+#include "gdcmFile.h"
+#include "gdcmDocument.h"
+#include "gdcmDebug.h"
+#include "gdcmUtil.h"
+#include "gdcmBinEntry.h"
+#include "gdcmHeader.h"
+#include "gdcmPixelReadConvert.h"
+#include "gdcmPixelWriteConvert.h"
+#include "gdcmDocEntryArchive.h"
+
+#include <fstream>
+
+namespace gdcm
+{
+typedef std::pair<TagDocEntryHT::iterator,TagDocEntryHT::iterator> IterHT;
+
+//-------------------------------------------------------------------------
+// Constructor / Destructor
+/**
+ * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
+ * file (Header only deals with the ... header)
+ * Opens (in read only and when possible) an existing file and checks
+ * for DICOM compliance. Returns NULL on failure.
+ * It will be up to the user to load the pixels into memory
+ * (see GetImageData, GetImageDataRaw)
+ * \note the in-memory representation of all available tags found in
+ * the DICOM header is post-poned to first header information access.
+ * This avoid a double parsing of public part of the header when
+ * one sets an a posteriori shadow dictionary (efficiency can be
+ * seen as a side effect).
+ */
+File::File( )
+{
+ HeaderInternal = new Header( );
+ SelfHeader = true;
+ Initialise();
+}
+
+/**
+ * \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
+ */
+File::File(Header *header)
+{
+ HeaderInternal = header;
+ SelfHeader = false;
+ Initialise();
+}
+
+/**
+ * \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
+ */
+File::File(std::string const & filename )
+{
+ HeaderInternal = new Header( filename );
+ SelfHeader = true;
+ Initialise();
+}
+
+/**
+ * \brief canonical destructor
+ * \note If the Header was created by the File constructor,
+ * it is destroyed by the File
+ */
+File::~File()
+{
+ if( PixelReadConverter )
+ {
+ delete PixelReadConverter;
+ }
+ if( PixelWriteConverter )
+ {
+ delete PixelWriteConverter;
+ }
+ if( Archive )
+ {
+ delete Archive;
+ }
+
+ if( SelfHeader )
+ {
+ delete HeaderInternal;
+ }
+ HeaderInternal = 0;
+}
+
+//-----------------------------------------------------------------------------
+// Print
+void File::Print(std::ostream &os)
+{
+ HeaderInternal->SetPrintLevel(PrintLevel);
+ HeaderInternal->Print(os);
+
+ PixelReadConverter->SetPrintLevel(PrintLevel);
+ PixelReadConverter->Print(os);
+}
+
+//-----------------------------------------------------------------------------
+// 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
+ */
+size_t File::GetImageDataSize()
+{
+ if ( PixelWriteConverter->GetUserData() )
+ {
+ return PixelWriteConverter->GetUserDataSize();
+ }
+
+ return PixelReadConverter->GetRGBSize();
+}
+
+/**
+ * \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
+ */
+size_t File::GetImageDataRawSize()
+{
+ if ( PixelWriteConverter->GetUserData() )
+ {
+ return PixelWriteConverter->GetUserDataSize();
+ }
+
+ return PixelReadConverter->GetRawSize();
+}
+
+/**
+ * \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
+ */
+uint8_t* File::GetImageData()
+{
+ if ( PixelWriteConverter->GetUserData() )
+ {
+ return PixelWriteConverter->GetUserData();
+ }
+
+ if ( ! GetRaw() )
+ {
+ // If the decompression failed nothing can be done.
+ return 0;
+ }
+
+ if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
+ {
+ return PixelReadConverter->GetRGB();
+ }
+ else
+ {
+ // When no LUT or LUT conversion fails, return the Raw
+ return PixelReadConverter->GetRaw();
+ }
+}
+
+/**
+ * \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
+ */
+uint8_t* File::GetImageDataRaw ()
+{
+ return GetRaw();
+}
+
+/**
+ * \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 ( ! GetRaw() )
+ {
+ // If the decompression failed nothing can be done.
+ return 0;
+ }
+
+ if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
+ {
+ if ( PixelReadConverter->GetRGBSize() > maxSize )
+ {
+ dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
+ "than caller's expected MaxSize");
+ return 0;
+ }
+ memcpy( destination,
+ (void*)PixelReadConverter->GetRGB(),
+ PixelReadConverter->GetRGBSize() );
+ return PixelReadConverter->GetRGBSize();
+ }
+
+ // Either no LUT conversion necessary or LUT conversion failed
+ if ( PixelReadConverter->GetRawSize() > maxSize )
+ {
+ dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
+ "than caller's expected MaxSize");
+ return 0;
+ }
+ memcpy( destination,
+ (void*)PixelReadConverter->GetRaw(),
+ PixelReadConverter->GetRawSize() );
+ return PixelReadConverter->GetRawSize();
+}
+
+/**
+ * \brief Points the internal pointer to the callers inData
+ * image representation, BUT WITHOUT COPYING THE DATA.
+ * 'image' Pixels are presented as C-like 2D arrays : line per line.
+ * 'volume'Pixels are presented as C-like 3D arrays : plane per plane
+ * \warning Since the pixels are not copied, it is the caller's responsability
+ * not to deallocate it's data before gdcm uses them (e.g. with
+ * the Write() method.
+ * @param inData user supplied pixel area
+ * @param expectedSize total image size, in Bytes
+ *
+ * @return boolean
+ */
+void File::SetImageData(uint8_t* inData, size_t expectedSize)
+{
+ SetUserData(inData,expectedSize);
+}
+
+/**
+ * \brief Set the image datas defined by the user
+ * \warning When writting the file, this datas are get as default datas to write
+ */
+void File::SetUserData(uint8_t* data, size_t expectedSize)
+{
+ PixelWriteConverter->SetUserData(data,expectedSize);
+}
+
+/**
+ * \brief Get the image datas defined by the user
+ * \warning When writting the file, this datas are get as default datas to write
+ */
+uint8_t* File::GetUserData()
+{
+ return PixelWriteConverter->GetUserData();
+}
+
+/**
+ * \brief Get the image data size defined by the user
+ * \warning When writting the file, this datas are get as default datas to write
+ */
+size_t File::GetUserDataSize()
+{
+ return PixelWriteConverter->GetUserDataSize();
+}
+
+/**
+ * \brief Get the image datas from the file.
+ * If a LUT is found, the datas are expanded to be RGB
+ */
+uint8_t* File::GetRGBData()
+{
+ return PixelReadConverter->GetRGB();
+}
+
+/**
+ * \brief Get the image data size from the file.
+ * If a LUT is found, the datas are expanded to be RGB
+ */
+size_t File::GetRGBDataSize()
+{
+ return PixelReadConverter->GetRGBSize();
+}
+
+/**
+ * \brief Get the image datas from the file.
+ * If a LUT is found, the datas are not expanded !
+ */
+uint8_t* File::GetRawData()
+{
+ return PixelReadConverter->GetRaw();
+}
+
+/**
+ * \brief Get the image data size from the file.
+ * If a LUT is found, the datas are not expanded !
+ */
+size_t File::GetRawDataSize()
+{
+ return PixelReadConverter->GetRawSize();
+}
+
+/**
+ * \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
+ */
+
+bool File::WriteRawData(std::string const & fileName)
+{
+ std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary );
+ if (!fp1)
+ {
+ dbg.Verbose(2, "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());
+
+ fp1.close();
+
+ return true;
+}
+
+/**
+ * \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
+ */
+
+bool File::WriteDcmImplVR (std::string const & fileName)
+{
+ SetWriteTypeToDcmImplVR();
+ return Write(fileName);
+}
+
+/**
+* \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
+ */
+
+bool File::WriteDcmExplVR (std::string const & fileName)
+{
+ SetWriteTypeToDcmExplVR();
+ return Write(fileName);
+}
+
+/**
+ * \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
+ */
+
+bool File::WriteAcr (std::string const & fileName)
+{
+ SetWriteTypeToAcr();
+ return Write(fileName);
+}
+
+/**
+ * \brief Writes on disk A SINGLE Dicom file,
+ * @param fileName name of the file to be created
+ * (any already existing file is overwritten)
+ * @return false if write fails
+ */
+bool File::Write(std::string const& fileName)
+{
+ switch(WriteType)
+ {
+ case ImplicitVR:
+ SetWriteFileTypeToImplicitVR();
+ break;
+ case ExplicitVR:
+ SetWriteFileTypeToExplicitVR();
+ break;
+ case ACR:
+ case ACR_LIBIDO:
+ SetWriteFileTypeToACR();
+ break;
+ default:
+ SetWriteFileTypeToExplicitVR();
+ }
+
+ // --------------------------------------------------------------
+ // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
+ //
+ // if recognition code tells us we dealt with a LibIDO image
+ // we reproduce on disk the switch between lineNumber and columnNumber
+ // just before writting ...
+ /// \todo the best trick would be *change* the recognition code
+ /// but pb expected if user deals with, e.g. COMPLEX images
+ if( WriteType == ACR_LIBIDO )
+ {
+ SetWriteToLibido();
+ }
+ else
+ {
+ SetWriteToNoLibido();
+ }
+ // ----------------- End of Special Patch ----------------
+
+ switch(WriteMode)
+ {
+ case WMODE_RAW :
+ SetWriteToRaw();
+ break;
+ case WMODE_RGB :
+ SetWriteToRGB();
+ break;
+ }
+
+ bool check = CheckWriteIntegrity();
+ if(check)
+ {
+ check = HeaderInternal->Write(fileName,WriteType);
+ }
+
+ RestoreWrite();
+ RestoreWriteFileType();
+
+ // --------------------------------------------------------------
+ // 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 File::SetEntryByNumber(std::string const& content,
+ uint16_t group, uint16_t element)
+{
+ return HeaderInternal->SetEntryByNumber(content,group,element);
+}
+
+bool File::SetEntryByNumber(uint8_t* content, int lgth,
+ uint16_t group, uint16_t element)
+{
+ return HeaderInternal->SetEntryByNumber(content,lgth,group,element);
+}
+
+bool File::ReplaceOrCreateByNumber(std::string const& content,
+ uint16_t group, uint16_t element)
+{
+ return HeaderInternal->ReplaceOrCreateByNumber(content,group,element) != NULL;