Program: gdcm
Module: $RCSfile: gdcmPixelReadConvert.cxx,v $
Language: C++
- Date: $Date: 2005/01/07 22:06:47 $
- Version: $Revision: 1.18 $
+ Date: $Date: 2005/01/23 10:12:34 $
+ Version: $Revision: 1.32 $
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 "gdcmHeader.h"
+#include "gdcmFile.h"
+#include "gdcmGlobal.h"
+#include "gdcmTS.h"
#include "gdcmPixelReadConvert.h"
#include "gdcmDocEntry.h"
#include "gdcmRLEFramesInfo.h"
{
#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);
-
-#define JOCTET uint8_t
-// For JPEG 8 Bits, body in file gdcmJpeg8.cxx
-bool gdcm_read_JPEG_file8 (std::ifstream *fp, void *image_buffer);
-bool gdcm_read_JPEG_memory8 (const JOCTET *buffer, const size_t buflen,
- void *image_buffer,
- size_t *howManyRead, size_t *howManyWritten);
-//
-// For JPEG 12 Bits, body in file gdcmJpeg12.cxx
-bool gdcm_read_JPEG_file12 (std::ifstream *fp, void *image_buffer);
-bool gdcm_read_JPEG_memory12 (const JOCTET *buffer, const size_t buflen,
- void *image_buffer,
- size_t *howManyRead, size_t *howManyWritten);
-
-// 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);
-bool gdcm_read_JPEG_memory16 (const JOCTET *buffer, const size_t buflen,
- void* image_buffer,
- size_t *howManyRead, size_t *howManyWritten);
-
//-----------------------------------------------------------------------------
// Constructor / Destructor
/**
* \brief Try to deal with RLE 16 Bits.
- * We assume the RLE has allready been parsed and loaded in
+ * We assume the RLE has already been parsed and loaded in
* Raw (through \ref ReadAndDecompressJPEGFile ).
* We here need to make 16 Bits Pixels from Low Byte and
* High Byte 'Planes'...(for what it may mean)
/**
* \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 subRaw Sub region of \ref Raw where the de
- * decoded fragment should be placed.
+ * @param subRaw Sub region of \ref Raw where the decoded fragment
+ * should be placed.
* @param fragmentSize The length of the binary fragment as found on the disk.
* @param RawSegmentSize The expected length of the fragment ONCE
* Raw.
uint16_t *im16 = (uint16_t*)Raw;
switch( SwapCode )
{
- case 0:
- case 12:
case 1234:
break;
- case 21:
case 3412:
case 2143:
case 4321:
uint32_t* im32 = (uint32_t*)Raw;
switch ( SwapCode )
{
- case 0:
case 1234:
break;
case 4321:
}
/**
- * \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)( RawSize / ( BitsAllocated / 8 ) );
uint16_t *deb = (uint16_t *)Raw;
/**
* \brief Reads from disk the Pixel Data of JPEG Dicom encapsulated
- * file and decompress it. This funciton assumes that each
+ * file and decompress it. This function assumes that each
* jpeg fragment contains a whole frame (jpeg file).
* @param fp File Pointer
* @return Boolean
*/
bool PixelReadConvert::ReadAndDecompressJPEGFramesFromFile( std::ifstream *fp )
{
+ // Pointer to the Raw image
uint8_t *localRaw = Raw;
+
+ // Precompute the offset localRaw will be shifted with
+ int length = XSize * YSize * SamplesPerPixel;
+ int numberBytes = BitsAllocated / 8;
+
// Loop on the fragment[s]
for( JPEGFragmentsInfo::JPEGFragmentsList::iterator
it = JPEGInfo->Fragments.begin();
it != JPEGInfo->Fragments.end();
++it )
{
- fp->seekg( (*it)->Offset, std::ios::beg);
-
- if ( BitsStored == 8)
- {
- // JPEG Lossy : call to IJG 6b
- if ( ! gdcm_read_JPEG_file8( fp, localRaw ) )
- {
- return false;
- }
- }
- else if ( BitsStored <= 12)
- {
- // Reading Fragment pixels
- if ( ! gdcm_read_JPEG_file12 ( fp, localRaw ) )
- {
- return false;
- }
- }
- else if ( BitsStored <= 16)
- {
- // Reading Fragment pixels
- if ( ! gdcm_read_JPEG_file16 ( fp, localRaw ) )
- {
- return false;
- }
- //assert( IsJPEGLossless );
- }
- else
- {
- // other JPEG lossy not supported
- gdcmErrorMacro( "Unknown jpeg lossy compression ");
- return false;
- }
+ (*it)->DecompressJPEGFramesFromFile(fp, localRaw, BitsStored );
// Advance to next free location in Raw
// for next fragment decompression (if any)
- int length = XSize * YSize * SamplesPerPixel;
- int numberBytes = BitsAllocated / 8;
localRaw += length * numberBytes;
}
ReadAndDecompressJPEGSingleFrameFragmentsFromFile( std::ifstream *fp )
{
// Loop on the fragment[s] to get total length
- size_t totalLength = 0;
- JPEGFragmentsInfo::JPEGFragmentsList::iterator it;
- for( it = JPEGInfo->Fragments.begin();
- it != JPEGInfo->Fragments.end();
- ++it )
- {
- totalLength += (*it)->Length;
- }
+ size_t totalLength = JPEGInfo->GetFragmentsLength();
// Concatenate the jpeg fragments into a local buffer
JOCTET *buffer = new JOCTET [totalLength];
- JOCTET *p = buffer;
+ // Fill in the buffer:
+ JPEGInfo->ReadAllFragments(fp, buffer);
- // Loop on the fragment[s]
- for( it = JPEGInfo->Fragments.begin();
- it != JPEGInfo->Fragments.end();
- ++it )
- {
- fp->seekg( (*it)->Offset, std::ios::beg);
- size_t len = (*it)->Length;
- fp->read((char *)p,len);
- p += len;
- }
-
- size_t howManyRead = 0;
- size_t howManyWritten = 0;
-
- if ( BitsStored == 8)
- {
- if ( ! gdcm_read_JPEG_memory8( buffer, totalLength, Raw,
- &howManyRead, &howManyWritten ) )
- {
- gdcmErrorMacro( "Failed to read jpeg8 ");
- delete [] buffer;
- return false;
- }
- }
- else if ( BitsStored <= 12)
- {
- if ( ! gdcm_read_JPEG_memory12( buffer, totalLength, Raw,
- &howManyRead, &howManyWritten ) )
- {
- gdcmErrorMacro( "Failed to read jpeg12 ");
- delete [] buffer;
- return false;
- }
- }
- else if ( BitsStored <= 16)
- {
-
- if ( ! gdcm_read_JPEG_memory16( buffer, totalLength, Raw,
- &howManyRead, &howManyWritten ) )
- {
- gdcmErrorMacro( "Failed to read jpeg16 ");
- delete [] buffer;
- return false;
- }
- }
- else
- {
- // other JPEG lossy not supported
- gdcmErrorMacro( "Unknown jpeg lossy compression ");
- delete [] buffer;
- return false;
- }
+ // kludge: // FIXME
+ JPEGFragmentsInfo::JPEGFragmentsList::const_iterator it = JPEGInfo->Fragments.begin();
+ (*it)->DecompressJPEGSingleFrameFragmentsFromFile(buffer, totalLength, Raw, BitsStored);
// free local buffer
delete [] buffer;
ReadAndDecompressJPEGFragmentedFramesFromFile( std::ifstream *fp )
{
// Loop on the fragment[s] to get total length
- size_t totalLength = 0;
- JPEGFragmentsInfo::JPEGFragmentsList::iterator it;
- for( it = JPEGInfo->Fragments.begin();
- it != JPEGInfo->Fragments.end();
- ++it )
- {
- totalLength += (*it)->Length;
- }
+ size_t totalLength = JPEGInfo->GetFragmentsLength();
// Concatenate the jpeg fragments into a local buffer
JOCTET *buffer = new JOCTET [totalLength];
- JOCTET *p = buffer;
-
- // Loop on the fragment[s]
- for( it = JPEGInfo->Fragments.begin();
- it != JPEGInfo->Fragments.end();
- ++it )
- {
- fp->seekg( (*it)->Offset, std::ios::beg);
- size_t len = (*it)->Length;
- fp->read((char *)p,len);
- p+=len;
- }
+ // Fill in the buffer:
+ JPEGInfo->ReadAllFragments(fp, buffer);
size_t howManyRead = 0;
size_t howManyWritten = 0;
size_t fragmentLength = 0;
+ JPEGFragmentsInfo::JPEGFragmentsList::const_iterator it;
for( it = JPEGInfo->Fragments.begin() ;
(it != JPEGInfo->Fragments.end()) && (howManyRead < totalLength);
++it )
fragmentLength += (*it)->Length;
if (howManyRead > fragmentLength) continue;
-
- if ( BitsStored == 8)
- {
- if ( ! gdcm_read_JPEG_memory8( buffer+howManyRead, totalLength-howManyRead,
- Raw+howManyWritten,
- &howManyRead, &howManyWritten ) )
- {
- gdcmErrorMacro( "Failed to read jpeg8");
- delete [] buffer;
- return false;
- }
- }
- else if ( BitsStored <= 12)
- {
-
- if ( ! gdcm_read_JPEG_memory12( buffer+howManyRead, totalLength-howManyRead,
- Raw+howManyWritten,
- &howManyRead, &howManyWritten ) )
- {
- gdcmErrorMacro( "Failed to read jpeg12");
- delete [] buffer;
- return false;
- }
- }
- else if ( BitsStored <= 16)
- {
- if ( ! gdcm_read_JPEG_memory16( buffer+howManyRead, totalLength-howManyRead,
- Raw+howManyWritten,
- &howManyRead, &howManyWritten ) )
- {
- gdcmErrorMacro( "Failed to read jpeg16 ");
- delete [] buffer;
- return false;
- }
- }
- else
- {
- // other JPEG lossy not supported
- gdcmErrorMacro( "Unknown jpeg lossy compression ");
- delete [] buffer;
- return false;
- }
+ (*it)->DecompressJPEGFragmentedFramesFromFile(buffer, Raw, BitsStored, howManyRead, howManyWritten, totalLength);
if (howManyRead < fragmentLength)
howManyRead = fragmentLength;
if ( IsJPEG2000 )
{
fp->seekg( (*JPEGInfo->Fragments.begin())->Offset, std::ios::beg);
- if ( ! gdcm_read_JPEG2000_file( fp,Raw ) )
+// if ( ! gdcm_read_JPEG2000_file( fp,Raw ) )
return false;
}
}
/**
- * \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()
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
+ // 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)
{
// 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
}
}
-void PixelReadConvert::GrabInformationsFromHeader( Header *header )
+void PixelReadConvert::GrabInformationsFromHeader( File *header )
{
// Number of Bits Allocated for storing a Pixel is defaulted to 16
// when absent from the header.
BitsAllocated = 16;
}
- // Number of "Bits Stored" defaulted to number of "Bits Allocated"
+ // Number of "Bits Stored", defaulted to number of "Bits Allocated"
// when absent from the header.
BitsStored = header->GetBitsStored();
if ( BitsStored == 0 )
BitsStored = BitsAllocated;
}
- // High Bit Position
+ // High Bit Position, defaulted to "Bits Allocated" - 1
HighBitPosition = header->GetHighBitPosition();
if ( HighBitPosition == 0 )
{
PixelSize = header->GetPixelSize();
PixelSign = header->IsSignedPixelData();
SwapCode = header->GetSwapCode();
- TransferSyntaxType ts = header->GetTransferSyntax();
+ std::string ts = header->GetTransferSyntax();
IsRaw =
( ! header->IsDicomV3() )
- || ts == ImplicitVRLittleEndian
- || ts == ImplicitVRLittleEndianDLXGE
- || ts == ExplicitVRLittleEndian
- || ts == ExplicitVRBigEndian
- || ts == DeflatedExplicitVRLittleEndian;
- IsJPEG2000 = header->IsJPEG2000();
- IsJPEGLossless = header->IsJPEGLossless();
- IsRLELossless = ( ts == RLELossless );
+ || 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 = header->GetPixelOffset();
PixelDataLength = header->GetPixelAreaLength();
RLEInfo = header->GetRLEInfo();
HasLUT = header->HasLUT();
if ( HasLUT )
{
- // Just in case some access to a Header element requires disk access.
- 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 = header->GetEntry( 0x0028, 0x1101 );
+ LutGreenDescriptor = header->GetEntry( 0x0028, 0x1102 );
+ LutBlueDescriptor = header->GetEntry( 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
////// Red round
header->LoadEntryBinArea(0x0028, 0x1201);
- LutRedData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1201 );
+ LutRedData = (uint8_t*)header->GetEntryBinArea( 0x0028, 0x1201 );
if ( ! LutRedData )
{
- gdcmVerboseMacro( "Unable to read red LUT data" );
+ gdcmVerboseMacro( "Unable to read Red LUT data" );
}
////// Green round:
header->LoadEntryBinArea(0x0028, 0x1202);
- LutGreenData = (uint8_t*)header->GetEntryBinAreaByNumber(0x0028, 0x1202 );
+ LutGreenData = (uint8_t*)header->GetEntryBinArea(0x0028, 0x1202 );
if ( ! LutGreenData)
{
- gdcmVerboseMacro( "Unable to read green LUT data" );
+ gdcmVerboseMacro( "Unable to read Green LUT data" );
}
////// Blue round:
header->LoadEntryBinArea(0x0028, 0x1203);
- LutBlueData = (uint8_t*)header->GetEntryBinAreaByNumber( 0x0028, 0x1203 );
+ LutBlueData = (uint8_t*)header->GetEntryBinArea( 0x0028, 0x1203 );
if ( ! LutBlueData )
{
- gdcmVerboseMacro( "Unable to read blue LUT data" );
+ gdcmVerboseMacro( "Unable to read Blue LUT data" );
}
}
}
/**
- * \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 )
{
- gdcmVerboseMacro( "Wrong red LUT descriptor" );
+ gdcmVerboseMacro( "Wrong Red LUT descriptor" );
}
int lengthG; // Green LUT length in Bytes
&lengthG, &debG, &nbitsG );
if( nbRead != 3 )
{
- gdcmVerboseMacro( "Wrong green LUT descriptor" );
+ gdcmVerboseMacro( "Wrong Green LUT descriptor" );
}
int lengthB; // Blue LUT length in Bytes
&lengthB, &debB, &nbitsB );
if( nbRead != 3 )
{
- gdcmVerboseMacro( "Wrong blue LUT descriptor" );
+ gdcmVerboseMacro( "Wrong Blue LUT descriptor" );
}
////////////////////////////////////////////////////////
// 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;
return true;
}
-/**
- * \brief Print self.
- * @param os Stream to print to.
- */
-void PixelReadConvert::Print( std::ostream &os )
-{
- Print("",os);
-}
-
/**
* \brief Print self.
* @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 -------------------------"
{
if ( RLEInfo )
{
- RLEInfo->Print( indent, os );
+ RLEInfo->Print( os, indent );
}
else
{
}
}
- if ( IsJPEG2000 || IsJPEGLossless )
+ if ( IsJPEG2000 || IsJPEGLossless || IsJPEGLossy || IsJPEGLS )
{
if ( JPEGInfo )
{
- JPEGInfo->Print( indent, os );
+ JPEGInfo->Print( os, indent );
}
else
{