gdcm::FileHelper Class Reference

In addition to Dicom header exploration, this class is designed for accessing the image/volume content. One can also use it to write Dicom/ACR-NEMA/RAW files. More...

#include <gdcmFileHelper.h>

Inheritance diagram for gdcm::FileHelper:

[legend]Collaboration diagram for gdcm::FileHelper:

[legend]List of all members.

Public Types
enum	FileMode { WMODE_RAW, WMODE_RGB }
Public Member Functions
void	Print (std::ostream &os=std::cout, std::string const &indent="")
	Prints the common part of DataEntry, SeqEntry.
File *	GetFile ()
	Accessor to File.
void	SetLoadMode (int loadMode)
	Sets the LoadMode of the internal gdcm::File as a boolean string. NO_SEQ, NO_SHADOW, NO_SHADOWSEQ ... (nothing more, right now) WARNING : before using NO_SHADOW, be sure *all* your files contain accurate values in the 0x0000 element (if any) of *each* Shadow Group. The parser will fail if the size is wrong !
void	SetFileName (std::string const &fileName)
	Sets the LoadMode of the internal gdcm::File.
bool	Load ()
	Loader.
void	SetUserFunction (VOID_FUNCTION_PUINT8_PFILE_POINTER userFunc)
	to allow user to modify pixel order (e.g. Mirror, UpsideDown,...)
bool	SetEntryString (std::string const &content, uint16_t group, uint16_t elem)
	Accesses an existing DataEntry through it's (group, element) and modifies it's content with the given value.
bool	SetEntryBinArea (uint8_t *content, int lgth, uint16_t group, uint16_t elem)
	Accesses an existing DataEntry through it's (group, element) and modifies it's content with the given value.
DataEntry *	InsertEntryString (std::string const &content, uint16_t group, uint16_t elem)
	Modifies the value of a given DataEntry when it exists. Creates it with the given value when unexistant.
DataEntry *	InsertEntryBinArea (uint8_t *binArea, int lgth, uint16_t group, uint16_t elem)
	Modifies the value of a given DataEntry when it exists. Creates it with the given value when unexistant. A copy of the binArea is made to be kept in the Document.
SeqEntry *	InsertSeqEntry (uint16_t group, uint16_t elem)
	Adds an empty SeqEntry (remove any existing entry with same group,elem).
size_t	GetImageDataSize ()
	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 (use GetImageDataRawSize if you want to be sure to get *only* the size of the pixels).
size_t	GetImageDataRawSize ()
	Get the size of the image data. If the image could be converted to RGB using a LUT, this transformation is not taken into account by GetImageDataRawSize (use GetImageDataSize if you wish).
uint8_t *	GetImageData ()
	brings pixels into memory : 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.
uint8_t *	GetImageDataRaw ()
	brings pixels into memory : Allocates necessary memory, Transforms YBR pixels (if any) into RGB pixels Transforms 3 planes R, G, B (if any) into a single RGB Plane Copies the pixel data (image[s]/volume[s]) to newly allocated zone. DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
	GDCM_LEGACY (size_t GetImageDataIntoVector(void *destination, size_t maxSize))
void	SetImageData (uint8_t *data, size_t expectedSize)
	Points the internal pointer to the callers inData image representation, BUT WITHOUT COPYING THE DATA. 'image' Pixels are presented as C-like 2D arrays : line per line. 'volume'Pixels are presented as C-like 3D arrays : plane per plane.
void	SetUserData (uint8_t *data, size_t expectedSize)
	Set the image data defined by the user.
uint8_t *	GetUserData ()
	Get the image data defined by the user.
size_t	GetUserDataSize ()
	Get the image data size defined by the user.
uint8_t *	GetRGBData ()
	Get the image data from the file. If a LUT is found, the data are expanded to be RGB.
size_t	GetRGBDataSize ()
	Get the image data size from the file. If a LUT is found, the data are expanded to be RGB.
uint8_t *	GetRawData ()
	Get the image data from the file. Even when a LUT is found, the data are not expanded to RGB!
size_t	GetRawDataSize ()
	Get the image data size from the file. Even when a LUT is found, the data are not expanded to RGB!
uint8_t *	GetLutRGBA ()
	Access to the underlying PixelReadConverter RGBA LUT.
int	GetLutItemNumber ()
	Access to the underlying PixelReadConverter RGBA LUT Item Number.
int	GetLutItemSize ()
	Access to the underlying PixelReadConverter RGBA LUT Item Size.
void	SetWriteModeToRaw ()
	Tells the writer we want to keep 'Grey pixels + Palettes color' when possible (as opposed to convert 'Palettes color' to RGB).
void	SetWriteModeToRGB ()
	Tells the writer we want to write RGB image when possible (as opposed to 'Grey pixels + Palettes color').
void	SetWriteMode (FileMode mode)
	Sets the Write Mode ( ).
FileMode	GetWriteMode ()
	Gets the Write Mode ( ).
void	SetWriteTypeToDcmImplVR ()
	Tells the writer we want to write as Implicit VR.
void	SetWriteTypeToDcmExplVR ()
	Tells the writer we want to write as Explicit VR.
void	SetWriteTypeToAcr ()
	Tells the writer we want to write as ACR-NEMA.
void	SetWriteTypeToAcrLibido ()
	Tells the writer we want to write as LibIDO.
void	SetWriteTypeToJPEG ()
	Tells the writer we want to write as JPEG.
void	SetWriteType (FileType format)
	Tells the writer which format we want to write (ImplicitVR, ExplicitVR, ACR, ACR_LIBIDO).
FileType	GetWriteType ()
	Gets the format we talled the write we wanted to write (ImplicitVR, ExplicitVR, ACR, ACR_LIBIDO).
bool	WriteRawData (std::string const &fileName)
	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.
bool	WriteDcmImplVR (std::string const &fileName)
	Writes on disk A SINGLE Dicom file, using the Implicit Value Representation convention NO test is performed on processor "Endianity".
bool	WriteDcmExplVR (std::string const &fileName)
	Writes on disk A SINGLE Dicom file, using the Explicit Value Representation convention NO test is performed on processor "Endiannity".
bool	WriteAcr (std::string const &fileName)
	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 ...
bool	Write (std::string const &fileName)
	Writes on disk A SINGLE Dicom file,.
void	SetKeepMediaStorageSOPClassUID (bool v)
	if user knows he didn't modify the pixels (e.g. he just anonymized the file), he is allowed to ask to keep the original 'Media Storage SOP Class UID' and 'Image Type'
void	CallStartMethod ()
	CallStartMethod.
void	CallProgressMethod ()
	CallProgressMethod.
void	CallEndMethod ()
	CallEndMethod.
void	Delete ()
	Delete the object.
void	Register ()
	Register the object.
void	Unregister ()
	Unregister the object.
const unsigned long &	GetRefCount () const
	Get the reference counting.
void	SetPrintLevel (int level)
	Sets the print level for the Dicom Header Elements.
int	GetPrintLevel ()
	Gets the print level for the Dicom Entries.
Static Public Member Functions
static FileHelper *	New ()
	Constructs a FileHelper with a RefCounter.
static FileHelper *	New (File *header)
	Constructs a FileHelper with a RefCounter from a fileHelper.
Protected Member Functions
	FileHelper ()
	Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 file (gdcm::File only deals with the ... header) Opens (in read only and when possible) an existing file and checks for DICOM compliance. Returns NULL on failure. It will be up to the user to load the pixels into memory ( GetImageDataSize() + GetImageData() methods).
	FileHelper (File *header)
	Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 file (File only deals with the ... header) Opens (in read only and when possible) an existing file and checks for DICOM compliance. Returns NULL on failure. It will be up to the user to load the pixels into memory ( GetImageDataSize() + GetImageData() methods).
	~FileHelper ()
	canonical destructor
bool	CheckWriteIntegrity ()
	Checks the write integrity.
void	SetWriteToRaw ()
	Updates the File to write RAW data (as opposed to RGB data) (modifies, when necessary, photochromatic interpretation, bits allocated, Pixels element VR).
void	SetWriteToRGB ()
	Updates the File to write RGB data (as opposed to RAW data) (modifies, when necessary, photochromatic interpretation, samples per pixel, Planar configuration, bits allocated, bits stored, high bit -ACR 24 bits- Pixels element VR, pushes out the LUT, ).
void	RestoreWrite ()
	Restore the File write mode.
void	SetWriteFileTypeToACR ()
	Pushes out the whole group 0002 FIXME : better, set a flag to tell the writer not to write it ... FIXME : method should probably have an other name ! SetWriteFileTypeToACR is NOT opposed to SetWriteFileTypeToExplicitVR and SetWriteFileTypeToImplicitVR.
void	SetWriteFileTypeToJPEG ()
	Sets in the File the TransferSyntax to 'Explicit VR Little Endian".
void	SetWriteFileTypeToExplicitVR ()
void	SetWriteFileTypeToImplicitVR ()
	Sets in the File the TransferSyntax to 'Implicit VR Little Endian".
void	RestoreWriteFileType ()
	Restore in the File the initial group 0002.
void	SetWriteToLibido ()
	Set the Write not to Libido format.
void	SetWriteToNoLibido ()
	Set the Write not to No Libido format.
void	RestoreWriteOfLibido ()
	Restore the Write format.
DataEntry *	CopyDataEntry (uint16_t group, uint16_t elem, const TagName &vr=GDCM_VRUNKNOWN)
	Duplicates a DataEntry or creates it.
void	CheckMandatoryElements ()
	This method is called automatically, just before writting in order to produce a 'True Dicom V3' image.
void	CheckMandatoryEntry (uint16_t group, uint16_t elem, std::string value)
void	SetMandatoryEntry (uint16_t group, uint16_t elem, std::string value)
void	CopyMandatoryEntry (uint16_t group, uint16_t elem, std::string value)
void	RestoreWriteMandatory ()
	Restore in the File the initial group 0002.
Protected Attributes
float	Progress
	value of the ??? for any progress bar
bool	Abort
int	PrintLevel
	Amount of printed details for each Dicom Entries : 0 : stands for the least detail level.
Private Member Functions
	gdcmTypeMacro (FileHelper)
void	Initialize ()
	Factorization for various forms of constructors.
uint8_t *	GetRaw ()
	Reads/[decompresses] the pixels, *without* making RGB from Palette Colors.
Private Attributes
File *	FileInternal
	gdcm::File to use to load the file
bool	Parsed
	Whether already parsed or not.
PixelReadConvert *	PixelReadConverter
	Pointer to the PixelReadConverter.
PixelWriteConvert *	PixelWriteConverter
	Pointer to the PixelWriteConverter.
DocEntryArchive *	Archive
	Pointer to the DocEntryArchive (used while writting process).
FileMode	WriteMode
	(WMODE_RAW, WMODE_RGB)
FileType	WriteType
	(ImplicitVR, ExplicitVR, ACR, ACR_LIBIDO)
VOID_FUNCTION_PUINT8_PFILE_POINTER	UserFunction
	Pointer to a user supplied function to allow modification of pixel order (e.g. : Mirror, UpsideDown, 90°Rotation, ...) use as : void userSuppliedFunction(uint8_t *im, gdcm::File *f) NB : the "uint8_t *" type of first param is just for prototyping. User will Cast it according what he founds with f->GetPixelType() See vtkgdcmSerieViewer for an example.
bool	KeepMediaStorageSOPClassUID
	if user knows he didn't modify the pixels (e.g. he just anonymized the file), he is allowed to ask to keep the original 'Media Storage SOP Class UID' and 'Image Type'

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Detailed Description

In addition to Dicom header exploration, this class is designed for accessing the image/volume content. One can also use it to write Dicom/ACR-NEMA/RAW files.

Definition at line 43 of file gdcmFileHelper.h.

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Member Enumeration Documentation

enum gdcm::FileHelper::FileMode

Enumerator: WMODE_RAW  WMODE_RGB  Definition at line 48 of file gdcmFileHelper.h. { WMODE_RAW, WMODE_RGB };

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Constructor & Destructor Documentation

gdcm::FileHelper::FileHelper (   )  [protected]

Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 file (gdcm::File only deals with the ... header) Opens (in read only and when possible) an existing file and checks for DICOM compliance. Returns NULL on failure. It will be up to the user to load the pixels into memory ( GetImageDataSize() + GetImageData() methods). Note: the in-memory representation of all available tags found in the DICOM header is post-poned to first header information access. This avoid a double parsing of public part of the header when one sets an a posteriori shadow dictionary (efficiency can be seen as a side effect). Definition at line 133 of file gdcmFileHelper.cxx. References FileInternal, Initialize(), and gdcm::File::New(). { FileInternal = File::New( ); Initialize(); }

gdcm::FileHelper::FileHelper (  File *  header  )  [protected]

Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 file (File only deals with the ... header) Opens (in read only and when possible) an existing file and checks for DICOM compliance. Returns NULL on failure. It will be up to the user to load the pixels into memory ( GetImageDataSize() + GetImageData() methods). Note: the in-memory representation of all available tags found in the DICOM header is post-poned to first header information access. This avoid a double parsing of public part of the header when user sets an a posteriori shadow dictionary (efficiency can be seen as a side effect). Parameters: header  already built Header Definition at line 153 of file gdcmFileHelper.cxx. References FileInternal, gdcmAssertMacro, gdcm::PixelReadConvert::GrabInformationsFromFile(), Initialize(), gdcm::File::IsReadable(), PixelReadConverter, and gdcm::RefCounter::Register(). { gdcmAssertMacro(header); FileInternal = header; FileInternal->Register(); Initialize(); if ( FileInternal->IsReadable() ) { PixelReadConverter->GrabInformationsFromFile( FileInternal, this ); } }

gdcm::FileHelper::~FileHelper (   )  [protected]

canonical destructor Note: If the header (gdcm::File) was created by the FileHelper constructor, it is destroyed by the FileHelper Definition at line 171 of file gdcmFileHelper.cxx. References Archive, FileInternal, PixelReadConverter, PixelWriteConverter, and gdcm::RefCounter::Unregister(). { if ( PixelReadConverter ) { delete PixelReadConverter; } if ( PixelWriteConverter ) { delete PixelWriteConverter; } if ( Archive ) { delete Archive; } FileInternal->Unregister(); }

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Member Function Documentation

void gdcm::FileHelper::CallEndMethod (   )

CallEndMethod. Definition at line 1751 of file gdcmFileHelper.cxx. References gdcm::CMD_ENDPROGRESS, gdcm::CommandManager::ExecuteCommand(), and Progress. { Progress = 1.0f; CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS); }

void gdcm::FileHelper::CallProgressMethod (   )

CallProgressMethod. Definition at line 1743 of file gdcmFileHelper.cxx. References gdcm::CMD_PROGRESS, and gdcm::CommandManager::ExecuteCommand(). { CommandManager::ExecuteCommand(this,CMD_PROGRESS); }

void gdcm::FileHelper::CallStartMethod (   )

CallStartMethod. Definition at line 1733 of file gdcmFileHelper.cxx. References Abort, gdcm::CMD_STARTPROGRESS, gdcm::CommandManager::ExecuteCommand(), and Progress. { Progress = 0.0f; Abort = false; CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS); }

void gdcm::FileHelper::CheckMandatoryElements (   )  [protected]

This method is called automatically, just before writting in order to produce a 'True Dicom V3' image. We cannot know *how* the user made the File : (reading an old ACR-NEMA file or a not very clean DICOM file ...) Just before writting : we check the Entries we create the mandatory entries if they are missing we modify the values if necessary we push the sensitive entries to the Archive The writing process will restore the entries as they where before entering FileHelper::CheckMandatoryElements, so the user will always see the entries just as they were before he decided to write. Note: Entries whose type is 1 are mandatory, with a mandatory value Entries whose type is 1c are mandatory-inside-a-Sequence, with a mandatory value Entries whose type is 2 are mandatory, with an optional value Entries whose type is 2c are mandatory-inside-a-Sequence, with an optional value Entries whose type is 3 are optional Todo: warn the user if we had to add some entries : even if a mandatory entry is missing, we add it, with a default value (we don't want to give up the writting process if user forgot to specify Lena's Patient ID, for instance ...) read the whole PS 3.3 Part of DICOM (890 pages) and write a *full* checker (probably one method per Modality ...) Any contribution is welcome. write a user callable full checker, to allow post reading and/or pre writting image consistency check. Definition at line 1327 of file gdcmFileHelper.cxx. References gdcm::ACR, gdcm::ACR_LIBIDO, gdcm::SQItem::AddEntry(), gdcm::SeqEntry::AddSQItem(), Archive, CheckMandatoryEntry(), CopyDataEntry(), CopyMandatoryEntry(), gdcm::Util::CreateUniqueUID(), gdcm::RefCounter::Delete(), FileInternal, gdcm::GDCM_UNFOUND, gdcmWarningMacro, gdcm::File::GetBitsAllocated(), gdcm::File::GetBitsStored(), gdcm::Util::GetCurrentDate(), gdcm::Util::GetCurrentTime(), gdcm::DocEntrySet::GetDataEntry(), gdcm::Global::GetDicts(), gdcm::DocEntrySet::GetEntryString(), gdcm::Util::GetFileMetaInformationVersion(), gdcm::File::GetHighBitPosition(), gdcm::Orientation::GetOrientation(), gdcm::DataEntry::GetString(), gdcm::Util::GetVersion(), KeepMediaStorageSOPClassUID, gdcm::Orientation::New(), gdcm::DataEntry::New(), gdcm::SQItem::New(), gdcm::SeqEntry::New(), gdcm::DocEntryArchive::Push(), gdcm::DataEntry::SetBinArea(), gdcm::DocEntry::SetLength(), gdcm::DataEntry::SetString(), and WriteType. Referenced by Write(). { std::string sop = Util::CreateUniqueUID(); // just to remember : 'official' 0002 group if ( WriteType != ACR && WriteType != ACR_LIBIDO ) { // Group 000002 (Meta Elements) already pushed out //0002 0000 UL 1 Meta Group Length //0002 0001 OB 1 File Meta Information Version //0002 0002 UI 1 Media Stored SOP Class UID //0002 0003 UI 1 Media Stored SOP Instance UID //0002 0010 UI 1 Transfer Syntax UID //0002 0012 UI 1 Implementation Class UID //0002 0013 SH 1 Implementation Version Name //0002 0016 AE 1 Source Application Entity Title //0002 0100 UI 1 Private Information Creator //0002 0102 OB 1 Private Information // Create them if not found // Always modify the value // Push the entries to the archive. CopyMandatoryEntry(0x0002,0x0000,"0"); DataEntry *e_0002_0001 = CopyDataEntry(0x0002,0x0001, "OB"); e_0002_0001->SetBinArea((uint8_t*)Util::GetFileMetaInformationVersion(), false); e_0002_0001->SetLength(2); Archive->Push(e_0002_0001); e_0002_0001->Delete(); if ( KeepMediaStorageSOPClassUID) // It up to the use to *know* whether he modified the pixels or not. // he is allowed to keep the original 'Media Storage SOP Class UID' CheckMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7"); else // Potentialy this is a post-processed image // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage] CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7"); // 'Media Storage SOP Instance UID' CopyMandatoryEntry(0x0002,0x0003,sop); // 'Implementation Class UID' // FIXME : in all examples we have, 0x0002,0x0012 is not so long : // semms to be Root UID + 4 digits (?) CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID()); // 'Implementation Version Name' std::string version = "GDCM "; version += Util::GetVersion(); CopyMandatoryEntry(0x0002,0x0013,version); } // Push out 'LibIDO-special' entries, if any Archive->Push(0x0028,0x0015); Archive->Push(0x0028,0x0016); Archive->Push(0x0028,0x0017); Archive->Push(0x0028,0x00199); // Deal with the pb of (Bits Stored = 12) // - we're gonna write the image as Bits Stored = 16 if ( FileInternal->GetEntryString(0x0028,0x0100) == "12") { CopyMandatoryEntry(0x0028,0x0100,"16"); } // Check if user wasn't drunk ;-) std::ostringstream s; // check 'Bits Allocated' vs decent values int nbBitsAllocated = FileInternal->GetBitsAllocated(); if ( nbBitsAllocated == 0 || nbBitsAllocated > 32) { CopyMandatoryEntry(0x0028,0x0100,"16"); gdcmWarningMacro("(0028,0100) changed from " << nbBitsAllocated << " to 16 for consistency purpose"); nbBitsAllocated = 16; } // check 'Bits Stored' vs 'Bits Allocated' int nbBitsStored = FileInternal->GetBitsStored(); if ( nbBitsStored == 0 || nbBitsStored > nbBitsAllocated ) { s.str(""); s << nbBitsAllocated; CopyMandatoryEntry(0x0028,0x0101,s.str()); gdcmWarningMacro("(0028,0101) changed from " << nbBitsStored << " to " << nbBitsAllocated << " for consistency purpose" ); nbBitsStored = nbBitsAllocated; } // check 'Hight Bit Position' vs 'Bits Allocated' and 'Bits Stored' int highBitPosition = FileInternal->GetHighBitPosition(); if ( highBitPosition == 0 || highBitPosition > nbBitsAllocated-1 || highBitPosition < nbBitsStored-1 ) { s.str(""); s << nbBitsStored - 1; CopyMandatoryEntry(0x0028,0x0102,s.str()); gdcmWarningMacro("(0028,0102) changed from " << highBitPosition << " to " << nbBitsAllocated-1 << " for consistency purpose"); } std::string pixelSpacing = FileInternal->GetEntryString(0x0028,0x0030); if ( pixelSpacing == GDCM_UNFOUND ) { pixelSpacing = "1.0\\1.0"; // if missing, Pixel Spacing forced to "1.0\1.0" CopyMandatoryEntry(0x0028,0x0030,pixelSpacing); } // 'Imager Pixel Spacing' : defaulted to 'Pixel Spacing' // --> This one is the *legal* one ! // FIXME : we should write it only when we are *sure* the image comes from // an imager (see also 0008,0x0064) CheckMandatoryEntry(0x0018,0x1164,pixelSpacing); // Samples Per Pixel (type 1) : default to grayscale CheckMandatoryEntry(0x0028,0x0002,"1"); // --- Check UID-related Entries --- // If 'SOP Class UID' exists ('true DICOM' image) // we create the 'Source Image Sequence' SeqEntry // to hold informations about the Source Image DataEntry *e_0008_0016 = FileInternal->GetDataEntry(0x0008, 0x0016); if ( e_0008_0016 ) { // Create 'Source Image Sequence' SeqEntry SeqEntry *sis = SeqEntry::New ( Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x2112) ); SQItem *sqi = SQItem::New(1); // (we assume 'SOP Instance UID' exists too) // create 'Referenced SOP Class UID' DataEntry *e_0008_1150 = DataEntry::New( Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) ); e_0008_1150->SetString( e_0008_0016->GetString()); sqi->AddEntry(e_0008_1150); e_0008_1150->Delete(); // create 'Referenced SOP Instance UID' DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018); DataEntry *e_0008_1155 = DataEntry::New( Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1155) ); e_0008_1155->SetString( e_0008_0018->GetString()); sqi->AddEntry(e_0008_1155); e_0008_1155->Delete(); sis->AddSQItem(sqi,1); sqi->Delete(); // temporarily replaces any previous 'Source Image Sequence' Archive->Push(sis); sis->Delete(); // FIXME : is 'Image Type' *really* depending on the presence of'SOP Class UID'? if ( KeepMediaStorageSOPClassUID) // It up to the use to *know* whether he modified the pixels or not. // he is allowed to keep the original 'Media Storage SOP Class UID' // and 'Image Type' as well CheckMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY"); else // Potentialy this is a post-processed image // (The written image is no longer an 'ORIGINAL' one) CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY"); } // At the end, not to overwrite the original ones, // needed by 'Referenced SOP Instance UID', 'Referenced SOP Class UID' // 'SOP Instance UID' CopyMandatoryEntry(0x0008,0x0018,sop); // the gdcm written image is a [Secondary Capture Image Storage] // except if user told us he dind't modify the pixels, and, therefore // he want to keep the 'Media Storage SOP Class UID' // 'Media Storage SOP Class UID' : [Secondary Capture Image Storage] if ( KeepMediaStorageSOPClassUID) { // It up to the use to *know* whether he modified the pixels or not. // he is allowed to keep the original 'Media Storage SOP Class UID' CheckMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7"); } else { // Potentialy this is a post-processed image // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage] CopyMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7"); // FIXME : Must we Force Value, or Default value ? // Is it Type 1 for any Modality ? // --> Answer seems to be NO :-( // FIXME : we should write it only when we are *sure* the image // *does not* come from an imager (see also 0018,0x1164) // Conversion Type. // Other possible values are : // See PS 3.3, Page 408 // DV = Digitized Video // DI = Digital Interface // DF = Digitized Film // WSD = Workstation // SD = Scanned Document // SI = Scanned Image // DRW = Drawing // SYN = Synthetic Image CheckMandatoryEntry(0x0008,0x0064,"SYN"); } // ---- The user will never have to take any action on the following ---- // new value for 'SOP Instance UID' //SetMandatoryEntry(0x0008,0x0018,Util::CreateUniqueUID()); // Instance Creation Date const std::string &date = Util::GetCurrentDate(); CopyMandatoryEntry(0x0008,0x0012,date); // Instance Creation Time const std::string &time = Util::GetCurrentTime(); CopyMandatoryEntry(0x0008,0x0013,time); // Study Date CheckMandatoryEntry(0x0008,0x0020,date); // Study Time CheckMandatoryEntry(0x0008,0x0030,time); // Accession Number //CopyMandatoryEntry(0x0008,0x0050,""); CheckMandatoryEntry(0x0008,0x0050,""); // ----- Add Mandatory Entries if missing --- // Entries whose type is 1 are mandatory, with a mandatory value // Entries whose type is 1c are mandatory-inside-a-Sequence, // with a mandatory value // Entries whose type is 2 are mandatory, with an optional value // Entries whose type is 2c are mandatory-inside-a-Sequence, // with an optional value // Entries whose type is 3 are optional // 'Study Instance UID' // Keep the value if exists // The user is allowed to create his own Study, // keeping the same 'Study Instance UID' for various images // The user may add images to a 'Manufacturer Study', // adding new Series to an already existing Study CheckMandatoryEntry(0x0020,0x000d,Util::CreateUniqueUID()); // 'Serie Instance UID' // Keep the value if exists // The user is allowed to create his own Series, // keeping the same 'Serie Instance UID' for various images // The user shouldn't add any image to a 'Manufacturer Serie' // but there is no way no to prevent him for doing that CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID()); // Study ID CheckMandatoryEntry(0x0020,0x0010,""); // Series Number CheckMandatoryEntry(0x0020,0x0011,""); // Instance Number CheckMandatoryEntry(0x0020,0x0013,""); // Patient Orientation // Can be computed from (0020|0037) : Image Orientation (Patient) gdcm::Orientation *o = gdcm::Orientation::New(); std::string ori = o->GetOrientation ( FileInternal ); o->Delete(); if (ori != "\\" ) CheckMandatoryEntry(0x0020,0x0020,ori); else CheckMandatoryEntry(0x0020,0x0020,""); // Modality : if missing we set it to 'OTher' CheckMandatoryEntry(0x0008,0x0060,"OT"); // Manufacturer : if missing we set it to 'GDCM Factory' CheckMandatoryEntry(0x0008,0x0070,"GDCM Factory"); // Institution Name : if missing we set it to 'GDCM Hospital' CheckMandatoryEntry(0x0008,0x0080,"GDCM Hospital"); // Patient's Name : if missing, we set it to 'GDCM^Patient' CheckMandatoryEntry(0x0010,0x0010,"GDCM^Patient"); // Patient ID CheckMandatoryEntry(0x0010,0x0020,""); // Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory CheckMandatoryEntry(0x0010,0x0030,""); // Patient's Sex :'type 2' entry -> must exist, value not mandatory CheckMandatoryEntry(0x0010,0x0040,""); // Referring Physician's Name :'type 2' entry -> must exist, value not mandatory CheckMandatoryEntry(0x0008,0x0090,""); // Remove some inconstencies (probably some more will be added) // if (0028 0008)Number of Frames exists // Push out (0020 0052),Frame of Reference UID // (only meaningfull within a Serie) DataEntry *e_0028_0008 = FileInternal->GetDataEntry(0x0028, 0x0008); if ( !e_0028_0008 ) { Archive->Push(0x0020, 0x0052); } // Deal with element 0x0000 (group length) of each group. // First stage : get all the different Groups /* GroupHT grHT; DocEntry *d = FileInternal->GetFirstEntry(); while(d) { grHT[d->GetGroup()] = 0; d=FileInternal->GetNextEntry(); } // Second stage : add the missing ones (if any) for (GroupHT::iterator it = grHT.begin(); it != grHT.end(); ++it) { CheckMandatoryEntry(it->first, 0x0000, "0"); } // Third stage : update all 'zero level' groups length */ }

void gdcm::FileHelper::CheckMandatoryEntry (  uint16_t  group, uint16_t  elem, std::string  value )  [protected]

Definition at line 1664 of file gdcmFileHelper.cxx. References Archive, gdcm::RefCounter::Delete(), FileInternal, gdcm::DocEntrySet::GetDataEntry(), gdcm::Global::GetDicts(), gdcm::DataEntry::New(), gdcm::DocEntryArchive::Push(), and gdcm::DataEntry::SetString(). Referenced by CheckMandatoryElements(). { DataEntry *entry = FileInternal->GetDataEntry(group,elem); if ( !entry ) { entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); entry->SetString(value); Archive->Push(entry); entry->Delete(); } }

bool gdcm::FileHelper::CheckWriteIntegrity (   )  [protected]

Checks 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 Returns: true if check is successfull Definition at line 749 of file gdcmFileHelper.cxx. References FileInternal, gdcmWarningMacro, gdcm::File::GetBitsAllocated(), gdcm::File::GetSamplesPerPixel(), gdcm::PixelWriteConvert::GetUserData(), gdcm::PixelWriteConvert::GetUserDataSize(), gdcm::File::GetXSize(), gdcm::File::GetYSize(), gdcm::File::GetZSize(), gdcm::File::HasLUT(), PixelWriteConverter, WMODE_RAW, WMODE_RGB, and WriteMode. Referenced by Write(). { if ( PixelWriteConverter->GetUserData() ) { int numberBitsAllocated = FileInternal->GetBitsAllocated(); if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 ) { gdcmWarningMacro( "numberBitsAllocated changed from " << numberBitsAllocated << " to 16 " << " for consistency purpose" ); numberBitsAllocated = 16; } size_t decSize = FileInternal->GetXSize() * FileInternal->GetYSize() * FileInternal->GetZSize() * FileInternal->GetSamplesPerPixel() * ( numberBitsAllocated / 8 ); size_t rgbSize = decSize; if ( FileInternal->HasLUT() ) rgbSize = decSize * 3; switch(WriteMode) { case WMODE_RAW : if ( decSize!=PixelWriteConverter->GetUserDataSize() ) { gdcmWarningMacro( "Data size (Raw) is incorrect. Should be " << decSize << " / Found :" << PixelWriteConverter->GetUserDataSize() ); return false; } break; case WMODE_RGB : if ( rgbSize!=PixelWriteConverter->GetUserDataSize() ) { gdcmWarningMacro( "Data size (RGB) is incorrect. Should be " << decSize << " / Found " << PixelWriteConverter->GetUserDataSize() ); return false; } break; } } return true; }

DataEntry * gdcm::FileHelper::CopyDataEntry (  uint16_t  group, uint16_t  elem, const TagName &  vr = GDCM_VRUNKNOWN )  [protected]

Duplicates a DataEntry or creates it. Parameters: group  Group number of the Entry elem  Element number of the Entry vr  Value Representation of the Entry FIXME : what is it used for? Returns: pointer to the new Bin Entry (NULL when creation failed). Definition at line 1124 of file gdcmFileHelper.cxx. References gdcm::DataEntry::Copy(), FileInternal, gdcm::GDCM_VRUNKNOWN, gdcm::DocEntry::GetDictEntry(), gdcm::ElementSet::GetDocEntry(), GetFile(), gdcm::DocEntry::GetVR(), gdcm::DataEntry::New(), and gdcm::DocEntrySet::NewDataEntry(). Referenced by CheckMandatoryElements(), CopyMandatoryEntry(), SetWriteFileTypeToExplicitVR(), SetWriteFileTypeToImplicitVR(), SetWriteFileTypeToJPEG(), SetWriteToLibido(), SetWriteToNoLibido(), SetWriteToRaw(), and SetWriteToRGB(). { DocEntry *oldE = FileInternal->GetDocEntry(group, elem); DataEntry *newE; if ( oldE && vr != GDCM_VRUNKNOWN ) if ( oldE->GetVR() != vr ) oldE = NULL; if ( oldE ) { newE = DataEntry::New(oldE->GetDictEntry()); newE->Copy(oldE); } else { newE = GetFile()->NewDataEntry(group, elem, vr); } return newE; }

void gdcm::FileHelper::CopyMandatoryEntry (  uint16_t  group, uint16_t  elem, std::string  value )  [protected]

Definition at line 1684 of file gdcmFileHelper.cxx. References Archive, CopyDataEntry(), gdcm::RefCounter::Delete(), gdcm::DocEntryArchive::Push(), and gdcm::DataEntry::SetString(). Referenced by CheckMandatoryElements(). { DataEntry *entry = CopyDataEntry(group,elem); entry->SetString(value); Archive->Push(entry); entry->Delete(); }

void gdcm::RefCounter::Delete (   )  [inline, inherited]

Delete the object. Remarks: The object is deleted only if its reference counting is to zero Definition at line 39 of file gdcmRefCounter.h. Referenced by gdcm::SerieHelper::AddFileName(), gdcm::Document::Backtrack(), CheckMandatoryElements(), CheckMandatoryEntry(), CopyMandatoryEntry(), gdcm::DicomDir::CreateDicomDirChainedList(), gdcm::File::DoTheLoadingJob(), gdcm::Dict::DoTheLoadingJob(), gdcm::DicomDirObject::FillObject(), gdcm::DocEntrySet::InsertEntryBinArea(), gdcm::DocEntrySet::InsertEntryString(), gdcm::DocEntrySet::InsertSeqEntry(), vtkGdcmReader::LoadFileInformation(), vtkGdcmReader::LoadImageInMemory(), main(), gdcm::DicomDir::NewMeta(), gdcm::DicomDirStudy::NewVisit(), gdcm::Document::ParseDES(), gdcm::Document::ParseSQ(), gdcm::Document::ReadNextDocEntry(), gdcm::DicomDir::SetElement(), SetMandatoryEntry(), SetWriteFileTypeToExplicitVR(), SetWriteFileTypeToImplicitVR(), SetWriteFileTypeToJPEG(), SetWriteToLibido(), SetWriteToNoLibido(), SetWriteToRaw(), SetWriteToRGB(), vtkGdcmWriter::WriteDcmFile(), gdcm::DicomDir::~DicomDir(), and gdcm::Global::~Global(). { Unregister(); }

gdcm::FileHelper::GDCM_LEGACY (  size_t   GetImageDataIntoVector(void *destination, size_t maxSize)  )

gdcm::FileHelper::gdcmTypeMacro (  FileHelper   )  [private]

File* gdcm::FileHelper::GetFile (   )  [inline]

Accessor to File. Definition at line 63 of file gdcmFileHelper.h. Referenced by CopyDataEntry(), vtkGdcmReader::LoadImageInMemory(), RestoreWrite(), SetLoadMode(), SetWriteToRaw(), and SetWriteToRGB(). { return FileInternal; }

uint8_t * gdcm::FileHelper::GetImageData (   )

brings pixels into memory : 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. Returns: Pointer to newly allocated pixel data. (uint8_t is just for prototyping. feel free to cast) NULL if alloc fails Definition at line 347 of file gdcmFileHelper.cxx. References gdcm::PixelReadConvert::BuildRGBImage(), FileInternal, gdcm::PixelReadConvert::GetRaw(), GetRaw(), gdcm::PixelReadConvert::GetRGB(), gdcm::PixelWriteConvert::GetUserData(), gdcm::File::HasLUT(), PixelReadConverter, and PixelWriteConverter. Referenced by vtkGdcmReader::LoadImageInMemory(). { if ( PixelWriteConverter->GetUserData() ) { return PixelWriteConverter->GetUserData(); } if ( ! GetRaw() ) { // If the decompression failed nothing can be done. return 0; } if ( FileInternal->HasLUT() && PixelReadConverter->BuildRGBImage() ) { return PixelReadConverter->GetRGB(); } else { // When no LUT or LUT conversion fails, return the Raw return PixelReadConverter->GetRaw(); } }

uint8_t * gdcm::FileHelper::GetImageDataRaw (   )

brings pixels into memory : Allocates necessary memory, Transforms YBR pixels (if any) into RGB pixels Transforms 3 planes R, G, B (if any) into a single RGB Plane Copies the pixel data (image[s]/volume[s]) to newly allocated zone. DOES NOT transform Grey plane + 3 Palettes into a RGB Plane Returns: Pointer to newly allocated pixel data. (uint8_t is just for prototyping. feel free to cast) NULL if alloc fails Definition at line 382 of file gdcmFileHelper.cxx. References GetRaw(). Referenced by vtkGdcmReader::LoadImageInMemory(). { return GetRaw(); }

size_t gdcm::FileHelper::GetImageDataRawSize (   )

Get the size of the image data. If the image could be converted to RGB using a LUT, this transformation is not taken into account by GetImageDataRawSize (use GetImageDataSize if you wish). Returns: The raw image size Definition at line 326 of file gdcmFileHelper.cxx. References gdcm::PixelReadConvert::GetRawSize(), gdcm::PixelWriteConvert::GetUserData(), gdcm::PixelWriteConvert::GetUserDataSize(), PixelReadConverter, and PixelWriteConverter. { if ( PixelWriteConverter->GetUserData() ) { return PixelWriteConverter->GetUserDataSize(); } return PixelReadConverter->GetRawSize(); }

size_t gdcm::FileHelper::GetImageDataSize (   )

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 (use GetImageDataRawSize if you want to be sure to get *only* the size of the pixels). Returns: The image size Definition at line 310 of file gdcmFileHelper.cxx. References gdcm::PixelReadConvert::GetRGBSize(), gdcm::PixelWriteConvert::GetUserData(), gdcm::PixelWriteConvert::GetUserDataSize(), PixelReadConverter, and PixelWriteConverter. Referenced by vtkGdcmReader::LoadImageInMemory(). { if ( PixelWriteConverter->GetUserData() ) { return PixelWriteConverter->GetUserDataSize(); } return PixelReadConverter->GetRGBSize(); }

int gdcm::FileHelper::GetLutItemNumber (   )

Access to the underlying PixelReadConverter RGBA LUT Item Number. Definition at line 546 of file gdcmFileHelper.cxx. References gdcm::PixelReadConvert::GetLutItemNumber(), and PixelReadConverter. { return PixelReadConverter->GetLutItemNumber(); }

int gdcm::FileHelper::GetLutItemSize (   )

Access to the underlying PixelReadConverter RGBA LUT Item Size. Definition at line 554 of file gdcmFileHelper.cxx. References gdcm::PixelReadConvert::GetLutItemSize(), and PixelReadConverter. { return PixelReadConverter->GetLutItemSize(); }

uint8_t * gdcm::FileHelper::GetLutRGBA (   )

Access to the underlying PixelReadConverter RGBA LUT. Definition at line 536 of file gdcmFileHelper.cxx. References gdcm::PixelReadConvert::BuildLUTRGBA(), gdcm::PixelReadConvert::GetLutRGBA(), and PixelReadConverter. Referenced by vtkGdcmReader::LoadImageInMemory(). { if ( PixelReadConverter->GetLutRGBA() ==0 ) PixelReadConverter->BuildLUTRGBA(); return PixelReadConverter->GetLutRGBA(); }

int gdcm::Base::GetPrintLevel (   )  [inline, inherited]

Gets the print level for the Dicom Entries. Definition at line 50 of file gdcmBase.h. { return PrintLevel; }

uint8_t * gdcm::FileHelper::GetRaw (   )  [private]

Reads/[decompresses] the pixels, *without* making RGB from Palette Colors. Returns: the pixels area, whatever its type (uint8_t is just for prototyping : feel free to Cast it) Definition at line 1781 of file gdcmFileHelper.cxx. References gdcm::Document::CloseFile(), FileInternal, gdcmWarningMacro, gdcm::PixelReadConvert::GetRaw(), gdcm::Document::OpenFile(), PixelReadConverter, gdcm::PixelReadConvert::ReadAndDecompressPixelData(), gdcm::PixelReadConvert::SetUserFunction(), and UserFunction. Referenced by GetImageData(), and GetImageDataRaw(). { PixelReadConverter->SetUserFunction( UserFunction ); uint8_t *raw = PixelReadConverter->GetRaw(); if ( ! raw ) { // The Raw image migth not be loaded yet: std::ifstream *fp = FileInternal->OpenFile(); PixelReadConverter->ReadAndDecompressPixelData( fp ); if ( fp ) FileInternal->CloseFile(); raw = PixelReadConverter->GetRaw(); if ( ! raw ) { gdcmWarningMacro( "Read/decompress of pixel data apparently went wrong."); return 0; } } return raw; }

uint8_t * gdcm::FileHelper::GetRawData (   )

Get the image data from the file. Even when a LUT is found, the data are not expanded to RGB! Definition at line 519 of file gdcmFileHelper.cxx. References gdcm::PixelReadConvert::GetRaw(), and PixelReadConverter. { return PixelReadConverter->GetRaw(); }

size_t gdcm::FileHelper::GetRawDataSize (   )

Get the image data size from the file. Even when a LUT is found, the data are not expanded to RGB! Definition at line 528 of file gdcmFileHelper.cxx. References gdcm::PixelReadConvert::GetRawSize(), and PixelReadConverter. { return PixelReadConverter->GetRawSize(); }

const unsigned long& gdcm::RefCounter::GetRefCount (   )  const [inline, inherited]

Get the reference counting. Returns: Reference count Definition at line 56 of file gdcmRefCounter.h. { return RefCount; }

uint8_t * gdcm::FileHelper::GetRGBData (   )

Get the image data from the file. If a LUT is found, the data are expanded to be RGB. Definition at line 501 of file gdcmFileHelper.cxx. References gdcm::PixelReadConvert::GetRGB(), and PixelReadConverter. { return PixelReadConverter->GetRGB(); }

size_t gdcm::FileHelper::GetRGBDataSize (   )

Get the image data size from the file. If a LUT is found, the data are expanded to be RGB. Definition at line 510 of file gdcmFileHelper.cxx. References gdcm::PixelReadConvert::GetRGBSize(), and PixelReadConverter. { return PixelReadConverter->GetRGBSize(); }

uint8_t * gdcm::FileHelper::GetUserData (   )

Get the image data defined by the user. Warning: When writting the file, this data are get as default data to write Definition at line 483 of file gdcmFileHelper.cxx. References gdcm::PixelWriteConvert::GetUserData(), and PixelWriteConverter. Referenced by vtkGdcmWriter::WriteDcmFile(). { return PixelWriteConverter->GetUserData(); }

size_t gdcm::FileHelper::GetUserDataSize (   )

Get the image data size defined by the user. Warning: When writting the file, this data are get as default data to write Definition at line 492 of file gdcmFileHelper.cxx. References gdcm::PixelWriteConvert::GetUserDataSize(), and PixelWriteConverter. Referenced by vtkGdcmWriter::WriteDcmFile(). { return PixelWriteConverter->GetUserDataSize(); }

FileMode gdcm::FileHelper::GetWriteMode (   )  [inline]

Gets the Write Mode ( ). Definition at line 122 of file gdcmFileHelper.h. { return WriteMode; }

FileType gdcm::FileHelper::GetWriteType (   )  [inline]

Gets the format we talled the write we wanted to write (ImplicitVR, ExplicitVR, ACR, ACR_LIBIDO). Definition at line 141 of file gdcmFileHelper.h. { return WriteType; }

void gdcm::FileHelper::Initialize (   )  [private]

Factorization for various forms of constructors. Definition at line 1762 of file gdcmFileHelper.cxx. References Archive, gdcm::ExplicitVR, FileInternal, KeepMediaStorageSOPClassUID, PixelReadConverter, PixelWriteConverter, UserFunction, WMODE_RAW, WriteMode, and WriteType. Referenced by FileHelper(). { UserFunction = 0; KeepMediaStorageSOPClassUID = false; WriteMode = WMODE_RAW; WriteType = ExplicitVR; PixelReadConverter = new PixelReadConvert; PixelWriteConverter = new PixelWriteConvert; Archive = new DocEntryArchive( FileInternal ); }

DataEntry * gdcm::FileHelper::InsertEntryBinArea (  uint8_t *  binArea, int  lgth, uint16_t  group, uint16_t  elem )

Modifies the value of a given DataEntry when it exists. Creates it with the given value when unexistant. A copy of the binArea is made to be kept in the Document. Parameters: binArea  (binary)value to be set lgth  new value length group  Group number of the Entry elem  Element number of the Entry Returns: pointer to the modified/created DataEntry (NULL when creation failed). Definition at line 283 of file gdcmFileHelper.cxx. References FileInternal, and gdcm::DocEntrySet::InsertEntryBinArea(). { return FileInternal->InsertEntryBinArea(binArea, lgth, group, elem); }

DataEntry * gdcm::FileHelper::InsertEntryString (  std::string const &  content, uint16_t  group, uint16_t  elem )

Modifies the value of a given DataEntry when it exists. Creates it with the given value when unexistant. Parameters: content  (string) value to be set group  Group number of the Entry elem  Element number of the Entry Returns: pointer to the modified/created DataEntry (NULL when creation failed). Definition at line 266 of file gdcmFileHelper.cxx. References FileInternal, and gdcm::DocEntrySet::InsertEntryString(). Referenced by SetImageInformation(). { return FileInternal->InsertEntryString(content, group, elem); }

SeqEntry * gdcm::FileHelper::InsertSeqEntry (  uint16_t  group, uint16_t  elem )

Adds an empty SeqEntry (remove any existing entry with same group,elem). Parameters: group  Group number of the Entry elem  Element number of the Entry Returns: pointer to the created SeqEntry (NULL when creation failed). Definition at line 297 of file gdcmFileHelper.cxx. References FileInternal, and gdcm::DocEntrySet::InsertSeqEntry(). { return FileInternal->InsertSeqEntry(group, elem); }

bool gdcm::FileHelper::Load (   )

Loader. Returns: false if file cannot be open or no swap info was found, or no tag was found. Definition at line 218 of file gdcmFileHelper.cxx. References FileInternal, gdcm::PixelReadConvert::GrabInformationsFromFile(), gdcm::File::Load(), and PixelReadConverter. { if ( !FileInternal->Load() ) return false; PixelReadConverter->GrabInformationsFromFile( FileInternal, this ); return true; }

static FileHelper* gdcm::FileHelper::New (  File *  header  )  [inline, static]

Constructs a FileHelper with a RefCounter from a fileHelper. Definition at line 58 of file gdcmFileHelper.h. {return new FileHelper(header);}

static FileHelper* gdcm::FileHelper::New (   )  [inline, static]

Constructs a FileHelper with a RefCounter. Definition at line 56 of file gdcmFileHelper.h. Referenced by vtkGdcmReader::LoadImageInMemory(), and vtkGdcmWriter::WriteDcmFile(). {return new FileHelper();}

void gdcm::FileHelper::Print (  std::ostream &  os = std::cout, std::string const &  indent = "" )  [virtual]

Prints the common part of DataEntry, SeqEntry. Parameters: os  ostream we want to print in indent  (unused) Reimplemented from gdcm::Base. Definition at line 1810 of file gdcmFileHelper.cxx. References FileInternal, gdcm::File::IsReadable(), PixelReadConverter, gdcm::PixelReadConvert::Print(), gdcm::ElementSet::Print(), gdcm::Base::PrintLevel, and gdcm::Base::SetPrintLevel(). { FileInternal->SetPrintLevel(PrintLevel); FileInternal->Print(os); if ( FileInternal->IsReadable() ) { PixelReadConverter->SetPrintLevel(PrintLevel); PixelReadConverter->Print(os); } }

void gdcm::RefCounter::Register (   )  [inline, inherited]

Register the object. Remarks: It increments the reference counting Definition at line 44 of file gdcmRefCounter.h. Referenced by gdcm::SQItem::AddEntry(), gdcm::ElementSet::AddEntry(), gdcm::Dict::AddEntry(), gdcm::SeqEntry::AddSQItem(), gdcm::SeqEntry::Copy(), gdcm::DicomDir::Copy(), gdcm::DocEntry::DocEntry(), FileHelper(), gdcm::DocEntrySet::GetDictEntry(), gdcm::CommandManager::InSetCommand(), gdcm::DocEntryArchive::Push(), gdcm::Dict::ReplaceEntry(), and gdcm::SeqEntry::SetDelimitationItem(). { RefCount++; }

void gdcm::FileHelper::RestoreWrite (   )  [protected]

Restore the File write mode. Definition at line 940 of file gdcmFileHelper.cxx. References Archive, GetFile(), and gdcm::DocEntryArchive::Restore(). Referenced by Write(). { Archive->Restore(0x0028,0x0002); Archive->Restore(0x0028,0x0004); Archive->Restore(0x0028,0x0006); Archive->Restore(GetFile()->GetGrPixel(),GetFile()->GetNumPixel()); // For old ACR-NEMA (24 bits problem) Archive->Restore(0x0028,0x0100); Archive->Restore(0x0028,0x0101); Archive->Restore(0x0028,0x0102); // 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); // For the Palette Color Lookup Table UID Archive->Restore(0x0028,0x1203); // group 0002 may be pushed out for ACR-NEMA writting purposes Archive->Restore(0x0002,0x0000); Archive->Restore(0x0002,0x0001); Archive->Restore(0x0002,0x0002); Archive->Restore(0x0002,0x0003); Archive->Restore(0x0002,0x0010); Archive->Restore(0x0002,0x0012); Archive->Restore(0x0002,0x0013); Archive->Restore(0x0002,0x0016); Archive->Restore(0x0002,0x0100); Archive->Restore(0x0002,0x0102); }

void gdcm::FileHelper::RestoreWriteFileType (   )  [protected]

Restore in the File the initial group 0002. Definition at line 1044 of file gdcmFileHelper.cxx. Referenced by Write(). { }

void gdcm::FileHelper::RestoreWriteMandatory (   )  [protected]

Restore in the File the initial group 0002. Definition at line 1695 of file gdcmFileHelper.cxx. References Archive, and gdcm::DocEntryArchive::Restore(). Referenced by Write(). { // group 0002 may be pushed out for ACR-NEMA writting purposes Archive->Restore(0x0002,0x0000); Archive->Restore(0x0002,0x0001); Archive->Restore(0x0002,0x0002); Archive->Restore(0x0002,0x0003); Archive->Restore(0x0002,0x0010); Archive->Restore(0x0002,0x0012); Archive->Restore(0x0002,0x0013); Archive->Restore(0x0002,0x0016); Archive->Restore(0x0002,0x0100); Archive->Restore(0x0002,0x0102); // FIXME : Check if none is missing ! Archive->Restore(0x0008,0x0012); Archive->Restore(0x0008,0x0013); Archive->Restore(0x0008,0x0016); Archive->Restore(0x0008,0x0018); Archive->Restore(0x0008,0x0060); Archive->Restore(0x0008,0x0070); Archive->Restore(0x0008,0x0080); Archive->Restore(0x0008,0x0090); Archive->Restore(0x0008,0x2112); Archive->Restore(0x0010,0x0010); Archive->Restore(0x0010,0x0030); Archive->Restore(0x0010,0x0040); Archive->Restore(0x0020,0x000d); Archive->Restore(0x0020,0x000e); }

void gdcm::FileHelper::RestoreWriteOfLibido (   )  [protected]

Restore the Write format. Definition at line 1103 of file gdcmFileHelper.cxx. References Archive, and gdcm::DocEntryArchive::Restore(). Referenced by Write(). { Archive->Restore(0x0028,0x0010); Archive->Restore(0x0028,0x0011); Archive->Restore(0x0008,0x0010); // Restore 'LibIDO-special' entries, if any Archive->Restore(0x0028,0x0015); Archive->Restore(0x0028,0x0016); Archive->Restore(0x0028,0x0017); Archive->Restore(0x0028,0x00199); }

bool gdcm::FileHelper::SetEntryBinArea (  uint8_t *  content, int  lgth, uint16_t  group, uint16_t  elem )

Accesses an existing DataEntry through it's (group, element) and modifies it's content with the given value. Parameters: content  new value (void* -> uint8_t*) to substitute with lgth  new value length group  group number of the Dicom Element to modify elem  element number of the Dicom Element to modify Returns: false if DataEntry not found Definition at line 251 of file gdcmFileHelper.cxx. References FileInternal, and gdcm::DocEntrySet::SetEntryBinArea(). { return FileInternal->SetEntryBinArea(content, lgth, group, elem); }

bool gdcm::FileHelper::SetEntryString (  std::string const &  content, uint16_t  group, uint16_t  elem )

Accesses an existing DataEntry through it's (group, element) and modifies it's content with the given value. Parameters: content  new value (string) to substitute with group  group number of the Dicom Element to modify elem  element number of the Dicom Element to modify Returns: false if DataEntry not found Definition at line 235 of file gdcmFileHelper.cxx. References FileInternal, and gdcm::DocEntrySet::SetEntryString(). { return FileInternal->SetEntryString(content, group, elem); }

void gdcm::FileHelper::SetFileName (  std::string const &  fileName  )

Sets the LoadMode of the internal gdcm::File. Parameters: fileName  name of the file to be open Definition at line 208 of file gdcmFileHelper.cxx. References FileInternal, and gdcm::Document::SetFileName(). { FileInternal->SetFileName( fileName ); }

void gdcm::FileHelper::SetImageData (  uint8_t *  inData, size_t  expectedSize )

Points the internal pointer to the callers inData image representation, BUT WITHOUT COPYING THE DATA. 'image' Pixels are presented as C-like 2D arrays : line per line. 'volume'Pixels are presented as C-like 3D arrays : plane per plane. Warning: Since the pixels are not copied, it is the caller's responsability not to deallocate its data before gdcm uses them (e.g. with the Write() method ) Parameters: inData  user supplied pixel area (uint8_t* is just for the compiler. user is allowed to pass any kind of pixelsn since the size is given in bytes) expectedSize  total image size, *in Bytes* Definition at line 461 of file gdcmFileHelper.cxx. References SetUserData(). { SetUserData(inData, expectedSize); }

void gdcm::FileHelper::SetKeepMediaStorageSOPClassUID (  bool  v  )  [inline]

if user knows he didn't modify the pixels (e.g. he just anonymized the file), he is allowed to ask to keep the original 'Media Storage SOP Class UID' and 'Image Type' Definition at line 154 of file gdcmFileHelper.h. { KeepMediaStorageSOPClassUID = v; }

void gdcm::FileHelper::SetLoadMode (  int  loadMode  )

Sets the LoadMode of the internal gdcm::File as a boolean string. NO_SEQ, NO_SHADOW, NO_SHADOWSEQ ... (nothing more, right now) WARNING : before using NO_SHADOW, be sure *all* your files contain accurate values in the 0x0000 element (if any) of *each* Shadow Group. The parser will fail if the size is wrong ! Parameters: loadMode  Load mode to be used Definition at line 200 of file gdcmFileHelper.cxx. References GetFile(), and gdcm::Document::SetLoadMode(). { GetFile()->SetLoadMode( loadMode ); }

void gdcm::FileHelper::SetMandatoryEntry (  uint16_t  group, uint16_t  elem, std::string  value )  [protected]

Definition at line 1676 of file gdcmFileHelper.cxx. References Archive, gdcm::RefCounter::Delete(), gdcm::Global::GetDicts(), gdcm::DataEntry::New(), gdcm::DocEntryArchive::Push(), and gdcm::DataEntry::SetString(). { DataEntry *entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); entry->SetString(value); Archive->Push(entry); entry->Delete(); }

void gdcm::Base::SetPrintLevel (  int  level  )  [inline, inherited]

Sets the print level for the Dicom Header Elements. Note: 0 for Light Print; 1 for 'medium' Print, 2 for Heavy Print Definition at line 47 of file gdcmBase.h. Referenced by gdcm::SQItem::Print(), gdcm::SeqEntry::Print(), Print(), gdcm::ElementSet::Print(), and gdcm::DicomDir::Print(). { PrintLevel = level; }

void gdcm::FileHelper::SetUserData (  uint8_t *  inData, size_t  expectedSize )

Set the image data defined by the user. Warning: When writting the file, this data are get as default data to write Parameters: inData  user supplied pixel area (uint8_t* is just for the compiler. user is allowed to pass any kind of pixels since the size is given in bytes) expectedSize  total image size, *in Bytes* Definition at line 474 of file gdcmFileHelper.cxx. References PixelWriteConverter, and gdcm::PixelWriteConvert::SetUserData(). Referenced by SetImageData(), and SetImageInformation(). { PixelWriteConverter->SetUserData(inData, expectedSize); }

void gdcm::FileHelper::SetUserFunction (  VOID_FUNCTION_PUINT8_PFILE_POINTER  userFunc  )  [inline]

to allow user to modify pixel order (e.g. Mirror, UpsideDown,...) Definition at line 70 of file gdcmFileHelper.h. Referenced by vtkGdcmReader::LoadImageInMemory(). { UserFunction = userFunc; }

void gdcm::FileHelper::SetWriteFileTypeToACR (   )  [protected]

Pushes out the whole group 0002 FIXME : better, set a flag to tell the writer not to write it ... FIXME : method should probably have an other name ! SetWriteFileTypeToACR is NOT opposed to SetWriteFileTypeToExplicitVR and SetWriteFileTypeToImplicitVR. Definition at line 984 of file gdcmFileHelper.cxx. References Archive, and gdcm::DocEntryArchive::Push(). Referenced by Write(). { Archive->Push(0x0002,0x0000); Archive->Push(0x0002,0x0001); Archive->Push(0x0002,0x0002); Archive->Push(0x0002,0x0003); Archive->Push(0x0002,0x0010); Archive->Push(0x0002,0x0012); Archive->Push(0x0002,0x0013); Archive->Push(0x0002,0x0016); Archive->Push(0x0002,0x0100); Archive->Push(0x0002,0x0102); }

void gdcm::FileHelper::SetWriteFileTypeToExplicitVR (   )  [protected]

Definition at line 1013 of file gdcmFileHelper.cxx. References Archive, CopyDataEntry(), gdcm::RefCounter::Delete(), gdcm::Util::DicomString(), gdcm::Global::GetTS(), gdcm::DocEntryArchive::Push(), and gdcm::DataEntry::SetString(). Referenced by Write(). { std::string ts = Util::DicomString( Global::GetTS()->GetSpecialTransferSyntax(TS::ExplicitVRLittleEndian) ); DataEntry *tss = CopyDataEntry(0x0002,0x0010); tss->SetString(ts); Archive->Push(tss); tss->Delete(); }

void gdcm::FileHelper::SetWriteFileTypeToImplicitVR (   )  [protected]

Sets in the File the TransferSyntax to 'Implicit VR Little Endian". Definition at line 1028 of file gdcmFileHelper.cxx. References Archive, CopyDataEntry(), gdcm::RefCounter::Delete(), gdcm::Util::DicomString(), gdcm::Global::GetTS(), gdcm::DocEntryArchive::Push(), and gdcm::DataEntry::SetString(). Referenced by Write(). { std::string ts = Util::DicomString( Global::GetTS()->GetSpecialTransferSyntax(TS::ImplicitVRLittleEndian) ); DataEntry *tss = CopyDataEntry(0x0002,0x0010); tss->SetString(ts); Archive->Push(tss); tss->Delete(); }

void gdcm::FileHelper::SetWriteFileTypeToJPEG (   )  [protected]

Sets in the File the TransferSyntax to 'Explicit VR Little Endian". Definition at line 1001 of file gdcmFileHelper.cxx. References Archive, CopyDataEntry(), gdcm::RefCounter::Delete(), gdcm::Util::DicomString(), gdcm::Global::GetTS(), gdcm::DocEntryArchive::Push(), and gdcm::DataEntry::SetString(). Referenced by Write(). { std::string ts = Util::DicomString( Global::GetTS()->GetSpecialTransferSyntax(TS::JPEGBaselineProcess1) ); DataEntry *tss = CopyDataEntry(0x0002,0x0010); tss->SetString(ts); Archive->Push(tss); tss->Delete(); }

void gdcm::FileHelper::SetWriteMode (  FileMode  mode  )  [inline]

Sets the Write Mode ( ). Definition at line 120 of file gdcmFileHelper.h. { WriteMode = mode; }

void gdcm::FileHelper::SetWriteModeToRaw (   )  [inline]

Tells the writer we want to keep 'Grey pixels + Palettes color' when possible (as opposed to convert 'Palettes color' to RGB). Definition at line 115 of file gdcmFileHelper.h. { SetWriteMode(WMODE_RAW); }

void gdcm::FileHelper::SetWriteModeToRGB (   )  [inline]

Tells the writer we want to write RGB image when possible (as opposed to 'Grey pixels + Palettes color'). Definition at line 118 of file gdcmFileHelper.h. { SetWriteMode(WMODE_RGB); }

void gdcm::FileHelper::SetWriteToLibido (   )  [protected]

Set the Write not to Libido format. Definition at line 1051 of file gdcmFileHelper.cxx. References Archive, gdcm::DataEntry::Copy(), CopyDataEntry(), gdcm::RefCounter::Delete(), FileInternal, gdcm::DocEntrySet::GetDataEntry(), gdcm::DocEntry::GetDictEntry(), gdcm::DataEntry::GetString(), gdcm::DataEntry::New(), gdcm::DocEntryArchive::Push(), and gdcm::DataEntry::SetString(). Referenced by Write(). { DataEntry *oldRow = FileInternal->GetDataEntry(0x0028, 0x0010); DataEntry *oldCol = FileInternal->GetDataEntry(0x0028, 0x0011); if ( oldRow && oldCol ) { std::string rows, columns; DataEntry *newRow=DataEntry::New(oldRow->GetDictEntry()); DataEntry *newCol=DataEntry::New(oldCol->GetDictEntry()); newRow->Copy(oldCol); newCol->Copy(oldRow); newRow->SetString(oldCol->GetString()); newCol->SetString(oldRow->GetString()); Archive->Push(newRow); Archive->Push(newCol); newRow->Delete(); newCol->Delete(); } DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010); libidoCode->SetString("ACRNEMA_LIBIDO_1.1"); Archive->Push(libidoCode); libidoCode->Delete(); }

void gdcm::FileHelper::SetWriteToNoLibido (   )  [protected]

Set the Write not to No Libido format. Definition at line 1085 of file gdcmFileHelper.cxx. References Archive, CopyDataEntry(), gdcm::RefCounter::Delete(), FileInternal, gdcm::DocEntrySet::GetDataEntry(), gdcm::DataEntry::GetString(), gdcm::DocEntryArchive::Push(), and gdcm::DataEntry::SetString(). Referenced by Write(). { DataEntry *recCode = FileInternal->GetDataEntry(0x0008,0x0010); if ( recCode ) { if ( recCode->GetString() == "ACRNEMA_LIBIDO_1.1" ) { DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010); libidoCode->SetString(""); Archive->Push(libidoCode); libidoCode->Delete(); } } }

void gdcm::FileHelper::SetWriteToRaw (   )  [protected]

Updates the File to write RAW data (as opposed to RGB data) (modifies, when necessary, photochromatic interpretation, bits allocated, Pixels element VR). Definition at line 802 of file gdcmFileHelper.cxx. References Archive, CopyDataEntry(), gdcm::RefCounter::Delete(), FileInternal, gdcm::DataEntry::FLAG_PIXELDATA, gdcm::File::GetBitsAllocated(), gdcm::PixelWriteConvert::GetData(), gdcm::PixelWriteConvert::GetDataSize(), GetFile(), gdcm::File::GetNumberOfScalarComponents(), gdcm::PixelReadConvert::GetRaw(), gdcm::PixelReadConvert::GetRawSize(), gdcm::File::HasLUT(), PixelReadConverter, PixelWriteConverter, gdcm::DocEntryArchive::Push(), gdcm::DataEntry::SetBinArea(), gdcm::DataEntry::SetFlag(), gdcm::DocEntry::SetLength(), gdcm::PixelWriteConvert::SetReadData(), gdcm::DataEntry::SetString(), and SetWriteToRGB(). Referenced by SetWriteToRGB(), and Write(). { if ( FileInternal->GetNumberOfScalarComponents() == 3 && !FileInternal->HasLUT() ) { SetWriteToRGB(); } else { DataEntry *photInt = CopyDataEntry(0x0028,0x0004); if (FileInternal->HasLUT() ) { photInt->SetString("PALETTE COLOR "); } else { photInt->SetString("MONOCHROME2 "); } PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(), PixelReadConverter->GetRawSize()); std::string vr = "OB"; if ( FileInternal->GetBitsAllocated()>8 ) vr = "OW"; if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files vr = "OB"; DataEntry *pixel = CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr); pixel->SetFlag(DataEntry::FLAG_PIXELDATA); pixel->SetBinArea(PixelWriteConverter->GetData(),false); pixel->SetLength(PixelWriteConverter->GetDataSize()); Archive->Push(photInt); Archive->Push(pixel); photInt->Delete(); pixel->Delete(); } }

void gdcm::FileHelper::SetWriteToRGB (   )  [protected]

Updates the File to write RGB data (as opposed to RAW data) (modifies, when necessary, photochromatic interpretation, samples per pixel, Planar configuration, bits allocated, bits stored, high bit -ACR 24 bits- Pixels element VR, pushes out the LUT, ). Definition at line 850 of file gdcmFileHelper.cxx. References Archive, gdcm::PixelReadConvert::BuildRGBImage(), CopyDataEntry(), gdcm::RefCounter::Delete(), FileInternal, gdcm::DataEntry::FLAG_PIXELDATA, gdcm::File::GetBitsAllocated(), gdcm::PixelWriteConvert::GetData(), gdcm::PixelWriteConvert::GetDataSize(), GetFile(), gdcm::File::GetNumberOfScalarComponents(), gdcm::PixelReadConvert::GetRaw(), gdcm::PixelReadConvert::GetRawSize(), gdcm::PixelReadConvert::GetRGB(), gdcm::PixelReadConvert::GetRGBSize(), PixelReadConverter, PixelWriteConverter, gdcm::DocEntryArchive::Push(), gdcm::DataEntry::SetBinArea(), gdcm::DataEntry::SetFlag(), gdcm::DocEntry::SetLength(), gdcm::PixelWriteConvert::SetReadData(), gdcm::DataEntry::SetString(), and SetWriteToRaw(). Referenced by SetWriteToRaw(), and Write(). { if ( FileInternal->GetNumberOfScalarComponents()==3 ) { PixelReadConverter->BuildRGBImage(); DataEntry *spp = CopyDataEntry(0x0028,0x0002); spp->SetString("3 "); DataEntry *planConfig = CopyDataEntry(0x0028,0x0006); planConfig->SetString("0 "); DataEntry *photInt = CopyDataEntry(0x0028,0x0004); photInt->SetString("RGB "); if ( PixelReadConverter->GetRGB() ) { PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(), PixelReadConverter->GetRGBSize()); } else // Raw data { PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(), PixelReadConverter->GetRawSize()); } std::string vr = "OB"; if ( FileInternal->GetBitsAllocated()>8 ) vr = "OW"; if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files vr = "OB"; DataEntry *pixel = CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr); pixel->SetFlag(DataEntry::FLAG_PIXELDATA); pixel->SetBinArea(PixelWriteConverter->GetData(),false); pixel->SetLength(PixelWriteConverter->GetDataSize()); Archive->Push(spp); Archive->Push(planConfig); Archive->Push(photInt); Archive->Push(pixel); spp->Delete(); planConfig->Delete(); photInt->Delete(); pixel->Delete(); // Remove any LUT Archive->Push(0x0028,0x1101); Archive->Push(0x0028,0x1102); Archive->Push(0x0028,0x1103); Archive->Push(0x0028,0x1201); Archive->Push(0x0028,0x1202); Archive->Push(0x0028,0x1203); // push out Palette Color Lookup Table UID, if any Archive->Push(0x0028,0x1199); // For old '24 Bits' ACR-NEMA // Thus, we have a RGB image and the bits allocated = 24 and // samples per pixels = 1 (in the read file) if ( FileInternal->GetBitsAllocated()==24 ) { DataEntry *bitsAlloc = CopyDataEntry(0x0028,0x0100); bitsAlloc->SetString("8 "); DataEntry *bitsStored = CopyDataEntry(0x0028,0x0101); bitsStored->SetString("8 "); DataEntry *highBit = CopyDataEntry(0x0028,0x0102); highBit->SetString("7 "); Archive->Push(bitsAlloc); Archive->Push(bitsStored); Archive->Push(highBit); bitsAlloc->Delete(); bitsStored->Delete(); highBit->Delete(); } } else { SetWriteToRaw(); } }

void gdcm::FileHelper::SetWriteType (  FileType  format  )  [inline]

Tells the writer which format we want to write (ImplicitVR, ExplicitVR, ACR, ACR_LIBIDO). Definition at line 138 of file gdcmFileHelper.h. { WriteType = format; }

void gdcm::FileHelper::SetWriteTypeToAcr (   )  [inline]

Tells the writer we want to write as ACR-NEMA. Definition at line 131 of file gdcmFileHelper.h. References gdcm::ACR. Referenced by WriteAcr(), and vtkGdcmWriter::WriteDcmFile(). { SetWriteType(ACR); }

void gdcm::FileHelper::SetWriteTypeToAcrLibido (   )  [inline]

Tells the writer we want to write as LibIDO. Definition at line 133 of file gdcmFileHelper.h. References gdcm::ACR_LIBIDO. Referenced by vtkGdcmWriter::WriteDcmFile(). { SetWriteType(ACR_LIBIDO); }

void gdcm::FileHelper::SetWriteTypeToDcmExplVR (   )  [inline]

Tells the writer we want to write as Explicit VR. Definition at line 129 of file gdcmFileHelper.h. References gdcm::ExplicitVR. Referenced by WriteDcmExplVR(), and vtkGdcmWriter::WriteDcmFile(). { SetWriteType(ExplicitVR); }

void gdcm::FileHelper::SetWriteTypeToDcmImplVR (   )  [inline]

Tells the writer we want to write as Implicit VR. Definition at line 127 of file gdcmFileHelper.h. References gdcm::ImplicitVR. Referenced by vtkGdcmWriter::WriteDcmFile(), and WriteDcmImplVR(). { SetWriteType(ImplicitVR); }

void gdcm::FileHelper::SetWriteTypeToJPEG (   )  [inline]

Tells the writer we want to write as JPEG. Definition at line 135 of file gdcmFileHelper.h. References gdcm::JPEG. { SetWriteType(JPEG); }

void gdcm::RefCounter::Unregister (   )  [inline, inherited]

Unregister the object. Remarks: It decrements the reference counting Definition at line 48 of file gdcmRefCounter.h. Referenced by gdcm::SeqEntry::ClearSQItem(), gdcm::DicomDir::Copy(), gdcm::DocEntrySet::GetDictEntry(), gdcm::CommandManager::InSetCommand(), gdcm::DocEntrySet::NewDataEntry(), gdcm::DocEntrySet::NewSeqEntry(), gdcm::Document::ReadNextDocEntry(), gdcm::SQItem::RemoveEntry(), gdcm::ElementSet::RemoveEntry(), gdcm::SeqEntry::SetDelimitationItem(), gdcm::DocEntry::~DocEntry(), and ~FileHelper(). { RefCount--; if(RefCount<=0) delete this; }

bool gdcm::FileHelper::Write (  std::string const &  fileName  )

Writes on disk A SINGLE Dicom file,. Parameters: fileName  name of the file to be created (any already existing file is overwritten) Returns: false if write fails Todo: the best trick would be *change* the recognition code but pb expected if user deals with, e.g. COMPLEX images Definition at line 657 of file gdcmFileHelper.cxx. References gdcm::ACR, gdcm::ACR_LIBIDO, CheckMandatoryElements(), CheckWriteIntegrity(), gdcm::ExplicitVR, FileInternal, gdcm::DocEntrySet::GetDataEntry(), gdcm::ImplicitVR, gdcm::DocEntrySet::InsertEntryString(), gdcm::JPEG, RestoreWrite(), RestoreWriteFileType(), RestoreWriteMandatory(), RestoreWriteOfLibido(), SetWriteFileTypeToACR(), SetWriteFileTypeToExplicitVR(), SetWriteFileTypeToImplicitVR(), SetWriteFileTypeToJPEG(), SetWriteToLibido(), SetWriteToNoLibido(), SetWriteToRaw(), SetWriteToRGB(), gdcm::Unknown, WMODE_RAW, WMODE_RGB, gdcm::File::Write(), WriteMode, and WriteType. Referenced by WriteAcr(), WriteDcmExplVR(), vtkGdcmWriter::WriteDcmFile(), and WriteDcmImplVR(). { switch(WriteType) { case ImplicitVR: SetWriteFileTypeToImplicitVR(); break; case Unknown: // should never happen; ExplicitVR is the default value case ExplicitVR: SetWriteFileTypeToExplicitVR(); break; case ACR: case ACR_LIBIDO: // NOTHING is done here just for LibIDO. // Just to avoid further trouble if user creates a file ex-nihilo, // wants to write it as an ACR-NEMA file, // and forgets to create any Entry belonging to group 0008 // (shame on him !) // We add Recognition Code (RET) if ( ! FileInternal->GetDataEntry(0x0008, 0x0010) ) FileInternal->InsertEntryString("ACR-NEMA V1.0 ", 0x0008, 0x0010); SetWriteFileTypeToACR(); // SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR ! break; case JPEG: SetWriteFileTypeToJPEG(); std::cerr << "Writting as JPEG" << std::endl; break; } CheckMandatoryElements(); // -------------------------------------------------------------- // 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 ... if ( WriteType == ACR_LIBIDO ) { SetWriteToLibido(); } else { SetWriteToNoLibido(); } // ----------------- End of Special Patch ---------------- switch(WriteMode) { case WMODE_RAW : SetWriteToRaw(); // modifies and pushes to the archive, when necessary break; case WMODE_RGB : SetWriteToRGB(); // modifies and pushes to the archive, when necessary break; } bool check = CheckWriteIntegrity(); // verifies length if (WriteType == JPEG ) check = true; if (check) { check = FileInternal->Write(fileName,WriteType); } RestoreWrite(); RestoreWriteFileType(); RestoreWriteMandatory(); // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images // // ...and we restore the header to be Dicom Compliant again // just after writting RestoreWriteOfLibido(); // ----------------- End of Special Patch ---------------- return check; }

bool gdcm::FileHelper::WriteAcr (  std::string const &  fileName  )

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 NO TEST is performed on processor "Endiannity". Parameters: fileName  name of the file to be created (any already existing file is overwritten) Returns: false if write fails Definition at line 645 of file gdcmFileHelper.cxx. References SetWriteTypeToAcr(), and Write(). { SetWriteTypeToAcr(); return Write(fileName); }

bool gdcm::FileHelper::WriteDcmExplVR (  std::string const &  fileName  )

Writes on disk A SINGLE Dicom file, using the Explicit Value Representation convention NO test is performed on processor "Endiannity". Parameters: fileName  name of the file to be created (any already existing file is overwritten) Returns: false if write fails Definition at line 625 of file gdcmFileHelper.cxx. References SetWriteTypeToDcmExplVR(), and Write(). { SetWriteTypeToDcmExplVR(); return Write(fileName); }

bool gdcm::FileHelper::WriteDcmImplVR (  std::string const &  fileName  )

Writes on disk A SINGLE Dicom file, using the Implicit Value Representation convention NO test is performed on processor "Endianity". Parameters: fileName  name of the file to be created (any already existing file is overwritten) Returns: false if write fails Definition at line 610 of file gdcmFileHelper.cxx. References SetWriteTypeToDcmImplVR(), and Write(). { SetWriteTypeToDcmImplVR(); return Write(fileName); }

bool gdcm::FileHelper::WriteRawData (  std::string const &  fileName  )

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. Parameters: fileName  name of the file to be created (any already existing file is over written) Returns: false if write fails Definition at line 567 of file gdcmFileHelper.cxx. References gdcmErrorMacro, gdcmWarningMacro, gdcm::PixelReadConvert::GetRaw(), gdcm::PixelReadConvert::GetRawSize(), gdcm::PixelReadConvert::GetRGB(), gdcm::PixelReadConvert::GetRGBSize(), gdcm::PixelWriteConvert::GetUserData(), gdcm::PixelWriteConvert::GetUserDataSize(), PixelReadConverter, and PixelWriteConverter. { std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary ); if (!fp1) { gdcmWarningMacro( "Fail to open (write) file:" << fileName.c_str()); return false; } if ( PixelWriteConverter->GetUserData() ) { fp1.write( (char *)PixelWriteConverter->GetUserData(), PixelWriteConverter->GetUserDataSize() ); } else if ( PixelReadConverter->GetRGB() ) { fp1.write( (char *)PixelReadConverter->GetRGB(), PixelReadConverter->GetRGBSize()); } else if ( PixelReadConverter->GetRaw() ) { fp1.write( (char *)PixelReadConverter->GetRaw(), PixelReadConverter->GetRawSize()); } else { gdcmErrorMacro( "Nothing written." ); } fp1.close(); return true; }

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Member Data Documentation

bool gdcm::FileHelper::Abort [mutable, protected]

Definition at line 200 of file gdcmFileHelper.h. Referenced by CallStartMethod().

DocEntryArchive* gdcm::FileHelper::Archive [private]

Pointer to the DocEntryArchive (used while writting process). Definition at line 218 of file gdcmFileHelper.h. Referenced by CheckMandatoryElements(), CheckMandatoryEntry(), CopyMandatoryEntry(), Initialize(), RestoreWrite(), RestoreWriteMandatory(), RestoreWriteOfLibido(), SetMandatoryEntry(), SetWriteFileTypeToACR(), SetWriteFileTypeToExplicitVR(), SetWriteFileTypeToImplicitVR(), SetWriteFileTypeToJPEG(), SetWriteToLibido(), SetWriteToNoLibido(), SetWriteToRaw(), SetWriteToRGB(), and ~FileHelper().

File* gdcm::FileHelper::FileInternal [private]

gdcm::File to use to load the file Definition at line 205 of file gdcmFileHelper.h. Referenced by CheckMandatoryElements(), CheckMandatoryEntry(), CheckWriteIntegrity(), CopyDataEntry(), FileHelper(), GetImageData(), GetRaw(), Initialize(), InsertEntryBinArea(), InsertEntryString(), InsertSeqEntry(), Load(), Print(), SetEntryBinArea(), SetEntryString(), SetFileName(), SetWriteToLibido(), SetWriteToNoLibido(), SetWriteToRaw(), SetWriteToRGB(), Write(), and ~FileHelper().

bool gdcm::FileHelper::KeepMediaStorageSOPClassUID [private]

if user knows he didn't modify the pixels (e.g. he just anonymized the file), he is allowed to ask to keep the original 'Media Storage SOP Class UID' and 'Image Type' Definition at line 238 of file gdcmFileHelper.h. Referenced by CheckMandatoryElements(), and Initialize().

bool gdcm::FileHelper::Parsed [private]

Whether already parsed or not. Definition at line 208 of file gdcmFileHelper.h.

PixelReadConvert* gdcm::FileHelper::PixelReadConverter [private]

Pointer to the PixelReadConverter. Definition at line 212 of file gdcmFileHelper.h. Referenced by FileHelper(), GetImageData(), GetImageDataRawSize(), GetImageDataSize(), GetLutItemNumber(), GetLutItemSize(), GetLutRGBA(), GetRaw(), GetRawData(), GetRawDataSize(), GetRGBData(), GetRGBDataSize(), Initialize(), Load(), Print(), SetWriteToRaw(), SetWriteToRGB(), WriteRawData(), and ~FileHelper().

PixelWriteConvert* gdcm::FileHelper::PixelWriteConverter [private]

Pointer to the PixelWriteConverter. Definition at line 214 of file gdcmFileHelper.h. Referenced by CheckWriteIntegrity(), GetImageData(), GetImageDataRawSize(), GetImageDataSize(), GetUserData(), GetUserDataSize(), Initialize(), SetUserData(), SetWriteToRaw(), SetWriteToRGB(), WriteRawData(), and ~FileHelper().

int gdcm::Base::PrintLevel [protected, inherited]

Amount of printed details for each Dicom Entries : 0 : stands for the least detail level. Definition at line 55 of file gdcmBase.h. Referenced by gdcm::SQItem::Print(), gdcm::SeqEntry::Print(), Print(), gdcm::ElementSet::Print(), gdcm::DocEntry::Print(), gdcm::DictEntry::Print(), gdcm::DicomDirStudy::Print(), gdcm::DicomDirSerie::Print(), gdcm::DicomDirPatient::Print(), gdcm::DicomDirMeta::Print(), gdcm::DicomDir::Print(), and gdcm::DataEntry::Print().

float gdcm::FileHelper::Progress [protected]

value of the ??? for any progress bar Definition at line 199 of file gdcmFileHelper.h. Referenced by CallEndMethod(), and CallStartMethod().

VOID_FUNCTION_PUINT8_PFILE_POINTER gdcm::FileHelper::UserFunction [private]

Pointer to a user supplied function to allow modification of pixel order (e.g. : Mirror, UpsideDown, 90°Rotation, ...) use as : void userSuppliedFunction(uint8_t *im, gdcm::File *f) NB : the "uint8_t *" type of first param is just for prototyping. User will Cast it according what he founds with f->GetPixelType() See vtkgdcmSerieViewer for an example. Definition at line 233 of file gdcmFileHelper.h. Referenced by GetRaw(), and Initialize().

FileMode gdcm::FileHelper::WriteMode [private]

(WMODE_RAW, WMODE_RGB) Definition at line 222 of file gdcmFileHelper.h. Referenced by CheckWriteIntegrity(), Initialize(), and Write().

FileType gdcm::FileHelper::WriteType [private]

(ImplicitVR, ExplicitVR, ACR, ACR_LIBIDO) Definition at line 225 of file gdcmFileHelper.h. Referenced by CheckMandatoryElements(), Initialize(), and Write().

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The documentation for this class was generated from the following files:

• gdcmFileHelper.h
• gdcmFileHelper.cxx

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