X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.cxx;h=acc5acfae523a4f2e110f0972f1f657e1b244aeb;hb=e7768bbebdc9a5972e396d71a3e848f5674ee378;hp=4921affdf3820fe2858911157c0295bcd9f98eaa;hpb=8da9df62c47908e7b9a67238a6c12b92ba6cae7a;p=gdcm.git diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx index 4921affd..acc5acfa 100644 --- a/src/gdcmFile.cxx +++ b/src/gdcmFile.cxx @@ -1,10 +1,10 @@ - /*========================================================================= +/*========================================================================= Program: gdcm Module: $RCSfile: gdcmFile.cxx,v $ Language: C++ - Date: $Date: 2004/11/25 13:12:02 $ - Version: $Revision: 1.164 $ + Date: $Date: 2007/10/23 15:52:33 $ + Version: $Revision: 1.341 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -16,778 +16,2356 @@ =========================================================================*/ +// +// -------------- 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 +// +// Image Position (Patient) (0020,0032) VM=3 +// --> +// The attribute Patient Orientation (0020,0020) from the General Image Module +// is of type 2C and has the condition Required if image does not require +// Image Orientation (0020,0037) and Image Position (0020,0032). +// However, if the image does require the attributes +// - Image Orientation (Patient) (0020,0037), VM=6 +// - Image Position (Patient) (0020,0032), VM=3 +// then attribute Patient Orientation (0020,0020) should not be present +// in the images. +// +// Remember also : +// Patient Position (0018,5100) values : + +// HFS = Head First-Supine, where increasing (positive axis direction) : +// X -> to the direction pointed to by the patient's oustretched left arm +// Y -> to the anterior-to-posterior direction in the patient's body +// Z -> to the feet-to-head direction in the patient's body + +// HFP = Head First-Prone, where increasing (positive axis direction) : +// X -> to the direction pointed to by the patient's oustretched left arm +// Y -> to the anterior-to-posterior direction in the patient's body +// Z -> to the feet-to-head direction in the patient's body + +// FFS = Feet First-Supine, where increasing (positive axis direction) : +// X -> to the direction pointed to by the patient's oustretched left arm +// Y -> to the anterior-to-posterion direction in the patient's body +// Z -> to the feet-to-head direction in the patient's body + +// FFP = Feet First-Prone, where increasing (positive axis direction) : +// X -> to the direction pointed to by the patient's oustretched left arm +// Y -> to the posterior-to-anterior direction in the patient's body +// Z -> to the feet-to-head direction in the patient's body + +// HFDR = Head First-Decubitus Right +// HFDL = Head First-Decubitus Left +// FFDR = Feet First-Decubitus Right +// FFDL = Feet First-Decubitus Left + +// we can also find (non standard!) + +// SEMIERECT +// SUPINE + +// CS 2 Patient Orientation (0020 0020) +// When the coordinates of the image +// are always present, this field is almost never used. +// Better we don't trust it too much ... +// Found Values are : +// L\P +// L\FP +// P\F +// L\F +// P\FR +// R\F +// +// (0020|0037) [Image Orientation (Patient)] [1\0\0\0\1\0 ] + + +// --------------------------------------------------------------- +// #include "gdcmFile.h" -#include "gdcmDocument.h" -#include "gdcmDebug.h" +#include "gdcmGlobal.h" #include "gdcmUtil.h" -#include "gdcmBinEntry.h" -#include - -namespace gdcm +#include "gdcmDebug.h" +#include "gdcmTS.h" +#include "gdcmSeqEntry.h" +#include "gdcmRLEFramesInfo.h" +#include "gdcmJPEGFragmentsInfo.h" +#include "gdcmDataEntry.h" +#include "gdcmSQItem.h" + +#include +#include //sscanf +#include // for atoi + +namespace GDCM_NAME_SPACE { -typedef std::pair IterHT; -//------------------------------------------------------------------------- +//----------------------------------------------------------------------------- // Constructor / Destructor + +/** + * \brief Constructor used when we want to generate dicom files from scratch + */ +File::File(): + Document() +{ + RLEInfo = new RLEFramesInfo; + JPEGInfo = new JPEGFragmentsInfo; + GrPixel = 0x7fe0; // to avoid further troubles + NumPixel = 0x0010; + BasicOffsetTableItemValue = 0; + FourthDimensionLocation = TagKey(0,0); +} + + /** - * \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 Canonical destructor. */ -File::File(Header *header) +File::~File() { - HeaderInternal = header; - SelfHeader = false; - Initialise(); + if ( RLEInfo ) + delete RLEInfo; + if ( JPEGInfo ) + delete JPEGInfo; + delete[] BasicOffsetTableItemValue; } +//----------------------------------------------------------------------------- +// Public /** - * \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 Loader + * @return false if file cannot be open or no swap info was found, + * or no tag was found. */ -File::File(std::string const & filename ) +bool File::Load( ) { - HeaderInternal = new Header( filename ); - SelfHeader = true; - Initialise(); + if ( ! this->Document::Load( ) ) + return false; + + return DoTheLoadingJob( ); } /** - * \brief Factorization for various forms of constructors. + * \brief Does the Loading Job (internal use only) + * @return false if file cannot be open or no swap info was found, + * or no tag was found. */ -void File::Initialise() +bool File::DoTheLoadingJob( ) { - WriteMode = WMODE_DECOMPRESSED; - WriteType = WTYPE_IMPL_VR; + // 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 = GetEntryString(0x0028, 0x0200); + if ( imgLocation == GDCM_UNFOUND ) + { + // default value + GrPixel = 0x7fe0; + } + else + { + GrPixel = (uint16_t) atoi( imgLocation.c_str() ); + } - PixelConverter = new PixelConvert; - Archive = new DocEntryArchive( HeaderInternal ); + // sometimes Image Location value doesn't follow + // the supposed processor endianness. + // see gdcmData/cr172241.dcm + if ( GrPixel == 0xe07f ) + { + GrPixel = 0x7fe0; + } - if ( HeaderInternal->IsReadable() ) + if ( GrPixel != 0x7fe0 ) + { + // This is a kludge for old dirty Philips imager. + NumPixel = 0x1010; + } + else { - PixelConverter->GrabInformationsFromHeader( HeaderInternal ); + NumPixel = 0x0010; } - Pixel_Data = 0; - ImageDataSize = 0; + // 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(); + const 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 DataEntry to change the DictEntry + // The changed DictEntry will have + // - a correct PixelVR OB or OW) + // - the name to "Pixel Data" + + //==>Take it easy! + //==> Just change the VR ! + +/* + DataEntry *oldEntry = dynamic_cast(entry); + if (oldEntry) + { + VRKey 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 = DictEntry::New(GrPixel,NumPixel, + // PixelVR,"1","Pixel Data"); + //DataEntry *newEntry = DataEntry::New(newDict); + //newDict->Delete(); + //newEntry->Copy(entry); + //newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea()); + //oldEntry->SetSelfArea(false); + + //RemoveEntry(oldEntry); + //AddEntry(newEntry); + //newEntry->Delete(); + } + } +*/ + VRKey PixelVR; + // 8 bits allocated is a 'OB(ytes)' , as well as 24 (old ACR-NEMA RGB) + // more than 8 (i.e 12, 16) is a 'OW(ords)' + if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 ) + PixelVR = "OB"; + else + PixelVR = "OW"; + // Change only made if usefull + if ( PixelVR != entry->GetVR() ) + { + entry->SetVR(PixelVR); + } + } + return true; } /** - * \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( PixelConverter ) +bool File::IsReadable() +{ + if ( !Document::IsReadable() ) + { + return false; + } + + const std::string &res = GetEntryString(0x0028, 0x0005); + if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) + { + gdcmWarningMacro("Wrong Image Dimensions" << res); + return false; // Image Dimensions + } + bool b0028_0100 = true; + if ( !GetDocEntry(0x0028, 0x0100) ) + { + gdcmWarningMacro("Bits Allocated (0028|0100) not found"); + //return false; // "Bits Allocated" + b0028_0100 = false; + } + bool b0028_0101 = true; + if ( !GetDocEntry(0x0028, 0x0101) ) + { + gdcmWarningMacro("Bits Stored (0028|0101) not found"); + //return false; // "Bits Stored" + b0028_0101 = false; + } + bool b0028_0102 = true; + if ( !GetDocEntry(0x0028, 0x0102) ) { - delete PixelConverter; + gdcmWarningMacro("Hight Bit (0028|0102) not found"); + //return false; // "High Bit" + b0028_0102 = false; } - if( Archive ) + bool b0028_0103 = true; + if ( !GetDocEntry(0x0028, 0x0103) ) { - delete Archive; + gdcmWarningMacro("Pixel Representation (0028|0103) not found"); + //return false; // "Pixel Representation" i.e. 'Sign' ( 0 : unsigned, 1 : signed) + b0028_0103 = false; } - if( SelfHeader ) + if ( !b0028_0100 && !b0028_0101 && !b0028_0102 && !b0028_0103) { - delete HeaderInternal; + gdcmWarningMacro("Too much mandatory Tags missing !"); + return false; } - HeaderInternal = 0; + + if ( !GetDocEntry(GrPixel, NumPixel) ) + { + gdcmWarningMacro("Pixel Dicom Element " << std::hex << + GrPixel << "|" << NumPixel << "not found"); + return false; // Pixel Dicom Element not found :-( + } + return true; } -//----------------------------------------------------------------------------- -// Print +/** + * \brief gets the info from 0020,0013 : Image Number else 0. + * @return image number + */ +int File::GetImageNumber() +{ + //0020 0013 : Image Number + std::string strImNumber = GetEntryString(0x0020,0x0013); + if ( strImNumber != GDCM_UNFOUND ) + { + return atoi( strImNumber.c_str() ); + } + return 0; //Hopeless +} -//----------------------------------------------------------------------------- -// 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 0008,0060 : Modality + * @return Modality Type */ -size_t File::GetImageDataSize() +ModalityType File::GetModality() { - return PixelConverter->GetRGBSize(); + // 0008 0060 : Modality + std::string strModality = GetEntryString(0x0008,0x0060); + if ( strModality != GDCM_UNFOUND ) + { + 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 Unknow; } /** - * \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 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 */ -size_t File::GetImageDataRawSize() +int File::GetXSize() { - return PixelConverter->GetDecompressedSize(); + DataEntry *entry = GetDataEntry(0x0028,0x0011); + if( entry ) + return (int)entry->GetValue(0); + return 0; } /** - * \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). */ -uint8_t* File::GetImageData() +int File::GetYSize() { - if ( ! GetDecompressed() ) + DataEntry *entry = GetDataEntry(0x0028,0x0010); + if( entry ) + return (int)entry->GetValue(0); + + if ( IsDicomV3() ) { - // If the decompression failed nothing can be done. return 0; } - if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) + // The Rows (0028,0010) entry was optional for ACR/NEMA. + // (at least some images didn't have it.) + // It might hence be a signal (1D image). So we default to 1: + return 1; +} + +/** + * \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). + */ +int File::GetZSize() +{ + // Both DicomV3 and ACR/Nema consider the "Number of Frames" + // as the third dimension. + DataEntry *entry = GetDataEntry(0x0028,0x0008); + if( entry ) + return (int)entry->GetValue(0); + + // We then consider the "Planes" entry as the third dimension + entry = GetDataEntry(0x0028,0x0012); + if( entry ) + return (int)entry->GetValue(0); + return 1; +} + +// Special case: +// ts["1.2.840.10008.5.1.4.1.1.4.1"] = "Enhanced MR Image Storage"; +bool File::GetSpacing(float &xspacing, float &yspacing, float &zspacing) +{ + xspacing = yspacing = zspacing = 1.0; + TS *ts = Global::GetTS(); + std::string sopclassuid_used; + // D 0002|0002 [UI] [Media Storage SOP Class UID] + + //const std::string &mediastoragesopclassuid_str = GetEntryValue(0x0002,0x0002); + const std::string &mediastoragesopclassuid_str = GetEntryString(0x0002,0x0002); + const std::string &mediastoragesopclassuid = ts->GetValue(mediastoragesopclassuid_str); + //D 0008|0016 [UI] [SOP Class UID] + const std::string &sopclassuid_str = GetEntryString(0x0008,0x0016); + const std::string &sopclassuid = ts->GetValue(sopclassuid_str); + if ( mediastoragesopclassuid == GDCM_UNFOUND && sopclassuid == GDCM_UNFOUND ) + { + return false; + } + else + { + if( mediastoragesopclassuid == sopclassuid ) + { + sopclassuid_used = mediastoragesopclassuid; + } + else + { + gdcmWarningMacro( "Inconsistant SOP Class UID: " + << mediastoragesopclassuid << " and " << sopclassuid ); + return false; + } + } + // ok we have now the correc SOP Class UID + if( sopclassuid_used == "Enhanced MR Image Storage" ) + { + SeqEntry *PerframeFunctionalGroupsSequence = GetSeqEntry(0x5200,0x9230); + unsigned int n = PerframeFunctionalGroupsSequence->GetNumberOfSQItems(); + if( !n ) return false; + SQItem *item1 = PerframeFunctionalGroupsSequence->GetFirstSQItem(); + DocEntry *p = item1->GetDocEntry(0x0028,0x9110); + if( !p ) return false; + SeqEntry *seq = dynamic_cast(p); + unsigned int n1 = seq->GetNumberOfSQItems(); + if( !n1 ) return false; + SQItem *item2 = seq->GetFirstSQItem(); + // D 0028|0030 [DS] [Pixel Spacing] [0.83333331346511\0.83333331346511 ] + DocEntry *p2 = item2->GetDocEntry(0x0028,0x0030); + if( !p2 ) return false; + DataEntry *entry = dynamic_cast(p2); + std::string spacing = entry->GetString(); + if ( sscanf( spacing.c_str(), "%f\\%f", &yspacing, &xspacing) != 2 ) + { + xspacing = yspacing = 1.; + return false; + } + // D 0018|0050 [DS] [Slice Thickness] [1 ] + DocEntry *p3 = item2->GetDocEntry(0x0018,0x0050); + if( !p3 ) return false; + DataEntry *entry2 = dynamic_cast(p3); + std::string thickness = entry2->GetString(); + if ( sscanf( thickness.c_str(), "%f", &zspacing) != 1 ) + { + zspacing = 1.; + return false; + } + return true; + } + return false; + } + +/** + * \brief Retrieve the -unnormalized- number of 'times' of '4D image'. + * User has to tell gdcm the location of this '4th Dimension component' + * using SetFourthDimensionLocation() method before. + * \warning The defaulted value is 1. + * @return The encountered size when found, 1 by default + * (The file doesn't contain a '4D image'.). + */ +int File::GetTSize() +{ + if (FourthDimensionLocation == TagKey(0,0) )// 4D location is not set : not a 4D object + return 1; + + DataEntry *entry = GetDataEntry(FourthDimensionLocation.GetGroup(), + FourthDimensionLocation.GetElement() ); + if( !entry ) { - return PixelConverter->GetRGB(); + gdcmWarningMacro( " FourthDimensionLocation not found at : " << + std::hex << FourthDimensionLocation.GetGroup() + << "|" << FourthDimensionLocation.GetElement()); + return 1; } else { - // When no LUT or LUT conversion fails, return the decompressed - return PixelConverter->GetDecompressed(); - } -} - -/** - * \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) -{ - if ( ! GetDecompressed() ) - { - // If the decompression failed nothing can be done. - return 0; - } + return (int)entry->GetValue(0); + } +} - if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() ) +/** + * \brief gets the info from 0018,1164 : ImagerPixelSpacing + * then 0028,0030 : Pixel Spacing + * else 1.0 + * @return X dimension of a pixel + */ +float File::GetXSpacing() +{ + float xspacing = 1.0; + float yspacing = 1.0; + float zspacing = 1.0; + + uint32_t nbValue; + DataEntry *entry; + bool ok = false; + if ( GetSpacing(xspacing,yspacing,zspacing) ) + { + return xspacing; + } + // else fallback + +/* +From:David Clunie - view profile +Date:Wed, May 24 2006 1:12 pm +Email:David Clunie +Groups:comp.protocols.dicom + +The short answer is that: + +- (0018,1164) describes a spacing equivalent to that which + would be measured off a film in projection radiography + +- (0018,7022) does not describe the image pixels themselves, + since detector elements may have been binned to produce + pixels + +- (0018,7020) may be different from (0018,7022) since there + may be non-sensitive material separating individual + detectors (i.e. the size is smaller than the spacing + between centers) + +Only (0018,1164) is relevant when measuring things; the +detector-specific attributes are there to describe the +acquisition. + +David + +PS. For ultrasound you need to use Region Calibration. +*/ + +/* +It *SHOULD* first find the IOD and then deduce which tags to read +Eg: Cross section this is in Pixel Spacing (0028,0030) +CR is in Imager Pixel Spacing (0018,1164) +US is in Pixel Aspect Ratio (0028,0034) +RT is in : +(3002,0011) Image Plane Pixel Spacing +(3002,0012) RT Image Position +and +(3004,000c) for deducing Z spacing +*/ + + std::string SOPClassUID = GetEntryString(0x0008,0x0016); + + /// \todo check the various SOP Class + /// to get the Pixel Spacing at the proper location + + ///\todo find images to check if it *actually* works + + if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6") + // Ultrasound Image Storage (Retired) + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6.1") + // Ultrasound Image Storage + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3") + // Ultrasound Multi-Frame Storage (Retired) + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3.1") ) + // Ultrasound Multi-FrameImage Storage { - if ( PixelConverter->GetRGBSize() > maxSize ) + // - check if SOPClassUID contains 2 parts (e.g. "4\3") + // - guess how to deduce the spacing (FOV ?, ??) + + entry = GetDataEntry(0x0028,0x0034); + if ( entry ) { - dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" - "than caller's expected MaxSize"); - return 0; + nbValue = entry->GetValueCount(); + if( nbValue !=2 ) { + gdcmWarningMacro("PixelAspectRatio (0x0028,0x0034) " + << "has a wrong number of values :" << nbValue); + } + xspacing = 1.0; // We get Pixel Aspect Ratio, not Spacing ... + ok = true; } - memcpy( destination, - (void*)PixelConverter->GetRGB(), - PixelConverter->GetRGBSize() ); - return PixelConverter->GetRGBSize(); + + if (ok) + return xspacing; } +/* + if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.1") ) + // Computed Radiography Image Storage + + // CR is in Imager Pixel Spacing (0018,1164)// - // Either no LUT conversion necessary or LUT conversion failed - if ( PixelConverter->GetDecompressedSize() > maxSize ) +*/ + // go on with old method ... + // --------------------- + // To follow David Clunie's advice, we first check ImagerPixelSpacing + + entry = GetDataEntry(0x0018,0x1164); + if( entry ) { - dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger" - "than caller's expected MaxSize"); - return 0; + nbValue = entry->GetValueCount(); + // Can't use IsValueCountValid because of the complex heuristic. + if( nbValue !=2 ) + gdcmWarningMacro("ImagerPixelSpacing (0x0018,0x1164) " + << "has a wrong number of values :" << nbValue); + + if( nbValue >= 3 ) + xspacing = (float)entry->GetValue(2); + else if( nbValue >= 2 ) + xspacing = (float)entry->GetValue(1); + else + xspacing = (float)entry->GetValue(0); + + if ( xspacing == 0.0 ) + xspacing = 1.0; + return xspacing; + } + else + { + gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" ); + } + + entry = GetDataEntry(0x0028,0x0030); + if( entry ) + { + nbValue = entry->GetValueCount(); + if( nbValue !=2 ) + gdcmWarningMacro("PixelSpacing (0x0018,0x0030) " + << "has a wrong number of values :" << nbValue); + + if( nbValue >= 3 ) + xspacing = (float)entry->GetValue(2); + else if( nbValue >= 2 ) + xspacing = (float)entry->GetValue(1); + else + xspacing = (float)entry->GetValue(0); + + if ( xspacing == 0.0 ) + xspacing = 1.0; + return xspacing; + } + else + { + gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); } - memcpy( destination, - (void*)PixelConverter->GetDecompressed(), - PixelConverter->GetDecompressedSize() ); - return PixelConverter->GetDecompressedSize(); + return xspacing; } /** - * \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 gets the info from 0018,1164 : ImagerPixelSpacing + * then from 0028,0030 : Pixel Spacing + * else 1.0 + * @return Y dimension of a pixel + */ +float File::GetYSpacing() +{ + float xspacing = 1., yspacing = 1.0, zspacing = 1.; + uint32_t nbValue; + DataEntry *entry; + bool ok = false; + if ( GetSpacing(xspacing,yspacing,zspacing) ) + { + return yspacing; + } + // else fallback + + std::string SOPClassUID = GetEntryString(0x0008,0x0016); + + /// \todo check the various SOP Class + /// to get the Pixel Spacing at the proper location + + ///\todo find images to check if it *actually* works + + if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6") + // Ultrasound Image Storage (Retired) + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6.1") + // Ultrasound Image Storage + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3") + // Ultrasound Multi-Frame Storage (Retired) + || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3.1") ) + // Ultrasound Multi-FrameImage Storage + { + // - check if SOPClassUID contains 2 parts (e.g. "4\3") + // - no way to deduce the spacing/ + + entry = GetDataEntry(0x0028,0x0034); + if ( entry ) + { + nbValue = entry->GetValueCount(); + if( nbValue ==2 ) { + yspacing = (float)entry->GetValue(0)/(float)entry->GetValue(1); + //std::cout << "ys " << yspacing << std::endl; + ok = true; + } + else + { + gdcmWarningMacro("PixelAspectRatio (0x0028,0x0034) " + << "has a wrong number of values :" << nbValue); + if (nbValue == 0 ) { + ok = false; + } + else if (nbValue == 1 ) { + yspacing = 1.0; // We get Pixel Aspect Ratio, not Spacing ... + ok = true; + } + } + } + + if (ok) + return yspacing; + } + + // go on with old method ... + // --------------------- + // To follow David Clunie's advice, we first check ImagerPixelSpacing + yspacing = 1.0; + // To follow David Clunie's advice, we first check ImagerPixelSpacing + + entry = GetDataEntry(0x0018,0x1164); + if( entry ) + { + yspacing = (float)entry->GetValue(0); + + if ( yspacing == 0.0 ) + yspacing = 1.0; + return yspacing; + } + else + { + gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" ); + } + + entry = GetDataEntry(0x0028,0x0030); + if( entry ) + { + yspacing = (float)entry->GetValue(0); + + if ( yspacing == 0.0 ) + yspacing = 1.0; + return yspacing; + } + else + { + gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); + } + + return yspacing; +} + +/** + * \brief gets the info from 0018,0088 : Space Between Slices + * else from 0018,0050 : Slice Thickness + * else 1.0 + * + * When an element is missing, we suppose slices join together + * (no overlapping, no interslice gap) but we have no way to check it ! + * For *Dicom* images, ZSpacing *should be* calculated using + * XOrigin, YOrigin, ZOrigin (of the top left image corner) + * of 2 consecutive images, and the Orientation + * Computing ZSpacing on a single image is not really meaningfull ! + * @return Z dimension of a voxel-to be */ -uint8_t* File::GetImageDataRaw () +float File::GetZSpacing() { - return GetDecompressed(); + + float xspacing = 1.0; + float yspacing = 1.0; + float zspacing = 1.0; + if ( GetSpacing(xspacing,yspacing,zspacing) ) + { + return zspacing; + } + + // Spacing Between Slices : distance between the middle of 2 slices + // Slices may be : + // jointives (Spacing between Slices = Slice Thickness) + // overlapping (Spacing between Slices < Slice Thickness) + // disjointes (Spacing between Slices > Slice Thickness) + // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal + // It only concerns the MRI guys, not people wanting to visualize volumes + // If Spacing Between Slices is missing, + // we suppose slices joint together + DataEntry *entry = GetDataEntry(0x0018,0x0088); + if( entry ) + { zspacing = (float)entry->GetValue(0); + + if ( zspacing == 0.0 ) + zspacing = 1.0; + return zspacing; + } + else + gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)"); + + // if no 'Spacing Between Slices' is found, + // we assume slices join together + // (no overlapping, no interslice gap) + entry = GetDataEntry(0x0018,0x0050); + if( entry ) + { + zspacing = (float)entry->GetValue(0); + + if ( zspacing == 0.0 ) + zspacing = 1.0; + return zspacing; + } + else + gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); + + // if no 'Spacing Between Slices' is found, + // we assume slices join together + // (no overlapping, no interslice gap) + entry = GetDataEntry(0x3004,0x000c); + if( entry ) + { + float z1 = (float)entry->GetValue(0); + float z2 = (float)entry->GetValue(1); + zspacing = z2 - z1; // can be negative... + + if ( zspacing == 0.0 ) + zspacing = 1.0; + return zspacing; + } + + return zspacing; } -uint8_t* File::GetDecompressed() +/** + * \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() { - uint8_t* decompressed = PixelConverter->GetDecompressed(); - if ( ! decompressed ) + DataEntry *entry = GetDataEntry(0x0020,0x0032); + if( !entry ) { - // The decompressed image migth not be loaded yet: - std::ifstream* fp = HeaderInternal->OpenFile(); - PixelConverter->ReadAndDecompressPixelData( fp ); - if(fp) - HeaderInternal->CloseFile(); - - decompressed = PixelConverter->GetDecompressed(); - if ( ! decompressed ) + gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); + entry = GetDataEntry(0x0020,0x0030); + if( !entry ) { - dbg.Verbose(0, "File::GetDecompressed: read/decompress of " - "pixel data apparently went wrong."); - return 0; + gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); + return 0.0f; } } - return decompressed; + if( entry->GetValueCount() == 3 ) + { + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(0); + } + return 0.0f; } /** - * \brief Points the internal Pixel_Data 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 + * \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 */ -bool File::SetImageData(uint8_t* inData, size_t expectedSize) +float File::GetYOrigin() { -// FIXME : if already allocated, memory leak ! - Pixel_Data = inData; - ImageDataSize = expectedSize; -// FIXME : 7fe0, 0010 IS NOT set ... - return true; + DataEntry *entry = GetDataEntry(0x0020,0x0032); + if( !entry ) + { + gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); + entry = GetDataEntry(0x0020,0x0030); + if( !entry ) + { + gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); + return 0.0f; + } + } + + if( entry->GetValueCount() == 3 ) + { + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(1); + } + return 0.0f; } /** - * \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 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() +{ + DataEntry *entry = GetDataEntry(0x0020,0x0032); + if( entry ) + { + if( entry->GetValueCount() == 3 ) + { + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(2); + } + gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); + return 0.0f; + } + + entry = GetDataEntry(0x0020,0x0030); + if( entry ) + { + if( entry->GetValueCount() == 3 ) + { + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(2); + } + gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); + return 0.0f; + } + + // for *very* old ACR-NEMA images + entry = GetDataEntry(0x0020,0x1041); + if( entry ) + { + if( entry->GetValueCount() == 1 ) + { + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(0); // VM=1 ! + } + gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); + return 0.0f; + } + + entry = GetDataEntry(0x0020,0x0050); + if( entry ) + { + if( entry->GetValueCount() == 1 ) + { + if (!entry->IsValueCountValid() ) + { + gdcmErrorMacro( "Invalid Value Count" ); + } + return (float)entry->GetValue(0); + } + gdcmWarningMacro( "Wrong Location (0020,0050)"); + return 0.0f; + } + return 0.; // Hopeless +} -bool File::WriteRawData(std::string const & fileName) +/** + * \brief gets the info from 0020,0037 : Image Orientation Patient + * or from 0020 0035 : Image Orientation (RET) + * + * (needed to organize DICOM files based on their x,y,z position) + * + * @param iop adress of the (6)float array to receive values. + * (defaulted as 1.,0.,0.,0.,1.,0. if nothing -or inconsistent stuff- + * is found. + * @return true when one of the tag -with consistent values- is found + * false when nothing or inconsistent stuff - is found + */ +bool File::GetImageOrientationPatient( float iop[6] ) { - std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary ); - if (!fp1) + std::string strImOriPat; + //iop is supposed to be float[6] + iop[0] = iop[4] = 1.; + iop[1] = iop[2] = iop[3] = iop[5] = 0.; + + // 0020 0037 DS REL Image Orientation (Patient) + if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND ) { - dbg.Verbose(2, "Fail to open (write) file:", fileName.c_str()); - return false; + 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." ); + return false; + } + return true; + } + //For ACR-NEMA + // 0020 0035 DS REL Image Orientation (RET) + else if ( (strImOriPat = GetEntryString(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." ); + return false; + } + return true; } - fp1.write((char*)Pixel_Data, ImageDataSize); - fp1.close(); + return false; +} - return true; +/** + * \brief gets the cosine of image X axis, against patient X axis + * (Sorry, but Python needs it :-( ) + * @return cosine of image X axis, against patient X axis + */ +float File::GetXCosineOnX() +{ + float iop[6]; + GetImageOrientationPatient( iop ); + return(iop[0]); } + +/** + * \brief gets the cosine of image X axis, against patient Y axis + * (Sorry, but Python needs it :-( ) + * @return cosine of image X axis, against patient Y axis + */ +float File::GetXCosineOnY() +{ + float iop[6]; + GetImageOrientationPatient( iop ); + return(iop[1]); +} /** - * \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 gets the cosine of image X axis, against patient Z axis + * (Sorry, but Python needs it :-( ) + * @return cosine of image X axis, against patient Z axis + */ +float File::GetXCosineOnZ() +{ + float iop[6]; + GetImageOrientationPatient( iop ); + return(iop[2]); +} -bool File::WriteDcmImplVR (std::string const & fileName) +/** + * \brief gets the cosine of image Y axis, against patient X axis + * (Sorry, but Python needs it :-( ) + * @return cosine of image Y axis, against patient X axis + */ +float File::GetYCosineOnX() +{ + float iop[6]; + GetImageOrientationPatient( iop ); + return(iop[3]); +} + +/** + * \brief gets the cosine of image Y axis, against patient Y axis + * (Sorry, but Python needs it :-( ) + * @return cosine of image Y axis, against patient Y axis + */ +float File::GetYCosineOnY() +{ + float iop[6]; + GetImageOrientationPatient( iop ); + return(iop[4]); +} + +/** + * \brief gets the cosine of image Y axis, against patient Z axis + * (Sorry, but Python needs it :-( ) + * @return cosine of image Y axis, against patient Z axis + */ +float File::GetYCosineOnZ() +{ + float iop[6]; + GetImageOrientationPatient( iop ); + return(iop[5]); +} +/** + * \brief gets the info from 0020,0032 : Image Position Patient + * or from 0020 0030 : Image Position (RET) + * + * @param ipp adress of the (3)float array to receive values. + * (defaulted as 0.,0.,0. if nothing -or inconsistent stuff- + * is found. + * @return true when one of the tag -with consistent values- is found + * false when nothing or inconsistent stuff - is found + */ +bool File::GetImagePositionPatient( float ipp[3] ) { - SetWriteTypeToDcmImplVR(); - return Write(fileName); + std::string strImPosiPat; + //ipp is supposed to be float[3] + ipp[0] = ipp[1] = ipp[2] = 0.; + + // 0020 0032 DS REL Image Position (Patient) + strImPosiPat = GetEntryString(0x0020,0x0032); + if ( strImPosiPat != GDCM_UNFOUND ) + { + if ( sscanf( strImPosiPat.c_str(), "%f \\ %f \\%f ", + &ipp[0], &ipp[1], &ipp[2]) != 3 ) + { + gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)." + << " Less than 3 values were found." ); + return false; + } + return true; + } + //For ACR-NEMA + // 0020 0030 DS REL Image Position (RET) + else if ( (strImPosiPat = GetEntryString(0x0020,0x0030)) != GDCM_UNFOUND ) + { + if ( sscanf( strImPosiPat.c_str(), "%f \\ %f \\%f ", + &ipp[0], &ipp[1], &ipp[2]) != 3 ) + { + gdcmWarningMacro( "wrong Image Position Patient (0020,0030). " + << "Less than 3 values were found." ); + return false; + } + return true; + } + return false; } /** -* \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 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 ! */ - -bool File::WriteDcmExplVR (std::string const & fileName) +int File::GetBitsStored() { - SetWriteTypeToDcmExplVR(); - return Write(fileName); + DataEntry *entry = GetDataEntry(0x0028,0x0101); + if( !entry ) + { + gdcmWarningMacro("BitsStored (0028,0101) is supposed to be mandatory"); + return 0; + } + return (int)entry->GetValue(0); } /** - * \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 Retrieve the number of Bits Allocated + * (8, 12 -compacted ACR-NEMA files-, 16, 24 -old RGB ACR-NEMA files-,) + * @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() +{ + DataEntry *entry = GetDataEntry(0x0028,0x0100); + if( !entry ) + { + gdcmWarningMacro("BitsAllocated (0028,0100) is supposed to be mandatory"); + return 0; + } + return (int)entry->GetValue(0); +} -bool File::WriteAcr (std::string const & fileName) +/** + * \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 position when present. 0 when missing. + */ +int File::GetHighBitPosition() { - SetWriteTypeToAcr(); - return Write(fileName); + DataEntry *entry = GetDataEntry(0x0028,0x0102); + if( !entry ) + { + gdcmWarningMacro("HighBitPosition (0028,0102) is supposed to be mandatory"); + return 0; + } + return (int)entry->GetValue(0); } -bool File::Write(std::string const& fileName) +/** + * \brief Retrieve the number of Samples Per Pixel + * (1 : gray level, 3 : RGB/YBR -1 or 3 Planes-) + * @return The encountered number of Samples Per Pixel, 1 by default. + * (we assume Gray level Pixels) + */ +int File::GetSamplesPerPixel() { - switch(WriteType) + DataEntry *entry = GetDataEntry(0x0028,0x0002); + if( !entry ) { - case WTYPE_IMPL_VR: - return WriteBase(fileName,ImplicitVR); - case WTYPE_EXPL_VR: - return WriteBase(fileName,ExplicitVR); - case WTYPE_ACR: - return WriteBase(fileName,ACR); + gdcmWarningMacro("SamplesPerPixel (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(false); + return (int)entry->GetValue(0); } /** - * \brief Access to the underlying \ref PixelConverter RGBA LUT + * \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. */ -uint8_t* File::GetLutRGBA() +int File::GetPlanarConfiguration() { - return PixelConverter->GetLutRGBA(); + DataEntry *entry = GetDataEntry(0x0028,0x0006); + if( !entry ) + { + return 0; + } + return (int)entry->GetValue(0); } -//----------------------------------------------------------------------------- -// 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, FileType type) -{ - switch(type) - { - case ImplicitVR: - SetWriteFileTypeToImplicitVR(); - break; - case ExplicitVR: - SetWriteFileTypeToExplicitVR(); - break; - case ACR: - SetWriteFileTypeToACR(); - break; - case ACR_LIBIDO: - SetWriteFileTypeToACRLibido(); - break; + * \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 ACR-NEMA RGB images) + assert( !(GetEntryString(0x0028,0x0100) == "24") ); + + std::string pixelType = GetPixelType(); + if ( pixelType == "8U" || pixelType == "8S" ) + { + return 1; } - - switch(WriteMode) + if ( pixelType == "16U" || pixelType == "16S") + { + return 2; + } + if ( pixelType == "32U" || pixelType == "32S") { - case WMODE_NATIVE : - SetWriteToNative(); - break; - case WMODE_DECOMPRESSED : - SetWriteToDecompressed(); - break; - case WMODE_RGB : - SetWriteToRGB(); - break; + return 4; } + if ( pixelType == "FD" ) + { + return 8; + } + gdcmWarningMacro( "Unknown pixel type: " << pixelType); + return 0; +} - // -------------------------------------------------------------- - // 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 ( HeaderInternal->GetFileType() == ACR_LIBIDO) +/** + * \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 + photochromatic interp ="RGB " + * + Planar Configuration = 0 + * @return 0S if nothing found. NOT USABLE file. The caller has to check + */ +std::string File::GetPixelType() +{ + std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated + if ( bitsAlloc == GDCM_UNFOUND ) { - SetWriteToLibido(); - }*/ - // ----------------- End of Special Patch ---------------- + gdcmWarningMacro( "Bits Allocated (0028,0100) supposed to be mandatory"); + bitsAlloc = "16"; // default and arbitrary value, not to polute the output + } - bool check = CheckWriteIntegrity(); - if(check) + else if ( bitsAlloc == "64" ) + { + return "FD"; + } + // useless since we have to bypass a bug ( >8 && < 16) + else if ( bitsAlloc == "12" ) + { + // It will be unpacked + bitsAlloc = "16"; + } + + else if ( bitsAlloc == "24" ) { - check = HeaderInternal->Write(fileName,type); + // (in order no to be messed up by old RGB images) + bitsAlloc = "8"; } - // -------------------------------------------------------------- - // 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 -/* if ( HeaderInternal->GetFileType() == ACR_LIBIDO ) + int i= atoi(bitsAlloc.c_str()); // fix a bug in some headers + if ( i > 8 && i < 16 ) { - RestoreWriteFromLibido(); - }*/ - // ----------------- End of Special Patch ---------------- + bitsAlloc = "16"; + } - RestoreWrite(); - RestoreWriteFileType(); + std::string sign; + if( IsSignedPixelData() ) + { + sign = "S"; + } + else + { + sign = "U"; + } + return bitsAlloc + sign; +} - return check; +/** + * \brief Check whether the pixels are signed (1) or UNsigned (0) data. + * \warning The method defaults to false (UNsigned) when tag 0028|0103 + * is missing. + * The responsability of checking this value is left to the caller + * (NO transformation is performed on the pixels to make then >0) + * @return True when signed, false when UNsigned + */ +bool File::IsSignedPixelData() +{ + DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation" + if( !entry ) + { + gdcmWarningMacro( "Pixel Representation (0028,0103) supposed to be " + << "mandatory"); + return false; + } + return entry->GetValue(0) != 0; } /** - * \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 Check whether this a monochrome picture (gray levels) or not, + * using "Photometric Interpretation" tag (0x0028,0x0004). + * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise. */ -bool File::CheckWriteIntegrity() +bool File::IsMonochrome() { - if(Pixel_Data) + const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); + if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") + || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") ) { - int numberBitsAllocated = HeaderInternal->GetBitsAllocated(); - if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 ) - { - numberBitsAllocated = 16; - } + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Photometric Interpretation (0028,0004) supposed to be " + << "mandatory"); + // to deal with old ACR-NEMA images + if (GetNumberOfScalarComponents() == 1) + return true; + } + return false; +} - int decSize = HeaderInternal->GetXSize() - * HeaderInternal->GetYSize() - * HeaderInternal->GetZSize() - * ( numberBitsAllocated / 8 ) - * HeaderInternal->GetSamplesPerPixel(); - int rgbSize = decSize; - if( HeaderInternal->HasLUT() ) - rgbSize = decSize * 3; +/** + * \brief Check whether this a MONOCHROME1 picture (high values = dark) + * or not using "Photometric Interpretation" tag (0x0028,0x0004). + * @return true when "MONOCHROME1" . False otherwise. + */ +bool File::IsMonochrome1() +{ + const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); + if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") ) + { + return true; + } + if ( PhotometricInterp == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Photometric Interpretation (0028,0004) : supposed to" + << " be mandatory! "); + } + return false; +} - switch(WriteMode) - { - case WMODE_NATIVE : - break; - case WMODE_DECOMPRESSED : - if( decSize!=ImageDataSize ) - { - dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect"); - //std::cerr<<"Dec : "<GetGrPixel(),GetHeader()->GetNumPixel()); - pixel->SetValue(GDCM_BINLOADED); - pixel->SetBinArea(Pixel_Data,false); - pixel->SetLength(ImageDataSize); + gdcmDebugMacro( "Not found : YBR Full (0028,0004)"); + } + return false; +} - Archive->Push(pixel); +/** + * \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; + } + // LutDescriptorGreen + if ( !GetDocEntry(0x0028,0x1102) ) + { + return false; + } + // LutDescriptorBlue + if ( !GetDocEntry(0x0028,0x1103) ) + { + return false; } + // Red Palette Color Lookup Table Data + bool segmented; + segmented = GetDocEntry(0x0028,0x1221) && + GetDocEntry(0x0028,0x1222) && + GetDocEntry(0x0028,0x1223); + if( segmented ) return true; + + 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; } -void File::SetWriteToDecompressed() +/** + * \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() { - if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT()) + 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 = GetEntryString(0x0028,0x1101); + if ( lutDescription == GDCM_UNFOUND ) { - SetWriteToRGB(); - } - else + return 0; + } + + 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; +} + +// Special case: +// ts["1.2.840.10008.5.1.4.1.1.4.1"] = "Enhanced MR Image Storage"; + bool File::GetRescaleSlopeIntercept(double &slope, double &intercept) { - ValEntry* photInt = CopyValEntry(0x0028,0x0004); - if(HeaderInternal->HasLUT()) - { - photInt->SetValue("PALETTE COLOR "); - photInt->SetLength(14); - } + slope = 1.0; + intercept = 0.0; + TS *ts = Global::GetTS(); + std::string sopclassuid_used; + // D 0002|0002 [UI] [Media Storage SOP Class UID] + const std::string &mediastoragesopclassuid_str = GetEntryString(0x0002,0x0002); + const std::string &mediastoragesopclassuid = ts->GetValue(mediastoragesopclassuid_str); + //D 0008|0016 [UI] [SOP Class UID] + const std::string &sopclassuid_str = GetEntryString(0x0008,0x0016); + const std::string &sopclassuid = ts->GetValue(sopclassuid_str); + if ( mediastoragesopclassuid == GDCM_UNFOUND && sopclassuid == GDCM_UNFOUND ) + { + return false; + } else - { - photInt->SetValue("MONOCHROME1 "); - photInt->SetLength(12); - } + { + if( mediastoragesopclassuid == sopclassuid ) + { + sopclassuid_used = mediastoragesopclassuid; + } + else + { + gdcmWarningMacro( "Inconsistant SOP Class UID: " + << mediastoragesopclassuid << " and " << sopclassuid ); + return false; + } + } + // ok we have now the correc SOP Class UID + if( sopclassuid_used == "Enhanced MR Image Storage" ) + { + SeqEntry *PerframeFunctionalGroupsSequence = GetSeqEntry(0x5200,0x9230); + unsigned int n = PerframeFunctionalGroupsSequence->GetNumberOfSQItems(); + if( !n ) return false; + SQItem *item1 = PerframeFunctionalGroupsSequence->GetFirstSQItem(); + DocEntry *p = item1->GetDocEntry(0x0028,0x9145); + if( !p ) return false; + SeqEntry *seq = dynamic_cast(p); + unsigned int n1 = seq->GetNumberOfSQItems(); + if( !n1 ) return false; + SQItem *item2 = seq->GetFirstSQItem(); + // D 0028|1052 [DS] [Rescale Intercept] [0 ] + DocEntry *p2 = item2->GetDocEntry(0x0028,0x1052); + if( !p2 ) return false; + DataEntry *entry = dynamic_cast(p2); + std::string intercept_str = entry->GetString(); + if ( sscanf( intercept_str.c_str(), "%lf", &intercept) != 1 ) + { + intercept = 0.; + return false; + } + // D 0028|1053 [DS] [Rescale Slope] [5.65470085470085] + DocEntry *p3 = item2->GetDocEntry(0x0028,0x1053); + if( !p3 ) return false; + DataEntry *entry2 = dynamic_cast(p3); + std::string slope_str = entry2->GetString(); + if ( sscanf( slope_str.c_str(), "%lf", &slope) != 1 ) + { + slope = 1.; + return false; + } + return true; + } + return false; + } - BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); - pixel->SetValue(GDCM_BINLOADED); - if(Pixel_Data) - { - pixel->SetBinArea(Pixel_Data,false); - pixel->SetLength(ImageDataSize); - } - else +/** + *\brief gets the info from 0028,1052 : Rescale Intercept + * @return Rescale Intercept. defaulted to 0.0 if not found or empty + */ +double File::GetRescaleIntercept() +{ + // 0028 1052 DS IMG Rescale Intercept + DataEntry *entry = GetDataEntry(0x0028, 0x1052); + if( !entry ) + { + gdcmWarningMacro( "Missing Rescale Intercept (0028,1052)"); + return 0.0f; + } + return (float)entry->GetValue(0); + +} + +/** + *\brief gets the info from 0028,1053 : Rescale Slope + * @return Rescale Slope. defaulted to 1.0 if not found or empty + */ +double File::GetRescaleSlope() +{ + double resInter = 0.; + double resSlope = 1.; + if ( GetRescaleSlopeIntercept(resSlope, resInter) ) + { + return resSlope; + } + //0028 1053 DS IMG Rescale Slope + std::string strRescSlope = GetEntryString(0x0028,0x1053); + if ( strRescSlope != GDCM_UNFOUND ) + { + if ( sscanf( strRescSlope.c_str(), "%lf ", &resSlope) != 1 ) { - pixel->SetBinArea(PixelConverter->GetDecompressed(),false); - pixel->SetLength(PixelConverter->GetDecompressedSize()); + // bug in the element 0x0028,0x1053 + gdcmWarningMacro( "Rescale Slope (0028,1053) is empty."); } - - 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, if no LUT found ...) + * \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 ) { - PixelConverter->BuildRGBImage(); - - ValEntry* spp = CopyValEntry(0x0028,0x0002); - spp->SetValue("3 "); - spp->SetLength(2); + return 3; + } - ValEntry* planConfig = CopyValEntry(0x0028,0x0006); - planConfig->SetValue("0 "); - planConfig->SetLength(2); + // 0028 0100 US IMG Bits Allocated + // (in order no to be messed up by old RGB images) + if ( GetEntryString(0x0028,0x0100) == "24" ) + { + return 3; + } - ValEntry* photInt = CopyValEntry(0x0028,0x0004); - photInt->SetValue("RGB "); - photInt->SetLength(4); + std::string strPhotometricInterpretation = GetEntryString(0x0028,0x0004); - BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel()); - pixel->SetValue(GDCM_BINLOADED); - if(Pixel_Data) - { - pixel->SetBinArea(Pixel_Data,false); - pixel->SetLength(ImageDataSize); - } - else if(PixelConverter->GetRGB()) + if ( ( strPhotometricInterpretation == "PALETTE COLOR ") ) + { + if ( HasLUT() )// PALETTE COLOR is NOT enough { - pixel->SetBinArea(PixelConverter->GetRGB(),false); - pixel->SetLength(PixelConverter->GetRGBSize()); + return 3; } - else // Decompressed data + else { - pixel->SetBinArea(PixelConverter->GetDecompressed(),false); - pixel->SetLength(PixelConverter->GetDecompressedSize()); + return 1; } + } - 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 "); - bitsAlloc->SetLength(2); - - ValEntry* bitsStored = CopyValEntry(0x0028,0x0101); - bitsStored->SetValue("8 "); - bitsStored->SetLength(2); - - ValEntry* highBit = CopyValEntry(0x0028,0x0102); - highBit->SetValue("7 "); - highBit->SetLength(2); - - 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 { - SetWriteToDecompressed(); + // 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::GetEntryString(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 + { + gdcmWarningMacro( "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); + return 0; + } } -void File::SetWriteFileTypeToACRLibido() +/** + * \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() { - SetWriteFileTypeToACR(); + DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel); + if ( pxlElement ) + { + return pxlElement->GetLength(); + } + else + { + gdcmWarningMacro( "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); + return 0; + } +} + +/** + * \brief Adds the characteristics of a new element we want to anonymize + * @param group Group number of the target tag. + * @param elem Element number of the target tag. + * @param value new value (string) to substitute with + */ +void File::AddAnonymizeElement (uint16_t group, uint16_t elem, + std::string const &value) +{ + DicomElement el; + el.Group = group; + el.Elem = elem; + el.Value = value; + UserAnonymizeList.push_back(el); } -void File::SetWriteFileTypeToExplicitVR() +/** + * \brief Overwrites in the file the values of the DicomElements + * held in the list + */ +void File::AnonymizeNoLoad() { - std::string ts = - Util::DicomString( TransferSyntaxStrings[ExplicitVRLittleEndian] ); + std::fstream *fp = new std::fstream(Filename.c_str(), + std::ios::in | std::ios::out | std::ios::binary); + GDCM_NAME_SPACE::DocEntry *d; + uint32_t offset; + uint32_t lgth; + uint32_t valLgth = 0; + std::string *spaces; + for (ListElements::iterator it = UserAnonymizeList.begin(); + it != UserAnonymizeList.end(); + ++it) + { + + //std::cout << "File::AnonymizeNoLoad -------" << std::hex <<(*it).Group <<"|"<< + // (*it).Elem + // << "[" << (*it).Value << "] "<< std::dec << std::endl; + d = GetDocEntry( (*it).Group, (*it).Elem); + + if ( d == NULL) + continue; + + if ( dynamic_cast(d) ) + { + gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry "); + continue; + } - ValEntry* tss = CopyValEntry(0x0002,0x0010); - tss->SetValue(ts); - tss->SetLength(ts.length()); + valLgth = (*it).Value.size(); + if (valLgth == 0) + continue; - Archive->Push(tss); + offset = d->GetOffset(); + lgth = d->GetLength(); + + //std::cout << "lgth " << lgth << " valLgth " << valLgth << std::endl; + if (valLgth < lgth) + { + spaces = new std::string( lgth-valLgth, ' '); + (*it).Value = (*it).Value + *spaces; + //std::cout << "[" << (*it).Value << "] " << lgth << std::endl; + 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 (remove Patient's personal info passed with + * AddAnonymizeElement() + * \note You cannot Anonymize a DataEntry (to be fixed) + */ +bool File::AnonymizeFile() { - std::string ts = - Util::DicomString( TransferSyntaxStrings[ImplicitVRLittleEndian] ); + // If Anonymisation list is empty, let's perform some basic anonymization + if ( UserAnonymizeList.begin() == UserAnonymizeList.end() ) + { + // If exist, replace by spaces + SetEntryString(" ",0x0010, 0x2154); // Telephone + SetEntryString(" ",0x0010, 0x1040); // Adress + SetEntryString(" ",0x0010, 0x0020); // Patient ID - ValEntry* tss = CopyValEntry(0x0002,0x0010); - tss->SetValue(ts); - tss->SetLength(ts.length()); + DocEntry *patientNameHE = GetDocEntry (0x0010, 0x0010); + + if ( patientNameHE ) // we replace it by Study Instance UID (why not ?) + { + std::string studyInstanceUID = GetEntryString (0x0020, 0x000d); + if ( studyInstanceUID != GDCM_UNFOUND ) + { + SetEntryString(studyInstanceUID, 0x0010, 0x0010); + } + else + { + SetEntryString("anonymized", 0x0010, 0x0010); + } + } + } + else + { + GDCM_NAME_SPACE::DocEntry *d; + for (ListElements::iterator it = UserAnonymizeList.begin(); + it != UserAnonymizeList.end(); + ++it) + { + d = GetDocEntry( (*it).Group, (*it).Elem); + + if ( d == NULL) + continue; + + if ( dynamic_cast(d) ) + { + gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry "); + continue; + } + + if ( dynamic_cast(d) ) + { + gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) "); + continue; + } + else + SetEntryString ((*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 writetype type of the file to be written + * (ACR, ExplicitVR, ImplicitVR) + */ +bool File::Write(std::string fileName, FileType writetype) { - ValEntry *oldRow = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010)); - ValEntry *oldCol = dynamic_cast(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011)); - - if( oldRow && oldCol ) + gdcmDebugMacro(" File::Write "); + std::ofstream *fp = new std::ofstream(fileName.c_str(), + std::ios::out | std::ios::binary); + if (*fp == NULL) { - std::string rows, columns; + gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str()); + return false; + } - ValEntry *newRow=new ValEntry(oldRow->GetDictEntry()); - ValEntry *newCol=new ValEntry(oldCol->GetDictEntry()); + // Entry : 0002|0000 = group length -> recalculated + DataEntry *e0000 = GetDataEntry(0x0002,0x0000); + if ( e0000 ) + { + std::ostringstream sLen; + sLen << ComputeGroup0002Length( ); + e0000->SetString(sLen.str()); + } - newRow->Copy(oldCol); - newCol->Copy(oldRow); + /// \todo FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx + if( writetype != JPEG && writetype != JPEG2000) + { + int i_lgPix = GetEntryLength(GrPixel, NumPixel); + if (i_lgPix != -2) /// \todo wtf "-2" ?!? + { + // no (GrPixel, NumPixel) element + std::string s_lgPix = Util::Format("%d", i_lgPix+12); + s_lgPix = Util::DicomString( s_lgPix.c_str() ); + InsertEntryString(s_lgPix,GrPixel, 0x0000, "UL"); + } + } + Document::WriteContent(fp, writetype,false,false); - newRow->SetValue(oldCol->GetValue()); - newCol->SetValue(oldRow->GetValue()); + fp->close(); + delete fp; - Archive->Push(newRow); - Archive->Push(newCol); - } + return true; } -void File::RestoreWriteFromLibido() -{ - Archive->Restore(0x0028,0x0010); - Archive->Restore(0x0028,0x0011); -} +//----------------------------------------------------------------------------- +// Protected -ValEntry* File::CopyValEntry(uint16_t group,uint16_t element) -{ - DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element); - ValEntry* newE; - if(oldE) +//----------------------------------------------------------------------------- +// Private +/** + * \brief Parse pixel data from disk of [multi-]fragment RLE encoding. + * Compute the RLE extra information and store it in RLEInfo + * for later pixel retrieval usage. + */ +void File::ComputeRLEInfo() +{ + std::string ts = GetTransferSyntax(); + if ( !Global::GetTS()->IsRLELossless(ts) ) { - newE = new ValEntry(oldE->GetDictEntry()); - newE->Copy(oldE); + return; } - else - { - newE = GetHeader()->NewValEntryByNumber(group,element); + + // 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" + ReadEncapsulatedBasicOffsetTable(); + + // 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; + int i=0; + uint32_t sum = 0; + while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) != 0 ) + { + // Since we have read the basic offset table, let's check the value were correct + // or else produce a warning: + if ( BasicOffsetTableItemValue ) + { + // If a BasicOffsetTableItemValue was read + uint32_t individualLength = BasicOffsetTableItemValue[i]; + assert( individualLength == sum ); // REMOVE that if this is a problem + if( individualLength != sum ) + { + gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght" ); + } + sum += frameLength + 8; + i++; + } + // 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(); // once per fragment + + 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 RLE Header and 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); } - return(newE); + // Make sure that we encounter a 'Sequence Delimiter Item' + // at the end of the item : + if ( !ReadTag(0xfffe, 0xe0dd) ) // once per RLE File + { + gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence"); + } } -BinEntry* File::CopyBinEntry(uint16_t group,uint16_t element) +/** + * \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 JPEGInfo for later pixel + * retrieval usage. + */ +void File::ComputeJPEGFragmentInfo() { - DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element); - BinEntry* newE; + // If you need to, look for comments of ComputeRLEInfo(). + std::string ts = GetTransferSyntax(); + if ( ! Global::GetTS()->IsJPEG(ts) ) + { + return; + } + + ReadEncapsulatedBasicOffsetTable(); + + // Loop on the fragments[s] and store the parsed information in a + // JPEGInfo. + long fragmentLength; + int i=0; + uint32_t sum = 0; + while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 ) + { + // Since we have read the basic offset table, let's check the value were correct + // or else produce a warning: + // A.4 Transfer syntaxes for encapsulation of encoded pixel data: + // When the Item Value is present, the Basic Offset Table Item Value shall contain + // concatenated 32-bit unsigned integer values that are byte offsets to the first + // byte of the Item Tag of the first fragment for each frame in the Sequence of + // Items. These offsets are measured from the first byte of the first Item Tag + // following the Basic Offset Table item (See Table A.4-2). + + if ( BasicOffsetTableItemValue ) + { + // If a BasicOffsetTableItemValue was read + uint32_t individualLength = BasicOffsetTableItemValue[i]; + //assert( individualLength == sum ); // Seems like 00191113.dcm is off by one ?? + if( individualLength != sum ) + { + gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght:" << + individualLength << " != " << sum ); + } + sum += fragmentLength + 8; + i++; + } + + long fragmentOffset = Fp->tellg(); // Once per fragment + // Store the collected info + JPEGFragment *newFragment = new JPEGFragment; + newFragment->SetOffset(fragmentOffset); + newFragment->SetLength(fragmentLength); + JPEGInfo->AddFragment(newFragment); + + SkipBytes(fragmentLength); + } - if(oldE) + // Make sure that we encounter a 'Sequence Delimiter Item' + // at the end of the item : + if ( !ReadTag(0xfffe, 0xe0dd) ) { - newE = new BinEntry(oldE->GetDictEntry()); - newE->Copy(oldE); + gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence"); } - else +} + +/** + * \brief Assuming the internal file pointer Document::Fp + * is placed at the beginning of a tag, check whether this + * tag is (TestGroup, TestElem). + * \warning On success the internal file pointer Document::Fp + * is modified to point after the tag. + * On failure (i.e. when the tag wasn't the expected tag + * (TestGroup, TestElem) the internal file pointer + * Document::Fp is restored to its original position. + * @param testGroup The expected group of the tag. + * @param testElem The expected Element of the tag. + * @return True on success, false otherwise. + */ +bool File::ReadTag(uint16_t testGroup, uint16_t testElem) +{ + long positionOnEntry = Fp->tellg(); // Only when reading fragments + //long currentPosition = positionOnEntry; // On debugging purposes + + // Read the Item Tag group and element, and make + // sure they are what we expected: + uint16_t itemTagGroup; + uint16_t itemTagElem; + try { - newE = GetHeader()->NewBinEntryByNumber(group,element); + itemTagGroup = ReadInt16(); + itemTagElem = ReadInt16(); } + catch ( FormatError ) + { + gdcmErrorMacro( "Can not read tag for " + << " We should have found tag (" + << DictEntry::TranslateToKey(testGroup,testElem) << ")" + ) ; + return false; + } + if ( itemTagGroup != testGroup || itemTagElem != testElem ) + { + // in order not to pollute output we don't warn on 'delimitors' + if (itemTagGroup != 0xfffe || testGroup != 0xfffe ) + gdcmWarningMacro( "Wrong Item Tag found:" + << " We should have found tag (" + << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl + << " but instead we encountered tag (" + << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")" + << " at address: " << " 0x(" << std::hex + << (unsigned int)positionOnEntry << std::dec << ")" + ) ; + Fp->seekg(positionOnEntry, std::ios::beg); - return(newE); + return false; + } + return true; } -//----------------------------------------------------------------------------- -// Private /** - * \brief Set the pixel datas in the good entry of the Header + * \brief Assuming the internal file pointer 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 Document::Fp + * is modified to point after the tag and its length. + * On failure (i.e. when the tag wasn't the expected tag + * (TestGroup, TestElement) the internal file pointer + * Document::Fp is restored to its original position. + * @param testGroup The expected Group of the tag. + * @param testElem The expected Element of the tag. + * @return On success returns the length associated to the tag. On failure + * returns 0. */ -void File::SetPixelData(uint8_t* data) +uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem) { - GetHeader()->SetEntryByNumber( GDCM_BINLOADED, - GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - // Will be 7fe0, 0010 in standard case - DocEntry* currentEntry = GetHeader()->GetDocEntryByNumber(GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel()); - if ( currentEntry ) + if ( !ReadTag(testGroup, testElem) ) { - if ( BinEntry* binEntry = dynamic_cast(currentEntry) ) - // Flag is to false because datas are kept in the gdcmPixelConvert - binEntry->SetBinArea( data, false ); + // Avoid polutting output + if ( testGroup != 0xfffe ) + gdcmErrorMacro( "ReadTag did not succeed for (" + << DictEntry::TranslateToKey(testGroup,testElem) + << ")..." ); + return 0; } + + //// Then read the associated Item Length + + // long currentPosition = Fp->tellg(); // save time // JPRx + uint32_t itemLength = ReadInt32(); + gdcmDebugMacro( "Basic Item Length is: " << itemLength +// << " 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::ReadEncapsulatedBasicOffsetTable() +{ + //// 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 its 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 *charBasicOffsetTableItemValue = new char[itemLength]; + Fp->read(charBasicOffsetTableItemValue, itemLength); + unsigned int nbEntries = itemLength/4; + assert( nbEntries*4 == itemLength); // Make sure this is a multiple + BasicOffsetTableItemValue = new uint32_t[nbEntries]; + + for (unsigned int i=0; i < nbEntries; i++ ) + { + BasicOffsetTableItemValue[i] = *((uint32_t*)(&charBasicOffsetTableItemValue[4*i])); +#if defined(GDCM_WORDS_BIGENDIAN) || defined(GDCM_FORCE_BIGENDIAN_EMULATION) + uint32_t val = BasicOffsetTableItemValue[i]; + BasicOffsetTableItemValue[i] + = ( (val<<24) | ((val<<8) & 0x00ff0000) | + ( (val>>8) & 0x0000ff00) | (val>>24) ); +#endif + gdcmDebugMacro( "Read one length for: " << + std::hex << BasicOffsetTableItemValue[i] ); + } + + delete[] charBasicOffsetTableItemValue; + } +} + +// These are the deprecated method that one day should be removed (after the next release) + +//#ifndef GDCM_LEGACY_REMOVE +/* + * \ brief Loader. (DEPRECATED : temporaryly kept not to break the API) + * @ param fileName file to be open for parsing + * @ return false if file cannot be open or no swap info was found, + * or no tag was found. + * @deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead + */ + /* +bool File::Load( std::string const &fileName ) +{ + GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2", + File::Load()); + SetFileName( fileName ); + if ( ! this->Document::Load( ) ) + return false; + + return DoTheLoadingJob( ); +} +#endif +*/ //----------------------------------------------------------------------------- -} // end namespace gdcm +// Print +//----------------------------------------------------------------------------- +} // end namespace gdcm