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gdcmPixmapReader.cxx
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gdcmPixmapReader.cxx
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/*=========================================================================
Program: GDCM (Grassroots DICOM). A DICOM library
Copyright (c) 2006-2011 Mathieu Malaterre
All rights reserved.
See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notice for more information.
=========================================================================*/
#include "gdcmPixmapReader.h"
#include "gdcmExplicitDataElement.h"
#include "gdcmImplicitDataElement.h"
#include "gdcmValue.h"
#include "gdcmFileMetaInformation.h"
#include "gdcmElement.h"
#include "gdcmPhotometricInterpretation.h"
#include "gdcmSegmentedPaletteColorLookupTable.h"
#include "gdcmTransferSyntax.h"
#include "gdcmLookupTable.h"
#include "gdcmAttribute.h"
#include "gdcmIconImage.h"
#include "gdcmPrivateTag.h"
#include "gdcmJPEGCodec.h"
#include "gdcmImageHelper.h"
namespace gdcm
{
PixmapReader::PixmapReader():PixelData(new Pixmap)
{
}
PixmapReader::~PixmapReader()
{
}
const Pixmap& PixmapReader::GetPixmap() const
{
return *PixelData;
}
Pixmap& PixmapReader::GetPixmap()
{
return *PixelData;
}
//void PixmapReader::SetPixmap(Pixmap const &img)
//{
// PixelData = img;
//}
bool PixmapReader::Read()
{
if( !Reader::Read() )
{
// cemra_bug/IM-0001-0066.dcm
// will return from the parser with an error
// but a partial Pixel Data can be seen
return false;
}
const FileMetaInformation &header = F->GetHeader();
const DataSet &ds = F->GetDataSet();
const TransferSyntax &ts = header.GetDataSetTransferSyntax();
// Need to set the type of image we are dealing with:
PixelData->SetTransferSyntax( ts );
bool res = false;
/* Does it really make sense to check for Media Storage SOP Class UID?
* I need then to check consistency with 0008 0016 Instance SOP Class UID
* ... I don't think there is an end.
* I'd rather go the old way check a bunch of tags (From Image Plane
* Module).
*/
MediaStorage ms = header.GetMediaStorage();
bool isImage = MediaStorage::IsImage( ms );
if( isImage )
{
// I cannot leave this here, since ELSCINT1 / LOSSLESS RICE declares CT Image Storage,
// when in fact this is a private Media Storage (no Pixel Data element)
//assert( ds.FindDataElement( Tag(0x7fe0,0x0010 ) ) );
assert( ts != TransferSyntax::TS_END && ms != MediaStorage::MS_END );
// Good it's the easy case. It's declared as an Image:
//PixelData->SetCompressionFromTransferSyntax( ts );
res = ReadImage(ms);
}
//else if( ms == MediaStorage::MRSpectroscopyStorage )
// {
// res = ReadImage(ms);
// }
else
{
MediaStorage ms2 = ds.GetMediaStorage();
//assert( !ds.FindDataElement( Tag(0x7fe0,0x0010 ) ) );
if( ms == MediaStorage::MediaStorageDirectoryStorage && ms2 == MediaStorage::MS_END )
{
gdcmDebugMacro( "DICOM file is not an Image file but a : " <<
MediaStorage::GetMSString(ms) << " SOP Class UID" );
res = false;
}
else if( ms == ms2 && ms != MediaStorage::MS_END )
{
gdcmDebugMacro( "DICOM file is not an Image file but a : " <<
MediaStorage::GetMSString(ms) << " SOP Class UID" );
res = false;
}
else
{
if( ms2 != MediaStorage::MS_END )
{
bool isImage2 = MediaStorage::IsImage( ms2 );
if( isImage2 )
{
gdcmDebugMacro( "After all it might be a DICOM file "
"(Mallinckrodt-like)" );
//PixelData->SetCompressionFromTransferSyntax( ts );
//PixelData->SetCompressionType( Compression::RAW );
res = ReadImage(ms2);
}
else
{
ms2.SetFromFile( *F );
if( MediaStorage::IsImage( ms2 ) )
{
res = ReadImage(ms2);
}
else
{
gdcmDebugMacro( "DICOM file is not an Image file but a : " <<
MediaStorage::GetMSString(ms2) << " SOP Class UID" );
res = false;
}
}
}
else if( ts == TransferSyntax::ImplicitVRBigEndianACRNEMA || header.IsEmpty() )
{
// Those transfer syntax have a high probability of being ACR NEMA
gdcmDebugMacro( "Looks like an ACR-NEMA file" );
// Hopefully all ACR-NEMA are RAW:
//PixelData->SetCompressionType( Compression::RAW );
res = ReadACRNEMAImage();
}
else // there is a Unknown Media Storage Syntax
{
assert( ts != TransferSyntax::TS_END && ms == MediaStorage::MS_END );
// god damit I don't know what to do...
gdcmWarningMacro( "Attempting to read this file as a DICOM file"
"\nDesperate attempt" );
MediaStorage ms3;
ms3.SetFromFile( GetFile() );
if( ms3 != MediaStorage::MS_END )
{
res = ReadImage(ms3);
}
else
{
// Giving up
res = false;
}
}
}
}
//if(res) PixelData->Print( std::cout );
return res;
}
// PICKER-16-MONO2-Nested_icon.dcm
void DoIconImage(const DataSet& rootds, Pixmap& image)
{
const Tag ticonimage(0x0088,0x0200);
IconImage &pixeldata = image.GetIconImage();
if( rootds.FindDataElement( ticonimage ) )
{
const DataElement &iconimagesq = rootds.GetDataElement( ticonimage );
//const SequenceOfItems* sq = iconimagesq.GetSequenceOfItems();
SmartPointer<SequenceOfItems> sq = iconimagesq.GetValueAsSQ();
// Is SQ empty ?
if( !sq ) return;
SequenceOfItems::ConstIterator it = sq->Begin();
const DataSet &ds = it->GetNestedDataSet();
// D 0028|0011 [US] [Columns] [512]
{
//const DataElement& de = ds.GetDataElement( Tag(0x0028, 0x0011) );
Attribute<0x0028,0x0011> at = { 0 };
at.SetFromDataSet( ds );
pixeldata.SetDimension(0, at.GetValue() );
}
// D 0028|0010 [US] [Rows] [512]
{
//const DataElement& de = ds.GetDataElement( Tag(0x0028, 0x0010) );
Attribute<0x0028,0x0010> at = { 0 };
at.SetFromDataSet( ds );
pixeldata.SetDimension(1, at.GetValue() );
}
PixelFormat pf;
// D 0028|0100 [US] [Bits Allocated] [16]
{
//const DataElement& de = ds.GetDataElement( Tag(0x0028, 0x0100) );
Attribute<0x0028,0x0100> at = { 0 };
at.SetFromDataSet( ds );
pf.SetBitsAllocated( at.GetValue() );
}
// D 0028|0101 [US] [Bits Stored] [12]
{
//const DataElement& de = ds.GetDataElement( Tag(0x0028, 0x0101) );
Attribute<0x0028,0x0101> at = { 0 };
at.SetFromDataSet( ds );
pf.SetBitsStored( at.GetValue() );
}
// D 0028|0102 [US] [High Bit] [11]
{
//const DataElement& de = ds.GetDataElement( Tag(0x0028, 0x0102) );
Attribute<0x0028,0x0102> at = { 0 };
at.SetFromDataSet( ds );
pf.SetHighBit( at.GetValue() );
}
// D 0028|0103 [US] [Pixel Representation] [0]
{
//const DataElement& de = ds.GetDataElement( Tag(0x0028, 0x0103) );
Attribute<0x0028,0x0103> at = { 0 };
at.SetFromDataSet( ds );
pf.SetPixelRepresentation( at.GetValue() );
}
// (0028,0002) US 1 # 2, 1 SamplesPerPixel
{
//if( ds.FindDataElement( Tag(0x0028, 0x0002) ) )
{
//const DataElement& de = ds.GetDataElement( Tag(0x0028, 0x0002) );
Attribute<0x0028,0x0002> at = { 1 };
at.SetFromDataSet( ds );
pf.SetSamplesPerPixel( at.GetValue() );
}
// else pf will default to 1...
}
pixeldata.SetPixelFormat( pf );
// D 0028|0004 [CS] [Photometric Interpretation] [MONOCHROME2 ]
const Tag tphotometricinterpretation(0x0028, 0x0004);
PhotometricInterpretation pi = PhotometricInterpretation::MONOCHROME2;
if( ds.FindDataElement( tphotometricinterpretation ) )
{
const ByteValue *photometricinterpretation = ds.GetDataElement( tphotometricinterpretation ).GetByteValue();
std::string photometricinterpretation_str(
photometricinterpretation->GetPointer(),
photometricinterpretation->GetLength() );
pi = PhotometricInterpretation::GetPIType(
photometricinterpretation_str.c_str());
}
assert( pi != PhotometricInterpretation::UNKNOWN);
pixeldata.SetPhotometricInterpretation( pi );
//
if ( pi == PhotometricInterpretation::PALETTE_COLOR )
{
SmartPointer<LookupTable> lut = new LookupTable;
const Tag testseglut(0x0028, (0x1221 + 0));
if( ds.FindDataElement( testseglut ) )
{
assert(0 && "Please report this image");
lut = new SegmentedPaletteColorLookupTable;
}
//SmartPointer<SegmentedPaletteColorLookupTable> lut = new SegmentedPaletteColorLookupTable;
lut->Allocate( pf.GetBitsAllocated() );
// for each red, green, blue:
for(int i=0; i<3; ++i)
{
// (0028,1101) US 0\0\16
// (0028,1102) US 0\0\16
// (0028,1103) US 0\0\16
const Tag tdescriptor(0x0028, (uint16_t)(0x1101 + i));
//const Tag tdescriptor(0x0028, 0x3002);
Element<VR::US,VM::VM3> el_us3;
// Now pass the byte array to a DICOMizer:
el_us3.SetFromDataElement( ds[tdescriptor] ); //.GetValue() );
lut->InitializeLUT( LookupTable::LookupTableType(i),
el_us3[0], el_us3[1], el_us3[2] );
// (0028,1201) OW
// (0028,1202) OW
// (0028,1203) OW
const Tag tlut(0x0028, (uint16_t)(0x1201 + i));
//const Tag tlut(0x0028, 0x3006);
// Segmented LUT
// (0028,1221) OW
// (0028,1222) OW
// (0028,1223) OW
const Tag seglut(0x0028, (uint16_t)(0x1221 + i));
if( ds.FindDataElement( tlut ) )
{
const ByteValue *lut_raw = ds.GetDataElement( tlut ).GetByteValue();
assert( lut_raw );
// LookupTableType::RED == 0
lut->SetLUT( LookupTable::LookupTableType(i),
(unsigned char*)lut_raw->GetPointer(), lut_raw->GetLength() );
//assert( pf.GetBitsAllocated() == el_us3.GetValue(2) );
unsigned long check =
(el_us3.GetValue(0) ? el_us3.GetValue(0) : 65536)
* el_us3.GetValue(2) / 8;
assert( check == lut_raw->GetLength() || 2 * check == lut_raw->GetLength()
|| check + 1 == lut_raw->GetLength() ); (void)check;
}
else if( ds.FindDataElement( seglut ) )
{
const ByteValue *lut_raw = ds.GetDataElement( seglut ).GetByteValue();
assert( lut_raw );
lut->SetLUT( LookupTable::LookupTableType(i),
(unsigned char*)lut_raw->GetPointer(), lut_raw->GetLength() );
//assert( pf.GetBitsAllocated() == el_us3.GetValue(2) );
//unsigned long check =
// (el_us3.GetValue(0) ? el_us3.GetValue(0) : 65536)
// * el_us3.GetValue(2) / 8;
//assert( check == lut_raw->GetLength() ); (void)check;
}
else
{
gdcmWarningMacro( "Icon Sequence is incomplete. Giving up" );
pixeldata.Clear();
return;
}
}
pixeldata.SetLUT(*lut);
}
const Tag tpixeldata = Tag(0x7fe0, 0x0010);
if( !ds.FindDataElement( tpixeldata ) )
{
gdcmWarningMacro( "Icon Sequence is incomplete. Giving up" );
pixeldata.Clear();
return;
}
const DataElement& de = ds.GetDataElement( tpixeldata );
pixeldata.SetDataElement( de );
// Pass TransferSyntax:
// Warning This is legal for the Icon to be uncompress in a compressed image
// We need to set the appropriate TS here:
const ByteValue *bv = de.GetByteValue();
if( bv )
pixeldata.SetTransferSyntax( TransferSyntax::ImplicitVRLittleEndian );
else
pixeldata.SetTransferSyntax( image.GetTransferSyntax() );
}
}
// GE_DLX-8-MONO2-Multiframe.dcm
void DoCurves(const DataSet& ds, Pixmap& pixeldata)
{
unsigned int numcurves;
if( (numcurves = Curve::GetNumberOfCurves( ds )) )
{
pixeldata.SetNumberOfCurves( numcurves );
Tag curve(0x5000,0x0000);
bool finished = false;
unsigned int idxcurves = 0;
while( !finished )
{
const DataElement &de = ds.FindNextDataElement( curve );
// Are we done:
if( de.GetTag().GetGroup() > 0x50FF ) // last possible curve curve
{
finished = true;
}
else if( de.GetTag().IsPrivate() ) // GEMS owns some 0x5003
{
// Move on to the next public one:
curve.SetGroup( (uint16_t)(de.GetTag().GetGroup() + 1) );
curve.SetElement( 0 );
}
else
{
// Yay! this is an curve element
Curve &ov = pixeldata.GetCurve(idxcurves);
++idxcurves; // move on to the next one
curve = de.GetTag();
uint16_t currentcurve = curve.GetGroup();
assert( !(currentcurve % 2) ); // 0x6001 is not an curve...
// Now loop on all element from this current group:
DataElement de2 = de;
while( de2.GetTag().GetGroup() == currentcurve )
{
ov.Update(de2);
curve.SetElement( (uint16_t)(de2.GetTag().GetElement() + 1) );
de2 = ds.FindNextDataElement( curve );
// Next element:
//curve.SetElement( curve.GetElement() + 1 );
}
// If we exit the loop we have pass the current curve and potentially point to the next one:
//curve.SetElement( curve.GetElement() + 1 );
//ov.Print( std::cout );
}
}
//std::cout << "Num of curves: " << numcurves << std::endl;
assert( idxcurves == numcurves );
}
}
unsigned int GetNumberOfOverlaysInternal(DataSet const & ds, std::vector<uint16_t> & overlaylist)
{
Tag overlay(0x6000,0x0000); // First possible overlay
bool finished = false;
unsigned int numoverlays = 0;
while( !finished )
{
const DataElement &de = ds.FindNextDataElement( overlay );
if( de.GetTag().GetGroup() > 0x60FF ) // last possible curve
{
finished = true;
}
else if( de.GetTag().IsPrivate() )
{
// Move on to the next public one:
overlay.SetGroup( (uint16_t)(de.GetTag().GetGroup() + 1) );
overlay.SetElement( 0 ); // reset just in case...
}
else
{
// Yeah this is a potential overlay element, let's check this is not a broken LEADTOOL image,
// or prova0001.dcm:
// (5000,0000) UL 0 # 4, 1 GenericGroupLength
// (6000,0000) UL 0 # 4, 1 GenericGroupLength
// (6001,0000) UL 28 # 4, 1 PrivateGroupLength
// (6001,0010) LT [PAPYRUS 3.0] # 12, 1 PrivateCreator
// (6001,1001) LT (no value available) # 0, 0 Unknown Tag & Data
/*
* FIXME:
* In order to support : gdcmData/SIEMENS_GBS_III-16-ACR_NEMA_1.acr
* gdcmDataExtra/gdcmSampleData/images_of_interest/XA_GE_JPEG_02_with_Overlays.dcm
* I cannot simply check for overlay_group,3000 this would not work
* I would need a strong euristick
*/
// Store found tag in overlay:
overlay = de.GetTag();
// heuristic based on either the Overlay Data or the Col/Row info
Tag toverlaydata(overlay.GetGroup(),0x3000 );
Tag toverlayrows(overlay.GetGroup(),0x0010 );
Tag toverlaycols(overlay.GetGroup(),0x0011 );
Tag toverlaybitpos(overlay.GetGroup(),0x0102 );
if( ds.FindDataElement( toverlaydata ) )
{
// ok so far so good...
const DataElement& overlaydata = ds.GetDataElement( toverlaydata );
//const DataElement& overlaydata = ds.GetDataElement(Tag(overlay.GetGroup(),0x0010));
if( !overlaydata.IsEmpty() )
{
++numoverlays;
overlaylist.push_back( overlay.GetGroup() );
}
}
else if( ds.FindDataElement( toverlayrows ) && ds.FindDataElement( toverlaycols )
&& ds.FindDataElement( toverlaybitpos ) )
{
// Overlay Pixel are in Unused Pixel
assert( !ds.FindDataElement( toverlaydata ) );
const DataElement& overlayrows = ds.GetDataElement( toverlayrows );
const DataElement& overlaycols = ds.GetDataElement( toverlaycols );
assert( ds.FindDataElement( toverlaybitpos ) );
const DataElement& overlaybitpos = ds.GetDataElement( toverlaybitpos );
if( !overlayrows.IsEmpty() && !overlaycols.IsEmpty() && !overlaybitpos.IsEmpty() )
{
++numoverlays;
overlaylist.push_back( overlay.GetGroup() );
}
}
// Move on to the next possible one:
overlay.SetGroup( (uint16_t)(overlay.GetGroup() + 2) );
// reset to element 0x0 just in case...
overlay.SetElement( 0 );
}
}
// at most one out of two :
assert( numoverlays < 0x00ff / 2 );
// PS 3.3 - 2004:
// C.9.2 Overlay plane module
// Each Overlay Plane is one bit deep. Sixteen separate Overlay Planes may be associated with an
// Image or exist as Standalone Overlays in a Series
assert( numoverlays <= 16 );
assert( numoverlays == overlaylist.size() );
return numoverlays;
}
bool DoOverlays(const DataSet& ds, Pixmap& pixeldata)
{
unsigned int numoverlays;
std::vector<uint16_t> overlaylist;
std::vector<bool> updateoverlayinfo;
if( (numoverlays = GetNumberOfOverlaysInternal( ds, overlaylist )) )
{
updateoverlayinfo.resize(numoverlays, false);
pixeldata.SetNumberOfOverlays( numoverlays );
for( unsigned int idxoverlays = 0; idxoverlays < numoverlays; ++idxoverlays )
{
Overlay &ov = pixeldata.GetOverlay(idxoverlays);
uint16_t currentoverlay = overlaylist[idxoverlays];
Tag overlay(0x6000,0x0000);
overlay.SetGroup( currentoverlay );
const DataElement &de = ds.FindNextDataElement( overlay );
assert( !(currentoverlay % 2) ); // 0x6001 is not an overlay...
// Now loop on all element from this current group:
DataElement de2 = de;
while( de2.GetTag().GetGroup() == currentoverlay )
{
ov.Update(de2);
overlay.SetElement( (uint16_t)(de2.GetTag().GetElement() + 1) );
de2 = ds.FindNextDataElement( overlay );
}
// Let's decode it:
std::ostringstream unpack;
ov.Decompress( unpack );
std::string s = unpack.str();
//size_t l = s.size();
// The following line will fail with images like XA_GE_JPEG_02_with_Overlays.dcm
// since the overlays are stored in the unused bit of the PixelData
if( !ov.IsEmpty() )
{
//assert( unpack.str().size() / 8 == ((ov.GetRows() * ov.GetColumns()) + 7 ) / 8 );
assert( ov.IsInPixelData( ) == false );
}
else
{
gdcmDebugMacro( "This image does not contains Overlay in the 0x60xx tags. "
<< "Instead the overlay is stored in the unused bit of the Pixel Data. "
<< "This is not supported right now"
<< std::endl );
ov.IsInPixelData( true );
// make sure Overlay is valid
if( ov.GetBitsAllocated() != pixeldata.GetPixelFormat().GetBitsAllocated() )
{
gdcmWarningMacro( "Bits Allocated are wrong. Correcting." );
ov.SetBitsAllocated( pixeldata.GetPixelFormat().GetBitsAllocated() );
}
if( !ov.GrabOverlayFromPixelData(ds) )
{
gdcmWarningMacro( "Could not extract Overlay from Pixel Data" );
//throw Exception("TODO: Could not extract Overlay Data");
}
updateoverlayinfo[idxoverlays] = true;
}
}
//std::cout << "Num of Overlays: " << numoverlays << std::endl;
}
// Now is good time to do some cleanup (eg. DX_GE_FALCON_SNOWY-VOI.dcm).
const PixelFormat &pf = pixeldata.GetPixelFormat();
// Yes I am using a call in the for() loop, because I internally modify the
// number of overlays:
for( size_t ov_idx = pixeldata.GetNumberOfOverlays(); ov_idx != 0; --ov_idx )
{
size_t ov = ov_idx - 1;
const Overlay& o = pixeldata.GetOverlay(ov);
if( o.IsInPixelData() )
{
unsigned short obp = o.GetBitPosition();
if( obp < pf.GetBitsStored() )
{
pixeldata.RemoveOverlay( ov );
updateoverlayinfo.erase( updateoverlayinfo.begin() + ov );
gdcmWarningMacro( "Invalid BitPosition: " << obp << " for overlay #" <<
ov << " removing it." );
}
}
}
for( size_t ov = 0;
ov < pixeldata.GetNumberOfOverlays() && updateoverlayinfo[ov] ; ++ov )
{
Overlay& o = pixeldata.GetOverlay(ov);
// We need to update information
if( o.GetBitsAllocated() == 16 )
{
o.SetBitsAllocated( 1 );
o.SetBitPosition( 0 );
}
else
{
gdcmErrorMacro( "Overlay #" << ov << " is not supported" );
return false;
}
}
return true;
}
bool PixmapReader::ReadImage(MediaStorage const &ms)
{
return ReadImageInternal(ms);
}
bool PixmapReader::ReadImageInternal(MediaStorage const &ms, bool handlepixeldata )
{
const DataSet &ds = F->GetDataSet();
std::string conversion;
bool isacrnema = false;
const Tag trecognitioncode(0x0008,0x0010);
if( ds.FindDataElement( trecognitioncode ) && !ds.GetDataElement( trecognitioncode ).IsEmpty() )
{
// PHILIPS_Gyroscan-12-MONO2-Jpeg_Lossless.dcm
// PHILIPS_Gyroscan-12-Jpeg_Extended_Process_2_4.dcm
gdcmDebugMacro( "Mixture of ACR NEMA and DICOM file" );
isacrnema = true;
const char *str = ds.GetDataElement( trecognitioncode ).GetByteValue()->GetPointer();
assert( strncmp( str, "ACR-NEMA", strlen( "ACR-NEMA" ) ) == 0 ||
strncmp( str, "ACRNEMA", strlen( "ACRNEMA" ) ) == 0 );
(void)str;//warning removal
}
std::vector<unsigned int> vdims = ImageHelper::GetDimensionsValue(*F);
unsigned int numberofframes = vdims[2];
// What should I do when numberofframes == 0 ?
if( numberofframes > 1 )
{
PixelData->SetNumberOfDimensions(3);
PixelData->SetDimension(2, numberofframes );
}
else
{
gdcmDebugMacro( "NumberOfFrames was specified with a value of: "
<< numberofframes );
PixelData->SetNumberOfDimensions(2);
}
// 2. What are the col & rows:
PixelData->SetDimension(0, vdims[0] );
PixelData->SetDimension(1, vdims[1] );
// 3. Pixel Format ?
PixelFormat pf;
// D 0028|0002 [US] [Samples per Pixel] [1]
{
Attribute<0x0028,0x0002> at = { 1 }; // By default assume 1 Samples Per Pixel
at.SetFromDataSet( ds );
pf.SetSamplesPerPixel( at.GetValue() );
}
if( ms == MediaStorage::MRSpectroscopyStorage )
{
pf.SetScalarType( PixelFormat::FLOAT32 );
}
else
{
assert( MediaStorage::IsImage( ms ) );
// D 0028|0100 [US] [Bits Allocated] [16]
//pf.SetBitsAllocated(
// ReadUSFromTag( Tag(0x0028, 0x0100), ss, conversion ) );
{
//const DataElement& de = ds.GetDataElement( Tag(0x0028, 0x0100) );
Attribute<0x0028,0x0100> at = { 0 };
at.SetFromDataSet( ds );
pf.SetBitsAllocated( at.GetValue() );
//assert( at.GetValue() == ReadUSFromTag( Tag(0x0028, 0x0100), ss, conversion ) );
}
// D 0028|0101 [US] [Bits Stored] [12]
//pf.SetBitsStored(
// ReadUSFromTag( Tag(0x0028, 0x0101), ss, conversion ) );
{
//const DataElement& de = ds.GetDataElement( Tag(0x0028, 0x0101) );
Attribute<0x0028,0x0101> at = { 0 };
at.SetFromDataSet( ds );
pf.SetBitsStored( at.GetValue() );
//assert( at.GetValue() == ReadUSFromTag( Tag(0x0028, 0x0101), ss, conversion ) );
}
// D 0028|0102 [US] [High Bit] [11]
//pf.SetHighBit(
// ReadUSFromTag( Tag(0x0028, 0x0102), ss, conversion ) );
{
//const DataElement& de = ds.GetDataElement( Tag(0x0028, 0x0102) );
Attribute<0x0028,0x0102> at = { 0 };
at.SetFromDataSet( ds );
pf.SetHighBit( at.GetValue() );
//assert( at.GetValue() == ReadUSFromTag( Tag(0x0028, 0x0102), ss, conversion ) );
}
// D 0028|0103 [US] [Pixel Representation] [0]
//Tag tpixelrep(0x0028, 0x0103);
//if( ds.FindDataElement( tpixelrep ) && !ds.GetDataElement( tpixelrep ).IsEmpty() )
{
//pf.SetPixelRepresentation(
// ReadUSFromTag( Tag(0x0028, 0x0103), ss, conversion ) );
//const DataElement& de = ds.GetDataElement( Tag(0x0028, 0x0103) );
Attribute<0x0028,0x0103> at = { 0 };
at.SetFromDataSet( ds );
pf.SetPixelRepresentation( at.GetValue() );
//assert( at.GetValue() == ReadUSFromTag( Tag(0x0028, 0x0103), ss, conversion ) );
}
// else
// {
// gdcmWarningMacro( "Pixel Representation was not found. Default to Unsigned Pixel Representation" );
// pf.SetPixelRepresentation( 0 );
// }
}
// 5. Photometric Interpretation
// D 0028|0004 [CS] [Photometric Interpretation] [MONOCHROME2 ]
const Tag tphotometricinterpretation(0x0028, 0x0004);
const ByteValue *photometricinterpretation
= ImageHelper::GetPointerFromElement( tphotometricinterpretation, *F );
PhotometricInterpretation pi = PhotometricInterpretation::UNKNOWN;
if( photometricinterpretation )
{
std::string photometricinterpretation_str(
photometricinterpretation->GetPointer(),
photometricinterpretation->GetLength() );
pi = PhotometricInterpretation::GetPIType( photometricinterpretation_str.c_str() );
// http://www.dominator.com/assets/003/5278.pdf
// JPEG 2000 lossless YUV_RCT
if( pi == PhotometricInterpretation::PI_END )
{
gdcmWarningMacro( "Discarding suspicious PhotometricInterpretation found: "
<< photometricinterpretation_str );
}
}
// try again harder:
if( !photometricinterpretation || pi == PhotometricInterpretation::PI_END )
{
if( pf.GetSamplesPerPixel() == 1 )
{
gdcmWarningMacro( "No PhotometricInterpretation found, default to MONOCHROME2" );
pi = PhotometricInterpretation::MONOCHROME2;
}
else if( pf.GetSamplesPerPixel() == 3 )
{
gdcmWarningMacro( "No PhotometricInterpretation found, default to RGB" );
pi = PhotometricInterpretation::RGB;
}
else if( pf.GetSamplesPerPixel() == 4 )
{
gdcmWarningMacro( "No PhotometricInterpretation found, default to ARGB" );
pi = PhotometricInterpretation::ARGB;
}
else
{
gdcmWarningMacro( "Impossible value for Samples Per Pixel: " << pf.GetSamplesPerPixel() );
return false;
}
}
assert( pi != PhotometricInterpretation::PI_END );
if( !pf.GetSamplesPerPixel() || (pi.GetSamplesPerPixel() != pf.GetSamplesPerPixel()) )
{
if( pi != PhotometricInterpretation::UNKNOWN )
{
pf.SetSamplesPerPixel( pi.GetSamplesPerPixel() );
}
else if ( isacrnema )
{
assert ( pf.GetSamplesPerPixel() == 0 );
assert ( pi == PhotometricInterpretation::UNKNOWN );
pf.SetSamplesPerPixel( 1 );
pi = PhotometricInterpretation::MONOCHROME2;
}
else
{
gdcmWarningMacro( "Cannot recognize image type. Does not looks like"
"ACR-NEMA and is missing both Sample Per Pixel AND PhotometricInterpretation."
"Please report" );
return false;
}
}
assert ( pf.GetSamplesPerPixel() != 0 );
// Very important to set the PixelFormat here before PlanarConfiguration
PixelData->SetPixelFormat( pf );
pf = PixelData->GetPixelFormat();
if( !pf.IsValid() )
{
return false;
}
if( pi == PhotometricInterpretation::UNKNOWN ) return false;
PixelData->SetPhotometricInterpretation( pi );
// 4. Planar Configuration
// D 0028|0006 [US] [Planar Configuration] [1]
const Tag planarconfiguration = Tag(0x0028, 0x0006);
// FIXME: Whatif planaconfiguration is send in a grayscale image... it would be empty...
// well hopefully :(
if( ds.FindDataElement( planarconfiguration ) && !ds.GetDataElement( planarconfiguration ).IsEmpty() )
{
const DataElement& de = ds.GetDataElement( planarconfiguration );
Attribute<0x0028,0x0006> at = { 0 };
at.SetFromDataElement( de );
//unsigned int pc = ReadUSFromTag( planarconfiguration, ss, conversion );
unsigned int pc = at.GetValue();
if( pc && PixelData->GetPixelFormat().GetSamplesPerPixel() != 3 )
{
gdcmDebugMacro( "Cannot have PlanarConfiguration=1, when Sample Per Pixel != 3" );
pc = 0;
}
PixelData->SetPlanarConfiguration( pc );
}
// Do the Palette Color:
// 1. Modality LUT Sequence
bool modlut = ds.FindDataElement(Tag(0x0028,0x3000) );
if( modlut )
{
gdcmWarningMacro( "Modality LUT (0028,3000) are not handled. Image will not be displayed properly" );
}
// 2. LUTData (0028,3006)
// technically I do not need to warn about LUTData since either modality lut XOR VOI LUT need to
// be sent to require a LUT Data...
bool lutdata = ds.FindDataElement(Tag(0x0028,0x3006) );
if( lutdata )
{
gdcmWarningMacro( "LUT Data (0028,3006) are not handled. Image will not be displayed properly" );
}
// 3. VOILUTSequence (0028,3010)
bool voilut = ds.FindDataElement(Tag(0x0028,0x3010) );
if( voilut )
{
gdcmWarningMacro( "VOI LUT (0028,3010) are not handled. Image will not be displayed properly" );
}
// (0028,0120) US 32767 # 2, 1 PixelPaddingValue
bool pixelpaddingvalue = ds.FindDataElement(Tag(0x0028,0x0120));
// PS 3.3 - 2008 / C.7.5.1.1.2 Pixel Padding Value and Pixel Padding Range Limit
if(pixelpaddingvalue)
{
// Technically if Pixel Padding Value is 0 on MONOCHROME2 image, then appearance should be fine...
bool vizissue = true;
if( pf.GetPixelRepresentation() == 0 )
{
Element<VR::US,VM::VM1> ppv;
if( !ds.GetDataElement(Tag(0x0028,0x0120) ).IsEmpty() )
{
ppv.SetFromDataElement( ds.GetDataElement(Tag(0x0028,0x0120)) ); //.GetValue() );
if( pi == PhotometricInterpretation::MONOCHROME2 && ppv.GetValue() == 0 )
{
vizissue = false;
}
}
}
else if( pf.GetPixelRepresentation() == 1 )
{
gdcmDebugMacro( "TODO" );
}
// test if there is any viz issue:
if( vizissue )
{
gdcmDebugMacro( "Pixel Padding Value (0028,0120) is not handled. Image will not be displayed properly" );
}
}
// 4. Palette Color Lookup Table Descriptor
if ( pi == PhotometricInterpretation::PALETTE_COLOR )
{
//const DataElement& modlutsq = ds.GetDataElement( Tag(0x0028,0x3000) );
//const SequenceOfItems* sq = modlutsq.GetSequenceOfItems();
//SequenceOfItems::ConstIterator it = sq->Begin();
//const DataSet &ds = it->GetNestedDataSet();
SmartPointer<LookupTable> lut = new LookupTable;
const Tag testseglut(0x0028, (0x1221 + 0));
if( ds.FindDataElement( testseglut ) )
{
lut = new SegmentedPaletteColorLookupTable;
}
//SmartPointer<SegmentedPaletteColorLookupTable> lut = new SegmentedPaletteColorLookupTable;
lut->Allocate( pf.GetBitsAllocated() );
// for each red, green, blue:
for(int i=0; i<3; ++i)
{
// (0028,1101) US 0\0\16
// (0028,1102) US 0\0\16
// (0028,1103) US 0\0\16
const Tag tdescriptor(0x0028, (uint16_t)(0x1101 + i));
//const Tag tdescriptor(0x0028, 0x3002);
Element<VR::US,VM::VM3> el_us3 = {{ 0, 0, 0}};
// Now pass the byte array to a DICOMizer:
el_us3.SetFromDataElement( ds[tdescriptor] ); //.GetValue() );
lut->InitializeLUT( LookupTable::LookupTableType(i),
el_us3[0], el_us3[1], el_us3[2] );
// (0028,1201) OW
// (0028,1202) OW
// (0028,1203) OW
const Tag tlut(0x0028, (uint16_t)(0x1201 + i));
//const Tag tlut(0x0028, 0x3006);
// Segmented LUT
// (0028,1221) OW
// (0028,1222) OW
// (0028,1223) OW
const Tag seglut(0x0028, (uint16_t)(0x1221 + i));
if( ds.FindDataElement( tlut ) )
{
const ByteValue *lut_raw = ds.GetDataElement( tlut ).GetByteValue();
if( lut_raw )
{
// LookupTableType::RED == 0
lut->SetLUT( LookupTable::LookupTableType(i),
(unsigned char*)lut_raw->GetPointer(), lut_raw->GetLength() );
//assert( pf.GetBitsAllocated() == el_us3.GetValue(2) );
}
else
{
lut->Clear();
}
unsigned long check =
(el_us3.GetValue(0) ? el_us3.GetValue(0) : 65536)
* el_us3.GetValue(2) / 8;
assert( !lut->Initialized() || check == lut_raw->GetLength() ); (void)check;
}
else if( ds.FindDataElement( seglut ) )
{
const ByteValue *lut_raw = ds.GetDataElement( seglut ).GetByteValue();
if( lut_raw )
{
lut->SetLUT( LookupTable::LookupTableType(i),
(unsigned char*)lut_raw->GetPointer(), lut_raw->GetLength() );
//assert( pf.GetBitsAllocated() == el_us3.GetValue(2) );
}
else
{
lut->Clear();
}
//unsigned long check =
// (el_us3.GetValue(0) ? el_us3.GetValue(0) : 65536)
// * el_us3.GetValue(2) / 8;
//assert( check == lut_raw->GetLength() ); (void)check;
}
else
{
gdcmAssertAlwaysMacro(0);
}
}
if( ! lut->Initialized() ) return false;
PixelData->SetLUT(*lut);
}
// TODO
//assert( pi.GetSamplesPerPixel() == pf.GetSamplesPerPixel() );
// 5.5 Do IconImage if any
assert( PixelData->GetIconImage().IsEmpty() );
DoIconImage(ds, *PixelData);
// 6. Do the Curves if any
DoCurves(ds, *PixelData);
// 7. Do the Overlays if any
if( !DoOverlays(ds, *PixelData) )
{
return false;
}
// 8. Do the PixelData
if( handlepixeldata )
{
if( ms == MediaStorage::MRSpectroscopyStorage )
{
const Tag spectdata = Tag(0x5600, 0x0020);
if( !ds.FindDataElement( spectdata ) )
{
gdcmWarningMacro( "No Spectroscopy Data Found" );
return false;
}
const DataElement& xde = ds.GetDataElement( spectdata );
//bool need = PixelData->GetTransferSyntax() == TransferSyntax::ImplicitVRBigEndianPrivateGE;
//PixelData->SetNeedByteSwap( need );
PixelData->SetDataElement( xde );
}
else
{
const Tag pixeldata = Tag(0x7fe0, 0x0010);
if( !ds.FindDataElement( pixeldata ) )
{
gdcmWarningMacro( "No Pixel Data Found" );
return false;
}
const DataElement& xde = ds.GetDataElement( pixeldata );
bool need = PixelData->GetTransferSyntax() == TransferSyntax::ImplicitVRBigEndianPrivateGE;
PixelData->SetNeedByteSwap( need );
PixelData->SetDataElement( xde );
// FIXME:
// We should check that when PixelData is RAW that Col * Dim == PixelData->GetLength()
//PixelFormat guesspf = PixelFormat->GuessPixelFormat();
}