Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2004/11/24 11:17:47 $
- Version: $Revision: 1.161 $
+ Date: $Date: 2004/11/26 10:55:04 $
+ Version: $Revision: 1.166 $
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"
*/
void File::Initialise()
{
- WriteMode = WMODE_RGB;
+ WriteMode = WMODE_DECOMPRESSED;
WriteType = WTYPE_IMPL_VR;
PixelConverter = new PixelConvert;
if ( HeaderInternal->IsReadable() )
{
- ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader();
- if ( HeaderInternal->HasLUT() )
- {
- ImageDataSize = 3 * ImageDataSizeRaw;
- }
- else
- {
- ImageDataSize = ImageDataSizeRaw;
- }
-
PixelConverter->GrabInformationsFromHeader( HeaderInternal );
}
- SaveInitialValues();
+ Pixel_Data = 0;
+ ImageDataSize = 0;
}
/**
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
//-----------------------------------------------------------------------------
// Public
-
/**
- * \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 (with a lut or by default), the size
+ * corresponds to the RGB image
+ * @return The image size
*/
-int File::ComputeDecompressedPixelDataSizeFromHeader()
+size_t File::GetImageDataSize()
{
- // 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;
- }
+ return PixelConverter->GetRGBSize();
+}
- int DecompressedSize = HeaderInternal->GetXSize()
- * HeaderInternal->GetYSize()
- * HeaderInternal->GetZSize()
- * ( numberBitsAllocated / 8 )
- * HeaderInternal->GetSamplesPerPixel();
-
- return DecompressedSize;
+/**
+ * \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()
+{
+ return PixelConverter->GetDecompressedSize();
}
/**
// If the decompression failed nothing can be done.
return 0;
}
-
+
if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
{
return PixelConverter->GetRGB();
// When no LUT or LUT conversion fails, return the decompressed
return PixelConverter->GetDecompressed();
}
-
-/* if ( ! GetDecompressed() )
- {
- // If the decompression failed nothing can be done.
- return 0;
- }
-
- uint8_t* pixelData;
- if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
- {
- pixelData = PixelConverter->GetRGB();
- }
- else
- {
- // When no LUT or LUT conversion fails, return the decompressed
- pixelData = PixelConverter->GetDecompressed();
- }
-
-// 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->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
- }
- 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
- }
- }
-
- // We say the value *is* loaded.
- SetPixelData(pixelData);
-// END PIXELCONVERT CLEANME
-
- return pixelData;*/
}
/**
uint8_t* File::GetImageDataRaw ()
{
return GetDecompressed();
-/* uint8_t* decompressed = GetDecompressed();
- if ( ! decompressed )
- {
- 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
- {
- 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);
- }
-
- // We say the value *is* loaded.
- SetPixelData(decompressed);
-
- PixelRead = 1; // PixelRaw
-// END PIXELCONVERT CLEANME
-
- return decompressed;*/
}
uint8_t* File::GetDecompressed()
// The decompressed image migth not be loaded yet:
std::ifstream* fp = HeaderInternal->OpenFile();
PixelConverter->ReadAndDecompressPixelData( fp );
- if(fp) HeaderInternal->CloseFile();
+ if(fp)
+ HeaderInternal->CloseFile();
+
decompressed = PixelConverter->GetDecompressed();
if ( ! decompressed )
{
- dbg.Verbose(0, "File::GetDecompressed: read/decompress of "
- "pixel data apparently went wrong.");
+ dbg.Verbose(0, "File::GetDecompressed: read/decompress of "
+ "pixel data apparently went wrong.");
return 0;
}
}
*/
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;
+ ImageDataSize = expectedSize;
// FIXME : 7fe0, 0010 IS NOT set ...
return true;
}
return(false);
}
+/**
+ * \brief Access to the underlying \ref PixelConverter RGBA LUT
+ */
+uint8_t* File::GetLutRGBA()
+{
+ return PixelConverter->GetLutRGBA();
+}
+
//-----------------------------------------------------------------------------
// Protected
/**
*/
bool File::WriteBase (std::string const & fileName, FileType type)
{
-/* 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 )
+ switch(type)
{
- // writing Dicom File Preamble
- char filePreamble[128];
- memset(filePreamble, 0, 128);
- fp1->write(filePreamble, 128);
- fp1->write("DICM", 4);
+ case ImplicitVR:
+ SetWriteFileTypeToImplicitVR();
+ break;
+ case ExplicitVR:
+ SetWriteFileTypeToExplicitVR();
+ break;
+ case ACR:
+ SetWriteFileTypeToACR();
+ break;
+ case ACR_LIBIDO:
+ SetWriteFileTypeToACRLibido();
+ break;
+ default:
+ SetWriteFileTypeToExplicitVR();
}
-
+
switch(WriteMode)
{
case WMODE_NATIVE :
// 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 ( HeaderInternal->GetFileType() == ACR_LIBIDO)
{
SetWriteToLibido();
- }
+ }*/
// ----------------- End of Special Patch ----------------
-
-/* uint16_t grPixel = HeaderInternal->GetGrPixel();
- uint16_t numPixel = HeaderInternal->GetNumPixel();;
-
- DocEntry* PixelElement =
- GetHeader()->GetDocEntryByNumber(grPixel, numPixel);
-
- if ( PixelRead == 1 )
+
+ bool check = CheckWriteIntegrity();
+ if(check)
{
- // we read pixel 'as is' (no tranformation LUT -> RGB)
- PixelElement->SetLength( ImageDataSizeRaw );
+ check = HeaderInternal->Write(fileName,type);
}
- else if ( PixelRead == 0 )
- {
- // we tranformed GrayLevel pixels + LUT into RGB Pixel
- PixelElement->SetLength( ImageDataSize );
- }*/
-
- HeaderInternal->Write(fp1, type);
// --------------------------------------------------------------
// Special Patch to allow gdcm to re-write ACR-LibIDO formated images
//
// ...and we restore the Header to be Dicom Compliant again
// just after writting
-
- if ( HeaderInternal->GetFileType() == ACR_LIBIDO )
+/* if ( HeaderInternal->GetFileType() == ACR_LIBIDO )
{
RestoreWriteFromLibido();
- }
+ }*/
// ----------------- End of Special Patch ----------------
RestoreWrite();
+ RestoreWriteFileType();
-
- fp1->close ();
- delete fp1;
-
- return true;
+ return check;
}
/**
- * \brief Access to the underlying \ref PixelConverter RGBA LUT
+ * \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
*/
-uint8_t* File::GetLutRGBA()
+bool File::CheckWriteIntegrity()
{
- return PixelConverter->GetLutRGBA();
-}
+ if(Pixel_Data)
+ {
+ int numberBitsAllocated = HeaderInternal->GetBitsAllocated();
+ if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
+ {
+ numberBitsAllocated = 16;
+ }
-//-----------------------------------------------------------------------------
-// Private
-/**
- * \brief Set the pixel datas in the good entry of the Header
- */
-void File::SetPixelData(uint8_t* data)
-{
- GetHeader()->SetEntryByNumber( GDCM_BINLOADED,
- GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
+ size_t decSize = HeaderInternal->GetXSize()
+ * HeaderInternal->GetYSize()
+ * HeaderInternal->GetZSize()
+ * ( numberBitsAllocated / 8 )
+ * HeaderInternal->GetSamplesPerPixel();
+ size_t rgbSize = decSize;
+ if( HeaderInternal->HasLUT() )
+ rgbSize = decSize * 3;
- // Will be 7fe0, 0010 in standard case
- DocEntry* currentEntry = GetHeader()->GetDocEntryByNumber(GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
- if ( currentEntry )
- {
- if ( BinEntry* binEntry = dynamic_cast<BinEntry *>(currentEntry) )
- // Flag is to false because datas are kept in the gdcmPixelConvert
- binEntry->SetBinArea( data, false );
+ switch(WriteMode)
+ {
+ case WMODE_NATIVE :
+ break;
+ case WMODE_DECOMPRESSED :
+ if( decSize!=ImageDataSize )
+ {
+ dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect");
+ //std::cerr<<"Dec : "<<decSize<<" | "<<ImageDataSize<<std::endl;
+ return false;
+ }
+ break;
+ case WMODE_RGB :
+ if( rgbSize!=ImageDataSize )
+ {
+ dbg.Verbose(0, "File::CheckWriteIntegrity: Data size is incorrect");
+ //std::cerr<<"RGB : "<<decSize<<" | "<<ImageDataSize<<std::endl;
+ return false;
+ }
+ break;
+ }
}
+
+ return true;
}
void File::SetWriteToNative()
{
-// Nothing to do
+ if(Pixel_Data)
+ {
+ BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+ pixel->SetValue(GDCM_BINLOADED);
+ pixel->SetBinArea(Pixel_Data,false);
+ pixel->SetLength(ImageDataSize);
+
+ Archive->Push(pixel);
+ }
}
void File::SetWriteToDecompressed()
{
-// 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);
+ if(HeaderInternal->HasLUT())
+ {
+ photInt->SetValue("PALETTE COLOR ");
+ photInt->SetLength(14);
+ }
+ else
+ {
+ photInt->SetValue("MONOCHROME1 ");
+ photInt->SetLength(12);
+ }
BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
pixel->SetValue(GDCM_BINLOADED);
- pixel->SetBinArea(PixelConverter->GetDecompressed(),false);
- pixel->SetLength(PixelConverter->GetDecompressedSize());
+ if(Pixel_Data)
+ {
+ pixel->SetBinArea(Pixel_Data,false);
+ pixel->SetLength(ImageDataSize);
+ }
+ else
+ {
+ pixel->SetBinArea(PixelConverter->GetDecompressed(),false);
+ pixel->SetLength(PixelConverter->GetDecompressedSize());
+ }
Archive->Push(photInt);
Archive->Push(pixel);
}
-/* else
- {
- SetWriteToRGB();
- } */
}
void File::SetWriteToRGB()
{
- if(PixelConverter->BuildRGBImage())
+ if(HeaderInternal->GetNumberOfScalarComponents()==3)
{
+ PixelConverter->BuildRGBImage();
+
ValEntry* spp = CopyValEntry(0x0028,0x0002);
spp->SetValue("3 ");
spp->SetLength(2);
- ValEntry* photInt = CopyValEntry(0x0028,0x0004);
- photInt->SetValue("RGB ");
- photInt->SetLength(4);
-
ValEntry* planConfig = CopyValEntry(0x0028,0x0006);
planConfig->SetValue("0 ");
planConfig->SetLength(2);
+ ValEntry* photInt = CopyValEntry(0x0028,0x0004);
+ photInt->SetValue("RGB ");
+ photInt->SetLength(4);
+
BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
pixel->SetValue(GDCM_BINLOADED);
- pixel->SetBinArea(PixelConverter->GetRGB(),false);
- pixel->SetLength(PixelConverter->GetRGBSize());
+ if(Pixel_Data)
+ {
+ pixel->SetBinArea(Pixel_Data,false);
+ pixel->SetLength(ImageDataSize);
+ }
+ else if(PixelConverter->GetRGB())
+ {
+ pixel->SetBinArea(PixelConverter->GetRGB(),false);
+ pixel->SetLength(PixelConverter->GetRGBSize());
+ }
+ else // Decompressed data
+ {
+ pixel->SetBinArea(PixelConverter->GetDecompressed(),false);
+ pixel->SetLength(PixelConverter->GetDecompressedSize());
+ }
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 ");
+ bitsAlloc->SetLength(2);
+
+ ValEntry* bitsStored = CopyValEntry(0x0028,0x0101);
+ bitsStored->SetValue("8 ");
+ bitsStored->SetLength(2);
+
+ ValEntry* highBit = CopyValEntry(0x0028,0x0102);
+ highBit->SetValue("7 ");
+ highBit->SetLength(2);
+
+ Archive->Push(bitsAlloc);
+ Archive->Push(bitsStored);
+ Archive->Push(highBit);
+ }
}
else
{
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::SetWriteFileTypeToACRLibido()
+{
+ SetWriteFileTypeToACR();
+}
+
+void File::SetWriteFileTypeToExplicitVR()
+{
+ std::string ts = Util::DicomString(
+ Document::GetTransferSyntaxValue(ExplicitVRLittleEndian).c_str() );
+
+ ValEntry* tss = CopyValEntry(0x0002,0x0010);
+ tss->SetValue(ts);
+ tss->SetLength(ts.length());
+
+ Archive->Push(tss);
+}
+
+void File::SetWriteFileTypeToImplicitVR()
+{
+ std::string ts = Util::DicomString(
+ Document::GetTransferSyntaxValue(ImplicitVRLittleEndian).c_str() );
+
+ ValEntry* tss = CopyValEntry(0x0002,0x0010);
+ tss->SetValue(ts);
+ tss->SetLength(ts.length());
+}
+
+void File::RestoreWriteFileType()
+{
+ Archive->Restore(0x0002,0x0010);
}
void File::SetWriteToLibido()
return(newE);
}
+//-----------------------------------------------------------------------------
+// Private
+
//-----------------------------------------------------------------------------
} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff