Program: gdcm
Module: $RCSfile: gdcmPixelReadConvert.cxx,v $
Language: C++
- Date: $Date: 2007/07/25 10:35:20 $
- Version: $Revision: 1.116 $
+ Date: $Date: 2007/10/03 09:31:08 $
+ Version: $Revision: 1.124 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmDocEntry.h"
#include "gdcmRLEFramesInfo.h"
#include "gdcmJPEGFragmentsInfo.h"
+#include "gdcmSegmentedPalette.h"
#include <fstream>
#include <stdio.h> //for sscanf
namespace GDCM_NAME_SPACE
{
-//bool ReadMPEGFile (std::ifstream *fp, char *inputdata, size_t lenght);
+//bool ReadMPEGFile (std::ifstream *fp, char *inputdata, size_t lenght);
bool gdcm_read_JPEG2000_file (void* raw,
char *inputdata, size_t inputlength);
//-----------------------------------------------------------------------------
// Public
/**
* \brief Predicate to know whether the image[s] (once Raw) is RGB.
- * \note See comments of \ref ConvertHandleColor
+ * \note See comments of ConvertHandleColor
*/
bool PixelReadConvert::IsRawRGB()
{
{
BitsAllocated = 16;
}
-
- else if (BitsAllocated > 8 && BitsAllocated < 16 && BitsAllocated != 12)
+ else if ( BitsAllocated > 8 && BitsAllocated < 16 && BitsAllocated != 12 )
{
BitsAllocated = 16;
- }
+ }
+
// Number of "Bits Stored", defaulted to number of "Bits Allocated"
// when absent from the file.
BitsStored = file->GetBitsStored();
}
// cache whether this is a strange GE transfer syntax (which uses
// a little endian transfer syntax for the header and a big endian
- // transfer syntax for the pixel data).
+ // transfer syntax for the pixel data).
IsPrivateGETransferSyntax =
( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRBigEndianPrivateGE );
- IsMPEG = IsJPEG2000 = IsJPEGLS = IsJPEGLossy = IsJPEGLossless = IsRLELossless = false;
+ IsMPEG = IsJPEG2000 = IsJPEGLS = IsJPEGLossy = IsJPEGLossless = IsRLELossless = false;
if (!IsRaw)
- {
+ {
while(true)
{
// mind the order : check the most usual first.
LutRedDescriptor = file->GetEntryString( 0x0028, 0x1101 );
LutGreenDescriptor = file->GetEntryString( 0x0028, 0x1102 );
LutBlueDescriptor = file->GetEntryString( 0x0028, 0x1103 );
-
- // FIXME : The following comment is probabely meaningless, since LUT are *always*
- // loaded at parsing time, whatever their length is.
-
- // 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 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. DataEntry::GetBinArea()) should force disk access from
- // within the [Bin|Val]Entry class itself. The only problem
- // is that the [Bin|Val]Entry is unaware of the FILE* is was
- // parsed from. Fix that. FIXME.
-
- // //// Red round
- file->LoadEntryBinArea(0x0028, 0x1201);
- LutRedData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1201 );
- if ( ! LutRedData )
- {
- gdcmWarningMacro("Unable to read Red Palette Color Lookup Table data");
- }
-
- // //// Green round:
- file->LoadEntryBinArea(0x0028, 0x1202);
- LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 );
- if ( ! LutGreenData)
- {
- gdcmWarningMacro("Unable to read Green Palette Color Lookup Table data");
- }
-
- // //// Blue round:
- file->LoadEntryBinArea(0x0028, 0x1203);
- LutBlueData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1203 );
- if ( ! LutBlueData )
- {
- gdcmWarningMacro("Unable to read Blue Palette Color Lookup Table data");
- }
+ if( file->GetDocEntry(0x0028,0x1221) ) // bla...
+ {
+ GDCM_NAME_SPACE::TagKey DCM_RedPaletteColorLookupTableDescriptor (0x0028, 0x1101);
+ GDCM_NAME_SPACE::TagKey DCM_GreenPaletteColorLookupTableDescriptor (0x0028, 0x1102);
+ GDCM_NAME_SPACE::TagKey DCM_BluePaletteColorLookupTableDescriptor (0x0028, 0x1103);
+
+ GDCM_NAME_SPACE::TagKey DCM_SegmentedRedPaletteColorLookupTableData (0x0028, 0x1221);
+ GDCM_NAME_SPACE::TagKey DCM_SegmentedGreenPaletteColorLookupTableData (0x0028, 0x1222);
+ GDCM_NAME_SPACE::TagKey DCM_SegmentedBluePaletteColorLookupTableData (0x0028, 0x1223);
+
+
+ LutRedData = new uint8_t[65535];
+ LutGreenData = new uint8_t[65535];
+ LutBlueData = new uint8_t[65535];
+ // TODO need to check file is indeed PALETTE COLOR:
+ ReadPaletteInto(file, DCM_RedPaletteColorLookupTableDescriptor,
+ DCM_SegmentedRedPaletteColorLookupTableData,LutRedData);
+ ReadPaletteInto(file, DCM_GreenPaletteColorLookupTableDescriptor,
+ DCM_SegmentedGreenPaletteColorLookupTableData,LutGreenData);
+ ReadPaletteInto(file, DCM_BluePaletteColorLookupTableDescriptor,
+ DCM_SegmentedBluePaletteColorLookupTableData,LutBlueData);
+
+ }
+ else
+ {
+
+ // FIXME : The following comment is probabely meaningless, since LUT are *always*
+ // loaded at parsing time, whatever their length is.
+
+ // 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 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. DataEntry::GetBinArea()) should force disk access from
+ // within the [Bin|Val]Entry class itself. The only problem
+ // is that the [Bin|Val]Entry is unaware of the FILE* is was
+ // parsed from. Fix that. FIXME.
+
+ // //// Red round
+ file->LoadEntryBinArea(0x0028, 0x1201);
+ LutRedData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1201 );
+ if ( ! LutRedData )
+ {
+ gdcmWarningMacro("Unable to read Red Palette Color Lookup Table data");
+ }
+
+ // //// Green round:
+ file->LoadEntryBinArea(0x0028, 0x1202);
+ LutGreenData = (uint8_t*)file->GetEntryBinArea(0x0028, 0x1202 );
+ if ( ! LutGreenData)
+ {
+ gdcmWarningMacro("Unable to read Green Palette Color Lookup Table data");
+ }
+
+ // //// Blue round:
+ file->LoadEntryBinArea(0x0028, 0x1203);
+ LutBlueData = (uint8_t*)file->GetEntryBinArea( 0x0028, 0x1203 );
+ if ( ! LutBlueData )
+ {
+ gdcmWarningMacro("Unable to read Blue Palette Color Lookup Table data");
+ }
+ }
}
FileInternal = file;
FH = fileHelper;
}
if (remainingLength !=0 )
fp->read( raw, remainingLength);
-
+
if ( fp->fail() || fp->eof())
{
gdcmWarningMacro( "Reading of Raw pixel data failed." );
delete [] Raw;
Raw = 0;
- if ( LutRGBA )
- delete [] LutRGBA;
- LutRGBA = 0;
+ //if ( LutRGBA )
+ // delete [] LutRGBA;
+ //LutRGBA = 0;
}
/**
// jpeg2000 stream to use jasper:
// I don't think we'll ever be able to deal with multiple fragments properly
- unsigned long inputlength = 0;
- JPEGFragment *jpegfrag = JPEGInfo->GetFirstFragment();
- while( jpegfrag )
- {
+ if( ZSize == 1 )
+ {
+ unsigned long inputlength = 0;
+ JPEGFragment *jpegfrag = JPEGInfo->GetFirstFragment();
+ while( jpegfrag )
+ {
inputlength += jpegfrag->GetLength();
jpegfrag = JPEGInfo->GetNextFragment();
- }
- gdcmAssertMacro( inputlength != 0);
- uint8_t *inputdata = new uint8_t[inputlength];
- char *pinputdata = (char*)inputdata;
- jpegfrag = JPEGInfo->GetFirstFragment();
- while( jpegfrag )
- {
+ }
+ gdcmAssertMacro( inputlength != 0);
+ uint8_t *inputdata = new uint8_t[inputlength];
+ char *pinputdata = (char*)inputdata;
+ jpegfrag = JPEGInfo->GetFirstFragment();
+ while( jpegfrag )
+ {
fp->seekg( jpegfrag->GetOffset(), std::ios::beg);
fp->read(pinputdata, jpegfrag->GetLength());
pinputdata += jpegfrag->GetLength();
jpegfrag = JPEGInfo->GetNextFragment();
- }
- // Warning the inputdata buffer is delete in the function
- if ( ! gdcm_read_JPEG2000_file( Raw,
- (char*)inputdata, inputlength ) )
- {
+ }
+ // Warning the inputdata buffer is deleted in the function
+ if ( gdcm_read_JPEG2000_file( Raw,
+ (char*)inputdata, inputlength ) )
+ {
return true;
- }
- // wow what happen, must be an error
- gdcmWarningMacro( "gdcm_read_JPEG2000_file() failed ");
- return false;
+ }
+ // wow what happen, must be an error
+ gdcmWarningMacro( "gdcm_read_JPEG2000_file() failed ");
+ return false;
+ }
+ else
+ {
+ if( (unsigned int)ZSize != JPEGInfo->GetFragmentCount() )
+ {
+ gdcmErrorMacro( "Sorry GDCM does not handle this type of fragments" );
+ return false;
+ }
+ // Hopefully every dicom fragment is *exactly* the j2k stream
+ JPEGFragment *jpegfrag = JPEGInfo->GetFirstFragment();
+ char *praw = (char*)Raw;
+ while( jpegfrag )
+ {
+ unsigned long inputlength = jpegfrag->GetLength();
+ char *inputdata = new char[inputlength];
+ fp->seekg( jpegfrag->GetOffset(), std::ios::beg);
+ fp->read(inputdata, jpegfrag->GetLength());
+ // Warning the inputdata buffer is deleted in the function
+ gdcm_read_JPEG2000_file( praw,
+ inputdata, inputlength) ;
+ praw += XSize*YSize*SamplesPerPixel*(BitsAllocated/8);
+ jpegfrag = JPEGInfo->GetNextFragment();
+ }
+ return true;
+ }
}
else if ( IsJPEGLS )
{
int length = XSize * YSize * ZSize * SamplesPerPixel;
int numberBytes = BitsAllocated / 8;
- JPEGInfo->DecompressFromFile(fp, Raw, BitsStored, numberBytes, length );
+ // to avoid major troubles when BitsStored == 8 && BitsAllocated==16 !
+ int dummy;
+ if (BitsStored == 8 && BitsAllocated==16)
+ dummy = 16;
+ else
+ dummy = BitsStored;
+ JPEGInfo->DecompressFromFile(fp, Raw, dummy, numberBytes, length );
return true;
}
}
}
/**
- * \brief Swap the bytes, according to \ref SwapCode.
+ * \brief Swap the bytes, according to SwapCode.
*/
void PixelReadConvert::ConvertSwapZone()
{
{
// pmask : to mask the 'unused bits' (may contain overlays)
uint16_t pmask = 0xffff;
- pmask = pmask >> ( BitsAllocated - BitsStored );
+
+ // It's up to the user to decide if he wants to ignore overlays (if any),
+ // not to gdcm, without asking.
+ // default is NOT TO LOAD, in order not to confuse ITK users (and others!).
+
+ if ( !FH->GetKeepOverlays() ) // mask spurious bits ! (overlay are NOT loaded!)
+ {
+ pmask = pmask >> ( BitsAllocated - BitsStored );
+ }
+ // else : it's up to the user to manage the 'pixels + overlays' he just loaded!
uint16_t *deb = (uint16_t*)Raw;
if ( !PixelSign ) // Pixels are unsigned
{
for(int i = 0; i<l; i++)
- {
+ {
*deb = (*deb >> (BitsStored - HighBitPosition - 1)) & pmask;
deb++;
}
}
else // Pixels are signed
{
+ // Hope there is never ACR-NEMA-like overlays within signed pixels (?!?)
+
// smask : to check the 'sign' when BitsStored != BitsAllocated
uint16_t smask = 0x0001;
smask = smask << ( 16 - (BitsAllocated - BitsStored + 1) );
// nmask : to propagate sign bit on negative values
int16_t nmask = (int16_t)0x8000;
nmask = nmask >> ( BitsAllocated - BitsStored - 1 );
-
+
for(int i = 0; i<l; i++)
{
*deb = *deb >> (BitsStored - HighBitPosition - 1);
// except for the few patches of color on the image.
// On such images, RLE achieves a compression ratio that is much better
// than the compression ratio on an equivalent RGB image.
-
+
gdcmWarningMacro("--> ConvertYcBcRPlanesToRGBPixels");
-
+
uint8_t *localRaw = Raw;
uint8_t *copyRaw = new uint8_t[ RawSize ];
memmove( copyRaw, localRaw, RawSize );
// ftp://medical.nema.org/medical/dicom/final/sup61_ft.pdf
// and be *very* affraid
//
-
+
/// \todo : find an example to see how 3rd dim and 4th dim work together
int l = XSize * YSize * TSize;
int nbFrames = ZSize;
int bitsAllocated = BitsAllocated;
// Number of "Bits Allocated" is fixed to 16 when it's 12, since
// in this case we will expand the image to 16 bits (see
- // \ref ReadAndDecompress12BitsTo16Bits() )
+ // ReadAndDecompress12BitsTo16Bits() )
if ( BitsAllocated == 12 )
{
bitsAllocated = 16;
else
{
RGBSize = RawSize;
-
}
RawSize += RawSize%2;
RGBSize += RGBSize%2;
CommandManager::ExecuteCommand(FH,CMD_ENDPROGRESS);
}
-
//-----------------------------------------------------------------------------
} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff