/*=========================================================================
-
+
Program: gdcm
Module: $RCSfile: gdcmPixelReadConvert.cxx,v $
Language: C++
- Date: $Date: 2004/12/03 10:21:55 $
- Version: $Revision: 1.1 $
+ Date: $Date: 2005/01/31 06:17:22 $
+ Version: $Revision: 1.42 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
=========================================================================*/
-////////////////// TEMPORARY NOTE
-// look for "fixMem" and convert that to a member of this class
-// Removing the prefix fixMem and dealing with allocations should do the trick
-//
-// grep PixelReadConvert everywhere and clean up !
-
#include "gdcmDebug.h"
+#include "gdcmFile.h"
+#include "gdcmGlobal.h"
+#include "gdcmTS.h"
#include "gdcmPixelReadConvert.h"
+#include "gdcmDocEntry.h"
+#include "gdcmRLEFramesInfo.h"
+#include "gdcmJPEGFragmentsInfo.h"
+
#include <fstream>
-#include <stdio.h>
+#include <stdio.h> //for sscanf
namespace gdcm
{
#define str2num(str, typeNum) *((typeNum *)(str))
-// For JPEG 2000, body in file gdcmJpeg2000.cxx
-bool gdcm_read_JPEG2000_file (std::ifstream* fp, void* image_buffer);
-
-// For JPEG 8 Bits, body in file gdcmJpeg8.cxx
-bool gdcm_read_JPEG_file8 (std::ifstream* fp, void* image_buffer);
-
-// For JPEG 12 Bits, body in file gdcmJpeg12.cxx
-bool gdcm_read_JPEG_file12 (std::ifstream* fp, void* image_buffer);
-
-// For JPEG 16 Bits, body in file gdcmJpeg16.cxx
-// Beware this is misleading there is no 16bits DCT algorithm, only
-// jpeg lossless compression exist in 16bits.
-bool gdcm_read_JPEG_file16 (std::ifstream* fp, void* image_buffer);
-
//-----------------------------------------------------------------------------
// Constructor / Destructor
{
RGB = 0;
RGBSize = 0;
- Decompressed = 0;
- DecompressedSize = 0;
+ Raw = 0;
+ RawSize = 0;
LutRGBA = 0;
LutRedData = 0;
LutGreenData = 0;
void PixelReadConvert::Squeeze()
{
if ( RGB )
- {
delete [] RGB;
- }
RGB = 0;
- if ( Decompressed )
- {
- delete [] Decompressed;
- }
- Decompressed = 0;
+ if ( Raw )
+ delete [] Raw;
+ Raw = 0;
if ( LutRGBA )
- {
delete [] LutRGBA;
- }
LutRGBA = 0;
}
void PixelReadConvert::AllocateRGB()
{
- if ( RGB ) {
+ if ( RGB )
delete [] RGB;
- }
- RGB = new uint8_t[ RGBSize ];
+ RGB = new uint8_t[RGBSize];
}
-void PixelReadConvert::AllocateDecompressed()
+void PixelReadConvert::AllocateRaw()
{
- if ( Decompressed ) {
- delete [] Decompressed;
- }
- Decompressed = new uint8_t[ DecompressedSize ];
+ if ( Raw )
+ delete [] Raw;
+ Raw = new uint8_t[RawSize];
}
/**
* \brief Read from file a 12 bits per pixel image and decompress it
* into a 16 bits per pixel image.
*/
-void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream* fp )
+void PixelReadConvert::ReadAndDecompress12BitsTo16Bits( std::ifstream *fp )
throw ( FormatError )
{
int nbPixels = XSize * YSize;
- uint16_t* localDecompres = (uint16_t*)Decompressed;
+ uint16_t* localDecompres = (uint16_t*)Raw;
for( int p = 0; p < nbPixels; p += 2 )
{
uint8_t b0, b1, b2;
fp->read( (char*)&b0, 1);
- if ( fp->fail() || fp->eof() )//Fp->gcount() == 1
+ if ( fp->fail() || fp->eof() )
{
throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
"Unfound first block" );
}
fp->read( (char*)&b1, 1 );
- if ( fp->fail() || fp->eof())//Fp->gcount() == 1
+ if ( fp->fail() || fp->eof())
{
throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
"Unfound second block" );
}
fp->read( (char*)&b2, 1 );
- if ( fp->fail() || fp->eof())//Fp->gcount() == 1
+ if ( fp->fail() || fp->eof())
{
throw FormatError( "PixelReadConvert::ReadAndDecompress12BitsTo16Bits()",
"Unfound second block" );
}
}
-/**
- * \brief Try to deal with RLE 16 Bits.
- * We assume the RLE has allready been parsed and loaded in
- * Decompressed (through \ref ReadAndDecompressJPEGFile ).
- * We here need to make 16 Bits Pixels from Low Byte and
- * High Byte 'Planes'...(for what it may mean)
- * @return Boolean
- */
-bool PixelReadConvert::DecompressRLE16BitsFromRLE8Bits( int NumberOfFrames )
-{
- size_t PixelNumber = XSize * YSize;
- size_t decompressedSize = XSize * YSize * NumberOfFrames;
-
- // We assumed Decompressed contains the decoded RLE pixels but as
- // 8 bits per pixel. In order to convert those pixels to 16 bits
- // per pixel we cannot work in place within Decompressed and hence
- // we copy it in a safe place, say copyDecompressed.
-
- uint8_t* copyDecompressed = new uint8_t[ decompressedSize * 2 ];
- memmove( copyDecompressed, Decompressed, decompressedSize * 2 );
-
- uint8_t* x = Decompressed;
- uint8_t* a = copyDecompressed;
- uint8_t* b = a + PixelNumber;
-
- for ( int i = 0; i < NumberOfFrames; i++ )
- {
- for ( unsigned int j = 0; j < PixelNumber; j++ )
- {
- *(x++) = *(b++);
- *(x++) = *(a++);
- }
- }
-
- delete[] copyDecompressed;
-
- /// \todo check that operator new []didn't fail, and sometimes return false
- return true;
-}
-
-/**
- * \brief Implementation of the RLE decoding algorithm for decompressing
- * a RLE fragment. [refer to PS 3.5-2003, section G.3.2 p 86]
- * @param subDecompressed Sub region of \ref Decompressed where the de
- * decoded fragment should be placed.
- * @param fragmentSize The length of the binary fragment as found on the disk.
- * @param decompressedSegmentSize The expected length of the fragment ONCE
- * decompressed.
- * @param fp File Pointer: on entry the position should be the one of
- * the fragment to be decoded.
- */
-bool PixelReadConvert::ReadAndDecompressRLEFragment( uint8_t* subDecompressed,
- long fragmentSize,
- long decompressedSegmentSize,
- std::ifstream* fp )
-{
- int8_t count;
- long numberOfOutputBytes = 0;
- long numberOfReadBytes = 0;
-
- while( numberOfOutputBytes < decompressedSegmentSize )
- {
- fp->read( (char*)&count, 1 );
- numberOfReadBytes += 1;
- if ( count >= 0 )
- // Note: count <= 127 comparison is always true due to limited range
- // of data type int8_t [since the maximum of an exact width
- // signed integer of width N is 2^(N-1) - 1, which for int8_t
- // is 127].
- {
- fp->read( (char*)subDecompressed, count + 1);
- numberOfReadBytes += count + 1;
- subDecompressed += count + 1;
- numberOfOutputBytes += count + 1;
- }
- else
- {
- if ( ( count <= -1 ) && ( count >= -127 ) )
- {
- int8_t newByte;
- fp->read( (char*)&newByte, 1);
- numberOfReadBytes += 1;
- for( int i = 0; i < -count + 1; i++ )
- {
- subDecompressed[i] = newByte;
- }
- subDecompressed += -count + 1;
- numberOfOutputBytes += -count + 1;
- }
- }
- // if count = 128 output nothing
-
- if ( numberOfReadBytes > fragmentSize )
- {
- dbg.Verbose(0, "PixelReadConvert::ReadAndDecompressRLEFragment: we "
- "read more bytes than the segment size.");
- return false;
- }
- }
- return true;
-}
-
-/**
- * \brief Reads from disk the Pixel Data of 'Run Length Encoded'
- * Dicom encapsulated file and decompress it.
- * @param fp already open File Pointer
- * at which the pixel data should be copied
- * @return Boolean
- */
-bool PixelReadConvert::ReadAndDecompressRLEFile( std::ifstream* fp )
-{
- uint8_t* subDecompressed = Decompressed;
- long decompressedSegmentSize = XSize * YSize;
-
- // Loop on the frame[s]
- for( RLEFramesInfo::RLEFrameList::iterator
- it = RLEInfo->Frames.begin();
- it != RLEInfo->Frames.end();
- ++it )
- {
- // Loop on the fragments
- for( unsigned int k = 1; k <= (*it)->NumberFragments; k++ )
- {
- fp->seekg( (*it)->Offset[k] , std::ios::beg );
- (void)ReadAndDecompressRLEFragment( subDecompressed,
- (*it)->Length[k],
- decompressedSegmentSize,
- fp );
- subDecompressed += decompressedSegmentSize;
- }
- }
-
- if ( BitsAllocated == 16 )
- {
- // Try to deal with RLE 16 Bits
- (void)DecompressRLE16BitsFromRLE8Bits( ZSize );
- }
-
- return true;
-}
/**
* \brief Swap the bytes, according to \ref SwapCode.
if( BitsAllocated == 16 )
{
- uint16_t* im16 = (uint16_t*)Decompressed;
+ uint16_t *im16 = (uint16_t*)Raw;
switch( SwapCode )
{
- case 0:
- case 12:
case 1234:
break;
- case 21:
case 3412:
case 2143:
case 4321:
- for( i = 0; i < DecompressedSize / 2; i++ )
+ for( i = 0; i < RawSize / 2; i++ )
{
im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
}
break;
default:
- dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value "
- "(16 bits) not allowed." );
+ gdcmVerboseMacro("SwapCode value (16 bits) not allowed.");
}
}
else if( BitsAllocated == 32 )
uint32_t s32;
uint16_t high;
uint16_t low;
- uint32_t* im32 = (uint32_t*)Decompressed;
+ uint32_t* im32 = (uint32_t*)Raw;
switch ( SwapCode )
{
- case 0:
case 1234:
break;
case 4321:
- for( i = 0; i < DecompressedSize / 4; i++ )
+ for( i = 0; i < RawSize / 4; i++ )
{
low = im32[i] & 0x0000ffff; // 4321
high = im32[i] >> 16;
}
break;
case 2143:
- for( i = 0; i < DecompressedSize / 4; i++ )
+ for( i = 0; i < RawSize / 4; i++ )
{
low = im32[i] & 0x0000ffff; // 2143
high = im32[i] >> 16;
}
break;
case 3412:
- for( i = 0; i < DecompressedSize / 4; i++ )
+ for( i = 0; i < RawSize / 4; i++ )
{
low = im32[i] & 0x0000ffff; // 3412
high = im32[i] >> 16;
}
break;
default:
- dbg.Verbose( 0, "PixelReadConvert::ConvertSwapZone: SwapCode value "
- "(32 bits) not allowed." );
+ gdcmVerboseMacro("SwapCode value (32 bits) not allowed." );
}
}
}
/**
- * \brief Deal with endianity i.e. re-arange bytes inside the integer
+ * \brief Deal with endianness i.e. re-arange bytes inside the integer
*/
void PixelReadConvert::ConvertReorderEndianity()
{
}
// Special kludge in order to deal with xmedcon broken images:
- if ( ( BitsAllocated == 16 )
- && ( BitsStored < BitsAllocated )
- && ( ! PixelSign ) )
+ if ( BitsAllocated == 16
+ && BitsStored < BitsAllocated
+ && !PixelSign )
{
- int l = (int)( DecompressedSize / ( BitsAllocated / 8 ) );
- uint16_t *deb = (uint16_t *)Decompressed;
+ int l = (int)( RawSize / ( BitsAllocated / 8 ) );
+ uint16_t *deb = (uint16_t *)Raw;
for(int i = 0; i<l; i++)
{
if( *deb == 0xffff )
/**
* \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
- & file and decompress it.
+ * file and decompress it.
* @param fp File Pointer
* @return Boolean
*/
-bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream* fp )
+bool PixelReadConvert::ReadAndDecompressJPEGFile( std::ifstream *fp )
{
- uint8_t* localDecompressed = Decompressed;
- // Loop on the fragment[s]
- for( JPEGFragmentsInfo::JPEGFragmentsList::iterator
- it = JPEGInfo->Fragments.begin();
- it != JPEGInfo->Fragments.end();
- ++it )
+ if ( IsJPEG2000 )
{
- fp->seekg( (*it)->Offset, std::ios::beg);
+ gdcmVerboseMacro( "Sorry, JPEG2000 not yet taken into account" );
+ fp->seekg( JPEGInfo->GetFirstFragment()->GetOffset(), std::ios::beg);
+// if ( ! gdcm_read_JPEG2000_file( fp,Raw ) )
+ return false;
+ }
- if ( IsJPEG2000 )
- {
- if ( ! gdcm_read_JPEG2000_file( fp,localDecompressed ) )
- {
- return false;
- }
- }
- else if ( BitsStored == 8)
- {
- // JPEG Lossy : call to IJG 6b
- if ( ! gdcm_read_JPEG_file8( fp, localDecompressed ) )
- {
- return false;
- }
- }
- else if ( BitsStored <= 12)
- {
- // Reading Fragment pixels
- if ( ! gdcm_read_JPEG_file12 ( fp, localDecompressed ) )
- {
- return false;
- }
- }
- else if ( BitsStored <= 16)
- {
- // Reading Fragment pixels
- if ( ! gdcm_read_JPEG_file16 ( fp, localDecompressed ) )
- {
- return false;
- }
- //assert( IsJPEGLossless );
- }
- else
- {
- // other JPEG lossy not supported
- dbg.Error("PixelReadConvert::ReadAndDecompressJPEGFile: unknown "
- "jpeg lossy compression ");
+ if ( IsJPEGLS )
+ {
+ gdcmVerboseMacro( "Sorry, JPEG-LS not yet taken into account" );
+ fp->seekg( JPEGInfo->GetFirstFragment()->GetOffset(), std::ios::beg);
+// if ( ! gdcm_read_JPEGLS_file( fp,Raw ) )
return false;
- }
+ }
- // Advance to next free location in Decompressed
- // for next fragment decompression (if any)
- int length = XSize * YSize * SamplesPerPixel;
- int numberBytes = BitsAllocated / 8;
+ // else ??
+ // Precompute the offset localRaw will be shifted with
+ int length = XSize * YSize * SamplesPerPixel;
+ int numberBytes = BitsAllocated / 8;
- localDecompressed += length * numberBytes;
- }
+ JPEGInfo->DecompressFromFile(fp, Raw, BitsStored, numberBytes, length );
return true;
}
{
if ( BitsStored != BitsAllocated )
{
- int l = (int)( DecompressedSize / ( BitsAllocated / 8 ) );
+ int l = (int)( RawSize / ( BitsAllocated / 8 ) );
if ( BitsAllocated == 16 )
{
uint16_t mask = 0xffff;
mask = mask >> ( BitsAllocated - BitsStored );
- uint16_t* deb = (uint16_t*)Decompressed;
+ uint16_t* deb = (uint16_t*)Raw;
for(int i = 0; i<l; i++)
{
*deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
{
uint32_t mask = 0xffffffff;
mask = mask >> ( BitsAllocated - BitsStored );
- uint32_t* deb = (uint32_t*)Decompressed;
+ uint32_t* deb = (uint32_t*)Raw;
for(int i = 0; i<l; i++)
{
*deb = (*deb >> (BitsStored - HighBitPosition - 1)) & mask;
}
else
{
- dbg.Verbose(0, "PixelReadConvert::ConvertReArrangeBits: weird image");
- throw FormatError( "PixelReadConvert::ConvertReArrangeBits()",
- "weird image !?" );
+ gdcmVerboseMacro("Weird image");
+ throw FormatError( "Weird image !?" );
}
}
return true;
}
/**
- * \brief Convert (Y plane, cB plane, cR plane) to RGB pixels
+ * \brief Convert (cY plane, cB plane, cR plane) to RGB pixels
* \warning Works on all the frames at a time
*/
void PixelReadConvert::ConvertYcBcRPlanesToRGBPixels()
{
- uint8_t* localDecompressed = Decompressed;
- uint8_t* copyDecompressed = new uint8_t[ DecompressedSize ];
- memmove( copyDecompressed, localDecompressed, DecompressedSize );
+ uint8_t *localRaw = Raw;
+ uint8_t *copyRaw = new uint8_t[ RawSize ];
+ memmove( copyRaw, localRaw, RawSize );
// to see the tricks about YBR_FULL, YBR_FULL_422,
// YBR_PARTIAL_422, YBR_ICT, YBR_RCT have a look at :
int l = XSize * YSize;
int nbFrames = ZSize;
- uint8_t* a = copyDecompressed;
- uint8_t* b = copyDecompressed + l;
- uint8_t* c = copyDecompressed + l + l;
+ uint8_t *a = copyRaw;
+ uint8_t *b = copyRaw + l;
+ uint8_t *c = copyRaw + l + l;
double R, G, B;
/// \todo : Replace by the 'well known' integer computation
if (G > 255.0) G = 255.0;
if (B > 255.0) B = 255.0;
- *(localDecompressed++) = (uint8_t)R;
- *(localDecompressed++) = (uint8_t)G;
- *(localDecompressed++) = (uint8_t)B;
+ *(localRaw++) = (uint8_t)R;
+ *(localRaw++) = (uint8_t)G;
+ *(localRaw++) = (uint8_t)B;
a++;
b++;
c++;
}
}
- delete[] copyDecompressed;
+ delete[] copyRaw;
}
/**
*/
void PixelReadConvert::ConvertRGBPlanesToRGBPixels()
{
- uint8_t* localDecompressed = Decompressed;
- uint8_t* copyDecompressed = new uint8_t[ DecompressedSize ];
- memmove( copyDecompressed, localDecompressed, DecompressedSize );
+ uint8_t *localRaw = Raw;
+ uint8_t *copyRaw = new uint8_t[ RawSize ];
+ memmove( copyRaw, localRaw, RawSize );
int l = XSize * YSize * ZSize;
- uint8_t* a = copyDecompressed;
- uint8_t* b = copyDecompressed + l;
- uint8_t* c = copyDecompressed + l + l;
+ uint8_t* a = copyRaw;
+ uint8_t* b = copyRaw + l;
+ uint8_t* c = copyRaw + l + l;
for (int j = 0; j < l; j++)
{
- *(localDecompressed++) = *(a++);
- *(localDecompressed++) = *(b++);
- *(localDecompressed++) = *(c++);
+ *(localRaw++) = *(a++);
+ *(localRaw++) = *(b++);
+ *(localRaw++) = *(c++);
}
- delete[] copyDecompressed;
+ delete[] copyRaw;
}
-bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream* fp )
+bool PixelReadConvert::ReadAndDecompressPixelData( std::ifstream *fp )
{
- // ComputeDecompressedAndRGBSizes is already made by
- // ::GrabInformationsFromHeader. So, the structure sizes are
+ // ComputeRawAndRGBSizes is already made by
+ // ::GrabInformationsFromfile. So, the structure sizes are
// correct
Squeeze();
//// First stage: get our hands on the Pixel Data.
if ( !fp )
{
- dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
- "unavailable file pointer." );
+ gdcmVerboseMacro( "Unavailable file pointer." );
return false;
}
fp->seekg( PixelOffset, std::ios::beg );
- if( fp->fail() || fp->eof()) //Fp->gcount() == 1
+ if( fp->fail() || fp->eof())
{
- dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
- "unable to find PixelOffset in file." );
+ gdcmVerboseMacro( "Unable to find PixelOffset in file." );
return false;
}
- AllocateDecompressed();
+ AllocateRaw();
//////////////////////////////////////////////////
//// Second stage: read from disk dans decompress.
{
ReadAndDecompress12BitsTo16Bits( fp);
}
- else if ( IsDecompressed )
+ else if ( IsRaw )
{
// This problem can be found when some obvious informations are found
- // after the field containing the image datas. In this case, these
- // bad datas are added to the size of the image (in the PixelDataLength
- // variable). But DecompressedSize is the right size of the image !
- if( PixelDataLength != DecompressedSize)
+ // after the field containing the image data. In this case, these
+ // bad data are added to the size of the image (in the PixelDataLength
+ // variable). But RawSize is the right size of the image !
+ if( PixelDataLength != RawSize)
{
- dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
- "Mismatch between PixelReadConvert and DecompressedSize." );
+ gdcmVerboseMacro( "Mismatch between PixelReadConvert and RawSize." );
}
- if( PixelDataLength > DecompressedSize)
+ if( PixelDataLength > RawSize)
{
- fp->read( (char*)Decompressed, DecompressedSize);
+ fp->read( (char*)Raw, RawSize);
}
else
{
- fp->read( (char*)Decompressed, PixelDataLength);
+ fp->read( (char*)Raw, PixelDataLength);
}
- if ( fp->fail() || fp->eof())//Fp->gcount() == 1
+ if ( fp->fail() || fp->eof())
{
- dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
- "reading of decompressed pixel data failed." );
+ gdcmVerboseMacro( "Reading of Raw pixel data failed." );
return false;
}
}
else if ( IsRLELossless )
{
- if ( ! ReadAndDecompressRLEFile( fp ) )
+ if ( ! RLEInfo->DecompressRLEFile( fp, Raw, XSize, YSize, ZSize, BitsAllocated ) )
{
- dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
- "RLE decompressor failed." );
+ gdcmVerboseMacro( "RLE decompressor failed." );
return false;
}
}
// Default case concerns JPEG family
if ( ! ReadAndDecompressJPEGFile( fp ) )
{
- dbg.Verbose( 0, "PixelReadConvert::ReadAndDecompressPixelData: "
- "JPEG decompressor failed." );
+ gdcmVerboseMacro( "JPEG decompressor failed." );
return false;
}
}
// formated Dicom) files (e.g. gdcmData/US-PAL-8-10x-echo.dcm) we encounter:
// - "Planar Configuration" = 0,
// - "Photometric Interpretation" = "PALETTE COLOR".
- // Hence gdcm shall use the folowing "heuristic" in order to be tolerant
+ // Hence gdcm will use the folowing "heuristic" in order to be tolerant
// towards Dicom-non-conformance files:
// << whatever the "Planar Configuration" value might be, a
// "Photometric Interpretation" set to "PALETTE COLOR" forces
// - [Planar 1] AND [Photo C] handled with ConvertYcBcRPlanesToRGBPixels()
// - [Planar 2] OR [Photo D] requires LUT intervention.
- if ( ! IsDecompressedRGB() )
+ if ( ! IsRawRGB() )
{
// [Planar 2] OR [Photo D]: LUT intervention done outside
return;
}
/**
- * \brief Predicate to know wether the image[s] (once decompressed) is RGB.
+ * \brief Predicate to know wether the image[s] (once Raw) is RGB.
* \note See comments of \ref ConvertHandleColor
*/
-bool PixelReadConvert::IsDecompressedRGB()
+bool PixelReadConvert::IsRawRGB()
{
if ( IsMonochrome
|| PlanarConfiguration == 2
return true;
}
-void PixelReadConvert::ComputeDecompressedAndRGBSizes()
+void PixelReadConvert::ComputeRawAndRGBSizes()
{
int bitsAllocated = BitsAllocated;
// Number of "Bits Allocated" is fixed to 16 when it's 12, since
bitsAllocated = 16;
}
- DecompressedSize = XSize * YSize * ZSize
+ RawSize = XSize * YSize * ZSize
* ( bitsAllocated / 8 )
* SamplesPerPixel;
if ( HasLUT )
{
- RGBSize = 3 * DecompressedSize;
+ RGBSize = 3 * RawSize;
}
else
{
- RGBSize = DecompressedSize;
+ RGBSize = RawSize;
}
}
-void PixelReadConvert::GrabInformationsFromHeader( Header* header )
+void PixelReadConvert::GrabInformationsFromFile( File *file )
{
- // Just in case some access to a Header element requires disk access.
- // Note: gdcmDocument::Fp is leaved open after OpenFile.
- std::ifstream* fp = header->OpenFile();
// Number of Bits Allocated for storing a Pixel is defaulted to 16
- // when absent from the header.
- BitsAllocated = header->GetBitsAllocated();
+ // when absent from the file.
+ BitsAllocated = file->GetBitsAllocated();
if ( BitsAllocated == 0 )
{
BitsAllocated = 16;
}
- // Number of "Bits Stored" defaulted to number of "Bits Allocated"
- // when absent from the header.
- BitsStored = header->GetBitsStored();
+ // Number of "Bits Stored", defaulted to number of "Bits Allocated"
+ // when absent from the file.
+ BitsStored = file->GetBitsStored();
if ( BitsStored == 0 )
{
BitsStored = BitsAllocated;
}
- // High Bit Position
- HighBitPosition = header->GetHighBitPosition();
+ // High Bit Position, defaulted to "Bits Allocated" - 1
+ HighBitPosition = file->GetHighBitPosition();
if ( HighBitPosition == 0 )
{
HighBitPosition = BitsAllocated - 1;
}
- XSize = header->GetXSize();
- YSize = header->GetYSize();
- ZSize = header->GetZSize();
- SamplesPerPixel = header->GetSamplesPerPixel();
- PixelSize = header->GetPixelSize();
- PixelSign = header->IsSignedPixelData();
- SwapCode = header->GetSwapCode();
- TransferSyntaxType ts = header->GetTransferSyntax();
- IsDecompressed =
- ( ! header->IsDicomV3() )
- || ts == ImplicitVRLittleEndian
- || ts == ImplicitVRLittleEndianDLXGE
- || ts == ExplicitVRLittleEndian
- || ts == ExplicitVRBigEndian
- || ts == DeflatedExplicitVRLittleEndian;
- IsJPEG2000 = header->IsJPEG2000();
- IsJPEGLossless = header->IsJPEGLossless();
- IsRLELossless = ( ts == RLELossless );
- PixelOffset = header->GetPixelOffset();
- PixelDataLength = header->GetPixelAreaLength();
- RLEInfo = header->GetRLEInfo();
- JPEGInfo = header->GetJPEGInfo();
-
- PlanarConfiguration = header->GetPlanarConfiguration();
- IsMonochrome = header->IsMonochrome();
- IsPaletteColor = header->IsPaletteColor();
- IsYBRFull = header->IsYBRFull();
+ XSize = file->GetXSize();
+ YSize = file->GetYSize();
+ ZSize = file->GetZSize();
+ SamplesPerPixel = file->GetSamplesPerPixel();
+ PixelSize = file->GetPixelSize();
+ PixelSign = file->IsSignedPixelData();
+ SwapCode = file->GetSwapCode();
+ std::string ts = file->GetTransferSyntax();
+ IsRaw =
+ ( ! file->IsDicomV3() )
+ || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian
+ || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndianDLXGE
+ || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRLittleEndian
+ || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian
+ || Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::DeflatedExplicitVRLittleEndian;
+
+ IsJPEG2000 = Global::GetTS()->IsJPEG2000(ts);
+ IsJPEGLS = Global::GetTS()->IsJPEGLS(ts);
+ IsJPEGLossy = Global::GetTS()->IsJPEGLossy(ts);
+ IsJPEGLossless = Global::GetTS()->IsJPEGLossless(ts);
+ IsRLELossless = Global::GetTS()->IsRLELossless(ts);
+
+ PixelOffset = file->GetPixelOffset();
+ PixelDataLength = file->GetPixelAreaLength();
+ RLEInfo = file->GetRLEInfo();
+ JPEGInfo = file->GetJPEGInfo();
+
+ PlanarConfiguration = file->GetPlanarConfiguration();
+ IsMonochrome = file->IsMonochrome();
+ IsPaletteColor = file->IsPaletteColor();
+ IsYBRFull = file->IsYBRFull();
/////////////////////////////////////////////////////////////////
// LUT section:
- HasLUT = header->HasLUT();
+ HasLUT = file->HasLUT();
if ( HasLUT )
{
- LutRedDescriptor = header->GetEntryByNumber( 0x0028, 0x1101 );
- LutGreenDescriptor = header->GetEntryByNumber( 0x0028, 0x1102 );
- LutBlueDescriptor = header->GetEntryByNumber( 0x0028, 0x1103 );
+ // Just in case some access to a File element requires disk access.
+ LutRedDescriptor = file->GetEntryValue( 0x0028, 0x1101 );
+ LutGreenDescriptor = file->GetEntryValue( 0x0028, 0x1102 );
+ LutBlueDescriptor = file->GetEntryValue( 0x0028, 0x1103 );
// Depending on the value of Document::MAX_SIZE_LOAD_ELEMENT_VALUE
// [ refer to invocation of Document::SetMaxSizeLoadEntry() in
// Document::Document() ], the loading of the value (content) of a
// [Bin|Val]Entry occurence migth have been hindered (read simply NOT
- // loaded). Hence, we first try to obtain the LUTs data from the header
- // and when this fails we read the LUTs data directely from disk.
- /// \todo Reading a [Bin|Val]Entry directly from disk is a kludge.
+ // loaded). Hence, we first try to obtain the LUTs data from the file
+ // and when this fails we read the LUTs data directly from disk.
+ /// \TODO Reading a [Bin|Val]Entry directly from disk is a kludge.
/// We should NOT bypass the [Bin|Val]Entry class. Instead
/// an access to an UNLOADED content of a [Bin|Val]Entry occurence
/// (e.g. BinEntry::GetBinArea()) should force disk access from
/// is that the [Bin|Val]Entry is unaware of the FILE* is was
/// parsed from. Fix that. FIXME.
- ////// Red round:
- LutRedData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1201 );
+ ////// Red round
+ file->LoadEntryBinArea(0x0028, 0x1201);
+ LutRedData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1201 );
if ( ! LutRedData )
{
- // Read the Lut Data from disk
- DocEntry* lutRedDataEntry = header->GetDocEntryByNumber( 0x0028,
- 0x1201 );
- LutRedData = new uint8_t[ lutRedDataEntry->GetLength() ];
- fp->seekg( lutRedDataEntry->GetOffset() ,std::ios::beg );
- fp->read( (char*)LutRedData, (size_t)lutRedDataEntry->GetLength());
- if ( fp->fail() || fp->eof())//Fp->gcount() == 1
- {
- dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: "
- "unable to read red LUT data" );
- }
+ gdcmVerboseMacro( "Unable to read Red LUT data" );
}
////// Green round:
- LutGreenData = (uint8_t*)header->GetEntryBinAreaByNumber(0x0028, 0x1202 );
+ file->LoadEntryBinArea(0x0028, 0x1202);
+ LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 );
if ( ! LutGreenData)
{
- // Read the Lut Data from disk
- DocEntry* lutGreenDataEntry = header->GetDocEntryByNumber( 0x0028,
- 0x1202 );
- LutGreenData = new uint8_t[ lutGreenDataEntry->GetLength() ];
- fp->seekg( lutGreenDataEntry->GetOffset() , std::ios::beg );
- fp->read( (char*)LutGreenData, (size_t)lutGreenDataEntry->GetLength() );
- if ( fp->fail() || fp->eof())//Fp->gcount() == 1
- {
- dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: "
- "unable to read green LUT data" );
- }
+ gdcmVerboseMacro( "Unable to read Green LUT data" );
}
////// Blue round:
- LutBlueData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1203 );
+ file->LoadEntryBinArea(0x0028, 0x1203);
+ LutBlueData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1203 );
if ( ! LutBlueData )
{
- // Read the Lut Data from disk
- DocEntry* lutBlueDataEntry = header->GetDocEntryByNumber( 0x0028,
- 0x1203 );
- LutBlueData = new uint8_t[ lutBlueDataEntry->GetLength() ];
- fp->seekg( lutBlueDataEntry->GetOffset() , std::ios::beg );
- fp->read( (char*)LutBlueData, (size_t)lutBlueDataEntry->GetLength() );
- if ( fp->fail() || fp->eof())//Fp->gcount() == 1
- {
- dbg.Verbose(0, "PixelReadConvert::GrabInformationsFromHeader: "
- "unable to read blue LUT data" );
- }
+ gdcmVerboseMacro( "Unable to read Blue LUT data" );
}
}
- ComputeDecompressedAndRGBSizes();
-
- if(fp)
- {
- header->CloseFile();
- }
+ ComputeRawAndRGBSizes();
}
/**
- * \brief Build Red/Green/Blue/Alpha LUT from Header
+ * \brief Build Red/Green/Blue/Alpha LUT from File
* when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
* and (0028,1101),(0028,1102),(0028,1102)
* - xxx Palette Color Lookup Table Descriptor - are found
&lengthR, &debR, &nbitsR );
if( nbRead != 3 )
{
- dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong red LUT descriptor");
+ gdcmVerboseMacro( "Wrong Red LUT descriptor" );
}
int lengthG; // Green LUT length in Bytes
&lengthG, &debG, &nbitsG );
if( nbRead != 3 )
{
- dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong green LUT descriptor");
+ gdcmVerboseMacro( "Wrong Green LUT descriptor" );
}
int lengthB; // Blue LUT length in Bytes
&lengthB, &debB, &nbitsB );
if( nbRead != 3 )
{
- dbg.Verbose(0, "PixelReadConvert::BuildLUTRGBA: wrong blue LUT descriptor");
+ gdcmVerboseMacro( "Wrong Blue LUT descriptor" );
}
////////////////////////////////////////////////////////
// forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
LutRGBA = new uint8_t[ 1024 ]; // 256 * 4 (R, G, B, Alpha)
if ( !LutRGBA )
- {
return;
- }
+
memset( LutRGBA, 0, 1024 );
int mult;
// if it works, we shall have to check the 3 Palettes
// to see which byte is ==0 (first one, or second one)
// and fix the code
- // We give up the checking to avoid some (useless ?)overhead
+ // We give up the checking to avoid some (useless ?) overhead
// (optimistic asumption)
int i;
uint8_t* a = LutRGBA + 0;
}
/**
- * \brief Build the RGB image from the Decompressed imagage and the LUTs.
+ * \brief Build the RGB image from the Raw imagage and the LUTs.
*/
bool PixelReadConvert::BuildRGBImage()
{
return true;
}
- if ( ! Decompressed )
+ if ( ! Raw )
{
// The job can't be done
return false;
// Build RGB Pixels
AllocateRGB();
uint8_t* localRGB = RGB;
- for (size_t i = 0; i < DecompressedSize; ++i )
+ for (size_t i = 0; i < RawSize; ++i )
{
- int j = Decompressed[i] * 4;
+ int j = Raw[i] * 4;
*localRGB++ = LutRGBA[j];
*localRGB++ = LutRGBA[j+1];
*localRGB++ = LutRGBA[j+2];
* @param indent Indentation string to be prepended during printing.
* @param os Stream to print to.
*/
-void PixelReadConvert::Print( std::string indent, std::ostream &os )
+void PixelReadConvert::Print( std::ostream &os, std::string const & indent )
{
os << indent
<< "--- Pixel information -------------------------"
<< std::endl;
os << indent
<< "Pixel Data: offset " << PixelOffset
- << " x" << std::hex << PixelOffset << std::dec
- << " length " << PixelDataLength
- << " x" << std::hex << PixelDataLength << std::dec
- << std::endl;
+ << " x(" << std::hex << PixelOffset << std::dec
+ << ") length " << PixelDataLength
+ << " x(" << std::hex << PixelDataLength << std::dec
+ << ")" << std::endl;
if ( IsRLELossless )
{
if ( RLEInfo )
{
- RLEInfo->Print( indent, os );
+ RLEInfo->Print( os, indent );
}
else
{
- dbg.Verbose(0, "PixelReadConvert::Print: set as RLE file "
- "but NO RLEinfo present.");
+ gdcmVerboseMacro("Set as RLE file but NO RLEinfo present.");
}
}
- if ( IsJPEG2000 || IsJPEGLossless )
+ if ( IsJPEG2000 || IsJPEGLossless || IsJPEGLossy || IsJPEGLS )
{
if ( JPEGInfo )
{
- JPEGInfo->Print( indent, os );
+ JPEGInfo->Print( os, indent );
}
else
{
- dbg.Verbose(0, "PixelReadConvert::Print: set as JPEG file "
- "but NO JPEGinfo present.");
+ gdcmVerboseMacro("Set as JPEG file but NO JPEGinfo present.");
}
}
}
// User
// ---> GetImageDataRaw
// ---> GetImageDataIntoVectorRaw
+
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff