Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2004/11/24 10:23:47 $
- Version: $Revision: 1.160 $
+ Date: $Date: 2005/01/06 20:03:27 $
+ Version: $Revision: 1.183 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
=========================================================================*/
#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
//-------------------------------------------------------------------------
// 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)
Initialise();
}
-/**
- * \brief Factorization for various forms of constructors.
- */
-void File::Initialise()
-{
- WriteMode = WMODE_RGB;
- WriteType = WTYPE_IMPL_VR;
-
- PixelConverter = new PixelConvert;
- Archive = new DocEntryArchive( HeaderInternal );
-
- if ( HeaderInternal->IsReadable() )
- {
- ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader();
- if ( HeaderInternal->HasLUT() )
- {
- ImageDataSize = 3 * ImageDataSizeRaw;
- }
- else
- {
- ImageDataSize = ImageDataSizeRaw;
- }
-
- PixelConverter->GrabInformationsFromHeader( HeaderInternal );
- }
-
- SaveInitialValues();
-}
-
/**
* \brief canonical destructor
* \note If the Header was created by the File constructor,
*/
File::~File()
{
- if( PixelConverter )
+ if( PixelReadConverter )
{
- delete PixelConverter;
+ delete PixelReadConverter;
+ }
+ if( PixelWriteConverter )
+ {
+ delete PixelWriteConverter;
}
if( Archive )
{
HeaderInternal = 0;
}
-/**
- * \brief Sets some initial values for the Constructor
- * \warning not end user intended
- */
-void File::SaveInitialValues()
-{
- PixelRead = -1; // no ImageData read yet.
- Pixel_Data = 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 computes the length (in bytes) we must ALLOCATE to receive the
- * image(s) pixels (multiframes taken into account)
- * \warning : it is NOT the group 7FE0 length
- * (no interest for compressed images).
+ * \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
*/
-int File::ComputeDecompressedPixelDataSizeFromHeader()
+size_t File::GetImageDataRawSize()
{
- // see PS 3.3-2003 : C.7.6.3.2.1
- //
- // MONOCHROME1
- // MONOCHROME2
- // PALETTE COLOR
- // RGB
- // HSV (Retired)
- // ARGB (Retired)
- // CMYK (Retired)
- // YBR_FULL
- // YBR_FULL_422 (no LUT, no Palette)
- // YBR_PARTIAL_422
- // YBR_ICT
- // YBR_RCT
-
- // LUT's
- // ex : gdcm-US-ALOKA-16.dcm
- // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data]
- // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data]
- // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data]
-
- // ex : OT-PAL-8-face.dcm
- // 0028|1201 [US] [Red Palette Color Lookup Table Data]
- // 0028|1202 [US] [Green Palette Color Lookup Table Data]
- // 0028|1203 [US] [Blue Palette Color Lookup Table Data]
-
- int numberBitsAllocated = HeaderInternal->GetBitsAllocated();
- // Number of "Bits Allocated" is fixed to 16 when:
- // - it is not defined (i.e. it's value is 0)
- // - it's 12, since we will expand the image to 16 bits (see
- // PixelConvert::ConvertDecompress12BitsTo16Bits() )
- if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
- {
- numberBitsAllocated = 16;
- }
+ if ( PixelWriteConverter->GetUserData() )
+ {
+ return PixelWriteConverter->GetUserDataSize();
+ }
- int DecompressedSize = HeaderInternal->GetXSize()
- * HeaderInternal->GetYSize()
- * HeaderInternal->GetZSize()
- * ( numberBitsAllocated / 8 )
- * HeaderInternal->GetSamplesPerPixel();
-
- return DecompressedSize;
+ return PixelReadConverter->GetRawSize();
}
/**
* @return Pointer to newly allocated pixel data.
* NULL if alloc fails
*/
-uint8_t* File::GetImageData()
+uint8_t *File::GetImageData()
{
- if ( ! GetDecompressed() )
- {
- // If the decompression failed nothing can be done.
- return 0;
- }
-
- uint8_t* pixelData;
- if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
+ if ( PixelWriteConverter->GetUserData() )
{
- pixelData = PixelConverter->GetRGB();
+ return PixelWriteConverter->GetUserData();
}
- else
+
+ if ( ! GetRaw() )
{
- // When no LUT or LUT conversion fails, return the decompressed
- pixelData = PixelConverter->GetDecompressed();
+ // If the decompression failed nothing can be done.
+ return 0;
}
-/*// PIXELCONVERT CLEANME
- // Restore the header in a disk-consistent state
- // (if user asks twice to get the pixels from disk)
- if ( PixelRead != -1 ) // File was "read" before
+ if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
{
- RestoreInitialValues();
- }
- if ( PixelConverter->GetRGB() )
- {
- // now, it's an RGB image
- // Lets's write it in the Header
- std::string spp = "3"; // Samples Per Pixel
- HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002);
- std::string rgb = "RGB "; // Photometric Interpretation
- HeaderInternal->SetEntryByNumber(rgb,0x0028,0x0004);
- std::string planConfig = "0"; // Planar Configuration
- HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006);
- PixelRead = 0; // no PixelRaw
+ return PixelReadConverter->GetRGB();
}
else
{
- if ( HeaderInternal->HasLUT() )
- {
- // The LUT interpretation failed
- std::string photometricInterpretation = Util::DicomString("MONOCHROME1");
- HeaderInternal->SetEntryByNumber( photometricInterpretation,
- 0x0028, 0x0004 );
- PixelRead = 0; // no PixelRaw
- }
- else
- {
- if ( PixelConverter->IsDecompressedRGB() )
- {
- ///////////////////////////////////////////////////
- // now, it's an RGB image
- // Lets's write it in the Header
- // Droping Palette Color out of the Header
- // has been moved to the Write process.
- // TODO : move 'values' modification to the write process
- // : save also (in order to be able to restore)
- // : 'high bit' -when not equal to 'bits stored' + 1
- // : 'bits allocated', when it's equal to 12 ?!
- std::string spp = "3"; // Samples Per Pixel
- std::string photInt = "RGB "; // Photometric Interpretation
- std::string planConfig = "0"; // Planar Configuration
- HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002);
- HeaderInternal->SetEntryByNumber(photInt,0x0028,0x0004);
- HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006);
- }
- PixelRead = 1; // PixelRaw
- }
+ // When no LUT or LUT conversion fails, return the Raw
+ return PixelReadConverter->GetRaw();
}
+}
- // We say the value *is* loaded.
- SetPixelData(pixelData);
-// END PIXELCONVERT CLEANME*/
-
- return pixelData;
+/**
+ * \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();
}
/**
* @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)
+size_t File::GetImageDataIntoVector (void *destination, size_t maxSize)
{
- if ( ! GetDecompressed() )
+ if ( ! GetRaw() )
{
// If the decompression failed nothing can be done.
return 0;
}
- if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
+ if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
{
- if ( PixelConverter->GetRGBSize() > maxSize )
+ if ( PixelReadConverter->GetRGBSize() > maxSize )
{
dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
"than caller's expected MaxSize");
return 0;
}
memcpy( destination,
- (void*)PixelConverter->GetRGB(),
- PixelConverter->GetRGBSize() );
- return PixelConverter->GetRGBSize();
+ (void*)PixelReadConverter->GetRGB(),
+ PixelReadConverter->GetRGBSize() );
+ return PixelReadConverter->GetRGBSize();
}
// Either no LUT conversion necessary or LUT conversion failed
- if ( PixelConverter->GetDecompressedSize() > maxSize )
+ if ( PixelReadConverter->GetRawSize() > maxSize )
{
dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
"than caller's expected MaxSize");
return 0;
}
memcpy( destination,
- (void*)PixelConverter->GetDecompressed(),
- PixelConverter->GetDecompressedSize() );
- return PixelConverter->GetDecompressedSize();
+ (void*)PixelReadConverter->GetRaw(),
+ PixelReadConverter->GetRawSize() );
+ return PixelReadConverter->GetRawSize();
}
/**
- * \brief Allocates necessary memory,
- * Transforms YBR pixels (if any) into RGB pixels
- * Transforms 3 planes R, G, B (if any) into a single RGB Plane
- * Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
- * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
- * @return Pointer to newly allocated pixel data.
- * \ NULL if alloc fails
+ * \brief 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
*/
-uint8_t* File::GetImageDataRaw ()
+void File::SetImageData(uint8_t *inData, size_t expectedSize)
{
- uint8_t* decompressed = GetDecompressed();
- if ( ! decompressed )
- {
- return 0;
- }
+ SetUserData(inData,expectedSize);
+}
-/*// PIXELCONVERT CLEANME
- // Restore the header in a disk-consistent state
- // (if user asks twice to get the pixels from disk)
- if ( PixelRead != -1 ) // File was "read" before
- {
- RestoreInitialValues();
- }
- if ( PixelConverter->IsDecompressedRGB() )
- {
- ///////////////////////////////////////////////////
- // now, it's an RGB image
- // Lets's write it in the Header
- // Droping Palette Color out of the Header
- // has been moved to the Write process.
- // TODO : move 'values' modification to the write process
- // : save also (in order to be able to restore)
- // : 'high bit' -when not equal to 'bits stored' + 1
- // : 'bits allocated', when it's equal to 12 ?!
- std::string spp = "3"; // Samples Per Pixel
- std::string photInt = "RGB "; // Photometric Interpretation
- std::string planConfig = "0"; // Planar Configuration
- HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002);
- HeaderInternal->SetEntryByNumber(photInt,0x0028,0x0004);
- HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006);
- }
+/**
+ * \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);
+}
- // We say the value *is* loaded.
- SetPixelData(decompressed);
-
- PixelRead = 1; // PixelRaw
-// END PIXELCONVERT CLEANME*/
+/**
+ * \brief Get the image datas defined by the user
+ * \warning When writting the file, this datas are get as default data to write
+ */
+uint8_t *File::GetUserData()
+{
+ return PixelWriteConverter->GetUserData();
+}
- return decompressed;
+/**
+ * \brief Get the image data size defined by the user
+ * \warning When writting the file, this datas are get as default data to write
+ */
+size_t File::GetUserDataSize()
+{
+ return PixelWriteConverter->GetUserDataSize();
}
-uint8_t* File::GetDecompressed()
+/**
+ * \brief Get the image datas from the file.
+ * If a LUT is found, the data are expanded to be RGB
+ */
+uint8_t *File::GetRGBData()
{
- uint8_t* decompressed = PixelConverter->GetDecompressed();
- if ( ! decompressed )
- {
- // The decompressed image migth not be loaded yet:
- std::ifstream* fp = HeaderInternal->OpenFile();
- PixelConverter->ReadAndDecompressPixelData( fp );
- if(fp) HeaderInternal->CloseFile();
- decompressed = PixelConverter->GetDecompressed();
- if ( ! decompressed )
- {
- dbg.Verbose(0, "File::GetDecompressed: read/decompress of "
- "pixel data apparently went wrong.");
- return 0;
- }
- }
+ return PixelReadConverter->GetRGB();
+}
- return decompressed;
+/**
+ * \brief Get the image data size from the file.
+ * If a LUT is found, the data are expanded to be RGB
+ */
+size_t File::GetRGBDataSize()
+{
+ return PixelReadConverter->GetRGBSize();
}
/**
- * \brief Points the internal Pixel_Data pointer to the callers inData
- * image representation, BUT WITHOUT COPYING THE DATA.
- * 'image' Pixels are presented as C-like 2D arrays : line per line.
- * 'volume'Pixels are presented as C-like 3D arrays : plane per plane
- * \warning Since the pixels are not copied, it is the caller's responsability
- * not to deallocate it's data before gdcm uses them (e.g. with
- * the Write() method.
- * @param inData user supplied pixel area
- * @param expectedSize total image size, in Bytes
- *
- * @return boolean
+ * \brief Get the image datas from the file.
+ * If a LUT is found, the datas are not expanded !
*/
-bool File::SetImageData(uint8_t* inData, size_t expectedSize)
-{
- HeaderInternal->SetImageDataSize( expectedSize );
-// FIXME : if already allocated, memory leak !
- Pixel_Data = inData;
- ImageDataSize = ImageDataSizeRaw = expectedSize;
- PixelRead = 1;
-// FIXME : 7fe0, 0010 IS NOT set ...
- return true;
+uint8_t *File::GetRawData()
+{
+ return PixelReadConverter->GetRaw();
+}
+
+/**
+ * \brief Get the image data size from the file.
+ * If a LUT is found, the data are not expanded !
+ */
+size_t File::GetRawDataSize()
+{
+ return PixelReadConverter->GetRawSize();
}
/**
* @return false if write fails
*/
-bool File::WriteRawData(std::string const & fileName)
+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;
}
- fp1.write((char*)Pixel_Data, ImageDataSize);
+
+ if(PixelWriteConverter->GetUserData())
+ fp1.write((char*)PixelWriteConverter->GetUserData(), PixelWriteConverter->GetUserDataSize());
+ else if(PixelReadConverter->GetRGB())
+ fp1.write((char*)PixelReadConverter->GetRGB(), PixelReadConverter->GetRGBSize());
+ else if(PixelReadConverter->GetRaw())
+ fp1.write((char*)PixelReadConverter->GetRaw(), PixelReadConverter->GetRawSize());
+
fp1.close();
return true;
* @return false if write fails
*/
-bool File::WriteDcmImplVR (std::string const & fileName)
+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
+ * 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)
+bool File::WriteDcmExplVR (std::string const &fileName)
{
SetWriteTypeToDcmExplVR();
return Write(fileName);
* @return false if write fails
*/
-bool File::WriteAcr (std::string const & fileName)
+bool File::WriteAcr (std::string const &fileName)
{
SetWriteTypeToAcr();
return Write(fileName);
}
-bool File::Write(std::string const& fileName)
-{
- switch(WriteType)
- {
- case WTYPE_IMPL_VR:
- return WriteBase(fileName,ImplicitVR);
- case WTYPE_EXPL_VR:
- return WriteBase(fileName,ExplicitVR);
- case WTYPE_ACR:
- return WriteBase(fileName,ACR);
- }
- return(false);
-}
-
-//-----------------------------------------------------------------------------
-// Protected
/**
- * \brief NOT a end user inteded function
- * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc)
+ * \brief Writes on disk A SINGLE Dicom file,
* @param fileName name of the file to be created
* (any already existing file is overwritten)
- * @param type file type (ExplicitVR, ImplicitVR, ...)
* @return false if write fails
*/
-bool File::WriteBase (std::string const & fileName, FileType type)
+bool File::Write(std::string const &fileName)
{
-/* if ( PixelRead == -1 && type != ExplicitVR)
- {
- return false;
- }*/
-
- std::ofstream* fp1 = new std::ofstream(fileName.c_str(),
- std::ios::out | std::ios::binary);
- if (fp1 == NULL)
- {
- dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str());
- return false;
- }
-
- if ( type == ImplicitVR || type == ExplicitVR )
- {
- // writing Dicom File Preamble
- char filePreamble[128];
- memset(filePreamble, 0, 128);
- fp1->write(filePreamble, 128);
- fp1->write("DICM", 4);
- }
-
- switch(WriteMode)
+ switch(WriteType)
{
- case WMODE_NATIVE :
- SetWriteToNative();
+ case ImplicitVR:
+ SetWriteFileTypeToImplicitVR();
break;
- case WMODE_DECOMPRESSED :
- SetWriteToDecompressed();
+ case ExplicitVR:
+ SetWriteFileTypeToExplicitVR();
break;
- case WMODE_RGB :
- SetWriteToRGB();
+ case ACR:
+ case ACR_LIBIDO:
+ SetWriteFileTypeToACR();
break;
+ default:
+ SetWriteFileTypeToExplicitVR();
}
// --------------------------------------------------------------
// if recognition code tells us we dealt with a LibIDO image
// we reproduce on disk the switch between lineNumber and columnNumber
// just before writting ...
-
/// \todo the best trick would be *change* the recognition code
/// but pb expected if user deals with, e.g. COMPLEX images
-
- std::string rows, columns;
- if ( HeaderInternal->GetFileType() == ACR_LIBIDO)
+ if( WriteType == ACR_LIBIDO )
{
SetWriteToLibido();
}
+ else
+ {
+ SetWriteToNoLibido();
+ }
// ----------------- End of Special Patch ----------------
-
-/* uint16_t grPixel = HeaderInternal->GetGrPixel();
- uint16_t numPixel = HeaderInternal->GetNumPixel();;
-
- DocEntry* PixelElement =
- GetHeader()->GetDocEntryByNumber(grPixel, numPixel);
-
- if ( PixelRead == 1 )
- {
- // we read pixel 'as is' (no tranformation LUT -> RGB)
- PixelElement->SetLength( ImageDataSizeRaw );
+
+ switch(WriteMode)
+ {
+ case WMODE_RAW :
+ SetWriteToRaw();
+ break;
+ case WMODE_RGB :
+ SetWriteToRGB();
+ break;
}
- else if ( PixelRead == 0 )
+
+ bool check = CheckWriteIntegrity();
+ if(check)
{
- // we tranformed GrayLevel pixels + LUT into RGB Pixel
- PixelElement->SetLength( ImageDataSize );
- }*/
-
- HeaderInternal->Write(fp1, type);
+ 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
-
- if ( HeaderInternal->GetFileType() == ACR_LIBIDO )
- {
- RestoreWriteFromLibido();
- }
+ RestoreWriteOfLibido();
// ----------------- End of Special Patch ----------------
- RestoreWrite();
+ return check;
+}
+/**
+ * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
+ * through it's (group, element) and modifies it's content with
+ * the given value.
+ * @param content new value (string) to substitute with
+ * @param group group number of the Dicom Element to modify
+ * @param element element number of the Dicom Element to modify
+ */
+bool File::SetEntryByNumber(std::string const &content,
+ uint16_t group, uint16_t element)
+{
+ return HeaderInternal->SetEntryByNumber(content,group,element);
+}
- fp1->close ();
- delete fp1;
- return true;
+/**
+ * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
+ * through it's (group, element) and modifies it's content with
+ * the given value.
+ * @param content new value (void* -> uint8_t*) to substitute with
+ * @param lgth new value length
+ * @param group group number of the Dicom Element to modify
+ * @param element element number of the Dicom Element to modify
+ */
+bool File::SetEntryByNumber(uint8_t *content, int lgth,
+ uint16_t group, uint16_t element)
+{
+ return HeaderInternal->SetEntryByNumber(content,lgth,group,element);
+}
+
+/**
+ * \brief Modifies the value of a given Doc Entry (Dicom Element)
+ * when it exists. Create it with the given value when unexistant.
+ * @param content (string) Value to be set
+ * @param group Group number of the Entry
+ * @param element Element number of the Entry
+ * \return pointer to the modified/created Header Entry (NULL when creation
+ * failed).
+ */
+bool File::ReplaceOrCreateByNumber(std::string const &content,
+ uint16_t group, uint16_t element)
+{
+ return HeaderInternal->ReplaceOrCreateByNumber(content,group,element) != NULL;
+}
+
+/*
+ * \brief Modifies the value of a given Header Entry (Dicom Element)
+ * when it exists. Create it with the given value when unexistant.
+ * A copy of the binArea is made to be kept in the Document.
+ * @param binArea (binary) value to be set
+ * @param group Group number of the Entry
+ * @param element Element number of the Entry
+ * \return pointer to the modified/created Header Entry (NULL when creation
+ * failed).
+ */
+bool File::ReplaceOrCreateByNumber(uint8_t *binArea, int lgth,
+ uint16_t group, uint16_t element)
+{
+ return HeaderInternal->ReplaceOrCreateByNumber(binArea,lgth,group,element) != NULL;
}
/**
- * \brief Access to the underlying \ref PixelConverter RGBA LUT
+ * \brief Access to the underlying \ref PixelReadConverter RGBA LUT
*/
uint8_t* File::GetLutRGBA()
{
- return PixelConverter->GetLutRGBA();
+ return PixelReadConverter->GetLutRGBA();
}
//-----------------------------------------------------------------------------
-// Private
+// Protected
+
/**
- * \brief Set the pixel datas in the good entry of the Header
+ * \brief Check the write integrity
+ *
+ * The tests made are :
+ * - verify the size of the image to write with the possible write
+ * when the user set an image data
+ * @return true if the check successfulls
*/
-void File::SetPixelData(uint8_t* data)
+bool File::CheckWriteIntegrity()
{
- GetHeader()->SetEntryByNumber( GDCM_BINLOADED,
- GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
-
- // Will be 7fe0, 0010 in standard case
- DocEntry* currentEntry = GetHeader()->GetDocEntryByNumber(GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
- if ( currentEntry )
+ if(PixelWriteConverter->GetUserData())
{
- if ( BinEntry* binEntry = dynamic_cast<BinEntry *>(currentEntry) )
- // Flag is to false because datas are kept in the gdcmPixelConvert
- binEntry->SetBinArea( data, false );
- }
-}
+ int numberBitsAllocated = HeaderInternal->GetBitsAllocated();
+ if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
+ {
+ numberBitsAllocated = 16;
+ }
-void File::SetWriteToNative()
-{
-// Nothing to do
+ size_t decSize = HeaderInternal->GetXSize()
+ * HeaderInternal->GetYSize()
+ * HeaderInternal->GetZSize()
+ * ( numberBitsAllocated / 8 )
+ * HeaderInternal->GetSamplesPerPixel();
+ size_t rgbSize = decSize;
+ if( HeaderInternal->HasLUT() )
+ rgbSize = decSize * 3;
+
+ switch(WriteMode)
+ {
+ case WMODE_RAW :
+ if( decSize!=PixelWriteConverter->GetUserDataSize() )
+ {
+ dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect (Raw)");
+ //std::cerr << "File::CheckWriteIntegrity: Data size is incorrect (Raw)\n"
+ // << decSize << " / " << PixelWriteConverter->GetUserDataSize() << "\n";
+ return false;
+ }
+ break;
+ case WMODE_RGB :
+ if( rgbSize!=PixelWriteConverter->GetUserDataSize() )
+ {
+ dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect (RGB)");
+ //std::cerr << "File::CheckWriteIntegrity: Data size is incorrect (RGB)\n"
+ // << decSize << " / " << PixelWriteConverter->GetUserDataSize() << "\n";
+ return false;
+ }
+ break;
+ }
+ }
+
+ return true;
}
-void File::SetWriteToDecompressed()
+void File::SetWriteToRaw()
{
-// if (( !HeaderInternal->HasLUT() ) || (!PixelConverter->BuildRGBImage()))
- if(HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage())
+ if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT())
{
SetWriteToRGB();
}
else
{
- ValEntry* photInt = CopyValEntry(0x0028,0x0004);
- photInt->SetValue("MONOCHROME1 ");
- photInt->SetLength(12);
+ ValEntry *photInt = CopyValEntry(0x0028,0x0004);
+ if(HeaderInternal->HasLUT())
+ {
+ photInt->SetValue("PALETTE COLOR ");
+ }
+ else
+ {
+ photInt->SetValue("MONOCHROME1 ");
+ }
- BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+ PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
+ PixelReadConverter->GetRawSize());
+
+ BinEntry *pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
pixel->SetValue(GDCM_BINLOADED);
- pixel->SetBinArea(PixelConverter->GetDecompressed(),false);
- pixel->SetLength(PixelConverter->GetDecompressedSize());
+ pixel->SetBinArea(PixelWriteConverter->GetData(),false);
+ pixel->SetLength(PixelWriteConverter->GetDataSize());
Archive->Push(photInt);
Archive->Push(pixel);
}
-/* else
- {
- SetWriteToRGB();
- } */
}
void File::SetWriteToRGB()
{
- if(PixelConverter->BuildRGBImage())
+ if(HeaderInternal->GetNumberOfScalarComponents()==3)
{
- ValEntry* spp = CopyValEntry(0x0028,0x0002);
+ PixelReadConverter->BuildRGBImage();
+
+ ValEntry *spp = CopyValEntry(0x0028,0x0002);
spp->SetValue("3 ");
- spp->SetLength(2);
- ValEntry* photInt = CopyValEntry(0x0028,0x0004);
+ ValEntry *planConfig = CopyValEntry(0x0028,0x0006);
+ planConfig->SetValue("0 ");
+
+ ValEntry *photInt = CopyValEntry(0x0028,0x0004);
photInt->SetValue("RGB ");
- photInt->SetLength(4);
- ValEntry* planConfig = CopyValEntry(0x0028,0x0006);
- planConfig->SetValue("0 ");
- planConfig->SetLength(2);
+ if(PixelReadConverter->GetRGB())
+ {
+ PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(),
+ PixelReadConverter->GetRGBSize());
+ }
+ else // Raw data
+ {
+ PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
+ PixelReadConverter->GetRawSize());
+ }
- BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+ BinEntry *pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
pixel->SetValue(GDCM_BINLOADED);
- pixel->SetBinArea(PixelConverter->GetRGB(),false);
- pixel->SetLength(PixelConverter->GetRGBSize());
+ pixel->SetBinArea(PixelWriteConverter->GetData(),false);
+ pixel->SetLength(PixelWriteConverter->GetDataSize());
Archive->Push(spp);
- Archive->Push(photInt);
Archive->Push(planConfig);
+ Archive->Push(photInt);
Archive->Push(pixel);
+
+ // Remove any LUT
+ Archive->Push(0x0028,0x1101);
+ Archive->Push(0x0028,0x1102);
+ Archive->Push(0x0028,0x1103);
+ Archive->Push(0x0028,0x1201);
+ Archive->Push(0x0028,0x1202);
+ Archive->Push(0x0028,0x1203);
+
+ // For old ACR-NEMA
+ // Thus, we have a RGB image and the bits allocated = 24 and
+ // samples per pixels = 1 (in the read file)
+ if(HeaderInternal->GetBitsAllocated()==24)
+ {
+ ValEntry *bitsAlloc = CopyValEntry(0x0028,0x0100);
+ bitsAlloc->SetValue("8 ");
+
+ ValEntry *bitsStored = CopyValEntry(0x0028,0x0101);
+ bitsStored->SetValue("8 ");
+
+ ValEntry *highBit = CopyValEntry(0x0028,0x0102);
+ highBit->SetValue("7 ");
+
+ Archive->Push(bitsAlloc);
+ Archive->Push(bitsStored);
+ Archive->Push(highBit);
+ }
}
else
{
- SetWriteToDecompressed();
+ SetWriteToRaw();
}
}
Archive->Restore(0x0028,0x0004);
Archive->Restore(0x0028,0x0006);
Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+
+ // For old ACR-NEMA (24 bits problem)
+ Archive->Restore(0x0028,0x0100);
+ Archive->Restore(0x0028,0x0101);
+ Archive->Restore(0x0028,0x0102);
+
+ // 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);
+}
+
+void File::SetWriteFileTypeToACR()
+{
+ Archive->Push(0x0002,0x0010);
+}
+
+void File::SetWriteFileTypeToExplicitVR()
+{
+ std::string ts = Util::DicomString(
+ Document::GetTransferSyntaxValue(ExplicitVRLittleEndian).c_str() );
+
+ ValEntry *tss = CopyValEntry(0x0002,0x0010);
+ tss->SetValue(ts);
+
+ Archive->Push(tss);
+}
+
+void File::SetWriteFileTypeToImplicitVR()
+{
+ std::string ts = Util::DicomString(
+ Document::GetTransferSyntaxValue(ImplicitVRLittleEndian).c_str() );
+
+ ValEntry *tss = CopyValEntry(0x0002,0x0010);
+ tss->SetValue(ts);
+
+ Archive->Push(tss);
+}
+
+void File::RestoreWriteFileType()
+{
+ Archive->Restore(0x0002,0x0010);
}
void File::SetWriteToLibido()
{
- ValEntry *oldRow = dynamic_cast<ValEntry *>(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010));
- ValEntry *oldCol = dynamic_cast<ValEntry *>(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011));
+ ValEntry *oldRow = dynamic_cast<ValEntry *>
+ (HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010));
+ ValEntry *oldCol = dynamic_cast<ValEntry *>
+ (HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011));
if( oldRow && oldCol )
{
Archive->Push(newRow);
Archive->Push(newCol);
}
+
+ ValEntry *libidoCode = CopyValEntry(0x0008,0x0010);
+ libidoCode->SetValue("ACRNEMA_LIBIDO_1.1");
+ Archive->Push(libidoCode);
+}
+
+void File::SetWriteToNoLibido()
+{
+ ValEntry *recCode = dynamic_cast<ValEntry *>
+ (HeaderInternal->GetDocEntryByNumber(0x0008,0x0010));
+ if( recCode )
+ {
+ if( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" )
+ {
+ ValEntry *libidoCode = CopyValEntry(0x0008,0x0010);
+ libidoCode->SetValue("");
+ Archive->Push(libidoCode);
+ }
+ }
}
-void File::RestoreWriteFromLibido()
+void File::RestoreWriteOfLibido()
{
Archive->Restore(0x0028,0x0010);
Archive->Restore(0x0028,0x0011);
+ Archive->Restore(0x0008,0x0010);
}
-ValEntry* File::CopyValEntry(uint16_t group,uint16_t element)
+ValEntry *File::CopyValEntry(uint16_t group,uint16_t element)
{
- DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element);
- ValEntry* newE;
+ DocEntry *oldE = HeaderInternal->GetDocEntryByNumber(group, element);
+ ValEntry *newE;
if(oldE)
{
return(newE);
}
-BinEntry* File::CopyBinEntry(uint16_t group,uint16_t element)
+BinEntry *File::CopyBinEntry(uint16_t group,uint16_t element)
{
- DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element);
- BinEntry* newE;
+ DocEntry *oldE = HeaderInternal->GetDocEntryByNumber(group, element);
+ BinEntry *newE;
if(oldE)
{
newE = GetHeader()->NewBinEntryByNumber(group,element);
}
-
return(newE);
}
+//-----------------------------------------------------------------------------
+// Protected
+/**
+ * \brief Factorization for various forms of constructors.
+ */
+void File::Initialise()
+{
+ WriteMode = WMODE_RAW;
+ WriteType = ExplicitVR;
+
+ PixelReadConverter = new PixelReadConvert;
+ PixelWriteConverter = new PixelWriteConvert;
+ Archive = new DocEntryArchive( HeaderInternal );
+
+ if ( HeaderInternal->IsReadable() )
+ {
+ PixelReadConverter->GrabInformationsFromHeader( HeaderInternal );
+ }
+}
+
+uint8_t *File::GetRaw()
+{
+ uint8_t *raw = PixelReadConverter->GetRaw();
+ if ( ! raw )
+ {
+ // The Raw image migth not be loaded yet:
+ std::ifstream *fp = HeaderInternal->OpenFile();
+ PixelReadConverter->ReadAndDecompressPixelData( fp );
+ if(fp)
+ HeaderInternal->CloseFile();
+
+ raw = PixelReadConverter->GetRaw();
+ if ( ! raw )
+ {
+ dbg.Verbose(0, "File::GetRaw: read/decompress of "
+ "pixel data apparently went wrong.");
+ return 0;
+ }
+ }
+
+ return raw;
+}
+
+//-----------------------------------------------------------------------------
+// Private
+
//-----------------------------------------------------------------------------
} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff