void HDF5IO::saveStdVector(const std::string& GroupName, const std::string& Name,
const std::vector<std::complex<double> >& V)
{
try{
H5::CompType ComplexDataType = openCompType("complex");
hsize_t Dim[1] = {hsize_t(V.size())};
H5::DataSpace dataspace(1,Dim);
H5::Group FG = getGroup( GroupName.c_str() );
try{
H5::Exception::dontPrint();
H5::DataSet dataset = FG.openDataSet(Name.c_str());
dataset.write(V.data(), ComplexDataType, dataspace);
} catch( const H5::GroupIException not_found_error ){
H5::DataSet dataset = FG.createDataSet(Name.c_str(), ComplexDataType,
dataspace);
dataset.write(V.data(), ComplexDataType);
} catch( const H5::FileIException error){
error.printError();
} catch( const H5::DataSetIException error){
error.printError();
}
FG.close();
} catch( const H5::Exception err ){
err.printError();
RUNTIME_ERROR("HDF5IO::saveComplexStdVector. ");
}
}
void HDF5IO::saveMatrix(const std::string& GroupName, const std::string& Name,
const ComplexMatrixType& M)
{
try{
H5::CompType ComplexDataType = this->openCompType("complex");
hsize_t Dims[2] = {hsize_t(M.rows()),hsize_t(M.cols())};
H5::DataSpace dataspace(2,Dims);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet dset = FG.openDataSet(Name.c_str());
// dset.extend( Dims );not working
dset.write(M.data(), ComplexDataType);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet dset = FG.createDataSet(Name.c_str(), ComplexDataType, dataspace);
dset.write(M.data(), ComplexDataType);
} catch ( const H5::DataSetIException error ){
error.printError();
RUNTIME_ERROR("HDF5IO::saveComplexMatrix at ");
}
FG.close();
} catch( const H5::Exception error ){
error.printError();
RUNTIME_ERROR("HDF5IO::saveComplexMatrix at ");
}
}
void HDF5IO::saveNumber(const std::string& GroupName, const std::string& Name,
unsigned long x)
{
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet dataset = FG.openDataSet( Name.c_str() );
dataset.write(&x, H5::PredType::NATIVE_ULONG);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet dataset = FG.createDataSet( Name.c_str(), H5::PredType::NATIVE_ULONG, H5::DataSpace());
dataset.write(&x, H5::PredType::NATIVE_ULONG);
}
FG.close();
}
void addrow( H5::DataSet& ds, const std::vector<double>& rowtowrite )
{
//Get the space (since it may have grown in length since last time of course )
H5::DataSpace origspace = ds.getSpace();
//get the rank, even though I know it is 2
int rank = origspace.getSimpleExtentNdims();
//Get the actual dimensions of the ranks.
hsize_t dims[rank];
int ndims = origspace.getSimpleExtentDims( dims, NULL);
//Want to ADD a row, so need to offset at row = nrows, and col = 0;
hsize_t offset[rank] = { dims[0], 0 };
hsize_t dims_toadd[rank] = { 1, rowtowrite.size() }; //will write 1 row, ncols columns.
//Compute "new" size (extended by 1 row).
hsize_t size[rank] = { dims[0]+dims_toadd[0], rowtowrite.size() };
//Do the extension.
ds.extend( size );
//Get the new (extended) space, and select the hyperslab to write the row to.
origspace = ds.getSpace();
origspace.selectHyperslab( H5S_SELECT_SET, dims_toadd, offset );
//Make the "memory" data space?
H5::DataSpace toaddspace(rank, dims_toadd);
ds.write( rowtowrite.data(), H5::PredType::NATIVE_DOUBLE, toaddspace, origspace );
//Can close toaddspace/origspace with no effect.
//Can also close/open data set at the beginning of each time with no effect.
}
void hdfutil::WriteString(const H5::CommonFG& group, const std::string & dsname, const std::string & str) {
hsize_t dims[] = {1};
H5::DataSpace dataspace(1, dims); // 1 string
H5::StrType strtype (0, str.size()); // string length
H5::DataSet dset = group.createDataSet(dsname, strtype, dataspace, CreatePropList());
dset.write(&str[0], strtype);
}
void writeArray(H5::Group &group, const std::string &name,
const std::string &value) {
StrType dataType(0, value.length() + 1);
DataSpace dataSpace = getDataSpace(1);
H5::DataSet data = group.createDataSet(name, dataType, dataSpace);
data.write(value, dataType);
}
bool CompartmentReportHDF5::writeCompartments( const uint32_t gid,
const uint16_ts& counts )
{
lunchbox::ScopedWrite mutex( detail::_hdf5Lock );
try
{
const size_t compCount = std::accumulate( counts.begin(),
counts.end(), 0 );
LBASSERT( !counts.empty( ));
LBASSERTINFO( compCount > 0, gid );
H5::DataSet dataset = _createDataset( gid, compCount );
const size_t sections = counts.size();
LBASSERT( sections > 0 );
dataset.openAttribute( 1 ).write( H5::PredType::NATIVE_INT, §ions );
// dataset.openAttribute( 2 ).write( H5::PredType::NATIVE_INT, &somas );
// dataset.openAttribute( 3 ).write( H5::PredType::NATIVE_INT, &axons );
// dataset.openAttribute( 4 ).write( H5::PredType::NATIVE_INT, &basals );
// dataset.openAttribute( 5 ).write( H5::PredType::NATIVE_INT, &apics );
boost::scoped_array< float > mapping( new float[compCount] );
size_t i = 0;
for( size_t j = 0; j < counts.size(); ++j )
for( size_t k = 0; k < counts[j]; ++k )
mapping[i++] = j;
dataset.write( mapping.get(), H5::PredType::NATIVE_FLOAT );
return true;
}
CATCH_HDF5ERRORS
return false;
}
/* only for Eigen3 matrix/vector */
void HDF5IO::saveVector(const std::string& GroupName,
const std::string& Name, const RealVectorType& V)
{
hsize_t Dim[1] = {hsize_t(V.size())};
H5::DataSpace dspace(1,Dim);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
DataSet.write(V.data(),H5::PredType::NATIVE_DOUBLE, dspace);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet DataSet = FG.createDataSet(Name.c_str(),
H5::PredType::NATIVE_DOUBLE,dspace);
DataSet.write(V.data(),H5::PredType::NATIVE_DOUBLE);
}
FG.close();
}
void HDF5IO::saveNumber(const std::string& GroupName, const std::string& Name,
ComplexType C)
{
H5::CompType ComplexDataType = openCompType("complex");
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet dataset = FG.openDataSet(Name.c_str());
RealType RealImag[2] = {real(C),imag(C)};
dataset.write(RealImag, ComplexDataType);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet dataset = FG.createDataSet(Name.c_str(), ComplexDataType, H5::DataSpace());
RealType RealImag[2] = {real(C),imag(C)};
dataset.write(RealImag, ComplexDataType);
}
FG.close();
}
void HDF5IO::saveMatrix(const std::string& GroupName, const std::string& Name,
const RealMatrixType& M)
{
try{
hsize_t Dims[2] = {hsize_t(M.rows()),hsize_t(M.cols())};
H5::DataSpace dataspace(2,Dims);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
DataSet.write(M.data(),H5::PredType::NATIVE_DOUBLE,dataspace);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet DataSet = FG.createDataSet(Name.c_str(),H5::PredType::NATIVE_DOUBLE,dataspace);
DataSet.write(M.data(),H5::PredType::NATIVE_DOUBLE);
}
FG.close();
} catch( const H5::Exception err ){
RUNTIME_ERROR("HDF5IO::saveRealMatrix");
}
}
void HDF5IO::saveStdVector(const std::string& GroupName, const std::string& Name,
const std::vector<double>& V)
{
try{
hsize_t Dim[1] = {hsize_t(V.size())};
H5::DataSpace dataspace(1,Dim);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet dataset = FG.openDataSet(Name.c_str());
dataset.write(V.data(),H5::PredType::NATIVE_DOUBLE, dataspace);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet dataset = FG.createDataSet(Name.c_str(),
H5::PredType::NATIVE_DOUBLE,dataspace);
dataset.write(V.data(),H5::PredType::NATIVE_DOUBLE);
}
FG.close();
} catch( const H5::Exception err ){
RUNTIME_ERROR("HDF5IO::saveRealStdVector");
}
}
void HDF5IO::saveVector(const std::string& GroupName,
const std::string& Name, const ComplexVectorType& V)
{
try{
H5::CompType ComplexDataType = this->openCompType("complex");
hsize_t Dim[1] = {hsize_t(V.size())};
H5::DataSpace dspace(1,Dim);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
DataSet.write(V.data(), ComplexDataType, dspace);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet DataSet = FG.createDataSet(Name.c_str(), ComplexDataType,
dspace);
DataSet.write(V.data(), ComplexDataType);
}
FG.close();
} catch ( const H5::DataSetIException error ){
error.printError();
RUNTIME_ERROR("HDF5IO::saveComplexVector at ");
}
}
void TImgWriteBuffer::write(const std::string& fname, const std::string& group, const std::string& img) {
H5::H5File* h5file = H5Utils::openFile(fname);
H5::Group* h5group = H5Utils::openGroup(h5file, group);
// Dataset properties: optimized for reading/writing entire buffer at once
int rank = 3;
hsize_t dim[3] = {length_, rect_.N_bins[0], rect_.N_bins[1]};
hsize_t chunk_dim[3] = {length_, rect_.N_bins[0], rect_.N_bins[1]};
if(length_ > 1000) {
float div = ceil((float)length_ / 1000.);
chunk_dim[0] = (int)ceil(length_ / div);
std::cerr << "! Changing chunk length to " << chunk_dim[0] << " stars." << std::endl;
}
H5::DataSpace dspace(rank, &(dim[0]));
H5::DSetCreatPropList plist;
plist.setDeflate(9); // gzip compression level
plist.setChunk(rank, &(chunk_dim[0]));
float fillvalue = 0;
plist.setFillValue(H5::PredType::NATIVE_FLOAT, &fillvalue);
H5::DataSet* dataset = new H5::DataSet(h5group->createDataSet(img, H5::PredType::NATIVE_FLOAT, dspace, plist));
dataset->write(buf, H5::PredType::NATIVE_FLOAT);
/*
* Attributes
*/
hsize_t att_dim = 2;
H5::DataSpace att_dspace(1, &att_dim);
H5::PredType att_dtype = H5::PredType::NATIVE_UINT32;
H5::Attribute att_N = dataset->createAttribute("nPix", att_dtype, att_dspace);
att_N.write(att_dtype, &(rect_.N_bins));
att_dtype = H5::PredType::NATIVE_DOUBLE;
H5::Attribute att_min = dataset->createAttribute("min", att_dtype, att_dspace);
att_min.write(att_dtype, &(rect_.min));
att_dtype = H5::PredType::NATIVE_DOUBLE;
H5::Attribute att_max = dataset->createAttribute("max", att_dtype, att_dspace);
att_max.write(att_dtype, &(rect_.max));
delete dataset;
delete h5group;
delete h5file;
}
void Bundle2::saveGeometry(const boost::filesystem::path& fileName) const {
H5::H5File bundleFile;
bundleFile.openFile(fileName.string(), H5F_ACC_RDWR);
H5::Group rootGroup = bundleFile.openGroup("/");
// If the group "Geometry" exists, delete it!
if(checkGeometry_(bundleFile)) {
rootGroup.unlink("Geometry");
}
// Creating group Geometry
H5::Group geometryGroup = rootGroup.createGroup("Geometry");
// Saving poses
const hsize_t posesChunkDim[] = { 3, 12 };
H5::DSetCreatPropList posesPropList;
posesPropList.setLayout(H5D_CHUNKED);
posesPropList.setChunk(2, posesChunkDim);
posesPropList.setDeflate(9);
const hsize_t posesMaxDim[] = { H5S_UNLIMITED, 12 };
const hsize_t posesCurDim[] = { frames_.size(), 12 };
H5::DataSpace posesDS(2, posesCurDim, posesMaxDim);
H5::DataSet posesDataSet = geometryGroup.createDataSet("Poses", H5::PredType::IEEE_F64LE, posesDS, posesPropList);
double* posesData = (double*)malloc(frames_.size()*12*sizeof(double));
size_t i = 0;
for(deque<Frame*>::const_iterator it = frames_.begin(); it != frames_.end(); it++) {
posesData[i*12] = (*it)->pose()->t().x();
posesData[i*12 + 1] = (*it)->pose()->t().y();
posesData[i*12 + 2] = (*it)->pose()->t().z();
core::Matrix<double> R = (*it)->pose()->R();
posesData[i*12 + 3] = R[0][0];
posesData[i*12 + 4] = R[1][0];
posesData[i*12 + 5] = R[2][0];
posesData[i*12 + 6] = R[0][1];
posesData[i*12 + 7] = R[1][1];
posesData[i*12 + 8] = R[2][1];
posesData[i*12 + 9] = R[0][2];
posesData[i*12 + 10] = R[1][2];
posesData[i*12 + 11] = R[2][2];
++i;
}
posesDataSet.write((const void*)posesData, H5::PredType::NATIVE_DOUBLE, H5::DataSpace::ALL, H5::DataSpace::ALL);
free((void*)posesData);
posesDataSet.close();
posesDS.close();
// Saving points
const hsize_t pointsChunkDim[] = {10, 3};
H5::DSetCreatPropList pointsPropList;
pointsPropList.setLayout(H5D_CHUNKED);
pointsPropList.setChunk(2, pointsChunkDim);
pointsPropList.setDeflate(9);
const hsize_t pointsMaxDim[] = { H5S_UNLIMITED, 3 };
const hsize_t pointsCurDim[] = { tracks_.size(), 3 };
H5::DataSpace pointsDS(2, pointsCurDim, pointsMaxDim);
H5::DataSet pointsDataSet = geometryGroup.createDataSet("Points", H5::PredType::IEEE_F64LE, pointsDS, pointsPropList);
double* pointsData = (double*)malloc(tracks_.size()*3*sizeof(double));
i = 0;
for(deque<Track*>::const_iterator it = tracks_.begin(); it != tracks_.end(); it++) {
pointsData[i*3] = (*it)->point()->coords().x();
pointsData[i*3 + 1] = (*it)->point()->coords().y();
pointsData[i*3 + 2] = (*it)->point()->coords().z();
++i;
}
pointsDataSet.write((const void*)pointsData, H5::PredType::NATIVE_DOUBLE, H5::DataSpace::ALL, H5::DataSpace::ALL);
free((void*)pointsData);
pointsDataSet.close();
pointsDS.close();
// Saving inlier information
const hsize_t inliersChunkDim[] = { 3 };
H5::DSetCreatPropList inliersPropList;
inliersPropList.setLayout(H5D_CHUNKED);
inliersPropList.setChunk(1, inliersChunkDim);
inliersPropList.setDeflate(9);
const hsize_t inliersMaxDim[] = { H5S_UNLIMITED };
const hsize_t inliersCurDim[] = { frames_.size() };
H5::DataSpace inliersDS(1, inliersCurDim, inliersMaxDim);
H5::VarLenType inliersType(&H5::PredType::STD_U8LE);
H5::DataSet inliersDataSet = geometryGroup.createDataSet("Inliers", inliersType, inliersDS, inliersPropList);
i = 0;
for(deque<Frame*>::const_iterator it = frames_.begin(); it != frames_.end(); it++) {
hvl_t inliersLine;
size_t inliersLineSize = 0;
for(size_t j = 0; j < (*it)->size(); ++j) {
View& v = (**it)[j];
for(unsigned int cam = 0; cam < v.numCameras(); ++cam) {
if(v.inCamera(cam)) ++inliersLineSize;
}
}
inliersLine.len = inliersLineSize;
inliersLine.p = malloc(inliersLineSize*sizeof(unsigned char));
size_t k = 0;
for(size_t j = 0; j < (*it)->size(); ++j) {
View& v = (**it)[j];
for(unsigned int cam = 0; cam < v.numCameras(); ++cam) {
if(v.inCamera(cam)) {
((unsigned char*)(inliersLine.p))[k] = v.ray(cam).inlier()?1:0;
++k;
}
}
}
const hsize_t dsOffset[] = { i };
const hsize_t dsCount[] = { 1 };
H5::DataSpace inliersCurDS = inliersDataSet.getSpace();
inliersCurDS.selectHyperslab(H5S_SELECT_SET, dsCount, dsOffset);
const hsize_t memDim[] = { 1 };
H5::DataSpace memDS(1, memDim, memDim);
H5::VarLenType memType(&H5::PredType::NATIVE_UCHAR);
inliersDataSet.write((const void*)&inliersLine, memType, memDS, inliersCurDS);
memType.close();
memDS.close();
inliersCurDS.close();
free(inliersLine.p);
++i;
}
inliersDataSet.close();
inliersType.close();
inliersDS.close();
// Saving curves
if(!curves_.empty()) {
const hsize_t chunkDim[] = { 5 };
H5::DSetCreatPropList propList;
propList.setLayout(H5D_CHUNKED);
propList.setChunk(1, chunkDim);
propList.setDeflate(9);
H5::VarLenType curveDatasetType(&H5::PredType::STD_U64LE);
hsize_t curvesDim[] = { curves_.size() };
hsize_t curvesMaxDim[] = { H5S_UNLIMITED };
H5::DataSpace curvesDataspace(1, curvesDim, curvesMaxDim);
H5::DataSet curvesDataset = geometryGroup.createDataSet("Curves", curveDatasetType, curvesDataspace, propList);
for(size_t i = 0; i < curves_.size(); ++i) {
hvl_t curveLine;
curveLine.len = curves_[i].size();
curveLine.p = malloc(curves_[i].size()*sizeof(size_t));
for(size_t j = 0; j < curves_[i].size(); ++j) ((size_t*)(curveLine.p))[j] = curves_[i].track(j);
const hsize_t dsOffset[] = { i };
const hsize_t dsCount[] = { 1 };
H5::DataSpace curDS = curvesDataset.getSpace();
curDS.selectHyperslab(H5S_SELECT_SET, dsCount, dsOffset);
const hsize_t memDim[] = { 1 };
H5::DataSpace memDS(1, memDim, memDim);
H5::VarLenType memType(&H5::PredType::NATIVE_HSIZE);
curvesDataset.write((const void*)&curveLine, memType, memDS, curDS);
memType.close();
memDS.close();
curDS.close();
free(curveLine.p);
}
curvesDataset.close();
curvesDataspace.close();
curveDatasetType.close();
propList.close();
}
geometryGroup.close();
rootGroup.close();
bundleFile.close();
}
int main( int argCount, char *argVec[] )
{
//declare *default* input file, output file, and length of radial profiles
std::string inFile;
std::string outFile;
const int radialProfileLength = 101;
//options for command line input are defined here
po::options_description optDesc("Allowed options");
optDesc.add_options()
("help","produce help message")
("in",po::value<std::string>(&inFile)->default_value("analytic.yaml"), "input file name")
("out",po::value<std::string>(&outFile)->default_value("gtcInputEq.h5"), "output file name")
;
po::variables_map varMap;
po::store(po::parse_command_line(argCount, argVec, optDesc), varMap);
po::notify(varMap);
if (varMap.count("help")) {
std::cout << optDesc << "\n";
return 1;
}
//declare YAML nodes to work with input file
YAML::Node magEq;
YAML::Node oneDim;
YAML::Node twoDim;
//declare variables to hold and manipulate intermediate data
int i; //loop index
double psi[radialProfileLength] = {0.0};
double dat[radialProfileLength] = {0.0};
//declare vars to manipulate HDF5 output file
H5::H5File outfile( outFile, H5F_ACC_TRUNC );
hsize_t dim[1] = { (unsigned int)radialProfileLength };
H5::DataSpace datspace1D( 1, dim );
H5::IntType dattype( H5::PredType::NATIVE_DOUBLE );
H5::DataSet datset;
//read in the YAML eq file
magEq = YAML::LoadFile( inFile );
//generate radial coords
for ( i=0; i<radialProfileLength; i++ )
psi[i] = i/(radialProfileLength - 1.0);
//do some parsing
//first check for 1D and 2D data in the eq file
//if the exist, generate profiles from polynomial coefficients
if(magEq["1D profiles"]){
oneDim = magEq["1D profiles"];
for(YAML::const_iterator iter=oneDim.begin(); iter!=oneDim.end(); ++iter){
for( i=0; i<radialProfileLength; i++)
dat[i] = iter->second[0].as<double>()
+ iter->second[1].as<double>()*psi[i]
+ iter->second[2].as<double>()*psi[i]*psi[i];
datset = outfile.createDataSet( iter->first.as<std::string>(), dattype, datspace1D );
datset.write( dat, H5::PredType::NATIVE_DOUBLE );
}
}
if(magEq["2d profiles"]){
twoDim = magEq["2D profiles"];
// do some more parsing if we need this part...
}
return 0;
}
bool saveStackHDF5( const char* fileName, const My4DImage& img, Codec_Mapping* mapping )
{
try
{
#ifdef USE_HDF5
H5::Exception::dontPrint();
H5::H5File file( fileName, H5F_ACC_TRUNC );
H5::Group* group = new H5::Group( file.createGroup( "/Channels" ) );
Image4DProxy<My4DImage> proxy( const_cast<My4DImage*>( &img ) );
long scaledHeight = nearestPowerOfEight( proxy.sy );
long scaledWidth = nearestPowerOfEight( proxy.sx );
// Initialize the upper and lower bounds
long pad_right = ( scaledWidth - proxy.sx ) ;
long pad_bottom = ( scaledHeight - proxy.sy );
hsize_t dims[1] = { 1 };
H5::DataSpace attr_ds = H5::DataSpace( 1, dims );
H5::Attribute attr = group->createAttribute( "width", H5::PredType::STD_I64LE, attr_ds );
attr.write( H5::PredType::NATIVE_INT, &( proxy.sx ) );
attr = group->createAttribute( "height", H5::PredType::STD_I64LE, attr_ds );
attr.write( H5::PredType::NATIVE_INT, &( proxy.sy ) );
attr = group->createAttribute( "frames", H5::PredType::STD_I64LE, attr_ds );
attr.write( H5::PredType::NATIVE_INT, &( proxy.sz ) );
attr = group->createAttribute( "pad_right", H5::PredType::STD_I64LE, attr_ds );
attr.write( H5::PredType::NATIVE_INT, &( pad_right ) );
attr = group->createAttribute( "pad_bottom", H5::PredType::STD_I64LE, attr_ds );
attr.write( H5::PredType::NATIVE_INT, &( pad_bottom ) );
Codec_Mapping* imap = mapping;
if ( !mapping )
{
imap = new Codec_Mapping();
generate_codec_mapping( *imap, proxy.sc );
}
for ( int c = 0; c < proxy.sc; ++c )
{
double default_irange = 1.0; // assumes data range is 0-255.0
if ( proxy.su > 1 )
{
default_irange = 1.0 / 16.0; // 0-4096, like our microscope images
}
std::vector<double> imin( proxy.sc, 0.0 );
std::vector<double> irange2( proxy.sc, default_irange );
// rescale if converting from 16 bit to 8 bit
if ( proxy.su > 1 )
{
if ( img.p_vmin && img.p_vmax )
proxy.set_minmax( img.p_vmin, img.p_vmax );
if ( proxy.has_minmax() )
{
imin[c] = proxy.vmin[c];
irange2[c] = 255.0 / ( proxy.vmax[c] - proxy.vmin[c] );
}
}
FFMpegEncoder encoder( NULL, scaledWidth, scaledHeight,
( *imap )[c].first, ( *imap )[c].second );
// If the image needs padding, fill the expanded border regions with black
for ( int z = 0; z < proxy.sz; ++z )
{
for ( int y = 0; y < scaledHeight; ++y )
{
for ( int x = 0; x < scaledWidth; ++x )
{
// If inside the area with valid data
if ( x < proxy.sx && y < proxy.sy )
{
int ic = c;
double val = proxy.value_at( x, y, z, ic );
val = ( val - imin[ic] ) * irange2[ic]; // rescale to range 0-255
for ( int cc = 0; cc < 3; ++cc )
encoder.setPixelIntensity( x, y, cc, ( int )val );
}
else
for ( int cc = 0; cc < 3; ++cc )
encoder.setPixelIntensity( x, y, cc, 0 );
}
}
encoder.write_frame();
}
for ( int rem = encoder.encoded_frames(); rem < proxy.sz; rem++ )
encoder.encode();
encoder.close();
hsize_t dims[1];
dims[0] = encoder.buffer_size();
H5::DataSpace dataspace( 1, dims );
std: stringstream name;
name << "Channel_" << c;
H5::DataSet dataset = group->createDataSet( name.str(), H5::PredType::NATIVE_UINT8, dataspace );
dataset.write( encoder.buffer(), H5::PredType::NATIVE_UINT8 );
dataset.close();
std::cout << "Encoded channel is " << encoder.buffer_size() << " bytes." << std::endl;
// Uncomment this if you want to dump the individual movies to a temp file
}
#endif
if ( !mapping )
delete imap;
file.close();
return true;
}
catch ( ... ) {}
return false;
}
bool TStellarData::save(const std::string& fname, const std::string& group, const std::string &dset, int compression) {
if((compression < 0) || (compression > 9)) {
std::cerr << "! Invalid gzip compression level: " << compression << std::endl;
return false;
}
hsize_t nstars = star.size();
if(nstars == 0) {
std::cerr << "! No stars to write." << std::endl;
return false;
}
H5::Exception::dontPrint();
H5::H5File *file = H5Utils::openFile(fname);
if(file == NULL) { return false; }
H5::Group *gp = H5Utils::openGroup(file, group);
if(gp == NULL) {
delete file;
return false;
}
/*
* Photometry
*/
// Datatype
hsize_t nbands = NBANDS;
H5::ArrayType f4arr(H5::PredType::NATIVE_FLOAT, 1, &nbands);
H5::ArrayType u4arr(H5::PredType::NATIVE_FLOAT, 1, &nbands);
H5::CompType dtype(sizeof(TFileData));
dtype.insertMember("obj_id", HOFFSET(TFileData, obj_id), H5::PredType::NATIVE_UINT64);
dtype.insertMember("l", HOFFSET(TFileData, l), H5::PredType::NATIVE_DOUBLE);
dtype.insertMember("b", HOFFSET(TFileData, b), H5::PredType::NATIVE_DOUBLE);
dtype.insertMember("mag", HOFFSET(TFileData, mag), f4arr);
dtype.insertMember("err", HOFFSET(TFileData, err), f4arr);
dtype.insertMember("maglimit", HOFFSET(TFileData, maglimit), f4arr);
dtype.insertMember("nDet", HOFFSET(TFileData, N_det), u4arr);
dtype.insertMember("EBV", HOFFSET(TFileData, EBV), H5::PredType::NATIVE_FLOAT);
// Dataspace
hsize_t dim = nstars;
H5::DataSpace dspace(1, &dim);
// Property List
H5::DSetCreatPropList plist;
plist.setChunk(1, &nstars);
plist.setDeflate(compression);
// Dataset
H5::DataSet dataset = gp->createDataSet(dset, dtype, dspace, plist);
// Write dataset
TFileData* data = new TFileData[nstars];
for(size_t i=0; i<nstars; i++) {
data[i].obj_id = star[i].obj_id;
data[i].l = star[i].l;
data[i].b = star[i].b;
for(size_t k=0; k<NBANDS; k++) {
data[i].mag[k] = star[i].m[k];
data[i].err[k] = star[i].err[k];
data[i].maglimit[k] = star[i].maglimit[k];
}
data[i].EBV = star[i].EBV;
}
dataset.write(data, dtype);
/*
* Attributes
*/
dim = 1;
H5::DataSpace att_dspace(1, &dim);
H5::PredType att_dtype = H5::PredType::NATIVE_UINT64;
H5::Attribute att_healpix_index = dataset.createAttribute("healpix_index", att_dtype, att_dspace);
att_healpix_index.write(att_dtype, &healpix_index);
att_dtype = H5::PredType::NATIVE_UINT32;
H5::Attribute att_nside = dataset.createAttribute("nside", att_dtype, att_dspace);
att_nside.write(att_dtype, &nside);
att_dtype = H5::PredType::NATIVE_UCHAR;
H5::Attribute att_nested = dataset.createAttribute("nested", att_dtype, att_dspace);
att_nested.write(att_dtype, &nested);
att_dtype = H5::PredType::NATIVE_DOUBLE;
H5::Attribute att_l = dataset.createAttribute("l", att_dtype, att_dspace);
att_l.write(att_dtype, &l);
att_dtype = H5::PredType::NATIVE_DOUBLE;
H5::Attribute att_b = dataset.createAttribute("b", att_dtype, att_dspace);
att_b.write(att_dtype, &b);
att_dtype = H5::PredType::NATIVE_DOUBLE;
H5::Attribute att_EBV = dataset.createAttribute("EBV", att_dtype, att_dspace);
att_EBV.write(att_dtype, &EBV);
file->close();
delete[] data;
delete gp;
delete file;
return true;
}
bool save_mat_image(cv::Mat& img, TRect& rect, std::string fname, std::string group_name,
std::string dset_name, std::string dim1, std::string dim2, int compression) {
assert((img.dims == 2) && (img.rows == rect.N_bins[0]) && (img.cols == rect.N_bins[1]));
if((compression<0) || (compression > 9)) {
std::cerr << "! Invalid gzip compression level: " << compression << std::endl;
return false;
}
H5::Exception::dontPrint();
H5::H5File *file = H5Utils::openFile(fname);
if(file == NULL) { return false; }
H5::Group *group = H5Utils::openGroup(file, group_name);
if(group == NULL) {
delete file;
return false;
}
/*
* Image Data
*/
// Creation property list
H5::DSetCreatPropList plist;
int rank = 2;
hsize_t dim[2] = {rect.N_bins[0], rect.N_bins[1]};
plist.setDeflate(compression); // gzip compression level
float fillvalue = 0;
plist.setFillValue(H5::PredType::NATIVE_FLOAT, &fillvalue);
plist.setChunk(rank, &(dim[0]));
H5::DataSpace dspace(rank, &(dim[0]));
H5::DataSet* dataset;
try {
dataset = new H5::DataSet(group->createDataSet(dset_name, H5::PredType::NATIVE_FLOAT, dspace, plist));
} catch(H5::FileIException create_dset_err) {
std::cerr << "Unable to create dataset '" << dset_name << "'." << std::endl;
delete group;
delete file;
return false;
}
float *buf = new float[rect.N_bins[0]*rect.N_bins[1]];
for(size_t j=0; j<rect.N_bins[0]; j++) {
for(size_t k=0; k<rect.N_bins[1]; k++) {
buf[rect.N_bins[1]*j + k] = img.at<double>(j,k);
/*float tmp = img.at<double>(j,k);
if(tmp > 0.) {
std::cerr << j << ", " << k << " --> " << j + rect.N_bins[0]*k << " --> " << tmp << std::endl;
}*/
}
}
dataset->write(buf, H5::PredType::NATIVE_FLOAT);
/*
* Attributes
*/
hsize_t att_dim = 2;
H5::DataSpace att_dspace(1, &att_dim);
H5::PredType att_dtype = H5::PredType::NATIVE_UINT32;
H5::Attribute att_N = dataset->createAttribute("N_pix", att_dtype, att_dspace);
att_N.write(att_dtype, &(rect.N_bins));
att_dtype = H5::PredType::NATIVE_DOUBLE;
H5::Attribute att_min = dataset->createAttribute("min", att_dtype, att_dspace);
att_min.write(att_dtype, &(rect.min));
att_dtype = H5::PredType::NATIVE_DOUBLE;
H5::Attribute att_max = dataset->createAttribute("max", att_dtype, att_dspace);
att_max.write(att_dtype, &(rect.max));
att_dim = 1;
H5::StrType vls_type(0, H5T_VARIABLE);
H5::DataSpace att_space_str(H5S_SCALAR);
H5::Attribute att_name_1 = dataset->createAttribute("dim_name_1", vls_type, att_space_str);
att_name_1.write(vls_type, dim1);
H5::Attribute att_name_2 = dataset->createAttribute("dim_name_2", vls_type, att_space_str);
att_name_2.write(vls_type, dim2);
file->close();
delete[] buf;
delete dataset;
delete group;
delete file;
return true;
}
void Bundle2::initGeometryStream_() {
// Creating group Geometry
H5::Group geometryGroup = streamFile_->createGroup("/Geometry");
// Saving poses
const hsize_t posesChunkDim[] = { 3, 12 };
H5::DSetCreatPropList posesPropList;
posesPropList.setLayout(H5D_CHUNKED);
posesPropList.setChunk(2, posesChunkDim);
posesPropList.setDeflate(9);
const hsize_t posesMaxDim[] = { H5S_UNLIMITED, 12 };
const hsize_t posesCurDim[] = { frames_.size(), 12 };
H5::DataSpace posesDS(2, posesCurDim, posesMaxDim);
H5::DataSet posesDataSet = geometryGroup.createDataSet("Poses", H5::PredType::IEEE_F64LE, posesDS, posesPropList);
double* posesData = (double*)malloc(frames_.size()*12*sizeof(double));
size_t i = 0;
for(deque<Frame*>::const_iterator it = frames_.begin(); it != frames_.end(); it++) {
posesData[i*12] = (*it)->pose()->t().x();
posesData[i*12 + 1] = (*it)->pose()->t().y();
posesData[i*12 + 2] = (*it)->pose()->t().z();
core::Matrix<double> R = (*it)->pose()->R();
posesData[i*12 + 3] = R[0][0];
posesData[i*12 + 4] = R[1][0];
posesData[i*12 + 5] = R[2][0];
posesData[i*12 + 6] = R[0][1];
posesData[i*12 + 7] = R[1][1];
posesData[i*12 + 8] = R[2][1];
posesData[i*12 + 9] = R[0][2];
posesData[i*12 + 10] = R[1][2];
posesData[i*12 + 11] = R[2][2];
++i;
}
posesDataSet.write((const void*)posesData, H5::PredType::NATIVE_DOUBLE, H5::DataSpace::ALL, H5::DataSpace::ALL);
free((void*)posesData);
posesDataSet.close();
posesDS.close();
// Creating points dataset
const hsize_t pointsChunkDim[] = {10, 3};
H5::DSetCreatPropList pointsPropList;
pointsPropList.setLayout(H5D_CHUNKED);
pointsPropList.setChunk(2, pointsChunkDim);
pointsPropList.setDeflate(9);
const hsize_t pointsMaxDim[] = { H5S_UNLIMITED, 3 };
const hsize_t pointsCurDim[] = { 0, 3 };
H5::DataSpace pointsDS(2, pointsCurDim, pointsMaxDim);
H5::DataSet pointsDataSet = geometryGroup.createDataSet("Points", H5::PredType::IEEE_F64LE, pointsDS, pointsPropList);
pointsDataSet.close();
pointsDS.close();
// Creating inliers dataset
const hsize_t inliersChunkDim[] = { 3 };
H5::DSetCreatPropList inliersPropList;
inliersPropList.setLayout(H5D_CHUNKED);
inliersPropList.setChunk(1, inliersChunkDim);
inliersPropList.setDeflate(9);
const hsize_t inliersMaxDim[] = { H5S_UNLIMITED };
const hsize_t inliersCurDim[] = { frames_.size() };
H5::DataSpace inliersDS(1, inliersCurDim, inliersMaxDim);
H5::VarLenType inliersType(&H5::PredType::STD_U8LE);
H5::DataSet inliersDataSet = geometryGroup.createDataSet("Inliers", inliersType, inliersDS, inliersPropList);
inliersDataSet.close();
inliersType.close();
inliersDS.close();
// Creating curve dataset
const hsize_t chunkDim[] = { 5 };
H5::DSetCreatPropList propList;
propList.setLayout(H5D_CHUNKED);
propList.setChunk(1, chunkDim);
propList.setDeflate(9);
H5::VarLenType curveDatasetType(&H5::PredType::STD_U64LE);
hsize_t curvesDim[] = { 0 };
hsize_t curvesMaxDim[] = { H5S_UNLIMITED };
H5::DataSpace curvesDataspace(1, curvesDim, curvesMaxDim);
H5::DataSet curvesDataset = geometryGroup.createDataSet("Curves", curveDatasetType, curvesDataspace, propList);
curvesDataset.close();
curvesDataspace.close();
curveDatasetType.close();
propList.close();
geometryGroup.close();
}
void TChainWriteBuffer::write(const std::string& fname, const std::string& group, const std::string& chain, const std::string& meta) {
H5::H5File* h5file = H5Utils::openFile(fname);
H5::Group* h5group = H5Utils::openGroup(h5file, group);
// Dataset properties: optimized for reading/writing entire buffer at once
int rank = 3;
hsize_t dim[3] = {length_, nSamples_+2, nDim_};
H5::DataSpace dspace(rank, &(dim[0]));
H5::DSetCreatPropList plist;
plist.setDeflate(9); // gzip compression level
plist.setChunk(rank, &(dim[0]));
float fillvalue = 0;
plist.setFillValue(H5::PredType::NATIVE_FLOAT, &fillvalue);
H5::DataSet* dataset = NULL;
try {
dataset = new H5::DataSet(h5group->createDataSet(chain, H5::PredType::NATIVE_FLOAT, dspace, plist));
} catch(H5::GroupIException &group_exception) {
std::cerr << "Could not create dataset for chain." << std::endl;
std::cerr << "Dataset '" << group << "/" << chain << "' most likely already exists." << std::endl;
throw;
}
dataset->write(buf, H5::PredType::NATIVE_FLOAT);
if(meta == "") { // Store metadata as attributes
bool *converged = new bool[length_];
float *lnZ = new float[length_];
for(unsigned int i=0; i<length_; i++) {
converged[i] = metadata[i].converged;
lnZ[i] = metadata[i].lnZ;
}
// Allow large attributes to be stored in dense storage, versus compact (which has 64 kB limit)
//if(length_ > 5) {
// hid_t dID = dataset->getCreatePlist().getId();
// herr_t res = H5Pset_attr_phase_change(dID, 0, 0);
// std::cerr << res << std::endl;
// if(res < 0) {
// std::cerr << "Failed to specify dense storage." << std::endl;
// }
//}
H5::DataSpace convSpace(1, &(dim[0]));
H5::Attribute convAtt = dataset->createAttribute("converged", H5::PredType::NATIVE_CHAR, convSpace);
convAtt.write(H5::PredType::NATIVE_CHAR, reinterpret_cast<char*>(converged));
H5::DataSpace lnZSpace(1, &(dim[0]));
H5::Attribute lnZAtt = dataset->createAttribute("ln(Z)", H5::PredType::NATIVE_FLOAT, lnZSpace);
lnZAtt.write(H5::PredType::NATIVE_FLOAT, lnZ);
delete[] converged;
delete[] lnZ;
} else { // Store metadata as separate dataset
H5::CompType metaType(sizeof(TChainMetadata));
metaType.insertMember("converged", HOFFSET(TChainMetadata, converged), H5::PredType::NATIVE_CHAR);
metaType.insertMember("ln(Z)", HOFFSET(TChainMetadata, lnZ), H5::PredType::NATIVE_FLOAT);
rank = 1;
H5::DataSpace metaSpace(rank, &(dim[0]));
H5::DSetCreatPropList metaProp;
TChainMetadata emptyMetadata = {0, 0};
metaProp.setFillValue(metaType, &emptyMetadata);
metaProp.setDeflate(9);
metaProp.setChunk(rank, &(dim[0]));
H5::DataSet* metaDataset = new H5::DataSet(h5group->createDataSet(meta, metaType, metaSpace, metaProp));
metaDataset->write(metadata.data(), metaType);
delete metaDataset;
metaDataset = NULL;
}
delete dataset;
delete h5group;
delete h5file;
//std::cerr << "Cleaned up." << std::endl;
}
void WriteTable(void* data){
//write data and close data set
dSet_.write(data, dType_, dSpace_);
dSet_.close();
}
