v8::Local<v8::Object> DOMTypedArray<WTFTypedArray, V8TypedArray>::wrap(v8::Isolate* isolate, v8::Local<v8::Object> creationContext)
{
// It's possible that no one except for the new wrapper owns this object at
// this moment, so we have to prevent GC to collect this object until the
// object gets associated with the wrapper.
RefPtr<ThisType> protect(this);
ASSERT(!DOMDataStore::containsWrapper(this, isolate));
const WrapperTypeInfo* wrapperTypeInfo = this->wrapperTypeInfo();
RefPtr<DOMArrayBufferBase> buffer = this->bufferBase();
v8::Local<v8::Value> v8Buffer = toV8(buffer.get(), creationContext, isolate);
if (v8Buffer.IsEmpty())
return v8::Local<v8::Object>();
ASSERT(isShared() == v8Buffer->IsSharedArrayBuffer());
v8::Local<v8::Object> wrapper;
if (isShared()) {
wrapper = V8TypedArray::New(v8Buffer.As<v8::SharedArrayBuffer>(), byteOffset(), length());
} else {
wrapper = V8TypedArray::New(v8Buffer.As<v8::ArrayBuffer>(), byteOffset(), length());
}
return associateWithWrapper(isolate, wrapperTypeInfo, wrapper);
}
JSArrayBufferView* DataView::wrap(ExecState* exec, JSGlobalObject* globalObject)
{
#if 0
return JSDataView::create(
exec, globalObject->typedArrayStructure(TypeDataView), buffer(), byteOffset(),
byteLength());
#else
return 0;
#endif
}
static VOID ProcessAddress (ADDRINT name, UINT32 size, ADDRINT ea, UINT32 bitIndex)
{
// Work out the base address of the array being accessed
if (baseAddr == 0)
{
baseAddr = ea - byteOffset(size,bitIndex);
return;
}
tests++;
// Check that the position agrees with what we think it should be.
if (baseAddr+byteOffset(size,bitIndex) != ea)
{
errors++;
out << (const char *)name << ": Bad EA "; printHex(ea);
out << " Expected "; printHex (baseAddr+byteOffset(size,bitIndex));
out << " Bit offset " << bitIndex << " Access size " << size << endl;
}
}
PassRefPtr<DataView> JSDataView::typedImpl()
{
return DataView::create(buffer(), byteOffset(), length());
}
JSArrayBufferView* DataView::wrap(ExecState* exec, JSGlobalObject* globalObject)
{
return JSDataView::create(
exec, globalObject->typedArrayStructure(TypeDataView), possiblySharedBuffer(), byteOffset(),
byteLength());
}
// niftiManager::readVector():reads 1D nifti vector
ValueType niftiManager::readVector(const std::string& vectorFilenameRef, std::vector<float>* vectorPointer) const
{
std::vector<float>& vector = *vectorPointer;
std::string vectorFilename( vectorFilenameRef );
std::string vectorFilenameZipped( vectorFilenameRef );
std::string extension;
std::string zipExtension( boost::filesystem::path(vectorFilename).extension().string() );
if ( zipExtension == ".gz" )
{
vectorFilename.resize(vectorFilename.size()-3);
// Variables for calling system commands
std::string sysCommand( "gzip -dcf " + vectorFilenameZipped + " > " + vectorFilename );
int success(system(sysCommand.c_str()));
extension = ( boost::filesystem::path(vectorFilename).extension().string() );
}
else if ( zipExtension == getFileExtension( ETFull ) || zipExtension == getFileExtension( ETCompact ) )
{
extension = zipExtension;
}
else
{
std::cerr << "File \"" << vectorFilenameZipped << "\" has no recognized extension (\"" << zipExtension << "\") stopping." << std::endl;
return VTError;
}
ValueType vectorValueType;
if( extension == getFileExtension( ETFull ) )
{
nifti_image* niftiImage = NULL;
boost::mutex& ioMutex(boost::detail::thread::singleton<boost::mutex>::instance()) ;
ioMutex.lock();
{
niftiImage = nifti_image_read(vectorFilename.c_str(), 1);
}
ioMutex.unlock();
if( !niftiImage )
{
std::cerr<< "ERROR @ niftiManager::readVector(): there was an error calling nifti_image_read() on vector "<< vectorFilename <<std::endl;
return VTError;
}
if( niftiImage->ndim != 1 )
{
std::cerr << "ERROR @ niftiManager::readVector(): nifti file has more than 1 dimension (" << niftiImage->ndim <<"): "<< niftiImage->nx <<" "<< niftiImage->ny <<" "<< niftiImage->nz <<" "<< niftiImage->nt <<" "<< niftiImage->nu <<" "<< niftiImage->nv <<std::endl;
return VTError;
}
const size_t repType( niftiImage->datatype );
const size_t repByteSize( niftiImage->nbyper );
const size_t dataSize( niftiImage->nvox );
if( repType == DT_FLOAT32 )
{
vectorValueType = VTFloat32;
}
else if ( repType == DT_UINT8 )
{
vectorValueType = VTUINT8;
}
else
{
std::cerr<< "ERROR @ niftiManager::readVector(): vector representation type not recognized (not FLOAT32 nor UNIT8)" << std::endl;
return VTError;
}
const size_t dimx( niftiImage->nx );
if( dimx != dataSize )
{
std::cerr<< "ERROR @ niftiManager::readVector(): vector dimension does not match data size" << std::endl;
return VTError;
}
vector.clear();
vector.resize(dataSize,0);
void* niftiData(niftiImage->data);
for (int i=0 ; i<dataSize ; ++i) {
size_t byteOffset( i * repByteSize );
if( byteOffset >= dataSize )
{
std::cerr<< "ERROR @ niftiManager::readVector():: pointer offset was too high when loading nifti data" << std::endl;
return VTError;
}
void* dataPos = static_cast<unsigned char*>(niftiData) + byteOffset;
if (repType == DT_UINT8)
{
unsigned char datapoint = *(static_cast<unsigned char*>(dataPos));
vector[i] = (float)datapoint;
}
else if (repType == DT_FLOAT32)
{
float datapoint = *(static_cast<float*>(dataPos));
vector[i] = datapoint;
}
else
{
std::cerr<< "ERROR @ niftiManager::readVector(): vector representation type not recognized (not FLOAT32 nor UNIT8)" << std::endl;
return VTError;
}
}
// clean up
nifti_image_free( niftiImage );
}
else if ( extension == getFileExtension( ETCompact ) )
{
std::ifstream inFile;
inFile.open( vectorFilename.c_str(), std::ios::in | std::ios::binary | std::ios::ate );
if( !inFile.is_open() )
{
std::stringstream errormessage;
errormessage << "ERROR @ niftiManager::readVector(): there was an error opening the input image file "<< vectorFilename <<std::endl;
throw std::runtime_error( errormessage.str() );
}
size_t dataSize = inFile.tellg();
void* data = malloc( dataSize );
inFile.seekg( 0, std::ios::beg );
boost::mutex& ioMutex(boost::detail::thread::singleton<boost::mutex>::instance()) ;
ioMutex.lock();
{
inFile.read( static_cast<char*>(data), dataSize );
}
ioMutex.unlock();
inFile.close();
const size_t headerSize = UINT32_SIZE + UINT32_SIZE;
void* dataPos = static_cast<unsigned char*>(data);
const size_t repType = *(static_cast<uint32_t*>(dataPos));
dataPos = static_cast<unsigned char*>(data) + UINT32_SIZE;
const size_t dimx = *(static_cast<uint32_t*>(dataPos));
size_t repByteSize( 0 );
if( repType == (FLOAT_SIZE * CHAR_BIT) )
{
vectorValueType = VTFloat32;
repByteSize = FLOAT_SIZE;
}
else if ( repType == (UINT8_SIZE * CHAR_BIT) )
{
vectorValueType = VTUINT8;
repByteSize = UINT8_SIZE;
}
else
{
std::cerr<< "ERROR @ niftiManager::readVector(): vector representation type not recognized: " << repType << " (not FLOAT32 nor UNIT8)" << std::endl;
return VTError;
}
const size_t dataSizeTest = headerSize + ( dimx * repByteSize );
if( dataSize != dataSizeTest )
{
std::stringstream errormessage;
errormessage << "ERROR @ niftiManager::readVector(): file data as read: "<< dataSize << " is different as file data according to header: " << dataSizeTest <<std::endl;
errormessage<<" headerSize: "<< headerSize <<" dimx: "<< dimx <<" repSize: "<<repByteSize << std::endl;
throw std::runtime_error( errormessage.str() );
}
vector.clear();
vector.resize(dimx,0);
for( size_t i = 0; i < dimx; ++i )
{
size_t byteOffset( headerSize + ( i * repByteSize ) );
if( byteOffset >= dataSize )
{
std::cerr<< "ERROR @ niftiManager::readVector():: pointer offset was too high when loading nifti data" << std::endl;
return VTError;
}
dataPos = static_cast<unsigned char*>(data) + byteOffset;
if ( vectorValueType == VTUINT8 )
{
uint8_t datapoint = *(static_cast<uint8_t*>(dataPos));
vector[i] = (float)datapoint;
}
else if ( vectorValueType == VTFloat32 )
{
float datapoint = *(static_cast<float*>(dataPos));
vector[i] = datapoint;
}
else
{
std::cerr<< "ERROR @ niftiManager::readVector(): vector representation type not recognized (not FLOAT32 nor UNIT8)" << std::endl;
return VTError;
}
}
// clean up
free( data );
}
else
{
std::cerr << "File \"" << vectorFilename << "\" has no recognized extension (\"" << extension << "\") stopping." << std::endl;
return VTError;
}
if ( zipExtension == ".gz" )
{
// Variables for calling system commands
std::string sysCommand( "rm -f " + vectorFilename );
int success(system(sysCommand.c_str()));
}
return vectorValueType;
}// end niftiManager::readVector() ----------------------------------------------------------------
// "writeImage()": writes a 3D image
void niftiManager::writeImage( const std::string& imageFilename, const ValueType dataValueType, const std::vector<std::vector<std::vector<float> > >& image, bool doZip ) const
{
if (image.empty())
{
std::cerr<< "ERROR @ niftiManager::writeImage(): image matrix is empty, image has not been written" <<std::endl;
return;
}
const size_t dimx = image.size();
const size_t dimy = image[0].size();
const size_t dimz = image[0][0].size();
nifti_1_header imageHeader;
imageHeader.sizeof_hdr = 0;
if(m_header.sizeof_hdr != 0)
{
imageHeader = m_header;
}
generateHeader( dimx, dimy, dimz, dataValueType, &imageHeader);
nifti_image* niftiImage = nifti_convert_nhdr2nim( imageHeader, NULL);
const size_t repByteSize( niftiImage->nbyper );
const size_t dataSize( niftiImage->nvox );
const size_t repType( niftiImage->datatype );
if ( dataSize != (dimx*dimy*dimz) )
{
throw std::runtime_error( "niftiManager::writeImage(): image header nvox and matrix size do not match" );
}
if ( repType != imageHeader.datatype )
{
throw std::runtime_error( "niftiManager::writeImage(): created header datatype and input argument dont match" );
}
if(niftiImage->data != NULL)
{
throw std::runtime_error( "niftiManager::writeVector(): nifti_convert_nhdr2nim had already allocated memory" );
}
niftiImage->data = malloc (dataSize * repByteSize);
for (int i=0 ; i<dimz ; ++i)
{
for (int j=0 ; j<dimy ; ++j)
{
for (int k=0 ; k<dimx ; ++k)
{
size_t voxOffset( (i*dimy*dimx) + (j*dimx) + k );
if( voxOffset >= dataSize )
{
throw std::runtime_error( "ERROR @ niftiManager::writeImage():: pointer offset was too high when loading nifti data");
}
size_t byteOffset( voxOffset * repByteSize );
void* dataPos = static_cast<unsigned char*>(niftiImage->data) + byteOffset;
if (repType == DT_UINT8)
{
unsigned char datapoint = (unsigned char)image[k][j][i];
*(static_cast<unsigned char*>(dataPos)) = datapoint;
}
else if (repType == DT_FLOAT32)
{
float datapoint = image[k][j][i];
*(static_cast<float*>(dataPos)) = datapoint;
}
else
{
throw std::runtime_error("ERROR @ niftiManager::writeImage(): image representation type not recognized (neither UINT8 nor FLOAT32)");
}
}
}
}
if( nifti_set_filenames(niftiImage, imageFilename.c_str(), 0, 1) )
{
std::stringstream errormessage;
errormessage << "ERROR @ niftiManager::writeImage(): there was an error calling nifti_set_filenames() on output image file "<< imageFilename <<std::endl;
throw std::runtime_error( errormessage.str() );
}
boost::mutex& ioMutex(boost::detail::thread::singleton<boost::mutex>::instance()) ;
ioMutex.lock();
{
nifti_image_write( niftiImage );
}
ioMutex.unlock();
// clean up
nifti_image_free( niftiImage );
if (doZip)
{ // zip file
// Variables for calling system commands
std::string gzipString("gzip -f ");
std::string sysCommand(gzipString + imageFilename);
int success(system(sysCommand.c_str()));
}
return;
}// end niftiManager::writeImage() -----------------------------------------------------------------
// "readImage()": reads a 3D image
ValueType niftiManager::readImage( const std::string& imageFilenameRef, std::vector<std::vector<std::vector<float> > >* imagePointer ) const
{
std::vector<std::vector<std::vector<float> > >& image( *imagePointer );
std::string imageFilename( imageFilenameRef );
std::string imageFilenameZipped( imageFilenameRef );
std::string extension( boost::filesystem::path(imageFilename).extension().string() );
if ( extension == ".gz" )
{
imageFilename.resize(imageFilename.size()-3);
// Variables for calling system commands
std::string sysCommand( "gzip -dcf " + imageFilenameZipped + " > " + imageFilename );
int success(system(sysCommand.c_str()));
}
else if ( extension == getFileExtension( ETFull ) )
{
}
else
{
std::cerr << "File \"" << imageFilenameZipped << "\" has no recognized extension (\"" << extension << "\") stopping." << std::endl;
return VTError;
}
nifti_image* niftiImage = NULL;
boost::mutex& ioMutex(boost::detail::thread::singleton<boost::mutex>::instance()) ;
ioMutex.lock();
{
niftiImage = nifti_image_read(imageFilename.c_str(), 1);
}
ioMutex.unlock();
if( !niftiImage )
{
std::cerr<< "ERROR @ niftiManager::readImage(): there was an error calling nifti_image_read() on image file "<< imageFilename <<std::endl;
return VTError;
}
if( niftiImage->ndim > 3 )
{
std::cerr << "ERROR @ niftiManager::readImage(): nifti file has more than 3 dimensions (" << niftiImage->ndim <<"): "<< niftiImage->nx <<" "<< niftiImage->ny <<" "<< niftiImage->nz <<" "<< niftiImage->nt <<" "<< niftiImage->nu <<" "<< niftiImage->nv <<std::endl;
return VTError;
}
const size_t repType( niftiImage->datatype );
const size_t repByteSize( niftiImage->nbyper );
const size_t dataSize( niftiImage->nvox );
ValueType imageValueType;
if(repType == DT_UINT8 )
{
imageValueType = VTUINT8;
}
else if(repType == DT_FLOAT32 )
{
imageValueType = VTFloat32;
}
else
{
std::cerr<< "ERROR @ niftiManager::readImage(): image representation type not recognized (neither UINT8 nor FLOAT32)" << std::endl;
return VTError;
}
const size_t dimx( niftiImage->nx );
const size_t dimy( niftiImage->ny );
const size_t dimz( niftiImage->nz);
image.clear();
{
std::vector<float> zvector(dimz,0);
std::vector<std::vector<float> >yzmatrix(dimy,zvector);
image.resize(dimx,yzmatrix);
}
void* niftiData(niftiImage->data);
for (int i=0 ; i<dimz ; ++i)
{
for (int j=0 ; j<dimy ; ++j)
{
for (int k=0 ; k<dimx ; ++k)
{
size_t voxOffset( (i*dimy*dimx) + (j*dimx) + k );
if( voxOffset >= dataSize )
{
std::cerr<< "ERROR @ niftiManager::readImage():: pointer offset was too high when loading nifti data" << std::endl;
return VTError;
}
size_t byteOffset( voxOffset * repByteSize );
void* dataPos = static_cast<unsigned char*>(niftiData) + byteOffset;
if (repType == DT_UINT8)
{
unsigned char datapoint = *(static_cast<unsigned char*>(dataPos));
image[k][j][i] = (float)datapoint;
}
else if (repType == DT_FLOAT32)
{
float datapoint = *(static_cast<float*>(dataPos));
image[k][j][i] = datapoint;
}
else
{
std::cerr<< "ERROR @ niftiManager::readImage(): image representation type not recognized (neither UINT8 nor FLOAT32)" << std::endl;
return VTError;
}
}
}
}
// clean up
nifti_image_free( niftiImage );
if ( extension == ".gz" )
{
// Variables for calling system commands
std::string sysCommand( "rm -f " + imageFilename );
int success(system(sysCommand.c_str()));
}
return imageValueType;
}// end niftiManager::readImage() -----------------------------------------------------------------