (any already existing file is over written) - * @return false if write fails + * \brief Retrieve the high bit position. + * \warning The method defaults to 0 when information is Missing. + * The responsability of checking this value is left to the caller. + * @return The high bit positin when present. 0 when Missing. */ - -bool File::WriteRawData(std::string const & fileName) +int File::GetHighBitPosition() { - std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary ); - if (!fp1) + std::string strSize = GetEntryValue( 0x0028, 0x0102 ); + if ( strSize == GDCM_UNFOUND ) { - dbg.Verbose(2, "Fail to open (write) file:", fileName.c_str()); - return false; + gdcmWarningMacro( "(0028,0102) is supposed to be mandatory"); + return 0; } - - if(PixelWriteConverter->GetUserData()) - fp1.write((char*)PixelWriteConverter->GetUserData(), PixelWriteConverter->GetUserDataSize()); - else if(PixelReadConverter->GetRGB()) - fp1.write((char*)PixelReadConverter->GetRGB(), PixelReadConverter->GetRGBSize()); - else if(PixelReadConverter->GetRaw()) - fp1.write((char*)PixelReadConverter->GetRaw(), PixelReadConverter->GetRawSize()); - - fp1.close(); - - return true; + return atoi( strSize.c_str() ); } /** - * \brief Writes on disk A SINGLE Dicom file, - * using the Implicit Value Representation convention - * NO test is performed on processor "Endiannity". - * @param fileName name of the file to be created - * (any already existing file is overwritten) - * @return false if write fails + * \brief Retrieve the number of Samples Per Pixel + * (1 : gray level, 3 : RGB -1 or 3 Planes-) + * @return The encountered number of Samples Per Pixel, 1 by default. + * (Gray level Pixels) */ - -bool File::WriteDcmImplVR (std::string const & fileName) +int File::GetSamplesPerPixel() { - SetWriteTypeToDcmImplVR(); - return Write(fileName); + const std::string &strSize = GetEntryValue(0x0028,0x0002); + if ( strSize == GDCM_UNFOUND ) + { + gdcmWarningMacro( "(0028,0002) is supposed to be mandatory"); + return 1; // Well, it's supposed to be mandatory ... + // but sometimes it's missing : *we* assume Gray pixels + } + return atoi( strSize.c_str() ); } /** -* \brief Writes on disk A SINGLE Dicom file, - * using the Explicit Value Representation convention - * NO test is performed on processor "Endiannity". * @param fileName name of the file to be created - * (any already existing file is overwritten) - * @return false if write fails + * \brief Retrieve the Planar Configuration for RGB images + * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane) + * @return The encountered Planar Configuration, 0 by default. */ - -bool File::WriteDcmExplVR (std::string const & fileName) +int File::GetPlanarConfiguration() { - SetWriteTypeToDcmExplVR(); - return Write(fileName); + std::string strSize = GetEntryValue(0x0028,0x0006); + if ( strSize == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)"); + return 0; + } + return atoi( strSize.c_str() ); } /** - * \brief Writes on disk A SINGLE Dicom file, - * using the ACR-NEMA convention - * NO test is performed on processor "Endiannity". - * (a l'attention des logiciels cliniques - * qui ne prennent en entrée QUE des images ACR ... - * \warning if a DICOM_V3 header is supplied, - * groups < 0x0008 and shadow groups are ignored - * \warning NO TEST is performed on processor "Endiannity". - * @param fileName name of the file to be created - * (any already existing file is overwritten) - * @return false if write fails + * \brief Return the size (in bytes) of a single pixel of data. + * @return The size in bytes of a single pixel of data; 0 by default + * 0 means the file is NOT USABLE; the caller will have to check */ - -bool File::WriteAcr (std::string const & fileName) +int File::GetPixelSize() { - SetWriteTypeToAcr(); - return Write(fileName); + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + // if (File::GetEntryValue(0x0028,0x0100) == "24") + // return 3; + + std::string pixelType = GetPixelType(); + if ( pixelType == "8U" || pixelType == "8S" ) + { + return 1; + } + if ( pixelType == "16U" || pixelType == "16S") + { + return 2; + } + if ( pixelType == "32U" || pixelType == "32S") + { + return 4; + } + if ( pixelType == "FD" ) + { + return 8; + } + gdcmWarningMacro( "Unknown pixel type"); + return 0; } -bool File::Write(std::string const& fileName) +/** + * \brief Build the Pixel Type of the image. + * Possible values are: + * - 8U unsigned 8 bit, + * - 8S signed 8 bit, + * - 16U unsigned 16 bit, + * - 16S signed 16 bit, + * - 32U unsigned 32 bit, + * - 32S signed 32 bit, + * - FD floating double 64 bits (Not kosher DICOM, but so usefull!) + * \warning 12 bit images appear as 16 bit. + * 24 bit images appear as 8 bit + * @return 0S if nothing found. NOT USABLE file. The caller has to check + */ +std::string File::GetPixelType() { - return WriteBase(fileName); -} + std::string bitsAlloc = GetEntryValue(0x0028, 0x0100); // Bits Allocated + if ( bitsAlloc == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Missing Bits Allocated (0028,0100)"); + bitsAlloc = "16"; // default and arbitrary value, not to polute the output + } -bool File::SetEntryByNumber(std::string const& content, - uint16_t group, uint16_t element) -{ - return HeaderInternal->SetEntryByNumber(content,group,element); + if ( bitsAlloc == "64" ) + { + return "FD"; + } + else if ( bitsAlloc == "12" ) + { + // It will be unpacked + bitsAlloc = "16"; + } + else if ( bitsAlloc == "24" ) + { + // (in order no to be messed up + bitsAlloc = "8"; // by old RGB images) + } + + std::string sign = GetEntryValue(0x0028, 0x0103);//"Pixel Representation" + + if (sign == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Missing Pixel Representation (0028,0103)"); + sign = "U"; // default and arbitrary value, not to polute the output + } + else if ( sign == "0" ) + { + sign = "U"; + } + else + { + sign = "S"; + } + return bitsAlloc + sign; } -bool File::SetEntryByNumber(uint8_t* content, int lgth, - uint16_t group, uint16_t element) +/** + * \brief Check whether the pixels are signed or UNsigned data. + * \warning The method defaults to false (UNsigned) when information is Missing. + * The responsability of checking this value is left to the caller. + * @return True when signed, false when UNsigned + */ +bool File::IsSignedPixelData() { - return HeaderInternal->SetEntryByNumber(content,lgth,group,element); + std::string strSize = GetEntryValue( 0x0028, 0x0103 ); + if ( strSize == GDCM_UNFOUND ) + { + gdcmWarningMacro( "(0028,0103) is supposed to be mandatory"); + return false; + } + int sign = atoi( strSize.c_str() ); + if ( sign == 0 ) + { + return false; + } + return true; } -bool File::ReplaceOrCreateByNumber(std::string const& content, - uint16_t group, uint16_t element) +/** + * \brief Check whether this a monochrome picture or not by accessing + * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise. + */ +bool File::IsMonochrome() { - return HeaderInternal->ReplaceOrCreateByNumber(content,group,element) != NULL; + const std::string &PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") + || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)"); + } + return false; } -bool File::ReplaceOrCreateByNumber(uint8_t* binArea, int lgth, - uint16_t group, uint16_t element) +/** + * \brief Check whether this a "PALETTE COLOR" picture or not by accessing + * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * @return true when "PALETTE COLOR". False otherwise. + */ +bool File::IsPaletteColor() { - return HeaderInternal->ReplaceOrCreateByNumber(binArea,lgth,group,element) != NULL; + std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + if ( PhotometricInterp == "PALETTE COLOR " ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Not found : Palette color (0028,0004)"); + } + return false; } /** - * \brief Access to the underlying \ref PixelReadConverter RGBA LUT + * \brief Check whether this a "YBR_FULL" color picture or not by accessing + * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). + * @return true when "YBR_FULL". False otherwise. */ -uint8_t* File::GetLutRGBA() +bool File::IsYBRFull() { - return PixelReadConverter->GetLutRGBA(); + std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 ); + if ( PhotometricInterp == "YBR_FULL" ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Not found : YBR Full (0028,0004)"); + } + return false; } -//----------------------------------------------------------------------------- -// Protected /** - * \brief NOT a end user inteded function - * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc) - * @param fileName name of the file to be created - * (any already existing file is overwritten) - * @param type file type (ExplicitVR, ImplicitVR, ...) - * @return false if write fails - */ -bool File::WriteBase (std::string const & fileName) -{ - switch(WriteType) - { - case ImplicitVR: - SetWriteFileTypeToImplicitVR(); - break; - case ExplicitVR: - SetWriteFileTypeToExplicitVR(); - break; - case ACR: - case ACR_LIBIDO: - SetWriteFileTypeToACR(); - break; - default: - SetWriteFileTypeToExplicitVR(); - } - - // -------------------------------------------------------------- - // Special Patch to allow gdcm to re-write ACR-LibIDO formated images - // - // if recognition code tells us we dealt with a LibIDO image - // we reproduce on disk the switch between lineNumber and columnNumber - // 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 ) - { - SetWriteToLibido(); + * \brief tells us if LUT are used + * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data' + * are NOT considered as LUT, since nobody knows + * how to deal with them + * Please warn me if you know sbdy that *does* know ... jprx + * @return true if LUT Descriptors and LUT Tables were found + */ +bool File::HasLUT() +{ + // Check the presence of the LUT Descriptors, and LUT Tables + // LutDescriptorRed + if ( !GetDocEntry(0x0028,0x1101) ) + { + return false; } - else + // LutDescriptorGreen + if ( !GetDocEntry(0x0028,0x1102) ) { - SetWriteToNoLibido(); + return false; } - // ----------------- End of Special Patch ---------------- - - switch(WriteMode) + // LutDescriptorBlue + if ( !GetDocEntry(0x0028,0x1103) ) { - case WMODE_RAW : - SetWriteToRaw(); - break; - case WMODE_RGB : - SetWriteToRGB(); - break; + return false; } + // Red Palette Color Lookup Table Data + if ( !GetDocEntry(0x0028,0x1201) ) + { + return false; + } + // Green Palette Color Lookup Table Data + if ( !GetDocEntry(0x0028,0x1202) ) + { + return false; + } + // Blue Palette Color Lookup Table Data + if ( !GetDocEntry(0x0028,0x1203) ) + { + return false; + } + + // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent) + // NOT taken into account, but we don't know how to use it ... + return true; +} - bool check = CheckWriteIntegrity(); - if(check) +/** + * \brief gets the info from 0028,1101 : Lookup Table Desc-Red + * else 0 + * @return Lookup Table number of Bits , 0 by default + * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * @ return bit number of each LUT item + */ +int File::GetLUTNbits() +{ + std::vector tokens; + int lutNbits; + + //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red + // = Lookup Table Desc-Blue + // Consistency already checked in GetLUTLength + std::string lutDescription = GetEntryValue(0x0028,0x1101); + if ( lutDescription == GDCM_UNFOUND ) { - check = HeaderInternal->Write(fileName,WriteType); + return 0; } - RestoreWrite(); - RestoreWriteFileType(); + tokens.clear(); // clean any previous value + Util::Tokenize ( lutDescription, tokens, "\\" ); + //LutLength=atoi(tokens[0].c_str()); + //LutDepth=atoi(tokens[1].c_str()); - // -------------------------------------------------------------- - // Special Patch to allow gdcm to re-write ACR-LibIDO formated images - // - // ...and we restore the Header to be Dicom Compliant again - // just after writting - RestoreWriteOfLibido(); - // ----------------- End of Special Patch ---------------- + lutNbits = atoi( tokens[2].c_str() ); + tokens.clear(); - return check; + return lutNbits; } /** - * \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 gets the info from 0028,1052 : Rescale Intercept + * @return Rescale Intercept */ -bool File::CheckWriteIntegrity() +float File::GetRescaleIntercept() { - if(PixelWriteConverter->GetUserData()) + float resInter = 0.; + /// 0028 1052 DS IMG Rescale Intercept + const std::string &strRescInter = GetEntryValue(0x0028,0x1052); + if ( strRescInter != GDCM_UNFOUND ) { - int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); - if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 ) + if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 ) { - numberBitsAllocated = 16; - } - - size_t decSize = HeaderInternal->GetXSize() - * HeaderInternal->GetYSize() - * HeaderInternal->GetZSize() - * ( numberBitsAllocated / 8 ) - * HeaderInternal->GetSamplesPerPixel(); - size_t rgbSize = decSize; - if( HeaderInternal->HasLUT() ) - rgbSize = decSize * 3; - - switch(WriteMode) - { - case WMODE_RAW : - if( decSize!=PixelWriteConverter->GetUserDataSize() ) - { - dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect (Raw)"); - //std::cerr << "File::CheckWriteIntegrity: Data size is incorrect (Raw)\n" - // << decSize << " / " << PixelWriteConverter->GetUserDataSize() << "\n"; - return false; - } - break; - case WMODE_RGB : - if( rgbSize!=PixelWriteConverter->GetUserDataSize() ) - { - dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect (RGB)"); - //std::cerr << "File::CheckWriteIntegrity: Data size is incorrect (RGB)\n" - // << decSize << " / " << PixelWriteConverter->GetUserDataSize() << "\n"; - return false; - } - break; + // bug in the element 0x0028,0x1052 + gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." ); } } - - return true; + + return resInter; } -void File::SetWriteToRaw() +/** + *\brief gets the info from 0028,1053 : Rescale Slope + * @return Rescale Slope + */ +float File::GetRescaleSlope() { - if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT()) + float resSlope = 1.; + //0028 1053 DS IMG Rescale Slope + std::string strRescSlope = GetEntryValue(0x0028,0x1053); + if ( strRescSlope != GDCM_UNFOUND ) { - SetWriteToRGB(); - } - else - { - ValEntry* photInt = CopyValEntry(0x0028,0x0004); - if(HeaderInternal->HasLUT()) + if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1) { - photInt->SetValue("PALETTE COLOR "); + // bug in the element 0x0028,0x1053 + gdcmWarningMacro( "Rescale Slope (0028,1053) is empty."); } - else - { - photInt->SetValue("MONOCHROME1 "); - } - - PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(), - PixelReadConverter->GetRawSize()); - - BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); - pixel->SetValue(GDCM_BINLOADED); - pixel->SetBinArea(PixelWriteConverter->GetData(),false); - pixel->SetLength(PixelWriteConverter->GetDataSize()); - - Archive->Push(photInt); - Archive->Push(pixel); } + + return resSlope; } -void File::SetWriteToRGB() +/** + * \brief This function is intended to user who doesn't want + * to have to manage a LUT and expects to get an RBG Pixel image + * (or a monochrome one ...) + * \warning to be used with GetImagePixels() + * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR) + */ +int File::GetNumberOfScalarComponents() { - if(HeaderInternal->GetNumberOfScalarComponents()==3) + if ( GetSamplesPerPixel() == 3 ) { - PixelReadConverter->BuildRGBImage(); + return 3; + } - ValEntry* spp = CopyValEntry(0x0028,0x0002); - spp->SetValue("3 "); - - ValEntry* planConfig = CopyValEntry(0x0028,0x0006); - planConfig->SetValue("0 "); - - ValEntry* photInt = CopyValEntry(0x0028,0x0004); - photInt->SetValue("RGB "); + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if ( GetEntryValue(0x0028,0x0100) == "24" ) + { + return 3; + } + + std::string strPhotometricInterpretation = GetEntryValue(0x0028,0x0004); - if(PixelReadConverter->GetRGB()) + if ( ( strPhotometricInterpretation == "PALETTE COLOR ") ) + { + if ( HasLUT() )// PALETTE COLOR is NOT enough { - PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(), - PixelReadConverter->GetRGBSize()); + return 3; } - else // Raw data + else { - PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(), - PixelReadConverter->GetRawSize()); + return 1; } + } - BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); - pixel->SetValue(GDCM_BINLOADED); - pixel->SetBinArea(PixelWriteConverter->GetData(),false); - pixel->SetLength(PixelWriteConverter->GetDataSize()); - - Archive->Push(spp); - Archive->Push(planConfig); - Archive->Push(photInt); - Archive->Push(pixel); - - // Remove any LUT - Archive->Push(0x0028,0x1101); - Archive->Push(0x0028,0x1102); - Archive->Push(0x0028,0x1103); - Archive->Push(0x0028,0x1201); - Archive->Push(0x0028,0x1202); - Archive->Push(0x0028,0x1203); - - // For old ACR-NEMA - // Thus, we have a RGB image and the bits allocated = 24 and - // samples per pixels = 1 (in the read file) - if(HeaderInternal->GetBitsAllocated()==24) - { - ValEntry* bitsAlloc = CopyValEntry(0x0028,0x0100); - bitsAlloc->SetValue("8 "); - - ValEntry* bitsStored = CopyValEntry(0x0028,0x0101); - bitsStored->SetValue("8 "); - - ValEntry* highBit = CopyValEntry(0x0028,0x0102); - highBit->SetValue("7 "); - - Archive->Push(bitsAlloc); - Archive->Push(bitsStored); - Archive->Push(highBit); - } + // beware of trailing space at end of string + // DICOM tags are never of odd length + if ( strPhotometricInterpretation == GDCM_UNFOUND || + Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") || + Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") ) + { + return 1; } else { - SetWriteToRaw(); + // we assume that *all* kinds of YBR are dealt with + return 3; } } -void File::RestoreWrite() +/** + * \brief This function is intended to user that DOESN'T want + * to get RGB pixels image when it's stored as a PALETTE COLOR image + * - the (vtk) user is supposed to know how deal with LUTs - + * \warning to be used with GetImagePixelsRaw() + * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -) + */ +int File::GetNumberOfScalarComponentsRaw() { - Archive->Restore(0x0028,0x0002); - Archive->Restore(0x0028,0x0004); - Archive->Restore(0x0028,0x0006); - Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); - - // For old ACR-NEMA (24 bits problem) - Archive->Restore(0x0028,0x0100); - Archive->Restore(0x0028,0x0101); - Archive->Restore(0x0028,0x0102); + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if ( File::GetEntryValue(0x0028,0x0100) == "24" ) + { + return 3; + } - // For the LUT - Archive->Restore(0x0028,0x1101); - Archive->Restore(0x0028,0x1102); - Archive->Restore(0x0028,0x1103); - Archive->Restore(0x0028,0x1201); - Archive->Restore(0x0028,0x1202); - Archive->Restore(0x0028,0x1203); + // we assume that *all* kinds of YBR are dealt with + return GetSamplesPerPixel(); } -void File::SetWriteFileTypeToACR() +/** + * \brief Recover the offset (from the beginning of the file) + * of *image* pixels (not *icone image* pixels, if any !) + * @return Pixel Offset + */ +size_t File::GetPixelOffset() { - Archive->Push(0x0002,0x0010); + DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel); + if ( pxlElement ) + { + return pxlElement->GetOffset(); + } + else + { + gdcmDebugMacro( "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); + return 0; + } } -void File::SetWriteFileTypeToExplicitVR() +/** + * \brief Recover the pixel area length (in Bytes) + * @return Pixel Element Length, as stored in the header + * (NOT the memory space necessary to hold the Pixels + * -in case of embeded compressed image-) + * 0 : NOT USABLE file. The caller has to check. + */ +size_t File::GetPixelAreaLength() { - std::string ts = Util::DicomString( - Document::GetTransferSyntaxValue(ExplicitVRLittleEndian).c_str() ); + DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel); + if ( pxlElement ) + { + return pxlElement->GetLength(); + } + else + { + gdcmDebugMacro( "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); + return 0; + } +} + +/** + * \brief Adds the characteristics of a new element we want to anonymize + * + */ +void File::AddAnonymizeElement (uint16_t group, uint16_t elem, + std::string const &value) - ValEntry* tss = CopyValEntry(0x0002,0x0010); - tss->SetValue(ts); +{ + Element el; + el.Group = group; + el.Elem = elem; + el.Value = value; + AnonymizeList.push_back(el); +} - Archive->Push(tss); +/** + * \brief Overwrites in the file the values of the DicomElements + * held in the list + */ +void File::AnonymizeNoLoad() +{ + std::fstream *fp = new std::fstream(Filename.c_str(), + std::ios::in | std::ios::out | std::ios::binary); + + // TODO : FIXME + // how to white out disk space if longer than 50 ? + + + gdcm::DocEntry *d; + uint32_t offset; + uint32_t lgth; + uint32_t valLgth = 0; + std::string *spaces; + for (ListElements::iterator it = AnonymizeList.begin(); + it != AnonymizeList.end(); + ++it) + { + d = GetDocEntry( (*it).Group, (*it).Elem); + + if ( d == NULL) + continue; + + if ( dynamic_cast(d) + || dynamic_cast(d) ) + continue; + + offset = d->GetOffset(); + lgth = d->GetLength(); + if (valLgth < lgth) + { + spaces = new std::string( lgth-valLgth, ' '); + (*it).Value = (*it).Value + *spaces; + delete spaces; + } + fp->seekp( offset, std::ios::beg ); + fp->write( (*it).Value.c_str(), lgth ); + + } + fp->close(); + delete fp; } -void File::SetWriteFileTypeToImplicitVR() +/** + * \brief anonymize a File (removes Patient's personal info passed with + * AddAnonymizeElement() + */ +bool File::AnonymizeFile() { - std::string ts = Util::DicomString( - Document::GetTransferSyntaxValue(ImplicitVRLittleEndian).c_str() ); + // If Anonymisation list is empty, let's perform some basic anonymization + if ( AnonymizeList.begin() == AnonymizeList.end() ) + { + // If exist, replace by spaces + SetValEntry (" ",0x0010, 0x2154); // Telephone + SetValEntry (" ",0x0010, 0x1040); // Adress + SetValEntry (" ",0x0010, 0x0020); // Patient ID + + DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010); + + if ( patientNameHE ) // we replace it by Study Instance UID (why not ?) + { + std::string studyInstanceUID = GetEntryValue (0x0020, 0x000d); + if ( studyInstanceUID != GDCM_UNFOUND ) + { + SetValEntry(studyInstanceUID, 0x0010, 0x0010); + } + else + { + SetValEntry("anonymised", 0x0010, 0x0010); + } + } + } + else + { + gdcm::DocEntry *d; + for (ListElements::iterator it = AnonymizeList.begin(); + it != AnonymizeList.end(); + ++it) + { + d = GetDocEntry( (*it).Group, (*it).Elem); + + if ( d == NULL) + continue; - ValEntry* tss = CopyValEntry(0x0002,0x0010); - tss->SetValue(ts); + if ( dynamic_cast(d) + || dynamic_cast(d) ) + continue; - Archive->Push(tss); + SetValEntry ((*it).Value, (*it).Group, (*it).Elem); + } } -void File::RestoreWriteFileType() -{ - Archive->Restore(0x0002,0x0010); + // In order to make definitively impossible any further identification + // remove or replace all the stuff that contains a Date + +//0008 0012 DA ID Instance Creation Date +//0008 0020 DA ID Study Date +//0008 0021 DA ID Series Date +//0008 0022 DA ID Acquisition Date +//0008 0023 DA ID Content Date +//0008 0024 DA ID Overlay Date +//0008 0025 DA ID Curve Date +//0008 002a DT ID Acquisition Datetime +//0018 9074 DT ACQ Frame Acquisition Datetime +//0018 9151 DT ACQ Frame Reference Datetime +//0018 a002 DT ACQ Contribution Date Time +//0020 3403 SH REL Modified Image Date (RET) +//0032 0032 DA SDY Study Verified Date +//0032 0034 DA SDY Study Read Date +//0032 1000 DA SDY Scheduled Study Start Date +//0032 1010 DA SDY Scheduled Study Stop Date +//0032 1040 DA SDY Study Arrival Date +//0032 1050 DA SDY Study Completion Date +//0038 001a DA VIS Scheduled Admission Date +//0038 001c DA VIS Scheduled Discharge Date +//0038 0020 DA VIS Admitting Date +//0038 0030 DA VIS Discharge Date +//0040 0002 DA PRC Scheduled Procedure Step Start Date +//0040 0004 DA PRC Scheduled Procedure Step End Date +//0040 0244 DA PRC Performed Procedure Step Start Date +//0040 0250 DA PRC Performed Procedure Step End Date +//0040 2004 DA PRC Issue Date of Imaging Service Request +//0040 4005 DT PRC Scheduled Procedure Step Start Date and Time +//0040 4011 DT PRC Expected Completion Date and Time +//0040 a030 DT PRC Verification Date Time +//0040 a032 DT PRC Observation Date Time +//0040 a120 DT PRC DateTime +//0040 a121 DA PRC Date +//0040 a13a DT PRC Referenced Datetime +//0070 0082 DA ??? Presentation Creation Date +//0100 0420 DT ??? SOP Autorization Date and Time +//0400 0105 DT ??? Digital Signature DateTime +//2100 0040 DA PJ Creation Date +//3006 0008 DA SSET Structure Set Date +//3008 0024 DA ??? Treatment Control Point Date +//3008 0054 DA ??? First Treatment Date +//3008 0056 DA ??? Most Recent Treatment Date +//3008 0162 DA ??? Safe Position Exit Date +//3008 0166 DA ??? Safe Position Return Date +//3008 0250 DA ??? Treatment Date +//300a 0006 DA RT RT Plan Date +//300a 022c DA RT Air Kerma Rate Reference Date +//300e 0004 DA RT Review Date + + return true; } -void File::SetWriteToLibido() +/** + * \brief Performs some consistency checking on various 'File related' + * (as opposed to 'DicomDir related') entries + * then writes in a file all the (Dicom Elements) included the Pixels + * @param fileName file name to write to + * @param filetype Type of the File to be written + * (ACR, ExplicitVR, ImplicitVR) + */ +bool File::Write(std::string fileName, FileType filetype) { - ValEntry *oldRow = dynamic_cast - (HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010)); - ValEntry *oldCol = dynamic_cast - (HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011)); - - if( oldRow && oldCol ) + std::ofstream *fp = new std::ofstream(fileName.c_str(), + std::ios::out | std::ios::binary); + if (*fp == NULL) { - std::string rows, columns; - - ValEntry *newRow=new ValEntry(oldRow->GetDictEntry()); - ValEntry *newCol=new ValEntry(oldCol->GetDictEntry()); + gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str()); + return false; + } - newRow->Copy(oldCol); - newCol->Copy(oldRow); + // Entry : 0002|0000 = group length -> recalculated + ValEntry *e0002 = GetValEntry(0x0002,0x0000); + if( e0002 ) + { + std::ostringstream sLen; + sLen << ComputeGroup0002Length(filetype); + e0002->SetValue(sLen.str()); + } - newRow->SetValue(oldCol->GetValue()); - newCol->SetValue(oldRow->GetValue()); + // Bits Allocated + if ( GetEntryValue(0x0028,0x0100) == "12") + { + SetValEntry("16", 0x0028,0x0100); + } - Archive->Push(newRow); - Archive->Push(newCol); + int i_lgPix = GetEntryLength(GrPixel, NumPixel); + if (i_lgPix != -2) + { + // no (GrPixel, NumPixel) element + std::string s_lgPix = Util::Format("%d", i_lgPix+12); + s_lgPix = Util::DicomString( s_lgPix.c_str() ); + InsertValEntry(s_lgPix,GrPixel, 0x0000); } - ValEntry *libidoCode = CopyValEntry(0x0008,0x0010); - libidoCode->SetValue("ACRNEMA_LIBIDO_1.1"); - Archive->Push(libidoCode); -} + // FIXME : should be nice if we could move it to File + // (or in future gdcmPixelData class) -void File::SetWriteToNoLibido() -{ - ValEntry *recCode = dynamic_cast - (HeaderInternal->GetDocEntryByNumber(0x0008,0x0010)); - if( recCode ) + // Drop Palette Color, if necessary + if ( GetEntryValue(0x0028,0x0002).c_str()[0] == '3' ) { - if( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" ) + // if SamplesPerPixel = 3, sure we don't need any LUT ! + // Drop 0028|1101, 0028|1102, 0028|1103 + // Drop 0028|1201, 0028|1202, 0028|1203 + + DocEntry *e = GetDocEntry(0x0028,0x01101); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntry(0x0028,0x1102); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntry(0x0028,0x1103); + if (e) { - ValEntry *libidoCode = CopyValEntry(0x0008,0x0010); - libidoCode->SetValue(""); - Archive->Push(libidoCode); + RemoveEntryNoDestroy(e); + } + e = GetDocEntry(0x0028,0x01201); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntry(0x0028,0x1202); + if (e) + { + RemoveEntryNoDestroy(e); + } + e = GetDocEntry(0x0028,0x1203); + if (e) + { + RemoveEntryNoDestroy(e); } } + + Document::WriteContent(fp, filetype); + + fp->close(); + delete fp; + + return true; } -void File::RestoreWriteOfLibido() +//----------------------------------------------------------------------------- +// Protected +/** + * \brief Initialize a default DICOM File that should contain all the + * field require by other reader. DICOM standard does not + * explicitely defines those fields, heuristic has been choosen. + * This is not perfect as we are writting a CT image... + */ +void File::InitializeDefaultFile() { - Archive->Restore(0x0028,0x0010); - Archive->Restore(0x0028,0x0011); - Archive->Restore(0x0008,0x0010); + std::string date = Util::GetCurrentDate(); + std::string time = Util::GetCurrentTime(); + std::string uid = Util::CreateUniqueUID(); + std::string uidMedia = uid; + std::string uidInst = uid; + std::string uidClass = Util::CreateUniqueUID(); + std::string uidStudy = Util::CreateUniqueUID(); + std::string uidSerie = Util::CreateUniqueUID(); + + // Meta Element Group Length + InsertValEntry("146 ", 0x0002, 0x0000); + // Media Storage SOP Class UID (CT Image Storage) + InsertValEntry("1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002); + // Media Storage SOP Instance UID + InsertValEntry(uidMedia.c_str(), 0x0002, 0x0003); + // Transfer Syntax UID (Explicit VR Little Endian) + InsertValEntry("1.2.840.10008.1.2.1 ", 0x0002, 0x0010); + // META Implementation Class UID + InsertValEntry(uidClass.c_str(), 0x0002, 0x0012); + // Source Application Entity Title + InsertValEntry("GDCM", 0x0002, 0x0016); + + // Instance Creation Date + InsertValEntry(date.c_str(), 0x0008, 0x0012); + // Instance Creation Time + InsertValEntry(time.c_str(), 0x0008, 0x0013); + // SOP Class UID + InsertValEntry("1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016); + // SOP Instance UID + InsertValEntry(uidInst.c_str(), 0x0008, 0x0018); + // Modality + InsertValEntry("CT", 0x0008, 0x0060); + // Manufacturer + InsertValEntry("GDCM", 0x0008, 0x0070); + // Institution Name + InsertValEntry("GDCM", 0x0008, 0x0080); + // Institution Address + InsertValEntry("http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081); + + // Patient's Name + InsertValEntry("GDCM", 0x0010, 0x0010); + // Patient ID + InsertValEntry("GDCMID", 0x0010, 0x0020); + + // Study Instance UID + InsertValEntry(uidStudy.c_str(), 0x0020, 0x000d); + // Series Instance UID + InsertValEntry(uidSerie.c_str(), 0x0020, 0x000e); + // StudyID + InsertValEntry("1", 0x0020, 0x0010); + // SeriesNumber + InsertValEntry("1", 0x0020, 0x0011); + + // Samples per pixel 1 or 3 + InsertValEntry("1", 0x0028, 0x0002); + // photochromatic interpretation + InsertValEntry("MONOCHROME1", 0x0028, 0x0004); + // nbRows + InsertValEntry("0", 0x0028, 0x0010); + // nbCols + InsertValEntry("0", 0x0028, 0x0011); + // BitsAllocated 8 or 12 or 16 + InsertValEntry("8", 0x0028, 0x0100); + // BitsStored <= BitsAllocated + InsertValEntry("8", 0x0028, 0x0101); + // HighBit <= BitsAllocated - 1 + InsertValEntry("7", 0x0028, 0x0102); + // Pixel Representation 0(unsigned) or 1(signed) + InsertValEntry("0", 0x0028, 0x0103); + + // default value + // Special case this is the image (not a string) + GrPixel = 0x7fe0; + NumPixel = 0x0010; + InsertBinEntry(0, 0, GrPixel, NumPixel); } -ValEntry* File::CopyValEntry(uint16_t group,uint16_t element) +//----------------------------------------------------------------------------- +// Private +/** + * \brief Parse pixel data from disk of [multi-]fragment RLE encoding. + * Compute the RLE extra information and store it in \ref RLEInfo + * for later pixel retrieval usage. + */ +void File::ComputeRLEInfo() { - DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element); - ValEntry* newE; + std::string ts = GetTransferSyntax(); + if ( !Global::GetTS()->IsRLELossless(ts) ) + { + return; + } + + // Encoded pixel data: for the time being we are only concerned with + // Jpeg or RLE Pixel data encodings. + // As stated in PS 3.5-2003, section 8.2 p44: + // "If sent in Encapsulated Format (i.e. other than the Native Format) the + // value representation OB is used". + // Hence we expect an OB value representation. Concerning OB VR, + // the section PS 3.5-2003, section A.4.c p 58-59, states: + // "For the Value Representations OB and OW, the encoding shall meet the + // following specifications depending on the Data element tag:" + // [...snip...] + // - the first item in the sequence of items before the encoded pixel + // data stream shall be basic offset table item. The basic offset table + // item value, however, is not required to be present" + ReadAndSkipEncapsulatedBasicOffsetTable(); + + // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G) + // Loop on the individual frame[s] and store the information + // on the RLE fragments in a RLEFramesInfo. + // Note: - when only a single frame is present, this is a + // classical image. + // - when more than one frame are present, then we are in + // the case of a multi-frame image. + long frameLength; + while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) ) + { + // Parse the RLE Header and store the corresponding RLE Segment + // Offset Table information on fragments of this current Frame. + // Note that the fragment pixels themselves are not loaded + // (but just skipped). + long frameOffset = Fp->tellg(); + + uint32_t nbRleSegments = ReadInt32(); + if ( nbRleSegments > 16 ) + { + // There should be at most 15 segments (refer to RLEFrame class) + gdcmWarningMacro( "Too many segments."); + } + + uint32_t rleSegmentOffsetTable[16]; + for( int k = 1; k <= 15; k++ ) + { + rleSegmentOffsetTable[k] = ReadInt32(); + } + + // Deduce from both the RLE Header and the frameLength the + // fragment length, and again store this info in a + // RLEFramesInfo. + long rleSegmentLength[15]; + // skipping (not reading) RLE Segments + if ( nbRleSegments > 1) + { + for(unsigned int k = 1; k <= nbRleSegments-1; k++) + { + rleSegmentLength[k] = rleSegmentOffsetTable[k+1] + - rleSegmentOffsetTable[k]; + SkipBytes(rleSegmentLength[k]); + } + } + + rleSegmentLength[nbRleSegments] = frameLength + - rleSegmentOffsetTable[nbRleSegments]; + SkipBytes(rleSegmentLength[nbRleSegments]); + + // Store the collected info + RLEFrame *newFrame = new RLEFrame; + newFrame->SetNumberOfFragments(nbRleSegments); + for( unsigned int uk = 1; uk <= nbRleSegments; uk++ ) + { + newFrame->SetOffset(uk,frameOffset + rleSegmentOffsetTable[uk]); + newFrame->SetLength(uk,rleSegmentLength[uk]); + } + RLEInfo->AddFrame(newFrame); + } - if(oldE) + // Make sure that at the end of the item we encounter a 'Sequence + // Delimiter Item': + if ( !ReadTag(0xfffe, 0xe0dd) ) { - newE = new ValEntry(oldE->GetDictEntry()); - newE->Copy(oldE); + gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence"); } - else +} + +/** + * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding. + * Compute the jpeg extra information (fragment[s] offset[s] and + * length) and store it[them] in \ref JPEGInfo for later pixel + * retrieval usage. + */ +void File::ComputeJPEGFragmentInfo() +{ + // If you need to, look for comments of ComputeRLEInfo(). + std::string ts = GetTransferSyntax(); + if ( ! Global::GetTS()->IsJPEG(ts) ) { - newE = GetHeader()->NewValEntryByNumber(group,element); + return; + } + + ReadAndSkipEncapsulatedBasicOffsetTable(); + + // Loop on the fragments[s] and store the parsed information in a + // JPEGInfo. + long fragmentLength; + while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) ) + { + long fragmentOffset = Fp->tellg(); + + // Store the collected info + JPEGFragment *newFragment = new JPEGFragment; + newFragment->SetOffset(fragmentOffset); + newFragment->SetLength(fragmentLength); + JPEGInfo->AddFragment(newFragment); + + SkipBytes(fragmentLength); } - return(newE); + // Make sure that at the end of the item we encounter a 'Sequence + // Delimiter Item': + if ( !ReadTag(0xfffe, 0xe0dd) ) + { + gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence"); + } } -BinEntry* File::CopyBinEntry(uint16_t group,uint16_t element) +/** + * \brief Assuming the internal file pointer \ref Document::Fp + * is placed at the beginning of a tag check whether this + * tag is (TestGroup, TestElement). + * \warning On success the internal file pointer \ref Document::Fp + * is modified to point after the tag. + * On failure (i.e. when the tag wasn't the expected tag + * (TestGroup, TestElement) the internal file pointer + * \ref Document::Fp is restored to it's original position. + * @param testGroup The expected group of the tag. + * @param testElement The expected Element of the tag. + * @return True on success, false otherwise. + */ +bool File::ReadTag(uint16_t testGroup, uint16_t testElement) { - DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element); - BinEntry* newE; - - if(oldE) + long positionOnEntry = Fp->tellg(); + long currentPosition = Fp->tellg(); // On debugging purposes + + // Read the Item Tag group and element, and make + // sure they are what we expected: + uint16_t itemTagGroup; + uint16_t itemTagElement; + try { - newE = new BinEntry(oldE->GetDictEntry()); - newE->Copy(oldE); + itemTagGroup = ReadInt16(); + itemTagElement = ReadInt16(); } - else + catch ( FormatError e ) { - newE = GetHeader()->NewBinEntryByNumber(group,element); + //std::cerr << e << std::endl; + return false; } + if ( itemTagGroup != testGroup || itemTagElement != testElement ) + { + gdcmWarningMacro( "Wrong Item Tag found:" + << " We should have found tag (" + << std::hex << testGroup << "," << testElement << ")" << std::endl + << " but instead we encountered tag (" + << std::hex << itemTagGroup << "," << itemTagElement << ")" + << " at address: " << " 0x(" << (unsigned int)currentPosition << ")" + ) ; + Fp->seekg(positionOnEntry, std::ios::beg); - return(newE); + return false; + } + return true; } -//----------------------------------------------------------------------------- -// Protected /** - * \brief Factorization for various forms of constructors. + * \brief Assuming the internal file pointer \ref Document::Fp + * is placed at the beginning of a tag (TestGroup, TestElement), + * read the length associated to the Tag. + * \warning On success the internal file pointer \ref Document::Fp + * is modified to point after the tag and it's length. + * On failure (i.e. when the tag wasn't the expected tag + * (TestGroup, TestElement) the internal file pointer + * \ref Document::Fp is restored to it's original position. + * @param testGroup The expected group of the tag. + * @param testElement The expected Element of the tag. + * @return On success returns the length associated to the tag. On failure + * returns 0. */ -void File::Initialise() +uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElement) { - WriteMode = WMODE_RAW; - WriteType = ExplicitVR; - PixelReadConverter = new PixelReadConvert; - PixelWriteConverter = new PixelWriteConvert; - Archive = new DocEntryArchive( HeaderInternal ); - - if ( HeaderInternal->IsReadable() ) + if ( !ReadTag(testGroup, testElement) ) + { + return 0; + } + + //// Then read the associated Item Length + long currentPosition = Fp->tellg(); + uint32_t itemLength = ReadInt32(); { - PixelReadConverter->GrabInformationsFromHeader( HeaderInternal ); + gdcmWarningMacro( "Basic Item Length is: " + << itemLength << std::endl + << " at address: " << std::hex << (unsigned int)currentPosition); } + return itemLength; } -uint8_t* File::GetRaw() +/** + * \brief When parsing the Pixel Data of an encapsulated file, read + * the basic offset table (when present, and BTW dump it). + */ +void File::ReadAndSkipEncapsulatedBasicOffsetTable() { - uint8_t* raw = PixelReadConverter->GetRaw(); - if ( ! raw ) + //// Read the Basic Offset Table Item Tag length... + uint32_t itemLength = ReadTagLength(0xfffe, 0xe000); + + // When present, read the basic offset table itself. + // Notes: - since the presence of this basic offset table is optional + // we can't rely on it for the implementation, and we will simply + // trash it's content (when present). + // - still, when present, we could add some further checks on the + // lengths, but we won't bother with such fuses for the time being. + if ( itemLength != 0 ) { - // The Raw image migth not be loaded yet: - std::ifstream* fp = HeaderInternal->OpenFile(); - PixelReadConverter->ReadAndDecompressPixelData( fp ); - if(fp) - HeaderInternal->CloseFile(); + char *basicOffsetTableItemValue = new char[itemLength + 1]; + Fp->read(basicOffsetTableItemValue, itemLength); - raw = PixelReadConverter->GetRaw(); - if ( ! raw ) +#ifdef GDCM_DEBUG + for (unsigned int i=0; i < itemLength; i += 4 ) { - dbg.Verbose(0, "File::GetRaw: read/decompress of " - "pixel data apparently went wrong."); - return 0; + uint32_t individualLength = str2num( &basicOffsetTableItemValue[i], + uint32_t); + gdcmWarningMacro( "Read one length: " << + std::hex << individualLength ); } - } +#endif //GDCM_DEBUG - return raw; + delete[] basicOffsetTableItemValue; + } } //----------------------------------------------------------------------------- -// Private +// Print //----------------------------------------------------------------------------- } // end namespace gdcm -