bool ossimHdfGridModel::setGridNodes( H5::H5File* h5File,
const std::string& latDataSetName,
const std::string& lonDataSetName,
ossim_uint32 imageRows,
ossim_uint32 imageCols )
{
bool status = false;
if ( h5File )
{
H5::DataSet latDataSet = h5File->openDataSet( latDataSetName );
H5::DataSet lonDataSet = h5File->openDataSet( lonDataSetName );
try
{
status = setGridNodes( &latDataSet, &lonDataSet, imageRows, imageCols );
}
catch ( const ossimException& e )
{
if ( traceDebug() )
{
ossimNotify(ossimNotifyLevel_WARN)
<< "ossimHdfGridModel::setGridNodes caught exception\n"
<< e.what() << std::endl;
}
}
latDataSet.close();
lonDataSet.close();
}
return status;
}
void FeaturePointsRANSAC::loadModel(std::string modelPath)
{
H5::H5File h5Model;
try {
h5Model = H5::H5File(modelPath, H5F_ACC_RDONLY);
}
catch (H5::Exception& e) {
std::string msg( std::string( "Could not open HDF5 file \n" ) + e.getCDetailMsg() );
throw msg;
}
// Load the Shape
H5::Group modelReconstructive = h5Model.openGroup("/shape/ReconstructiveModel/model");
H5::DataSet dsMean = modelReconstructive.openDataSet("./mean");
hsize_t dims[1];
dsMean.getSpace().getSimpleExtentDims(dims, NULL); // dsMean.getSpace() leaks memory... maybe a hdf5 bug, maybe vlenReclaim(...) could be a fix. No idea.
//H5::DataSpace dsp = dsMean.getSpace();
//dsp.close();
std::cout << "Dims: " << dims[0] << std::endl; // TODO: I guess this whole part could be done A LOT better!
float* testData = new float[dims[0]];
dsMean.read(testData, H5::PredType::NATIVE_FLOAT);
this->modelMeanShp.reserve(dims[0]);
for (unsigned int i=0; i < dims[0]; ++i) {
modelMeanShp.push_back(testData[i]);
}
delete[] testData;
testData = NULL;
dsMean.close();
// // Load the Texture
H5::Group modelReconstructiveTex = h5Model.openGroup("/color/ReconstructiveModel/model");
H5::DataSet dsMeanTex = modelReconstructiveTex.openDataSet("./mean");
hsize_t dimsTex[1];
dsMeanTex.getSpace().getSimpleExtentDims(dimsTex, NULL);
std::cout << "Dims: " << dimsTex[0] << std::endl; // TODO: I guess this whole part could be done A LOT better!
float* testDataTex = new float[dimsTex[0]];
dsMeanTex.read(testDataTex, H5::PredType::NATIVE_FLOAT);
this->modelMeanTex.reserve(dimsTex[0]);
for (unsigned int i=0; i < dimsTex[0]; ++i) {
modelMeanTex.push_back(testDataTex[i]);
}
delete[] testDataTex;
testDataTex = NULL;
dsMeanTex.close();
h5Model.close();
}
ossimRefPtr<ossimImageGeometry> ossimH5Reader::getInternalImageGeometry()
{
ossimRefPtr<ossimImageGeometry> geom = new ossimImageGeometry();
if ( m_projection.valid() )
{
// Stored projection, currently shared by all entries.
geom->setProjection( m_projection.get() );
}
else if ( isOpen() )
{
// Find the "Latitude" and "Longitude" datasets if present.
std::string latName;
std::string lonName;
if ( getLatLonDatasetNames( m_h5File, latName, lonName ) )
{
H5::DataSet latDataSet = m_h5File->openDataSet( latName );
H5::DataSet lonDataSet = m_h5File->openDataSet( lonName );
// Get the valid rectangle of the dataset.
ossimIrect validRect = m_entries[m_currentEntry].getValidImageRect();
// Try for a coarse projection first:
ossimRefPtr<ossimProjection> proj =
processCoarseGridProjection( latDataSet,
lonDataSet,
validRect );
if ( proj.valid() == false )
{
ossimIrect rect;
proj = ossim_hdf5::getBilinearProjection( latDataSet, lonDataSet, validRect );
}
if ( proj.valid() )
{
// Store it for next time:
m_projection = proj;
// Set the geometry projection
geom->setProjection( proj.get() );
}
latDataSet.close();
lonDataSet.close();
}
}
return geom;
}
arma::Mat<uint16_t> readLUT(const std::string& path)
{
H5::H5File file (path.c_str(), H5F_ACC_RDONLY);
H5::DataSet ds = file.openDataSet("LUT");
H5::DataSpace filespace = ds.getSpace();
int ndims = filespace.getSimpleExtentNdims();
assert(ndims == 2);
hsize_t dims[2] = {1, 1};
filespace.getSimpleExtentDims(dims);
H5::DataSpace memspace (ndims, dims);
arma::Mat<uint16_t> res (dims[0], dims[1]);
ds.read(res.memptr(), H5::PredType::NATIVE_UINT16, memspace, filespace);
filespace.close();
memspace.close();
ds.close();
file.close();
// NOTE: Armadillo stores data in column-major order, while HDF5 uses
// row-major ordering. Above, we read the data directly from HDF5 into
// the arma matrix, so it was implicitly transposed. The next function
// fixes this problem.
arma::inplace_trans(res);
return res;
}
void pyne::Material::_load_comp_protocol0(H5::H5File * db, std::string datapath, int row)
{
H5::Group matgroup = (*db).openGroup(datapath);
H5::DataSet nucset;
double nucvalue;
hsize_t matG = matgroup.getNumObjs();
// Iterate over datasets in the group.
for (int matg = 0; matg < matG; matg++)
{
std::string nuckey = matgroup.getObjnameByIdx(matg);
nucset = matgroup.openDataSet(nuckey);
nucvalue = h5wrap::get_array_index<double>(&nucset, row);
if (nuckey == "Mass" || nuckey == "MASS" || nuckey == "mass")
mass = nucvalue;
else
comp[pyne::nucname::zzaaam(nuckey)] = nucvalue;
nucset.close();
};
// Set meta data
name = datapath.substr(datapath.rfind("/")+1, datapath.length());
atoms_per_mol = -1.0;
};
bool loadStackHDF5( const char* fileName, Image4DSimple& img )
{
#ifdef USE_HDF5
H5::Exception::dontPrint();
H5::H5File file( fileName, H5F_ACC_RDONLY );
for ( size_t i = 0; i < file.getObjCount(); i++ )
{
H5std_string name = file.getObjnameByIdx( i );
if ( name == "Channels" )
{
H5::Group channels = file.openGroup( name );
// Grab the attributes
H5::Attribute attr = channels.openAttribute( "width" );
H5::DataType type = attr.getDataType();
long width, height;
attr.read( type, &width );
attr.close();
attr = channels.openAttribute( "height" );
attr.read( type, &height );
attr.close();
int num_channels = 0;
// Count the number of channels
for ( size_t obj = 0; obj < channels.getNumObjs(); obj++ )
if ( channels.getObjTypeByIdx( obj ) == H5G_DATASET )
num_channels++;
int channel_idx = 0;
for ( size_t obj = 0; obj < channels.getNumObjs(); obj++ )
{
if ( channels.getObjTypeByIdx( obj ) == H5G_DATASET )
{
H5std_string ds_name = channels.getObjnameByIdx( obj );
H5::DataSet data = channels.openDataSet( ds_name );
uint8_t* buffer = new uint8_t[ data.getStorageSize() ];
data.read( buffer, data.getDataType() );
QByteArray qbarray( ( const char* )buffer, data.getStorageSize() );
data.close();
if ( !loadIndexedStackFFMpeg( &qbarray, img, channel_idx++, num_channels,
width, height ) )
{
v3d_msg( "Error happened in HDF file reading. Stop. \n", false );
return false;
}
delete [] buffer;
}
}
}
}
#endif
return true;
}
bool ossim_hdf5::getDatasetAttributeValue( H5::H5File* file,
const std::string& objectName,
const std::string& key,
std::string& value )
{
static const char MODULE[] = "ossim_hdf5::getDatasetAttributeValue";
bool result = false;
if ( file )
{
try // HDF5 library throws exceptions so wrap with try{}catch...
{
// Open the dataset:
H5::DataSet dataset = file->openDataSet( objectName );
// Lookw for key:
H5::Attribute attr = dataset.openAttribute( key );
std::string name = attr.getName();
H5::DataType type = attr.getDataType();
H5T_class_t typeClass = attr.getTypeClass();
if ( ( name == key ) && ( typeClass == H5T_STRING ) )
{
attr.read( type, value );
result = true;
}
// Cleanup:
attr.close();
dataset.close();
}
catch( const H5::Exception& e )
{
ossimNotify(ossimNotifyLevel_WARN)
<< MODULE << " WARNING: Caught exception!\n"
<< e.getDetailMsg() << std::endl;
}
catch( ... )
{
ossimNotify(ossimNotifyLevel_WARN)
<< MODULE << " WARNING: Caught unknown exception!" << std::endl;
}
}
return result;
} // End: ossim_hdf5::getDatasetAttributeValue
void ossimH5Reader::addImageDatasetEntries(const std::vector<std::string>& names)
{
if ( m_h5File && names.size() )
{
std::vector<std::string>::const_iterator i = names.begin();
while ( i != names.end() )
{
if ( ossim_hdf5::isExcludedDataset( *i ) == false )
{
H5::DataSet dataset = m_h5File->openDataSet( *i );
// Get the class of the datatype that is used by the dataset.
H5T_class_t type_class = dataset.getTypeClass();
if ( ( type_class == H5T_INTEGER ) || ( type_class == H5T_FLOAT ) )
{
// Get the extents:
std::vector<ossim_uint32> extents;
ossim_hdf5::getExtents( &dataset, extents );
if ( extents.size() >= 2 )
{
if ( ( extents[0] > 1 ) && ( extents[1] > 1 ) )
{
ossimH5ImageDataset hids;
hids.initialize( dataset, *i );
m_entries.push_back( hids );
}
}
}
dataset.close();
}
++i;
}
}
#if 0 /* Please leave for debug. (drb) */
std::vector<ossimH5ImageDataset>::const_iterator i = m_entries.begin();
while ( i != m_entries.end() )
{
std::cout << (*i) << endl;
++i;
}
#endif
} // End: ossimH5Reader::addImageDatasetEntries
bool ossim_hdf5::isLoadableAsImage( H5::H5File* file, const std::string& datasetName )
{
bool result = false;
// std::cout << "isLoadable entered..." << std::endl;
if ( file && datasetName.size() )
{
if ( isExcludedDataset( datasetName ) == false )
{
H5::DataSet dataset = file->openDataSet( datasetName );
// Get the class of the datatype that is used by the dataset.
H5T_class_t type_class = dataset.getTypeClass();
// std::cout << "Class type: " << ossim_hdf5::getDatatypeClassType( type_class )
// << std::endl;
if ( ( type_class == H5T_INTEGER ) || ( type_class == H5T_FLOAT ) )
{
// Get dataspace of the dataset.
// H5::DataSpace dataspace = dataset.getSpace();
// Get the extents:
std::vector<ossim_uint32> extents;
ossim_hdf5::getExtents( &dataset, extents );
if ( extents.size() >= 2 )
{
if ( ( extents[0] > 1 ) && ( extents[1] > 1 ) )
{
// std::cout << "Accepting dataset: " << datasetName << std::endl;
result = true;
}
}
}
dataset.close();
}
}
// std::cout << "isLoadable exit status: " << (result?"true":"false") << std::endl;
return result;
}
std::vector<double> readEloss(const std::string& path)
{
H5::H5File file (path.c_str(), H5F_ACC_RDONLY);
H5::DataSet ds = file.openDataSet("eloss");
H5::DataSpace filespace = ds.getSpace();
int ndims = filespace.getSimpleExtentNdims();
assert(ndims == 1);
hsize_t dim;
filespace.getSimpleExtentDims(&dim);
H5::DataSpace memspace (ndims, &dim);
std::vector<double> res (dim);
ds.read(res.data(), H5::PredType::NATIVE_DOUBLE, memspace, filespace);
filespace.close();
memspace.close();
ds.close();
file.close();
return res;
}
Bundle2::Bundle2(const boost::filesystem::path& fileName, bool loadGeometry):
version_(BUNDLE_VERSION), poiFirstFrame_(0) {
// Opening file
H5::H5File bundleFile;
bundleFile.openFile(fileName.string(), H5F_ACC_RDONLY);
loadParameters(bundleFile);
// Loading POI
H5::Group poiGroup = bundleFile.openGroup("/POI");
hsize_t count;
H5::Attribute attr = poiGroup.openAttribute("count");
attr.read(H5::PredType::NATIVE_HSIZE, &count);
attr.close();
for(size_t frame = 0; frame < count; ++frame) {
cout.flush();
const std::string frameGroupName = boost::str(boost::format("Frame %1$04d") % frame);
H5::Group frameGroup = poiGroup.openGroup(frameGroupName);
addPOIFrame();
for(size_t camera = 0; camera < numCameras_; ++camera)
poi_[poi_.size() - 1][camera].load(frameGroup, camera);
frameGroup.close();
}
poiGroup.close();
// Loading frames
H5::Group bundleGroup = bundleFile.openGroup("/Bundle");
H5::Group framesGroup = bundleGroup.openGroup("Frames");
attr = framesGroup.openAttribute("count");
attr.read(H5::PredType::NATIVE_HSIZE, &count);
attr.close();
for(size_t frame = 0; frame < count; ++frame) {
Frame* f = new Frame(framesGroup, frame, numCameras_);
frames_.push_back(f);
}
framesGroup.close();
// Loading tracks
H5::DataSet tracksDataset = bundleGroup.openDataSet("Tracks");
hsize_t tracksDim[2];
H5::DataSpace tracksDS = tracksDataset.getSpace();
tracksDS.getSimpleExtentDims(tracksDim);
tracksDS.close();
for(size_t i = 0; i < tracksDim[0]; ++i) {
size_t j = addTrack();
tracks_[j]->load(tracksDataset, frames_, i);
}
tracksDataset.close();
bundleGroup.close();
if(loadGeometry && checkGeometry_(bundleFile)) loadGeometry_(bundleFile);
bundleFile.close();
}
void ossim_hdf5::printObject( H5::H5File* file,
const std::string& objectName,
const std::string& prefix,
std::ostream& out )
{
#if 0
std::cout << "printObject entered..."
<< "\nobjectName: " << objectName
<< "\nprefix: " << prefix
<< std::endl;
#endif
H5::DataSet dataset = file->openDataSet( objectName );
// Get the class of the datatype that is used by the dataset.
H5T_class_t type_class = dataset.getTypeClass();
out << prefix << ".class_type: "
<< ossim_hdf5::getDatatypeClassType( type_class ) << std::endl;
const ossim_uint32 ATTRS_COUNT = dataset.getNumAttrs();
for ( ossim_uint32 aIdx = 0; aIdx < ATTRS_COUNT; ++aIdx )
{
H5::Attribute attr = dataset.openAttribute( aIdx );
ossim_hdf5::printAttribute( attr, prefix, out );
attr.close();
}
// Extents:
std::vector<ossim_uint32> extents;
ossim_hdf5::getExtents( &dataset, extents );
for ( ossim_uint32 i = 0; i < extents.size(); ++i )
{
ossimString os;
std::string exStr = ".extent";
exStr += os.toString(i).string();
out << prefix << exStr << ": " << extents[i] << std::endl;
}
// ossimScalarType scalar = getScalarType( type_class, dataset.getId() );
ossimScalarType scalar = ossim_hdf5::getScalarType( dataset.getId() );
if ( scalar != OSSIM_SCALAR_UNKNOWN)
{
out << prefix << "." << ossimKeywordNames::SCALAR_TYPE_KW << ": "
<< ossimScalarTypeLut::instance()->getEntryString( scalar ) << std::endl;
if ( ossim::scalarSizeInBytes( scalar ) > 1 )
{
ossimByteOrder byteOrder = ossim_hdf5::getByteOrder( &dataset );
std::string byteOrderString = "little_endian";
if ( byteOrder == OSSIM_BIG_ENDIAN )
{
byteOrderString = "big_endian";
}
out << prefix << "." <<ossimKeywordNames::BYTE_ORDER_KW << ": "
<< byteOrderString << std::endl;
}
}
#if 0
// Attributes:
int numberOfAttrs = dataset.getNumAttrs();
cout << "numberOfAttrs: " << numberOfAttrs << endl;
for ( ossim_int32 attrIdx = 0; attrIdx < numberOfAttrs; ++attrIdx )
{
H5::Attribute attribute = dataset.openAttribute( attrIdx );
cout << "attribute.from class: " << attribute.fromClass() << endl;
}
#endif
dataset.close();
} // End: printObject
H5RandomReader::H5RandomReader(const std::string fileName, const std::string groupPath) throw (InvalidFileException) {
try {
file.openFile(fileName, H5F_ACC_RDONLY);}
catch ( H5::FileIException ) {
throw InvalidFileException("Cannot acces file");}
try {
group = file.openGroup(groupPath);}
catch ( H5::GroupIException ) {
file.close();
throw InvalidFileException("Cannot access group");}
/*
* extract timeline. This is also necessary to get the nbSteps.
*/
try {
timeline = group.openDataSet("timeline");
nSteps = timeline.getSpace().getSimpleExtentNpoints();}
catch ( H5::DataSetIException error ) {
//error.printError();
group.close();
file.close();
throw InvalidFileException("Cannot access timeline dataset");}
if (logging::info)
std::cerr << "Opened group \"" << fileName << groupPath << "\" which has " << nSteps << " steps.\n";
/*
* extract objects names in the xpGroup
*/
std::vector<std::string> names;
H5Literate(group.getId(), H5_INDEX_NAME, H5_ITER_INC, NULL, iterInGroup, &names);
/*
* extract data from object in xpGroup
* these data can be of 3 types: matrix, translate or wrench
* each data are saved in related map
*/
for (unsigned int i=0; i<names.size(); i++){ //TODO: skip timeline
H5::DataSet dSet = group.openDataSet(names[i]);
if (H5Aexists(dSet.getId(), "ArborisViewerType")) {
H5::Attribute att = dSet.openAttribute("ArborisViewerType");
std::string type;
att.read(att.getDataType(), type);
if (type == "matrix"){
H5::DataSpace dSpace = dSet.getSpace();
bool dimension_ok = false;
if (dSpace.getSimpleExtentNdims()==3) {
hsize_t dims[3];
dSpace.getSimpleExtentDims (dims);
if (dims[0] == nSteps && dims[1] == 4 && dims[2] == 4)
dimension_ok = true;}
if (dimension_ok)
matrices[names[i]] = dSet;
else {
if (logging::warning)
std::cerr << "Skipping dataset \"" << names[i] << "\" which has wrong dimensions. I was expecting (" << nSteps << ",4,4).\n";
dSet.close();}}
else if (type == "translate"){
H5::DataSpace dSpace = dSet.getSpace();
bool dimension_ok = false;
if (dSpace.getSimpleExtentNdims()==2) {
hsize_t dims[2];
dSpace.getSimpleExtentDims (dims);
if (dims[0] == nSteps && dims[1] == 3)
dimension_ok = true;}
if (dimension_ok)
translates[names[i]] = dSet;
else {
if (logging::warning)
std::cerr << "Skipping dataset \"" << names[i] << "\" which has wrong dimensions. I was expecting (" << nSteps << ",3).\n";
dSet.close();}}
else if (type == "wrench") {
H5::DataSpace dSpace = dSet.getSpace();
bool dimension_ok = false;
if (dSpace.getSimpleExtentNdims()==2) {
hsize_t dims[2];
dSpace.getSimpleExtentDims (dims);
if (dims[0] == nSteps && dims[1] == 6)
dimension_ok = true;}
if (dimension_ok)
wrenches[names[i]] = dSet;
else {
if (logging::warning)
std::cerr << "Skipping dataset \"" << names[i] << "\" which as wrong dimensions. I was expecting (" << nSteps << ",6).\n";
dSet.close();}}
else {
if (logging::warning)
std::cerr << "Skipping dataset \"" << names[i] << "\" whose ArborisViewerType attribute as unknown value \"" << type << "\".\n";
dSet.close();}
att.close();
}
else {
if (logging::info)
std::cerr << "Skipping dataset \"" << names[i] << "\" which has no ArborisViewerType attribute.\n";
dSet.close();
}
}
};
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();
}
void Bundle2::loadGeometry_(H5::H5File& file) {
H5::Group geometryGroup = file.openGroup("/Geometry");
// Loading poses
H5::DataSet posesDataSet = geometryGroup.openDataSet("Poses");
double* posesData = (double*)malloc(frames_.size()*12*sizeof(double));
posesDataSet.read((void*)posesData, H5::PredType::NATIVE_DOUBLE, H5::DataSpace::ALL, H5::DataSpace::ALL);
posesDataSet.close();
size_t i = 0;
for(deque<Frame*>::iterator it = frames_.begin(); it != frames_.end(); ++it) {
Pose* pose = new Pose;
pose->sett(core::RealPoint3D<double>(posesData[i*12], posesData[i*12 + 1], posesData[i*12 + 2]));
core::Matrix<double> R(3, 3);
R[0][0] = posesData[i*12 + 3]; R[1][0] = posesData[i*12 + 4]; R[2][0] = posesData[i*12 + 5];
R[0][1] = posesData[i*12 + 6]; R[1][1] = posesData[i*12 + 7]; R[2][1] = posesData[i*12 + 8];
R[0][2] = posesData[i*12 + 9]; R[1][2] = posesData[i*12 + 10]; R[2][2] = posesData[i*12 + 11];
pose->setR(R);
pose->calcEulerAngles();
pose->setorientationSynchronWithAngles(true);
pose->setderivationsSynchronWithAngles(false);
(*it)->setpose(pose);
++i;
}
free((void*)posesData);
// Loading points
H5::DataSet pointsDataSet = geometryGroup.openDataSet("Points");
double* pointsData = (double*)malloc(tracks_.size()*3*sizeof(double));
pointsDataSet.read((void*)pointsData, H5::PredType::NATIVE_DOUBLE, H5::DataSpace::ALL, H5::DataSpace::ALL);
pointsDataSet.close();
i = 0;
for(deque<Track*>::iterator it = tracks_.begin(); it != tracks_.end(); it++) {
Point* point = new Point(core::RealPoint3D<double>(pointsData[i*3], pointsData[i*3 + 1], pointsData[i*3 + 2]));
(*it)->setpoint(point);
++i;
}
free((void*)pointsData);
// Loading inlier information
H5::DataSet inliersDataSet = geometryGroup.openDataSet("Inliers");
hvl_t* inliersData = (hvl_t*)malloc(frames_.size()*sizeof(hvl_t));
H5::VarLenType memType(&H5::PredType::NATIVE_UCHAR);
inliersDataSet.read((void*)inliersData, memType, H5::DataSpace::ALL, H5::DataSpace::ALL);
memType.close();
inliersDataSet.close();
i = 0;
for(deque<Frame*>::iterator it = frames_.begin(); it != frames_.end(); it++) {
unsigned char* inl = (unsigned char*)(inliersData[i].p);
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)) {
Ray ray;
if(inl[k]) ray.setinlier(true);
else ray.setinlier(false);
v.addRay(cam, ray);
++k;
}
}
}
++i;
}
for(size_t j = 0; j < frames_.size(); ++j) free(inliersData[j].p);
free((void*)inliersData);
// Loading curves if they exists
bool curvesFound = false;
const hsize_t maxObjs = geometryGroup.getNumObjs();
for(hsize_t obj = 0; obj < maxObjs; ++obj) {
string objName = geometryGroup.getObjnameByIdx(obj);
if(objName == string("Curves")) curvesFound = true;
}
if(curvesFound) {
H5::DataSet curvesDataSet = geometryGroup.openDataSet("Curves");
hsize_t curvesDim[1];
H5::DataSpace curvesDS = curvesDataSet.getSpace();
curvesDS.getSimpleExtentDims(curvesDim);
curvesDS.close();
hvl_t* curvesData = (hvl_t*)malloc(curvesDim[0]*sizeof(hvl_t));
H5::VarLenType memType(&H5::PredType::NATIVE_HSIZE);
curvesDataSet.read((void*)curvesData, memType, H5::DataSpace::ALL, H5::DataSpace::ALL);
memType.close();
curvesDataSet.close();
for(size_t c = 0; c < curvesDim[0]; ++c) {
const size_t cur_c = addCurve();
for(size_t p = 0; p < curvesData[c].len; ++p) {
curves_[cur_c].addPoint(((size_t*)(curvesData[c].p))[p]);
}
}
for(size_t i = 0; i < curvesDim[0]; ++i) free(curvesData[i].p);
free((void*)curvesData);
}
geometryGroup.close();
}
void WriteTable(void* data){
//write data and close data set
dSet_.write(data, dType_, dSpace_);
dSet_.close();
}
// Bundle management
void Bundle2::save(const boost::filesystem::path& fileName) const {
// Creating HDF5 file
H5::H5File bundleFile(fileName.string(), H5F_ACC_TRUNC);
storeParameters(bundleFile);
H5::DataSpace scalar;
// Saving POI
H5::Group poiGroup = bundleFile.createGroup("/POI");
H5::Attribute attr = poiGroup.createAttribute("count", H5::PredType::STD_U64LE, scalar);
hsize_t count = poi_.size();
attr.write(H5::PredType::NATIVE_HSIZE, &count);
attr.close();
for(size_t frame = 0; frame < poi_.size(); ++frame) {
const std::string frameGroupName = boost::str(boost::format("Frame %1$04d") % frame);
H5::Group frameGroup = poiGroup.createGroup(frameGroupName);
count = poi_[frame].size();
attr = frameGroup.createAttribute("count", H5::PredType::STD_U64LE, scalar);
attr.write(H5::PredType::NATIVE_HSIZE, &count);
attr.close();
for(size_t camera = 0; camera < poi_[frame].size(); ++camera)
poi_[frame][camera].save(frameGroup, camera);
frameGroup.close();
}
poiGroup.close();
// Saving key frames
H5::Group bundleGroup = bundleFile.createGroup("/Bundle");
H5::Group framesGroup = bundleGroup.createGroup("Frames");
count = frames_.size();
attr = framesGroup.createAttribute("count", H5::PredType::STD_U64LE, scalar);
attr.write(H5::PredType::NATIVE_HSIZE, &count);
attr.close();
for(deque<Frame*>::const_iterator it = frames_.begin(); it != frames_.end(); it++) {
(*it)->save(framesGroup);
}
framesGroup.close();
// Saving tracks
const hsize_t chunkDim[] = { 2, 1 };
H5::DSetCreatPropList propList;
propList.setLayout(H5D_CHUNKED);
propList.setChunk(2, chunkDim);
propList.setDeflate(9);
H5::VarLenType tracksDatasetType(&H5::PredType::STD_U64LE);
hsize_t tracksDim[] = { tracks_.size(), 2 };
hsize_t tracksMaxDim[] = { H5S_UNLIMITED, 2 };
H5::DataSpace tracksDataspace(2, tracksDim, tracksMaxDim);
H5::DataSet tracksDataset = bundleGroup.createDataSet("Tracks", tracksDatasetType, tracksDataspace, propList);
for(size_t i = 0; i < tracks_.size(); ++i)
tracks_[i]->save(tracksDataset, i);
tracksDataset.close();
tracksDataspace.close();
tracksDatasetType.close();
propList.close();
bundleGroup.close();
scalar.close();
bundleFile.close();
}
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 Bundle2::initFrameStream_() {
H5::DataSpace scalar;
// Creating datasets for each frame
H5::Group bundleGroup = streamFile_->createGroup("/Bundle");
H5::Group framesGroup = bundleGroup.createGroup("Frames");
hsize_t count = frames_.size();
H5::Attribute attr = framesGroup.createAttribute("count", H5::PredType::STD_U64LE, scalar);
attr.write(H5::PredType::NATIVE_HSIZE, &count);
attr.close();
// Defining frame dataset property
hsize_t chunkDim[] = { 1, 2, 10 };
H5::DSetCreatPropList propList;
propList.setLayout(H5D_CHUNKED);
propList.setChunk(3, chunkDim);
propList.setDeflate(9);
// Definig dataset dataspace
hsize_t max_dim[] = { numCameras_, 2, H5S_UNLIMITED };
hsize_t dim[] = { numCameras_, 2, 0 };
H5::DataSpace ds(3, dim, max_dim);
for(deque<Frame*>::const_iterator it = frames_.begin(); it != frames_.end(); it++) {
const std::string datasetName = boost::str(boost::format("Frame %1$04d") % (*it)->number());
// Creating dataset
H5::DataSet frameData = framesGroup.createDataSet(datasetName, H5::PredType::IEEE_F32LE, ds, propList);
// Writing global number
attr = frameData.createAttribute("globalNumber", H5::PredType::STD_U64LE, scalar);
count = (*it)->globalNumber();
attr.write(H5::PredType::NATIVE_HSIZE, &count);
attr.close();
// Clean up!
frameData.close();
}
// Clean up!
ds.close();
propList.close();
// Creating tracks dataset
hsize_t chunkDim2[] = { 2, 10 };
propList = H5::DSetCreatPropList();
propList.setLayout(H5D_CHUNKED);
propList.setChunk(2, chunkDim);
propList.setDeflate(9);
H5::VarLenType tracksDatasetType(&H5::PredType::STD_U64LE);
hsize_t tracksDim[] = { 0, 2 };
hsize_t tracksMaxDim[] = { H5S_UNLIMITED, 2 };
H5::DataSpace tracksDataspace(2, tracksDim, tracksMaxDim);
H5::DataSet tracksDataset = bundleGroup.createDataSet("Tracks", tracksDatasetType, tracksDataspace, propList);
tracksDataset.close();
tracksDataspace.close();
tracksDatasetType.close();
propList.close();
framesGroup.close();
bundleGroup.close();
scalar.close();
}
PcaModel PcaModel::loadStatismoModel(path h5file, PcaModel::ModelType modelType)
{
logging::Logger logger = Loggers->getLogger("shapemodels");
PcaModel model;
// Load the shape or color model from the .h5 file
string h5GroupType;
if (modelType == ModelType::SHAPE) {
h5GroupType = "shape";
} else if (modelType == ModelType::COLOR) {
h5GroupType = "color";
}
H5::H5File h5Model;
try {
h5Model = H5::H5File(h5file.string(), H5F_ACC_RDONLY);
}
catch (H5::Exception& e) {
string errorMessage = "Could not open HDF5 file: " + string(e.getCDetailMsg());
logger.error(errorMessage);
throw errorMessage;
}
// Load either the shape or texture mean
string h5Group = "/" + h5GroupType + "/model";
H5::Group modelReconstructive = h5Model.openGroup(h5Group);
// Read the mean
H5::DataSet dsMean = modelReconstructive.openDataSet("./mean");
hsize_t dims[2];
dsMean.getSpace().getSimpleExtentDims(dims, NULL); // dsMean.getSpace() leaks memory... maybe a hdf5 bug, maybe vlenReclaim(...) could be a fix. No idea.
//H5::DataSpace dsp = dsMean.getSpace();
//dsp.close();
Loggers->getLogger("shapemodels").debug("Dimensions of the model mean: " + lexical_cast<string>(dims[0]));
model.mean = Mat(1, dims[0], CV_32FC1); // Use a row-vector, because of faster memory access and I'm not sure the memory block is allocated contiguously if we have multiple rows.
dsMean.read(model.mean.ptr<float>(0), H5::PredType::NATIVE_FLOAT);
model.mean = model.mean.t(); // Transpose it to a col-vector
dsMean.close();
// Read the eigenvalues
dsMean = modelReconstructive.openDataSet("./pcaVariance");
dsMean.getSpace().getSimpleExtentDims(dims, NULL);
Loggers->getLogger("shapemodels").debug("Dimensions of the pcaVariance: " + lexical_cast<string>(dims[0]));
model.eigenvalues = Mat(1, dims[0], CV_32FC1);
dsMean.read(model.eigenvalues.ptr<float>(0), H5::PredType::NATIVE_FLOAT);
model.eigenvalues = model.eigenvalues.t();
dsMean.close();
// Read the PCA basis matrix
dsMean = modelReconstructive.openDataSet("./pcaBasis");
dsMean.getSpace().getSimpleExtentDims(dims, NULL);
Loggers->getLogger("shapemodels").debug("Dimensions of the PCA basis matrix: " + lexical_cast<string>(dims[0]) + ", " + lexical_cast<string>(dims[1]));
model.pcaBasis = Mat(dims[0], dims[1], CV_32FC1);
dsMean.read(model.pcaBasis.ptr<float>(0), H5::PredType::NATIVE_FLOAT);
dsMean.close();
modelReconstructive.close(); // close the model-group
// Read the noise variance (not implemented)
/*dsMean = modelReconstructive.openDataSet("./noiseVariance");
float noiseVariance = 10.0f;
dsMean.read(&noiseVariance, H5::PredType::NATIVE_FLOAT);
dsMean.close(); */
// Read the triangle-list
string representerGroupName = "/" + h5GroupType + "/representer";
H5::Group representerGroup = h5Model.openGroup(representerGroupName);
dsMean = representerGroup.openDataSet("./reference-mesh/triangle-list");
dsMean.getSpace().getSimpleExtentDims(dims, NULL);
Loggers->getLogger("shapemodels").debug("Dimensions of the triangle-list: " + lexical_cast<string>(dims[0]) + ", " + lexical_cast<string>(dims[1]));
Mat triangles(dims[0], dims[1], CV_32SC1);
dsMean.read(triangles.ptr<int>(0), H5::PredType::NATIVE_INT32);
dsMean.close();
representerGroup.close();
model.triangleList.resize(triangles.rows);
for (unsigned int i = 0; i < model.triangleList.size(); ++i) {
model.triangleList[i][0] = triangles.at<int>(i, 0);
model.triangleList[i][1] = triangles.at<int>(i, 1);
model.triangleList[i][2] = triangles.at<int>(i, 2);
}
// Load the landmarks mappings:
// load the reference-mesh
representerGroup = h5Model.openGroup(representerGroupName);
dsMean = representerGroup.openDataSet("./reference-mesh/vertex-coordinates");
dsMean.getSpace().getSimpleExtentDims(dims, NULL);
Loggers->getLogger("shapemodels").debug("Dimensions of the reference-mesh vertex-coordinates matrix: " + lexical_cast<string>(dims[0]) + ", " + lexical_cast<string>(dims[1]));
Mat referenceMesh(dims[0], dims[1], CV_32FC1);
dsMean.read(referenceMesh.ptr<float>(0), H5::PredType::NATIVE_FLOAT);
dsMean.close();
representerGroup.close();
// convert to 3 vectors with the x, y and z coordinates for easy searching
vector<float> refx(referenceMesh.col(0).clone());
vector<float> refy(referenceMesh.col(1).clone());
vector<float> refz(referenceMesh.col(2).clone());
// load the landmarks info (mapping name <-> reference (x, y, z)-coords)
H5::Group landmarksGroup = h5Model.openGroup("/metadata/landmarks");
dsMean = landmarksGroup.openDataSet("./text");
H5std_string outputString;
Loggers->getLogger("shapemodels").debug("Reading landmark information from the model.");
dsMean.read(outputString, dsMean.getStrType());
dsMean.close();
landmarksGroup.close();
vector<string> landmarkLines;
boost::split(landmarkLines, outputString, boost::is_any_of("\n"), boost::token_compress_on);
for (const auto& l : landmarkLines) {
if (l == "") {
continue;
}
vector<string> line;
boost::split(line, l, boost::is_any_of(" "), boost::token_compress_on);
string name = line[0];
int visibility = lexical_cast<int>(line[1]);
float x = lexical_cast<float>(line[2]);
float y = lexical_cast<float>(line[3]);
float z = lexical_cast<float>(line[4]);
// Find the x, y and z values in the reference
const auto ivx = std::find(begin(refx), end(refx), x);
const auto ivy = std::find(begin(refy), end(refy), y);
const auto ivz = std::find(begin(refz), end(refz), z);
// TODO Check for .end()!
const auto vertexIdX = std::distance(begin(refx), ivx);
const auto vertexIdY = std::distance(begin(refy), ivy);
const auto vertexIdZ = std::distance(begin(refz), ivz);
// assert vx=vy=vz
// Hmm this is not perfect. If there's another vertex where 1 or 2 coords are the same, it fails.
// We should do the search differently: Find _all_ the vertices that are equal, then take the one that has the right x, y and z.
model.landmarkVertexMap.insert(make_pair(name, vertexIdX));
}
h5Model.close();
return model;
}
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;
}
