X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=0644f92018c46f739ecf18e11103476ced81a41f;hb=f5c24f2018ff4775ff6ae006de753a394d8cae0f;hp=e94cb485419c56c470a8b5e397dbba115783d86a;hpb=020d769ac045f06318b7061bfdfa0e1adfd9edd5;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index e94cb485..0644f920 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -3,12 +3,12 @@ Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/09/13 07:49:36 $ - Version: $Revision: 1.125 $ + Date: $Date: 2005/02/06 14:39:35 $ + Version: $Revision: 1.213 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or - http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details. + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR @@ -16,1155 +16,1753 @@ =========================================================================*/ +// +// -------------- 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 "gdcmGlobal.h" +#include "gdcmUtil.h" #include "gdcmDebug.h" -#include "jpeg/ljpg/jpegless.h" +#include "gdcmTS.h" +#include "gdcmValEntry.h" +#include "gdcmBinEntry.h" +#include "gdcmSeqEntry.h" +#include "gdcmRLEFramesInfo.h" +#include "gdcmJPEGFragmentsInfo.h" -typedef std::pair IterHT; +#include //sscanf +#include -//------------------------------------------------------------------------- +namespace gdcm +{ +//----------------------------------------------------------------------------- // Constructor / Destructor /** - * \ingroup gdcmFile - * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 - * file (gdcmHeader 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 gdcmHeader + * \brief Constructor + * @param filename name of the file whose header we want to analyze */ -gdcmFile::gdcmFile(gdcmHeader *header) -{ - Header = header; - SelfHeader = false; - SetInitialValues(); +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); + } + } + } } /** - * \ingroup gdcmFile - * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 - * file (gdcmHeader 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 Constructor used when we want to generate dicom files from scratch */ -gdcmFile::gdcmFile(std::string const & filename ) +File::File(): + Document() { - Header = new gdcmHeader( filename ); - SelfHeader = true; - SetInitialValues(); + RLEInfo = new RLEFramesInfo; + JPEGInfo = new JPEGFragmentsInfo; + InitializeDefaultFile(); } /** - * \ingroup gdcmFile - * \brief Sets some initial for the Constructor + * \brief Canonical destructor. */ -void gdcmFile::SetInitialValues() -{ - PixelRead = -1; // no ImageData read yet. - LastAllocatedPixelDataLength = 0; - Pixel_Data = 0; - - InitialSpp = ""; - InitialPhotInt = ""; - InitialPlanConfig = ""; - InitialBitsAllocated = ""; - - InitialRedLUTDescr = 0; - InitialGreenLUTDescr = 0; - InitialBlueLUTDescr = 0; - InitialRedLUTData = 0; - InitialGreenLUTData = 0; - InitialBlueLUTData = 0; - - if ( Header->IsReadable() ) - { - SetPixelDataSizeFromHeader(); - - // the following values *may* be modified - // by gdcmFile::GetImageDataIntoVectorRaw - // we save their initial value. - InitialSpp = Header->GetEntryByNumber(0x0028,0x0002); - InitialPhotInt = Header->GetEntryByNumber(0x0028,0x0004); - InitialPlanConfig = Header->GetEntryByNumber(0x0028,0x0006); - InitialBitsAllocated = Header->GetEntryByNumber(0x0028,0x0100); - - // the following entries *may* be removed from the H table - // (NOT deleted ...) by gdcmFile::GetImageDataIntoVectorRaw - // we keep a pointer on them. - InitialRedLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1101); - InitialGreenLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1102); - InitialBlueLUTDescr = Header->GetDocEntryByNumber(0x0028,0x1103); - InitialRedLUTData = Header->GetDocEntryByNumber(0x0028,0x1201); - InitialGreenLUTData = Header->GetDocEntryByNumber(0x0028,0x1202); - InitialBlueLUTData = Header->GetDocEntryByNumber(0x0028,0x1203); - } +File::~File () +{ + if( RLEInfo ) + delete RLEInfo; + if( JPEGInfo ) + delete JPEGInfo; } +//----------------------------------------------------------------------------- +// Public /** - * \ingroup gdcmFile - * \brief canonical destructor - * \note If the gdcmHeader was created by the gdcmFile constructor, - * it is destroyed by the gdcmFile + * \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. */ -gdcmFile::~gdcmFile() -{ - if( SelfHeader ) +bool File::IsReadable() +{ + if( !Document::IsReadable() ) { - delete Header; + return false; } - Header = 0; -// InitialLutDescriptors and InitialLutData -// will have to be deleted if the don't belong any longer -// to the Header H table ... -} + const std::string &res = GetEntryValue(0x0028, 0x0005); + if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) + { + return false; // Image Dimensions + } + if ( !GetDocEntry(0x0028, 0x0100) ) + { + return false; // "Bits Allocated" + } + if ( !GetDocEntry(0x0028, 0x0101) ) + { + return false; // "Bits Stored" + } + if ( !GetDocEntry(0x0028, 0x0102) ) + { + return false; // "High Bit" + } + if ( !GetDocEntry(0x0028, 0x0103) ) + { + return false; // "Pixel Representation" i.e. 'Sign' + } -//----------------------------------------------------------------------------- -// Print + return true; +} -//----------------------------------------------------------------------------- -// Public +/** + * \brief gets the info from 0020,0013 : Image Number else 0. + * @return image number + */ +int File::GetImageNumber() +{ + // 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 atoi( strImNumber.c_str() ); + } + return 0; //Hopeless +} /** - * \ingroup gdcmFile - * \brief computes the length (in bytes) we must ALLOCATE to receive the - * image(s) pixels (multiframes taken into account) - * \warning : it is NOT the group 7FE0 length - * (no interest for compressed images). - * \warning : not end user intended ? + * \brief gets the info from 0008,0060 : Modality + * @return Modality Type */ -void gdcmFile::SetPixelDataSizeFromHeader() +ModalityType File::GetModality() { - // see PS 3.3-2003 : C.7.6.3.2.1 - // - // MONOCHROME1 - // MONOCHROME2 - // PALETTE COLOR - // RGB - // HSV (Retired) - // ARGB (Retired) - // CMYK (Retired) - // YBR_FULL - // YBR_FULL_422 (no LUT, no Palette) - // YBR_PARTIAL_422 - // YBR_ICT - // YBR_RCT - - // LUT's - // ex : gdcm-US-ALOKA-16.dcm - // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data] - // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data] - // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data] - - // ex : OT-PAL-8-face.dcm - // 0028|1201 [US] [Red Palette Color Lookup Table Data] - // 0028|1202 [US] [Green Palette Color Lookup Table Data] - // 0028|1203 [US] [Blue Palette Color Lookup Table Data] - - // Number of "Bits Allocated" - int nb; - std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); - - if ( str_nb == GDCM_UNFOUND ) - { - nb = 16; - } - else + // 0008 0060 CS ID Modality + std::string strModality = GetEntryValue(0x0008,0x0060); + if ( strModality != GDCM_UNFOUND ) { - nb = atoi( str_nb.c_str() ); - if (nb == 12) + 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 { - nb =16; + /// \todo throw error return value ??? + /// specified <> unknown in our database + return Unknow; } } - ImageDataSize = - ImageDataSizeRaw = Header->GetXSize() * Header->GetYSize() - * Header->GetZSize() * (nb/8) * Header->GetSamplesPerPixel(); - std::string str_PhotometricInterpretation = - Header->GetEntryByNumber(0x0028,0x0004); - - // if ( str_PhotometricInterpretation == "PALETTE COLOR " ), - // pb when undealt Segmented Palette Color - - if ( Header->HasLUT() ) + + return Unknow; +} + +/** + * \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 + */ +int File::GetXSize() +{ + const std::string &strSize = GetEntryValue(0x0028,0x0011); + if ( strSize == GDCM_UNFOUND ) { - ImageDataSize *= 3; + return 0; } + + return atoi( strSize.c_str() ); } /** - * \ingroup gdcmFile - * \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 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). */ -void *gdcmFile::GetImageData() +int File::GetYSize() { - // FIXME (Mathieu) - // I need to deallocate Pixel_Data before doing any allocation: - - if ( Pixel_Data ) - if ( LastAllocatedPixelDataLength != ImageDataSize ) - free(Pixel_Data); - if ( !Pixel_Data ) - Pixel_Data = new uint8_t[ImageDataSize]; - - if ( Pixel_Data ) - { - LastAllocatedPixelDataLength = ImageDataSize; - - // we load the pixels (and transform grey level + LUT into RGB) - GetImageDataIntoVector(Pixel_Data, ImageDataSize); - - // We say the value *is* loaded. - GetHeader()->SetEntryByNumber( GDCM_BINLOADED, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - - // Will be 7fe0, 0010 in standard case - GetHeader()->SetEntryVoidAreaByNumber( Pixel_Data, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - } - PixelRead = 0; // no PixelRaw - - return Pixel_Data; + const std::string &strSize = GetEntryValue(0x0028,0x0010); + if ( strSize != GDCM_UNFOUND ) + { + return atoi( strSize.c_str() ); + } + if ( IsDicomV3() ) + { + 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; } /** - * \ingroup gdcmFile - * \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. + * \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). */ -size_t gdcmFile::GetImageDataIntoVector (void* destination, size_t maxSize) +int File::GetZSize() { - GetImageDataIntoVectorRaw (destination, maxSize); - PixelRead = 0 ; // =0 : no ImageDataRaw - if ( !Header->HasLUT() ) + // 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 ImageDataSize; + return atoi( strSize.c_str() ); } - - // from Lut R + Lut G + Lut B - uint8_t *newDest = new uint8_t[ImageDataSize]; - uint8_t *a = (uint8_t *)destination; - uint8_t *lutRGBA = Header->GetLUTRGBA(); - if ( lutRGBA ) + // We then consider the "Planes" entry as the third dimension + const std::string &strSize2 = GetEntryValue(0x0028,0x0012); + if ( strSize2 != GDCM_UNFOUND ) { - int j; - // move Gray pixels to temp area - memmove(newDest, destination, ImageDataSizeRaw); - for (size_t i=0; iSetEntryByNumber(spp,0x0028,0x0002); - std::string rgb = "RGB "; // Photometric Interpretation - Header->SetEntryByNumber(rgb,0x0028,0x0004); - std::string planConfig = "0"; // Planar Configuration - Header->SetEntryByNumber(planConfig,0x0028,0x0006); + return xspacing; } - else // GetLUTRGBA() failed - { - // (gdcm-US-ALOKA-16.dcm), contains Segmented xxx Palette Color - // that are *more* than 65535 long ?!? - // No idea how to manage such an image ! - // Need to make RGB Pixels (?) from grey Pixels (?!) and Gray Lut (!?!) - // It seems that *no Dicom Viewer* has any idea :-( - - std::string photomInterp = "MONOCHROME1 "; // Photometric Interpretation - Header->SetEntryByNumber(photomInterp,0x0028,0x0004); - } - - /// \todo Drop Palette Color out of the Header? - return ImageDataSize; + + // to avoid troubles with David Clunie's-like images + if ( xspacing == 0. && yspacing == 0.) + return 1.; + + if ( xspacing == 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 ); + } + + return xspacing; } /** - * \ingroup gdcmFile - * \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 - */ -void * gdcmFile::GetImageDataRaw () + * \brief gets the info from 0028,0030 : Pixel Spacing + * else 1.0 + * @return Y dimension of a pixel + */ +float File::GetYSpacing() { - size_t imgDataSize; - if ( Header->HasLUT() ) - /// \todo Let gdcmHeader user a chance to get the right value - imgDataSize = ImageDataSizeRaw; - else - imgDataSize = ImageDataSize; - - // FIXME (Mathieu) - // I need to deallocate Pixel_Data before doing any allocation: - - if ( Pixel_Data ) - if ( LastAllocatedPixelDataLength != imgDataSize ) - free(Pixel_Data); - if ( !Pixel_Data ) - Pixel_Data = new uint8_t[imgDataSize]; - - if ( Pixel_Data ) + float yspacing = 1.; + std::string strSpacing = GetEntryValue(0x0028,0x0030); + + if ( strSpacing == GDCM_UNFOUND ) { - LastAllocatedPixelDataLength = imgDataSize; - - // we load the pixels ( grey level or RGB, but NO transformation) - GetImageDataIntoVectorRaw(Pixel_Data, imgDataSize); + gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)"); + return 1.; + } - // We say the value *is* loaded. - GetHeader()->SetEntryByNumber( GDCM_BINLOADED, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - - // will be 7fe0, 0010 in standard cases - GetHeader()->SetEntryVoidAreaByNumber(Pixel_Data, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - } - PixelRead = 1; // PixelRaw + // if sscanf cannot read any float value, it won't affect yspacing + sscanf( strSpacing.c_str(), "%f", &yspacing); - return Pixel_Data; -} + if ( yspacing == 0.0 ) + yspacing = 1.0; + + return yspacing; +} /** - * \ingroup gdcmFile - * \brief Copies at most MaxSize bytes of pixel data to caller's - * memory space. - * \warning This function was designed to avoid people that want to build - * a volume from an image stack to need 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 hace to call GetImageData - * \warning DOES NOT transform the Grey Plane + Palette Color (if any) - * into a single RGB Pixels Plane - * the (VTK) user will manage the palettes - * - * @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. + * \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 */ -size_t gdcmFile::GetImageDataIntoVectorRaw (void *destination, size_t maxSize) +float File::GetZSpacing() { - int nb, nbu, highBit, sign; - - // we save the initial values of the following - // in order to be able to restore the header in a disk-consistent state - // (if user asks twice to get the pixels from disk) - - if ( PixelRead == -1 ) // File was never "read" before - { - InitialSpp = Header->GetEntryByNumber(0x0028,0x0002); - InitialPhotInt = Header->GetEntryByNumber(0x0028,0x0004); - InitialPlanConfig = Header->GetEntryByNumber(0x0028,0x0006); - InitialBitsAllocated = Header->GetEntryByNumber(0x0028,0x0100); - } - else // File was already "read", the following *may* have been modified - // we restore them to be in a disk-consistent state - { - // FIXME : What happened with the LUTs ? - Header->SetEntryByNumber(InitialSpp,0x0028,0x0002); - Header->SetEntryByNumber(InitialPhotInt,0x0028,0x0004); - Header->SetEntryByNumber(InitialPlanConfig,0x0028,0x0006); - Header->SetEntryByNumber(InitialBitsAllocated,0x0028,0x0100); - } + // 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 - PixelRead = 1 ; // PixelRaw - - if ( ImageDataSize > maxSize ) + const std::string &strSpacingBSlices = GetEntryValue(0x0018,0x0088); + + if ( strSpacingBSlices == GDCM_UNFOUND ) { - dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: pixel data bigger" - "than caller's expected MaxSize"); - return (size_t)0; + 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() ); +} - ReadPixelData( destination ); +/** + * \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 + */ +float File::GetXOrigin() +{ + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryValue(0x0020,0x0032); - // Number of Bits Allocated for storing a Pixel - std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); - if ( str_nb == GDCM_UNFOUND ) + if ( strImPos == GDCM_UNFOUND ) { - nb = 16; - } - else - { - nb = atoi( str_nb.c_str() ); - // FIXME - // From reading SetPixelDataSizeFromHeader, it seems 12 should be treated - // separately, correct ? + 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.; + } } - // Number of Bits actually used - std::string str_nbu = Header->GetEntryByNumber(0x0028,0x0101); - if ( str_nbu == GDCM_UNFOUND ) - { - nbu = nb; - } - else + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) { - nbu = atoi( str_nbu.c_str() ); + return 0.; } - // High Bit Position - std::string str_highBit = Header->GetEntryByNumber(0x0028,0x0102); - if ( str_highBit == GDCM_UNFOUND ) - { - highBit = nb - 1; - } - else - { - highBit = atoi( str_highBit.c_str() ); - } + return xImPos; +} + +/** + * \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 + */ +float File::GetYOrigin() +{ + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryValue(0x0020,0x0032); - // Pixel sign - // 0 = Unsigned - // 1 = Signed - std::string str_sign = Header->GetEntryByNumber(0x0028,0x0103); - if ( str_sign == GDCM_UNFOUND ) + if ( strImPos == GDCM_UNFOUND) { - sign = 0; // default is unsigned + 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.; + } } - else + + if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 ) { - sign = atoi( str_sign.c_str() ); + return 0.; } - // re arange bytes inside the integer (processor endianity) - if ( nb != 8 ) + return yImPos; +} + +/** + * \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 + */ +float File::GetZOrigin() +{ + float xImPos, yImPos, zImPos; + std::string strImPos = GetEntryValue(0x0020,0x0032); + + if ( strImPos != GDCM_UNFOUND ) { - SwapZone(destination, Header->GetSwapCode(), ImageDataSize, nb); + 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; + } } - - // to avoid pb with some xmedcon breakers images - if ( nb == 16 && nbu < nb && sign == 0) + + strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos != GDCM_UNFOUND ) { - int l = (int)(ImageDataSize / (nb/8)); - uint16_t *deb = (uint16_t *)destination; - for(int i = 0; i> (nb-nbu); - uint16_t *deb = (uint16_t *)destination; - for(int i = 0; i> (nbu - highBit - 1)) & mask; - deb++; - } + gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); + return 0.; // bug in the element 0x0020,0x1041 + } + else + { + return zImPos; } - else if ( nb == 32 ) + } + gdcmWarningMacro( "Unfound Slice Location (0020,1041)"); + + std::string strLocation = GetEntryValue(0x0020,0x0050); + if ( strLocation != GDCM_UNFOUND ) + { + if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1) { - uint32_t mask = 0xffffffff; - mask = mask >> (nb - nbu); - uint32_t *deb = (uint32_t *)destination; - for(int i = 0; i> (nbu - highBit - 1)) & mask; - deb++; - } + gdcmWarningMacro( "Wrong Location (0020,0050)"); + return 0.; // bug in the element 0x0020,0x0050 } else { - dbg.Verbose(0, "gdcmFile::GetImageDataIntoVector: weird image"); - return 0; + return zImPos; } } -// DO NOT remove this code commented out. -// Nobody knows what's expecting you ... -// Just to 'see' what was actually read on disk :-( + gdcmWarningMacro( "Unfound Location (0020,0050)"); -// FILE * f2; -// f2 = fopen("SpuriousFile.RAW","wb"); -// fwrite(destination,ImageDataSize,1,f2); -// fclose(f2); + return 0.; // Hopeless +} - // Deal with the color - // ------------------- - - std::string str_PhotometricInterpretation = - Header->GetEntryByNumber(0x0028,0x0004); +/** + * \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] ) +{ + std::string strImOriPat; + //iop is supposed to be float[6] + iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.; - if ( str_PhotometricInterpretation == "MONOCHROME1 " - || str_PhotometricInterpretation == "MONOCHROME2 " ) + // 0020 0037 DS REL Image Orientation (Patient) + if ( (strImOriPat = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND ) { - return ImageDataSize; + 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." ); + } } - - // Planar configuration = 0 : Pixels are already RGB - // Planar configuration = 1 : 3 planes : R, G, B - // Planar configuration = 2 : 1 gray Plane + 3 LUT - - // Well ... supposed to be ! - // See US-PAL-8-10x-echo.dcm: PlanarConfiguration=0, - // PhotometricInterpretation=PALETTE COLOR - // and heuristic has to be 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." ); + } + } +} - int planConf = Header->GetPlanarConfiguration(); // 0028,0006 +/** + * \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 ! + */ +int File::GetBitsStored() +{ + 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() ); +} - // Whatever Planar Configuration is, - // "PALETTE COLOR " implies that we deal with the palette. - if ( str_PhotometricInterpretation == "PALETTE COLOR ") +/** + * \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 ! + */ +int File::GetBitsAllocated() +{ + std::string strSize = GetEntryValue(0x0028,0x0100); + if ( strSize == GDCM_UNFOUND ) { - planConf = 2; + 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() ); +} - switch ( planConf ) +/** + * \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. + */ +int File::GetHighBitPosition() +{ + std::string strSize = GetEntryValue( 0x0028, 0x0102 ); + if ( strSize == GDCM_UNFOUND ) { - case 0: - // Pixels are already RGB - break; - case 1: - if (str_PhotometricInterpretation == "YBR_FULL") - { - // Warning : YBR_FULL_422 acts as RGB - // : we need to make RGB Pixels from Planes Y,cB,cR - - // to see the tricks about YBR_FULL, YBR_FULL_422, - // YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at : - // ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf - // and be *very* affraid - // - int l = Header->GetXSize() * Header->GetYSize(); - int nbFrames = Header->GetZSize(); - - uint8_t* newDest = new uint8_t[ImageDataSize]; - uint8_t* x = newDest; - uint8_t* a = (uint8_t*)destination; - uint8_t* b = a + l; - uint8_t* c = b + l; - double R,G,B; - - /// \todo : Replace by the 'well known' integer computation - /// counterpart - /// see http://lestourtereaux.free.fr/papers/data/yuvrgb.pdf - /// for code optimisation - - for (int i = 0; i < nbFrames; i++) - { - for (int j = 0; j < l; j++) - { - R = 1.164 *(*a-16) + 1.596 *(*c -128) + 0.5; - G = 1.164 *(*a-16) - 0.813 *(*c -128) - 0.392 *(*b -128) + 0.5; - B = 1.164 *(*a-16) + 2.017 *(*b -128) + 0.5; - - if (R < 0.0) R = 0.0; - if (G < 0.0) G = 0.0; - if (B < 0.0) B = 0.0; - if (R > 255.0) R = 255.0; - if (G > 255.0) G = 255.0; - if (B > 255.0) B = 255.0; - - *(x++) = (uint8_t)R; - *(x++) = (uint8_t)G; - *(x++) = (uint8_t)B; - a++; b++; c++; - } - } - memmove(destination, newDest, ImageDataSize); - delete[] newDest; - } - else - { - // need to make RGB Pixels from R,G,B Planes - // (all the Frames at a time) - - int l = Header->GetXSize() * Header->GetYSize() * Header->GetZSize(); - - uint8_t *newDest = new uint8_t[ImageDataSize]; - uint8_t *x = newDest; - uint8_t *a = (uint8_t *)destination; - uint8_t *b = a + l; - uint8_t *c = b + l; - - for (int j = 0; j < l; j++) - { - *(x++) = *(a++); - *(x++) = *(b++); - *(x++) = *(c++); - } - memmove(destination, newDest, ImageDataSize); - delete[] newDest; - } - break; - case 2: - // Palettes were found - // Let the user deal with them ! - return ImageDataSize; + gdcmWarningMacro( "(0028,0102) is supposed to be mandatory"); + return 0; } - // now, it's an RGB image - // Lets's write it in the Header + return atoi( strSize.c_str() ); +} - // CreateOrReplaceIfExist ? +/** + * \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) + */ +int File::GetSamplesPerPixel() +{ + 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() ); +} - std::string spp = "3"; // Samples Per Pixel - std::string photInt = "RGB "; // Photometric Interpretation - std::string planConfig = "0"; // Planar Configuration +/** + * \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. + */ +int File::GetPlanarConfiguration() +{ + 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 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 + */ +int File::GetPixelSize() +{ + // 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; - - Header->SetEntryByNumber(spp,0x0028,0x0002); - Header->SetEntryByNumber(photInt,0x0028,0x0004); - Header->SetEntryByNumber(planConfig,0x0028,0x0006); - - /// \todo Drop Palette Color out of the Header? - return ImageDataSize; + 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; } /** - * \ingroup gdcmFile - * \brief performs a shalow copy (not a deep copy) of the user given - * pixel area. - * '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 user is kindly requested NOT TO 'free' the Pixel area - * @param inData user supplied pixel area - * @param expectedSize total image size, in Bytes - * - * @return boolean + * \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 */ -bool gdcmFile::SetImageData(void *inData, size_t expectedSize) +std::string File::GetPixelType() { - Header->SetImageDataSize( expectedSize ); -// FIXME : if already allocated, memory leak ! - Pixel_Data = inData; - ImageDataSize = ImageDataSizeRaw = expectedSize; - PixelRead = 1; -// FIXME : 7fe0, 0010 IS NOT set ... - return true; + 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 + } + + 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; } /** - * \ingroup gdcmFile - * \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 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 gdcmFile::WriteRawData(std::string const & fileName) +bool File::IsSignedPixelData() { - FILE *fp1 = fopen(fileName.c_str(), "wb"); - if (fp1 == NULL) + 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 ) { - printf("Fail to open (write) file [%s] \n", fileName.c_str()); return false; } - fwrite (Pixel_Data, ImageDataSize, 1, fp1); - fclose (fp1); - return true; } /** - * \ingroup gdcmFile - * \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 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 gdcmFile::WriteDcmImplVR (std::string const & fileName) +bool File::IsMonochrome() { - return WriteBase(fileName, gdcmImplicitVR); + 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; } /** - * \ingroup gdcmFile -* \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 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 gdcmFile::WriteDcmExplVR (std::string const & fileName) +bool File::IsPaletteColor() { - return WriteBase(fileName, gdcmExplicitVR); + 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; } /** - * \ingroup gdcmFile - * \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 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. */ - -bool gdcmFile::WriteAcr (std::string const & fileName) +bool File::IsYBRFull() { - return WriteBase(fileName, gdcmACR); + 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 /** - * \ingroup gdcmFile - * \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 gdcmFile::WriteBase (std::string const & fileName, FileType type) + * \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() { - if ( PixelRead == -1 && type != gdcmExplicitVR) + // Check the presence of the LUT Descriptors, and LUT Tables + // LutDescriptorRed + if ( !GetDocEntry(0x0028,0x1101) ) { return false; } - - FILE *fp1 = fopen(fileName.c_str(), "wb"); - if (fp1 == NULL) + // LutDescriptorGreen + if ( !GetDocEntry(0x0028,0x1102) ) { - printf("Failed to open (write) File [%s] \n", fileName.c_str()); return false; } - - if ( type == gdcmImplicitVR || type == gdcmExplicitVR ) + // LutDescriptorBlue + if ( !GetDocEntry(0x0028,0x1103) ) { - // writing Dicom File Preamble - uint8_t* filePreamble = new uint8_t[128]; - memset(filePreamble, 0, 128); - fwrite(filePreamble, 128, 1, fp1); - fwrite("DICM", 4, 1, fp1); - - delete[] filePreamble; + return false; } - - // -------------------------------------------------------------- - // 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 - - std::string rows, columns; - if ( Header->GetFileType() == gdcmACR_LIBIDO) + // Red Palette Color Lookup Table Data + if ( !GetDocEntry(0x0028,0x1201) ) { - rows = Header->GetEntryByNumber(0x0028, 0x0010); - columns = Header->GetEntryByNumber(0x0028, 0x0011); - - Header->SetEntryByNumber(columns, 0x0028, 0x0010); - Header->SetEntryByNumber(rows , 0x0028, 0x0011); + return false; } - // ----------------- End of Special Patch ---------------- - - uint16_t grPixel = Header->GetGrPixel(); - uint16_t numPixel = Header->GetNumPixel();; - - gdcmDocEntry* PixelElement = - GetHeader()->GetDocEntryByNumber(grPixel, numPixel); - - if ( PixelRead == 1 ) + // Green Palette Color Lookup Table Data + if ( !GetDocEntry(0x0028,0x1202) ) { - // we read pixel 'as is' (no tranformation LUT -> RGB) - PixelElement->SetLength( ImageDataSizeRaw ); + return false; } - else if ( PixelRead == 0 ) + // Blue Palette Color Lookup Table Data + if ( !GetDocEntry(0x0028,0x1203) ) { - // we tranformed GrayLevel pixels + LUT into RGB Pixel - PixelElement->SetLength( ImageDataSize ); + return false; } - - Header->Write(fp1, type); - // -------------------------------------------------------------- - // 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 + // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent) + // NOT taken into account, but we don't know how to use it ... + return true; +} - if ( Header->GetFileType() == gdcmACR_LIBIDO ) +/** + * \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 ) { - Header->SetEntryByNumber(rows , 0x0028, 0x0010); - Header->SetEntryByNumber(columns, 0x0028, 0x0011); + return 0; } - // ----------------- End of Special Patch ---------------- - - // fwrite(Pixel_Data, ImageDataSize, 1, fp1); // should be useless, now - fclose (fp1); - return true; + tokens.clear(); // clean any previous value + Util::Tokenize ( lutDescription, tokens, "\\" ); + //LutLength=atoi(tokens[0].c_str()); + //LutDepth=atoi(tokens[1].c_str()); + + lutNbits = atoi( tokens[2].c_str() ); + tokens.clear(); + + return lutNbits; } -//----------------------------------------------------------------------------- -// Private /** - * \ingroup gdcmFile - * \brief Swap the bytes, according to swap code. - * \warning not end user intended - * @param im area to deal with - * @param swap swap code - * @param lgr Area Length - * @param nb Pixels Bit number + *\brief gets the info from 0028,1052 : Rescale Intercept + * @return Rescale Intercept */ -void gdcmFile::SwapZone(void *im, int swap, int lgr, int nb) +float File::GetRescaleIntercept() { - int i; - - if( nb == 16 ) + float resInter = 0.; + /// 0028 1052 DS IMG Rescale Intercept + const std::string &strRescInter = GetEntryValue(0x0028,0x1052); + if ( strRescInter != GDCM_UNFOUND ) { - uint16_t* im16 = (uint16_t*)im; - switch( swap ) + if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 ) { - case 0: - case 12: - case 1234: - break; - case 21: - case 3412: - case 2143: - case 4321: - for(i=0; i < lgr/2; i++) - { - im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); - } - break; - default: - std::cout << "SWAP value (16 bits) not allowed :i" << swap << - std::endl; + // bug in the element 0x0028,0x1052 + gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." ); } } - else if( nb == 32 ) + + return resInter; +} + +/** + *\brief gets the info from 0028,1053 : Rescale Slope + * @return Rescale Slope + */ +float File::GetRescaleSlope() +{ + float resSlope = 1.; + //0028 1053 DS IMG Rescale Slope + std::string strRescSlope = GetEntryValue(0x0028,0x1053); + if ( strRescSlope != GDCM_UNFOUND ) { - uint32_t s32; - uint16_t fort, faible; - uint32_t* im32 = (uint32_t*)im; - switch ( swap ) + if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1) { - case 0: - case 1234: - break; - case 4321: - for(i = 0; i < lgr/4; i++) - { - faible = im32[i] & 0x0000ffff; // 4321 - fort = im32[i] >> 16; - fort = ( fort >> 8 ) | ( fort << 8 ); - faible = ( faible >> 8 ) | ( faible << 8); - s32 = faible; - im32[i] = ( s32 << 16 ) | fort; - } - break; - case 2143: - for(i = 0; i < lgr/4; i++) - { - faible = im32[i] & 0x0000ffff; // 2143 - fort = im32[i] >> 16; - fort = ( fort >> 8 ) | ( fort << 8 ); - faible = ( faible >> 8) | ( faible << 8); - s32 = fort; - im32[i] = ( s32 << 16 ) | faible; - } - break; - case 3412: - for(i = 0; i < lgr/4; i++) - { - faible = im32[i] & 0x0000ffff; // 3412 - fort = im32[i] >> 16; - s32 = faible; - im32[i] = ( s32 << 16 ) | fort; - } - break; - default: - std::cout << "SWAP value (32 bits) not allowed : " << swap << - std::endl; + // bug in the element 0x0028,0x1053 + gdcmWarningMacro( "Rescale Slope (0028,1053) is empty."); } } + + return resSlope; } /** - * \ingroup gdcmFile - * \brief Read pixel data from disk (optionaly decompressing) into the - * caller specified memory location. - * @param destination where the pixel data should be stored. - * + * \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) */ -bool gdcmFile::ReadPixelData(void *destination) +int File::GetNumberOfScalarComponents() { - FILE *fp = Header->OpenFile(); - - if ( !fp ) + if ( GetSamplesPerPixel() == 3 ) { - return false; + return 3; } - if ( fseek(fp, Header->GetPixelOffset(), SEEK_SET) == -1 ) + + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if ( GetEntryValue(0x0028,0x0100) == "24" ) { - Header->CloseFile(); - return false; + return 3; } + + std::string strPhotometricInterpretation = GetEntryValue(0x0028,0x0004); - // ---------------------- Compacted File (12 Bits Per Pixel) - // unpack 12 Bits pixels into 16 Bits pixels - // 2 pixels 12bit = [0xABCDEF] - // 2 pixels 16bit = [0x0ABD] + [0x0FCE] - - if ( Header->GetBitsAllocated() == 12 ) + if ( ( strPhotometricInterpretation == "PALETTE COLOR ") ) { - int nbPixels = Header->GetXSize() * Header->GetYSize(); - uint8_t b0, b1, b2; - - uint16_t* pdestination = (uint16_t*)destination; - for(int p = 0; p < nbPixels; p += 2 ) + if ( HasLUT() )// PALETTE COLOR is NOT enough { - fread(&b0,1,1,fp); - fread(&b1,1,1,fp); - fread(&b2,1,1,fp); - - //Two steps is necessary to please VC++ - *pdestination++ = ((b0 >> 4) << 8) + ((b0 & 0x0f) << 4) + (b1 & 0x0f); - // A B D - *pdestination++ = ((b2 & 0x0f) << 8) + ((b1 >> 4) << 4) + (b2 >> 4); - // F C E - - // Troubles expected on Big-Endian processors ? + return 3; } + else + { + return 1; + } + } - Header->CloseFile(); - return true; + // 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 + { + // we assume that *all* kinds of YBR are dealt with + return 3; + } +} + +/** + * \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() +{ + // 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; + } + + // we assume that *all* kinds of YBR are dealt with + return GetSamplesPerPixel(); +} - // ---------------------- Uncompressed File - if ( !Header->IsDicomV3() || - Header->IsImplicitVRLittleEndianTransferSyntax() || - Header->IsExplicitVRLittleEndianTransferSyntax() || - Header->IsExplicitVRBigEndianTransferSyntax() || - Header->IsDeflatedExplicitVRLittleEndianTransferSyntax() ) +/** + * \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() +{ + DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel); + if ( pxlElement ) { - size_t ItemRead = fread(destination, Header->GetPixelAreaLength(), 1, fp); - Header->CloseFile(); - if ( ItemRead != 1 ) + return pxlElement->GetOffset(); + } + else + { + gdcmDebugMacro( "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); + return 0; + } +} + +/** + * \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() +{ + 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) + +{ + Element el; + el.Group = group; + el.Elem = elem; + el.Value = value; + AnonymizeList.push_back(el); +} + +/** + * \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 ? + char spaces[50] = " "; + + gdcm::DocEntry *d; + uint32_t offset; + uint32_t lgth; + uint32_t lgtToWrite; + for (ListElements::iterator it = AnonymizeList.begin(); + it != AnonymizeList.end(); + ++it) + { + d = GetDocEntry( (*it).Group, (*it).Elem); + + if ( dynamic_cast(d) + || dynamic_cast(d) ) + continue; + + offset = d->GetOffset(); + lgth = d->GetLength(); + fp->seekp( offset, std::ios::beg ); + + if ( (*it).Value == "" ) { - return false; + lgtToWrite = lgth > 50 ? 50 : lgth; + fp->write( spaces, lgtToWrite ); } else { - return true; + // TODO : FIXME + // how to white out disk space if longer than 50 ? + (*it).Value = (*it).Value + spaces; + lgtToWrite = lgth > (*it).Value.length() ? (*it).Value.length() : lgth; + fp->write( (char *)(*it).Value.c_str(), lgtToWrite ); + } + fp->close(); + delete fp; } +} - // ---------------------- Run Length Encoding - if ( Header->IsRLELossLessTransferSyntax() ) - { - bool res = gdcm_read_RLE_file (fp,destination); - Header->CloseFile(); - return res; - } - - // --------------- SingleFrame/Multiframe JPEG Lossless/Lossy/2000 - int nb; - std::string str_nb = Header->GetEntryByNumber(0x0028,0x0100); - if ( str_nb == GDCM_UNFOUND ) +/** + * \brief anonymize a File (removes Patient's personal info passed with + * AddAnonymizeElement() + */ +bool File::AnonymizeFile() +{ + // If Anonymisation list is empty, let's perform some basic anonymisation + if ( AnonymizeList.begin() == AnonymizeList.end() ) { - nb = 16; + // 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 { - nb = atoi( str_nb.c_str() ); - if ( nb == 12 ) - { - nb = 16; // ?? 12 should be ACR-NEMA only + gdcm::DocEntry *d; + for (ListElements::iterator it = AnonymizeList.begin(); + it != AnonymizeList.end(); + ++it) + { + d = GetDocEntry( (*it).Group, (*it).Elem); + + if ( dynamic_cast(d) + || dynamic_cast(d) ) + continue; + + SetValEntry ((*it).Value, (*it).Group, (*it).Elem); } - } +} - int nBytes= nb/8; - int taille = Header->GetXSize() * Header->GetYSize() - * Header->GetSamplesPerPixel(); - long fragmentBegining; // for ftell, fseek + // 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 - bool jpg2000 = Header->IsJPEG2000(); - bool jpgLossless = Header->IsJPEGLossless(); + return true; +} - bool res = true; - uint16_t ItemTagGr, ItemTagEl; - int ln; - - // Position on begining of Jpeg Pixels - - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if(Header->GetSwapCode()) +/** + * \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) +{ + std::ofstream *fp = new std::ofstream(fileName.c_str(), + std::ios::out | std::ios::binary); + if (*fp == NULL) { - ItemTagGr = Header->SwapShort(ItemTagGr); - ItemTagEl = Header->SwapShort(ItemTagEl); + gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str()); + return false; } - fread(&ln,4,1,fp); - if( Header->GetSwapCode() ) + // Entry : 0002|0000 = group length -> recalculated + ValEntry *e0002 = GetValEntry(0x0002,0x0000); + if( e0002 ) { - ln = Header->SwapLong( ln ); // Basic Offset Table Item length + std::ostringstream sLen; + sLen << ComputeGroup0002Length(filetype); + e0002->SetValue(sLen.str()); } - if ( ln != 0 ) + // Bits Allocated + if ( GetEntryValue(0x0028,0x0100) == "12") { - // What is it used for ?!? - uint8_t* BasicOffsetTableItemValue = new uint8_t[ln+1]; - fread(BasicOffsetTableItemValue,ln,1,fp); - //delete[] BasicOffsetTableItemValue; + SetValEntry("16", 0x0028,0x0100); } - // first Fragment initialisation - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if( Header->GetSwapCode() ) + int i_lgPix = GetEntryLength(GrPixel, NumPixel); + if (i_lgPix != -2) { - ItemTagGr = Header->SwapShort( ItemTagGr ); - ItemTagEl = Header->SwapShort( ItemTagEl ); + // 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); } - // parsing fragments until Sequence Delim. Tag found - while ( ItemTagGr == 0xfffe && ItemTagEl != 0xe0dd ) + // FIXME : should be nice if we could move it to File + // (or in future gdcmPixelData class) + + // Drop Palette Color, if necessary + if ( GetEntryValue(0x0028,0x0002).c_str()[0] == '3' ) { - // --- for each Fragment - fread(&ln,4,1,fp); - if( Header->GetSwapCode() ) + // 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) { - ln = Header->SwapLong(ln); // Fragment Item length + RemoveEntryNoDestroy(e); } - fragmentBegining = ftell( fp ); - - if ( jpg2000 ) + e = GetDocEntry(0x0028,0x1102); + if (e) { - // JPEG 2000 : call to ??? - res = gdcm_read_JPEG2000_file (fp,destination); // Not Yet written - // ------------------------------------- endif (JPEG2000) + RemoveEntryNoDestroy(e); } - else if (jpgLossless) + e = GetDocEntry(0x0028,0x1103); + if (e) { - // JPEG LossLess : call to xmedcom Lossless JPEG - // Reading Fragment pixels - JPEGLosslessDecodeImage (fp, (uint16_t*)destination, - Header->GetPixelSize() * 8 * Header->GetSamplesPerPixel(), ln); - res = 1; // in order not to break the loop - - } // ------------------------------------- endif (JPEGLossless) - else + RemoveEntryNoDestroy(e); + } + e = GetDocEntry(0x0028,0x01201); + if (e) { - // JPEG Lossy : call to IJG 6b - if ( Header->GetBitsStored() == 8) - { - // Reading Fragment pixels - res = gdcm_read_JPEG_file (fp,destination); - } - else - { - // Reading Fragment pixels - res = gdcm_read_JPEG_file12 (fp,destination); - } - // ------------------------------------- endif (JPEGLossy) + RemoveEntryNoDestroy(e); + } + e = GetDocEntry(0x0028,0x1202); + if (e) + { + RemoveEntryNoDestroy(e); } + e = GetDocEntry(0x0028,0x1203); + if (e) + { + RemoveEntryNoDestroy(e); + } + } - if ( !res ) + +#ifdef GDCM_WORDS_BIGENDIAN + // Super Super hack that will make gdcm a BOMB ! but should + // Fix temporarily the dashboard + BinEntry *b = GetBinEntry(GrPixel,NumPixel); + if ( GetPixelSize() == 16 ) + { + uint16_t *im16 = (uint16_t *)b->GetBinArea(); + int lgth = b->GetLength(); + for( int i = 0; i < lgth / 2; i++ ) { - break; + im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); } - - // location in user's memory - // for next fragment (if any) - destination = (uint8_t*)destination + taille * nBytes; + } +#endif //GDCM_WORDS_BIGENDIAN - fseek(fp,fragmentBegining, SEEK_SET); // To be sure we start - fseek(fp,ln,SEEK_CUR); // at the begining of next fragment - - ItemTagGr = ItemTagEl = 0; - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if( Header->GetSwapCode() ) + + Document::WriteContent(fp, filetype); + + +#ifdef GDCM_WORDS_BIGENDIAN + // Flip back the pixel ... I told you this is a hack + if ( GetPixelSize() == 16 ) + { + uint16_t *im16 = (uint16_t*)b->GetBinArea(); + int lgth = b->GetLength(); + for( int i = 0; i < lgth / 2; i++ ) + { + im16[i]= (im16[i] >> 8) | (im16[i] << 8 ); + } + } +#endif //GDCM_WORDS_BIGENDIAN + + + fp->close(); + delete fp; + + return true; +} + +//----------------------------------------------------------------------------- +// 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() +{ + 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(uidClass.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); +} + +//----------------------------------------------------------------------------- +// 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() +{ + 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++ ) { - ItemTagGr = Header->SwapShort( ItemTagGr ); - ItemTagEl = Header->SwapShort( ItemTagEl ); + 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); + } + + // 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 RLE item sequence"); + } +} + +/** + * \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) ) + { + 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); + } + + // 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"); + } +} + +/** + * \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) +{ + 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 + { + itemTagGroup = ReadInt16(); + itemTagElement = ReadInt16(); + } + catch ( FormatError e ) + { + //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 false; } - // endWhile parsing fragments until Sequence Delim. Tag found + return true; +} + +/** + * \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. + */ +uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElement) +{ - Header->CloseFile(); - return res; + if ( !ReadTag(testGroup, testElement) ) + { + return 0; + } + + //// Then read the associated Item Length + long currentPosition = Fp->tellg(); + uint32_t itemLength = ReadInt32(); + { + gdcmWarningMacro( "Basic Item Length is: " + << itemLength << std::endl + << " at address: " << std::hex << (unsigned int)currentPosition); + } + return itemLength; } + +/** + * \brief When parsing the Pixel Data of an encapsulated file, read + * the basic offset table (when present, and BTW dump it). + */ +void File::ReadAndSkipEncapsulatedBasicOffsetTable() +{ + //// 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 ) + { + char *basicOffsetTableItemValue = new char[itemLength + 1]; + Fp->read(basicOffsetTableItemValue, itemLength); + +#ifdef GDCM_DEBUG + for (unsigned int i=0; i < itemLength; i += 4 ) + { + uint32_t individualLength = str2num( &basicOffsetTableItemValue[i], + uint32_t); + gdcmWarningMacro( "Read one length: " << + std::hex << individualLength ); + } +#endif //GDCM_DEBUG + + delete[] basicOffsetTableItemValue; + } +} + +//----------------------------------------------------------------------------- +// Print + //----------------------------------------------------------------------------- +} // end namespace gdcm