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 ossim_hdf5::getExtents( const H5::DataSet* dataset,
std::vector<ossim_uint32>& extents )
{
extents.clear();
if ( dataset )
{
// Get dataspace of the dataset.
H5::DataSpace dataspace = dataset->getSpace();
// Number of dimensions:
int ndims = dataspace.getSimpleExtentNdims();
if ( ndims )
{
//hsize_t dims_out[ndims];
std::vector<hsize_t> dims_out(ndims);
dataspace.getSimpleExtentDims( &dims_out.front(), 0 );
for ( ossim_int32 i = 0; i < ndims; ++i )
{
extents.push_back(static_cast<ossim_uint32>(dims_out[i]));
}
}
dataspace.close();
}
}
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;
}
UInt GetDatasetNDim(H5::CommonFG &parentGroup, std::string datasetName) {
HDFData tmpDataset;
tmpDataset.InitializeDataset(parentGroup, datasetName);
H5::DataSpace dataspace = tmpDataset.dataset.getSpace();
UInt nDims = dataspace.getSimpleExtentNdims();
dataspace.close();
tmpDataset.dataset.close();
return nDims;
}
int H5Signal::signal_count(void)
/*----------------------------*/
{
H5::DataSpace uspace = dataset.openAttribute("uri").getSpace() ;
int udims = uspace.getSimpleExtentNdims() ;
if (udims == 0) return 1 ; // SCALAR
else {
if (udims != 1) throw H5Exception("Dataset's 'uri' attribute has wrong shape: " + uri) ;
return uspace.getSimpleExtentNpoints() ;
}
}
/**
* @brief Returns a pointer to a std::vector<float> containing the values of the selected variable
*
* This allocates a new std::vector<float> pointer. Make sure you
* delete the contents when you done using it, or you will have a memory leak.
*
* @param variable
* @return std::vector<float> containing the values of the selected variable.
*/
std::vector<float>* HDF5FileReader::getVariable(const std::string& variable)
{
std::vector<float>* variableData = new std::vector<float>();
if (this->doesVariableExist(variable))
{
//std::cout << "reading " << variable << std::endl;
//get variable number
// long variableNum = this->getVariableID(variable);
//std::cout << "variableNum for " << variable << ": " << variableNum << std::endl;
//get dim sizes
H5::Group group = this->current_file->openGroup("Variables");
//cout << "variable: " << variable << ": " << counts[0] << endl;
H5::DataSet * dataset = new H5::DataSet(group.openDataSet(variable));
H5::DataSpace dataspace = dataset->getSpace();
int rank = dataspace.getSimpleExtentNdims(); //should be 1
hsize_t count[1];
hsize_t offset[1] = {0};
// int ndims = dataspace.getSimpleExtentDims(count, NULL);
//std::cout << "count[0]: " << count[0] << std::endl;
float * buffer = new float[count[0]];
dataspace.selectHyperslab(H5S_SELECT_SET, count, offset);
H5::DataSpace memspace( rank, count);
memspace.selectHyperslab(H5S_SELECT_SET, count, offset);
dataset->read(buffer, H5::PredType::NATIVE_FLOAT, memspace, dataspace);
//std::cout << "after read" << std::endl;
//add data to vector type, and delete original array
variableData->reserve(count[0]);
for (int i = 0; i < count[0]; i++)
{
variableData->push_back(buffer[i]);
}
//std::cout << "after adding to variableData vector" << std::endl;
delete[] buffer;
delete dataset;
//std::cout << "finished reading " << variable << std::endl;
//std::cout << "size of variable: " << variableData.size() << std::endl;
//std::cout << "dimSizes[0]: " << dimSizes[0] << std::endl;
}
return variableData;
}
const std::vector<hsize_t> TableDims(){
if(flags_ != hdf5::READ)
throw std::runtime_error("TableDims() is only valid in READ mode");
H5::DataSet dSet = file_->openDataSet("T00000000");
H5::DataSpace dSpace = dSet.getSpace();
std::vector<hsize_t> dims(dSpace.getSimpleExtentNdims());
dSpace.getSimpleExtentDims(&dims[0]);
return dims;
}
NDArray<T, Nd> NDArray<T,Nd>::ReadFromH5(const H5::DataSet& h5Dset) {
H5::DataSpace dspace = h5Dset.getSpace();
int ndim = dspace.getSimpleExtentNdims();
if (ndim>Nd)
throw std::range_error("Too many dimensions in H5 dataset for NDArray");
hsize_t dimSize[ndim];
dspace.getSimpleExtentDims(dimSize);
std::array<std::size_t, Nd> dimSizeArr;
for (int i=0; i<Nd; ++i) dimSizeArr[i] = dimSize[i];
NDArray<T, Nd> arr(dimSizeArr);
// Read in data here
H5::DataType h5DType = GetH5DataType<T>();
h5Dset.read(arr.mData, h5DType);
return arr;
}
void HDF5IO::loadStdVector(const std::string& GroupName, const std::string& Name,
std::vector<RealType>& V)
{
try{
H5::Group FG = getGroup( GroupName );
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
H5::DataSpace DataSpace = DataSet.getSpace();
if(DataSpace.getSimpleExtentNdims() != 1)
throw(H5::DataSpaceIException("HDF5IO::loadRealVector()","Unexpected multidimentional dataspace."));
V.resize(DataSpace.getSimpleExtentNpoints());
DataSet.read(V.data(),H5::PredType::NATIVE_DOUBLE);
FG.close();
} catch( const H5::Exception err ){
RUNTIME_ERROR("HDF5IO::loadRealStdVector");
}
}
void HDF5IO::loadVector(const std::string& GroupName, const std::string& Name,
RealVectorType& V)
{
H5::Group FG = getGroup( GroupName );
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
H5::DataSpace DataSpace = DataSet.getSpace();
if(DataSpace.getSimpleExtentNdims() != 1)
throw(H5::DataSpaceIException("HDF5IO::loadRealVector()",
"Unexpected multidimentional dataspace."));
V.resize(DataSpace.getSimpleExtentNpoints());
try{
DataSet.read(V.data(),H5::PredType::NATIVE_DOUBLE);
}catch( H5::GroupIException not_found_error ){
RUNTIME_ERROR("No dataset found in loadRealVector. ");
}
FG.close();
}
void HDF5IO::loadStdVector(const std::string& GroupName, const std::string& Name,
std::vector<ComplexType>& V)
{
try{
H5::CompType ComplexDataType = this->openCompType("complex");
H5::Group FG = getGroup( GroupName );
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
H5::DataSpace DataSpace = DataSet.getSpace();
if(DataSpace.getSimpleExtentNdims() != 1)
throw(H5::DataSpaceIException("HDF5IO::loadComplexVector()","Unexpected multidimentional dataspace."));
V.resize(DataSpace.getSimpleExtentNpoints());
DataSet.read(V.data(),ComplexDataType);
FG.close();
} catch( const H5::Exception err ){
RUNTIME_ERROR("HDF5IO::loadComplexStdVector");
}
}
/**
* @brief Returns a value in the flat array of the variable and index requested.
*
* Use this method on variables that have a type of int
*
* @param variable The variable in the file
* @param index The index in the variable's array in the file
*
* @return int of the value in the array.
*/
int HDF5FileReader::getVariableIntAtIndex(const std::string& variable, long index)
{
// long counts[1];
int value = std::numeric_limits<int>::min();
if (this->doesVariableExist(variable))
{
//std::cout << "reading " << variable << std::endl;
//get variable number
// long variableNum = this->getVariableID(variable);
//get dim sizes
H5::Group group = this->current_file->openGroup("Variables");
//cout << "variable: " << variable << ": " << counts[0] << endl;
H5::DataSet * dataset = new H5::DataSet(group.openDataSet(variable));
H5::DataSpace dataspace = dataset->getSpace();
int rank = dataspace.getSimpleExtentNdims(); //should be 1
hsize_t count[1] = {1};
hsize_t offset[1] = {0};
//int ndims = dataspace.getSimpleExtentDims(count, NULL);
float * buffer = new float[count[0]];
dataspace.selectHyperslab(H5S_SELECT_SET, count, offset);
hsize_t dim[] = {count[0]};
H5::DataSpace memspace( rank, dim);
memspace.selectHyperslab(H5S_SELECT_SET, dim, offset);
dataset->read(buffer, H5::PredType::NATIVE_INT, memspace, dataspace);
//add data to vector type, and delete original array
value = buffer[0];
delete[] buffer;
delete dataset;
}
return value;
//std::cout << "finished reading " << variable << std::endl;
//std::cout << "size of variable: " << variableData.size() << std::endl;
//std::cout << "dimSizes[0]: " << dimSizes[0] << std::endl;
}
size_t H5Signal::clock_size(void)
/*-----------------------------*/
{
try {
H5::Attribute attr = dataset.openAttribute("clock") ;
hobj_ref_t ref ;
attr.read(H5::PredType::STD_REF_OBJ, &ref) ;
attr.close() ;
H5::DataSet clk(H5Rdereference(H5Iget_file_id(dataset.getId()), H5R_OBJECT, &ref)) ;
H5::DataSpace cspace = clk.getSpace() ;
int cdims = cspace.getSimpleExtentNdims() ;
hsize_t cshape[cdims] ;
cspace.getSimpleExtentDims(cshape) ;
return cshape[0] ;
}
catch (H5::AttributeIException e) { }
return -1 ;
}
/** Retrieves the dimensions of the dataset */
int hdfutil::GetDsDims (const H5::DataSet & dataset, int dims[3]) {
H5::DataSpace dataspace = dataset.getSpace();
bool simple = dataspace.isSimple();
if (!simple)
throw std::runtime_error("complex HDF5 dataspace");
int rank = (int)dataspace.getSimpleExtentNdims();
if (rank > 3)
throw std::runtime_error("unsupported dimensionality");
hsize_t h5_dims[3];
dataspace.getSimpleExtentDims(h5_dims, NULL);
for (int i = 0; i < rank; i++)
dims[i] = (int)h5_dims[i];
for (int i = rank; i < 3; i++)
dims[i] = -1;
return rank;
}
/**
* Returns a pointer to a std::vector<float> containing the values of the selected variable
* in the range specified by the startIndex and count (the number of records to read) stored
* in the selected file. This allocates a new std::vector<float> pointer. Make sure you
* delete the contents when you done using it, or you will have a memory leak.
* @param variableID
* @param startIndex
* @param count
* @return std::vector<float> containing the values of the selected variable.
*/
std::vector<float>* HDF5FileReader::getVariable(long variable, long indexOffset, long count)
{
std::vector<float>* variableData = new std::vector<float>();
//get dim sizes
H5::Group group = this->current_file->openGroup("Variables");
//cout << "variable: " << variable << ": " << counts[0] << endl;
H5::DataSet * dataset = new H5::DataSet(group.openDataSet(group.getObjnameByIdx(variable)));
H5::DataSpace dataspace = dataset->getSpace();
int rank = dataspace.getSimpleExtentNdims(); //should be 1
hsize_t length[1] = {count};
hsize_t offset[1] = {indexOffset};
//int ndims = dataspace.getSimpleExtentDims(count, NULL);
float * buffer = new float[length[0]];
dataspace.selectHyperslab(H5S_SELECT_SET, length, offset);
hsize_t dim[] = {length[0]};
H5::DataSpace memspace( rank, dim);
memspace.selectHyperslab(H5S_SELECT_SET, dim, offset);
dataset->read(buffer, H5::PredType::NATIVE_FLOAT, memspace, dataspace);
//add data to vector type, and delete original array
variableData->reserve(length[0]);
for (int i = 0; i < length[0]; i++)
{
variableData->push_back(buffer[i]);
}
delete[] buffer;
delete dataset;
//std::cout << "finished reading " << variable << std::endl;
//std::cout << "size of variable: " << variableData.size() << std::endl;
//std::cout << "dimSizes[0]: " << dimSizes[0] << std::endl;
return variableData;
}
void HDF5IO::loadMatrix(const std::string& GroupName, const std::string& Name,
ComplexMatrixType& M)
{
try{
H5::CompType ComplexDataType = this->openCompType("complex");
H5::Group FG = getGroup( GroupName );
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
H5::DataSpace DataSpace = DataSet.getSpace();
if(DataSpace.getSimpleExtentNdims() != 2)
throw(H5::DataSpaceIException("HDF5IO::loadMatrix()","A dataspace must be precisely two-dimensional."));
hsize_t Dims[2];
DataSpace.getSimpleExtentDims(Dims);
M.resize(Dims[0],Dims[1]);
DataSet.read(M.data(), ComplexDataType);
FG.close();
} catch( const H5::Exception err ){
RUNTIME_ERROR("HDF5IO::loadComplexMatrix at ");
}
}
/// Return the attribute name of obj, and "" if the attribute does not exist.
inline std::string read_string_attribute (H5::H5Object const * obj, std::string name ) {
std::string value ="";
H5::Attribute attr;
if (H5LTfind_attribute(obj -> getId(), name.c_str() )==0) return value;// not present
// can not find how to get the size with hl. Using full interface
//herr_t err2 = H5LTget_attribute_string(gr.getId(), x.c_str(), name.c_str() , &(buf.front()) ) ;
//value.append( &(buf.front()) );
try { attr= obj->openAttribute(name.c_str());}
catch (H5::AttributeIException) { return value;}
try {
H5::DataSpace dataspace = attr.getSpace();
int rank = dataspace.getSimpleExtentNdims();
if (rank != 0) TRIQS_RUNTIME_ERROR << "Reading a string attribute and got rank !=0";
size_t size = attr.getStorageSize();
H5::StrType strdatatype(H5::PredType::C_S1, size+1);
std::vector<char> buf(size+1, 0x00);
attr.read(strdatatype, (void *)(&buf[0]));
value.append( &(buf.front()) );
}
TRIQS_ARRAYS_H5_CATCH_EXCEPTION;
return value;
}
static void read_attr(Attribute *attr, H5::Group g, cpath basename, cpath group_path, cpath name, BaseType &type)
{
int total = 1;
H5::Attribute h5attr = g.openAttribute(name.generic_string().c_str());
type = toBaseType(H5Aget_type(h5attr.getId()));
H5::DataSpace space = h5attr.getSpace();
int dimcount = space.getSimpleExtentNdims();
hsize_t *dims = new hsize_t[dimcount];
hsize_t *maxdims = new hsize_t[dimcount];
space.getSimpleExtentDims(dims, maxdims);
for(int i=0;i<dimcount;i++)
total *= dims[i];
group_path = remove_prefix(group_path, basename);
name = group_path / name;
//legacy attribute reading
if (dimcount == 1) {
void *buf = malloc(baseType_size(type)*total);
h5attr.read(toH5NativeDataType(type), buf);
attr->set<hsize_t>(name, dimcount, dims, type, buf);
}
else {
Mat m;
Mat_H5AttrRead(m, h5attr);
attr->setName(name);
attr->set(m);
}
delete[] dims;
delete[] maxdims;
}
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;
}
std::vector<double> readlastrow( H5::DataSet& ds )
{
H5::DataSpace origspace = ds.getSpace();
int rank = origspace.getSimpleExtentNdims();
hsize_t dims[rank];
int ndims = origspace.getSimpleExtentDims( dims, NULL);
hsize_t nrows=dims[0];
hsize_t ncols=dims[1];
std::vector<double> returnvect( ncols );
hsize_t targrowoffset = nrows-1;
hsize_t targcoloffset = 0;
hsize_t dimsmem[rank] = {1, ncols};
H5::DataSpace memspace(rank, dimsmem);
hsize_t offset[rank] = { targrowoffset, targcoloffset };
origspace.selectHyperslab( H5S_SELECT_SET, dimsmem, offset );
ds.read( returnvect.data(), H5::PredType::NATIVE_DOUBLE, memspace, origspace );
return returnvect;
}
bool ossimHdfGridModel::setGridNodes( H5::DataSet* latDataSet,
H5::DataSet* lonDataSet,
ossim_uint32 imageRows,
ossim_uint32 imageCols )
{
bool status = false;
if ( latDataSet && lonDataSet )
{
const ossim_uint32 GRID_SIZE = 32; // Only grab every 32nd value.
// Get dataspace of the dataset.
H5::DataSpace latDataSpace = latDataSet->getSpace();
H5::DataSpace lonDataSpace = lonDataSet->getSpace();
const ossim_int32 LAT_DIM_COUNT = latDataSpace.getSimpleExtentNdims();
const ossim_int32 LON_DIM_COUNT = latDataSpace.getSimpleExtentNdims();
// Number of dimensions of the input dataspace:
if ( ( LAT_DIM_COUNT == 2 ) && ( LON_DIM_COUNT == 2 ) )
{
//---
// Get the extents:
// dimsOut[0] is height, dimsOut[1] is width: //---
std::vector<hsize_t> latDimsOut(LAT_DIM_COUNT);
latDataSpace.getSimpleExtentDims( &latDimsOut.front(), 0 );
std::vector<hsize_t> lonDimsOut(LON_DIM_COUNT);
lonDataSpace.getSimpleExtentDims( &lonDimsOut.front(), 0 );
// Verify same as image:
if ( (latDimsOut[0] == imageRows) &&
(lonDimsOut[0] == imageRows) &&
(latDimsOut[1] == imageCols) &&
(lonDimsOut[1] == imageCols) )
{
//---
// Capture the rectangle:
// dimsOut[0] is height, dimsOut[1] is width:
//---
ossimIrect rect = ossimIrect( 0, 0,
static_cast<ossim_int32>( latDimsOut[1]-1 ),
static_cast<ossim_int32>( latDimsOut[0]-1 ) );
//----
// Initialize the ossimDblGrids:
//---
ossimDpt dspacing (GRID_SIZE, GRID_SIZE);
ossim_uint32 gridRows = imageRows / GRID_SIZE + 1;
ossim_uint32 gridCols = imageCols / GRID_SIZE + 1;
// Round up if size doesn't fall on end pixel.
if ( imageRows % GRID_SIZE) ++gridRows;
if ( imageCols % GRID_SIZE) ++gridCols;
ossimIpt gridSize (gridCols, gridRows);
// The grid as used in base class, has UV-space always at 0,0 origin
ossimDpt gridOrigin(0.0,0.0);
const ossim_float64 NULL_VALUE = -999.0;
theLatGrid.setNullValue(ossim::nan());
theLonGrid.setNullValue(ossim::nan());
theLatGrid.initialize(gridSize, gridOrigin, dspacing);
theLonGrid.initialize(gridSize, gridOrigin, dspacing);
std::vector<hsize_t> inputCount(LAT_DIM_COUNT);
std::vector<hsize_t> inputOffset(LAT_DIM_COUNT);
inputOffset[0] = 0; // row
inputOffset[1] = 0; // col
inputCount[0] = 1; // row
inputCount[1] = (hsize_t)imageCols; // col
// Output dataspace dimensions. Reading a line at a time.
const ossim_int32 OUT_DIM_COUNT = 3;
std::vector<hsize_t> outputCount(OUT_DIM_COUNT);
outputCount[0] = 1; // band
outputCount[1] = 1; // row
outputCount[2] = imageCols; // col
// Output dataspace offset.
std::vector<hsize_t> outputOffset(OUT_DIM_COUNT);
outputOffset[0] = 0;
outputOffset[1] = 0;
outputOffset[2] = 0;
ossimScalarType scalar = ossim_hdf5::getScalarType( latDataSet );
if ( scalar == OSSIM_FLOAT32 )
{
// Set the return status to true if we get here...
status = true;
// See if we need to swap bytes:
ossimEndian* endian = 0;
if ( ( ossim::byteOrder() != ossim_hdf5::getByteOrder( latDataSet ) ) )
{
endian = new ossimEndian();
}
// Native type:
H5::DataType latDataType = latDataSet->getDataType();
H5::DataType lonDataType = lonDataSet->getDataType();
// Output dataspace always the same, width of one line.
H5::DataSpace bufferDataSpace( OUT_DIM_COUNT, &outputCount.front());
bufferDataSpace.selectHyperslab( H5S_SELECT_SET,
&outputCount.front(),
&outputOffset.front() );
// Arrays to hold a single line of latitude longitude values.
vector<ossim_float32> latValue(imageCols);
vector<ossim_float32> lonValue(imageCols);
hsize_t row = 0;
// Line loop:
for ( ossim_uint32 y = 0; y < gridRows; ++y )
{
// row = line in image space
row = y*GRID_SIZE;
bool hitNans = false;
if ( row < imageRows )
{
inputOffset[0] = row;
latDataSpace.selectHyperslab( H5S_SELECT_SET,
&inputCount.front(),
&inputOffset.front() );
lonDataSpace.selectHyperslab( H5S_SELECT_SET,
&inputCount.front(),
&inputOffset.front() );
// Read data from file into the buffer.
latDataSet->read( &(latValue.front()), latDataType,
bufferDataSpace, latDataSpace );
lonDataSet->read( &(lonValue.front()), lonDataType,
bufferDataSpace, lonDataSpace );
if ( endian )
{
// If the endian pointer is initialized(not zero) swap the bytes.
endian->swap( &(latValue.front()), imageCols );
endian->swap( &(lonValue.front()), imageCols );
}
// Sample loop:
hsize_t col = 0;
for ( ossim_uint32 x = 0; x < gridCols; ++x )
{
ossim_float32 lat = ossim::nan();
ossim_float32 lon = ossim::nan();
// col = sample in image space
col = x*GRID_SIZE;
if ( col < imageCols )
{
if ( (latValue[col] > NULL_VALUE)&&(lonValue[col] > NULL_VALUE) )
{
lat = latValue[col];
lon = lonValue[col];
}
else
{
hitNans = true;
}
}
else // Last column is outside of image bounds.
{
ossim_float32 latSpacing = ossim::nan();
ossim_float32 lonSpacing = ossim::nan();
// Get the last two latitude values:
ossim_float32 lat1 = latValue[imageCols-2];
ossim_float32 lat2 = latValue[imageCols-1];
// Get the last two longitude values
ossim_float32 lon1 = lonValue[imageCols-2];
ossim_float32 lon2 = lonValue[imageCols-1];
if ( ( lat1 > NULL_VALUE ) && ( lat2 > NULL_VALUE ) )
{
// Delta between last two latitude values.
latSpacing = lat2 - lat1;
// Compute:
lat = lat2 + ( col - (imageCols-1) ) * latSpacing;
}
else
{
hitNans = true;
}
if ( ( lon1 > NULL_VALUE ) && ( lon2 > NULL_VALUE ) )
{
// Consider dateline crossing.
if ( (lon1 > 0.0) && ( lon2 < 0.0 ) )
{
lon2 += 360.0;
}
// Delta between last two longitude values.
lonSpacing = lon2 - lon1;
// Compute:
lon = lon2 + ( col - (imageCols-1) ) * lonSpacing;
// Check for wrap:
if ( lon > 180 )
{
lon -= 360.0;
}
}
else
{
hitNans = true;
}
#if 0 /* Please leave for debug. (drb) */
cout << "lat1: " << lat1 << " lat2 " << lat2
<< " lon1 " << lon1 << " lon2 " << lon2
<< "\n";
#endif
}
if ( hitNans )
{
std::string errMsg =
"ossimHdfGridModel::setGridNodes encountered nans!";
throw ossimException(errMsg);
}
// Assign the latitude and longitude.
theLatGrid.setNode( x, y, lat );
theLonGrid.setNode( x, y, lon );
#if 0 /* Please leave for debug. (drb) */
cout << "x,y,col,row,lat,lon:" << x << "," << y << ","
<< col << "," << row << ","
<< theLatGrid.getNode(x, y)
<< "," << theLonGrid.getNode( x, y) << "\n";
#endif
} // End sample loop.
}
else // Row is outside of image bounds:
{
// Read the last two rows in.
vector<ossim_float32> latValue2(imageCols);
vector<ossim_float32> lonValue2(imageCols);
inputOffset[0] = imageRows-2; // 2nd to last line
latDataSpace.selectHyperslab( H5S_SELECT_SET,
&inputCount.front(),
&inputOffset.front() );
lonDataSpace.selectHyperslab( H5S_SELECT_SET,
&inputCount.front(),
&inputOffset.front() );
// Read data from file into the buffer.
latDataSet->read( &(latValue.front()), latDataType,
bufferDataSpace, latDataSpace );
lonDataSet->read( &(lonValue.front()), lonDataType,
bufferDataSpace, lonDataSpace );
inputOffset[0] = imageRows-1; // last line
latDataSpace.selectHyperslab( H5S_SELECT_SET,
&inputCount.front(),
&inputOffset.front() );
lonDataSpace.selectHyperslab( H5S_SELECT_SET,
&inputCount.front(),
&inputOffset.front() );
// Read data from file into the buffer.
latDataSet->read( &(latValue2.front()), latDataType,
bufferDataSpace, latDataSpace );
lonDataSet->read( &(lonValue2.front()), lonDataType,
bufferDataSpace, lonDataSpace );
if ( endian )
{
// If the endian pointer is initialized(not zero) swap the bytes.
endian->swap( &(latValue.front()), imageCols );
endian->swap( &(lonValue.front()), imageCols );
endian->swap( &(latValue2.front()), imageCols );
endian->swap( &(lonValue2.front()), imageCols );
}
// Sample loop:
hsize_t col = 0;
for ( ossim_uint32 x = 0; x < gridCols; ++x )
{
col = x*GRID_SIZE; // Sample in image space.
ossim_float32 lat = ossim::nan();
ossim_float32 lat1 = ossim::nan();
ossim_float32 lat2 = ossim::nan();
ossim_float32 latSpacing = ossim::nan();
ossim_float32 lon = ossim::nan();
ossim_float32 lon1 = ossim::nan();
ossim_float32 lon2 = ossim::nan();
ossim_float32 lonSpacing = ossim::nan();
if ( col < imageCols )
{
lat1 = latValue[col];
lat2 = latValue2[col];
lon1 = lonValue[col];
lon2 = lonValue2[col];
}
else // Very last grid point.
{
// Compute the missing column for the last two image lines:
lat1 = latValue[imageCols-1] + ( col - (imageCols-1)) *
( latValue[imageCols-1] - latValue[imageCols-2] );
lat2 = latValue2[imageCols-1] + ( col - (imageCols-1)) *
( latValue2[imageCols-1] - latValue2[imageCols-2] );
lon1 = lonValue[imageCols-1] + ( col - (imageCols-1)) *
( lonValue[imageCols-1] - lonValue[imageCols-2] );
lon2 = lonValue2[imageCols-1] + ( col - (imageCols-1)) *
( lonValue2[imageCols-1] - lonValue2[imageCols-2] );
}
#if 0 /* Please leave for debug. (drb) */
cout << "lat1: " << lat1 << " lat2 " << lat2
<< " lon1 " << lon1 << " lon2 " << lon2
<< "\n";
#endif
if ( ( lon1 > NULL_VALUE ) && ( lon2 > NULL_VALUE ) )
{
// Consider dateline crossing.
if ( (lon1 > 0.0) && ( lon2 < 0.0 ) )
{
lon2 += 360.0;
}
// Delta between last two longitude values.
lonSpacing = lon2 - lon1;
// Compute:
lon = lon2 + ( row - (imageRows-1) ) * lonSpacing;
// Check for wrap:
if ( lon > 180 )
{
lon -= 360.0;
}
}
else
{
hitNans = true;
}
if ( ( lat1 > NULL_VALUE ) && ( lat2 > NULL_VALUE ) )
{
// Delta between last two latitude values.
latSpacing = lat2 - lat1;
// Compute:
lat = lat2 + ( row - (imageRows-1) ) * latSpacing;
}
else
{
hitNans = true;
}
if ( hitNans )
{
std::string errMsg =
"ossimHdfGridModel::setGridNodes encountered nans!";
throw ossimException(errMsg);
}
// Assign the latitude::
theLatGrid.setNode( x, y, lat );
// Assign the longitude.
theLonGrid.setNode( x, y, lon );
#if 0 /* Please leave for debug. (drb) */
cout << "x,y,col,row,lat,lon:" << x << "," << y << ","
<< col << "," << row << "," << lat << "," << lon << "\n";
#endif
} // End sample loop.
} // Matches if ( row < imageRows ){...}else{
} // End line loop.
latDataSpace.close();
lonDataSpace.close();
if ( status )
{
theLatGrid.enableExtrapolation();
theLonGrid.enableExtrapolation();
theHeightEnabledFlag = false;
ossimDrect imageRect(rect);
initializeModelParams(imageRect);
// debugDump();
}
} // Matches: if ( scalar == OSSIM_FLOAT32 )
} // Matches: if ( (latDimsOut[0] == imageRows) ...
} // Matches: if ( ( LAT_DIM_COUNT == 2 ) ...
} // Matches: if ( latDataSet && lonDataSet
return status;
} // End: bool ossimHdfGridModel::setGridNodes( H5::DataSet* latDataSet, ... )
bool ossimH5GridModel::setGridNodes( H5::DataSet* latDataSet,
H5::DataSet* lonDataSet,
const ossimIrect& validRect )
{
bool status = false;
if ( latDataSet && lonDataSet )
{
m_crossesDateline = ossim_hdf5::crossesDateline( *lonDataSet, validRect );
if ( m_crossesDateline )
{
theLonGrid.setDomainType(ossimDblGrid::WRAP_360);
}
else
{
theLonGrid.setDomainType(ossimDblGrid::WRAP_180);
}
// Get dataspace of the dataset.
H5::DataSpace latDataSpace = latDataSet->getSpace();
H5::DataSpace lonDataSpace = lonDataSet->getSpace();
const ossim_int32 LAT_DIM_COUNT = latDataSpace.getSimpleExtentNdims();
const ossim_int32 LON_DIM_COUNT = lonDataSpace.getSimpleExtentNdims();
// Number of dimensions of the input dataspace:
if ( ( LAT_DIM_COUNT == 2 ) && ( LON_DIM_COUNT == 2 ) )
{
const ossim_uint32 ROWS = validRect.height();
const ossim_uint32 COLS = validRect.width();
const ossim_uint32 GRID_SIZE = 4; // Only grab every 4th value.
//---
// Get the extents:
// dimsOut[0] is height, dimsOut[1] is width:
//---
std::vector<hsize_t> latDimsOut(LAT_DIM_COUNT);
latDataSpace.getSimpleExtentDims( &latDimsOut.front(), 0 );
std::vector<hsize_t> lonDimsOut(LON_DIM_COUNT);
lonDataSpace.getSimpleExtentDims( &lonDimsOut.front(), 0 );
// Verify valid rect within our bounds:
if ( (ROWS <= latDimsOut[0] ) && (ROWS <= lonDimsOut[0] ) &&
(COLS <= latDimsOut[1] ) && (COLS <= lonDimsOut[1] ) )
{
//----
// Initialize the ossimDblGrids:
//---
ossimDpt dspacing (GRID_SIZE, GRID_SIZE);
ossim_uint32 gridRows = ROWS / GRID_SIZE + 1;
ossim_uint32 gridCols = COLS / GRID_SIZE + 1;
// Round up if size doesn't fall on end pixel.
if ( ROWS % GRID_SIZE) ++gridRows;
if ( COLS % GRID_SIZE) ++gridCols;
ossimIpt gridSize (gridCols, gridRows);
// The grid as used in base class, has UV-space always at 0,0 origin
ossimDpt gridOrigin(0.0,0.0);
const ossim_float64 NULL_VALUE = -999.0;
theLatGrid.setNullValue(ossim::nan());
theLonGrid.setNullValue(ossim::nan());
theLatGrid.initialize(gridSize, gridOrigin, dspacing);
theLonGrid.initialize(gridSize, gridOrigin, dspacing);
std::vector<hsize_t> inputCount(LAT_DIM_COUNT);
std::vector<hsize_t> inputOffset(LAT_DIM_COUNT);
inputOffset[0] = 0; // row is set below.
inputOffset[1] = validRect.ul().x; // col
inputCount[0] = 1; // row
inputCount[1] = (hsize_t)COLS; // col
// Output dataspace dimensions. Reading a line at a time.
const ossim_int32 OUT_DIM_COUNT = 3;
std::vector<hsize_t> outputCount(OUT_DIM_COUNT);
outputCount[0] = 1; // band
outputCount[1] = 1; // row
outputCount[2] = COLS; // col
// Output dataspace offset.
std::vector<hsize_t> outputOffset(OUT_DIM_COUNT);
outputOffset[0] = 0;
outputOffset[1] = 0;
outputOffset[2] = 0;
ossimScalarType scalar = ossim_hdf5::getScalarType( latDataSet );
if ( scalar == OSSIM_FLOAT32 )
{
// Set the return status to true if we get here...
status = true;
// See if we need to swap bytes:
ossimEndian* endian = 0;
if ( ( ossim::byteOrder() != ossim_hdf5::getByteOrder( latDataSet ) ) )
{
endian = new ossimEndian();
}
// Native type:
H5::DataType latDataType = latDataSet->getDataType();
H5::DataType lonDataType = lonDataSet->getDataType();
// Output dataspace always the same, width of one line.
H5::DataSpace bufferDataSpace( OUT_DIM_COUNT, &outputCount.front());
bufferDataSpace.selectHyperslab( H5S_SELECT_SET,
&outputCount.front(),
&outputOffset.front() );
// Arrays to hold a single line of latitude longitude values.
vector<ossim_float32> latValue(COLS);
vector<ossim_float32> lonValue(COLS);
hsize_t row = 0;
// Line loop:
for ( ossim_uint32 y = 0; y < gridRows; ++y )
{
// row = line in image space
row = y*GRID_SIZE;
if ( row < ROWS )
{
inputOffset[0] = row + validRect.ul().y;
latDataSpace.selectHyperslab( H5S_SELECT_SET,
&inputCount.front(),
&inputOffset.front() );
lonDataSpace.selectHyperslab( H5S_SELECT_SET,
&inputCount.front(),
&inputOffset.front() );
// Read data from file into the buffer.
latDataSet->read( &(latValue.front()), latDataType,
bufferDataSpace, latDataSpace );
lonDataSet->read( &(lonValue.front()), lonDataType,
bufferDataSpace, lonDataSpace );
if ( endian )
{
// If the endian pointer is initialized(not zero) swap the bytes.
endian->swap( &(latValue.front()), COLS );
endian->swap( &(lonValue.front()), COLS );
}
// Sample loop:
hsize_t col = 0;
for ( ossim_uint32 x = 0; x < gridCols; ++x )
{
ossim_float32 lat = ossim::nan();
ossim_float32 lon = ossim::nan();
// col = sample in image space
col = x*GRID_SIZE;
if ( col < COLS )
{
if ( (latValue[col] > NULL_VALUE)&&(lonValue[col] > NULL_VALUE) )
{
lat = latValue[col];
lon = lonValue[col];
if ( m_crossesDateline )
{
if ( lon < 0.0 ) lon += 360;
}
}
else // Nulls in grid!
{
std::string errMsg =
"ossimH5GridModel::setGridNodes encountered nans!";
throw ossimException(errMsg);
}
}
else // Last column is outside of image bounds.
{
// Get the last two latitude values:
ossim_float32 lat1 = theLatGrid.getNode( x-2, y );
ossim_float32 lat2 = theLatGrid.getNode( x-1, y );
// Get the last two longitude values
ossim_float32 lon1 = theLonGrid.getNode( x-2, y );
ossim_float32 lon2 = theLonGrid.getNode( x-1, y );
if ( ( lat1 > NULL_VALUE ) && ( lat2 > NULL_VALUE ) )
{
// Delta between last two latitude grid values.
ossim_float32 latSpacing = lat2 - lat1;
// Compute:
lat = lat2 + latSpacing;
}
else // Nulls in grid!
{
std::string errMsg =
"ossimH5GridModel::setGridNodes encountered nans!";
throw ossimException(errMsg);
}
if ( ( lon1 > NULL_VALUE ) && ( lon2 > NULL_VALUE ) )
{
// Delta between last two longitude values.
ossim_float32 lonSpacing = lon2 - lon1;
// Compute:
lon = lon2 + lonSpacing;
// Check for wrap:
if ( !m_crossesDateline && ( lon > 180 ) )
{
lon -= 360.0;
}
}
else // Nulls in grid!
{
std::string errMsg =
"ossimH5GridModel::setGridNodes encountered nans!";
throw ossimException(errMsg);
}
#if 0 /* Please leave for debug. (drb) */
cout << "lat1: " << lat1 << " lat2 " << lat2
<< " lon1 " << lon1 << " lon2 " << lon2
<< "\n";
#endif
}
// Assign the latitude and longitude.
theLatGrid.setNode( x, y, lat );
theLonGrid.setNode( x, y, lon );
#if 0 /* Please leave for debug. (drb) */
cout << "x,y,col,row,lat,lon:" << x << "," << y << ","
<< col << "," << row << ","
<< theLatGrid.getNode(x, y)
<< "," << theLonGrid.getNode( x, y) << "\n";
#endif
} // End sample loop.
}
else // Row is outside of image bounds:
{
// Sample loop:
for ( ossim_uint32 x = 0; x < gridCols; ++x )
{
ossim_float32 lat = ossim::nan();
ossim_float32 lon = ossim::nan();
ossim_float32 lat1 = theLatGrid.getNode( x, y-2 );
ossim_float32 lat2 = theLatGrid.getNode( x, y-1 );
ossim_float32 lon1 = theLonGrid.getNode( x, y-2 );
ossim_float32 lon2 = theLonGrid.getNode( x, y-1 );
if ( ( lon1 > NULL_VALUE ) && ( lon2 > NULL_VALUE ) )
{
// Delta between last two longitude values.
ossim_float32 lonSpacing = lon2 - lon1;
// Compute:
lon = lon2 + lonSpacing;
// Check for wrap:
if ( !m_crossesDateline && ( lon > 180 ) )
{
lon -= 360.0;
}
}
else // Nulls in grid!
{
std::string errMsg =
"ossimH5GridModel::setGridNodes encountered nans!";
throw ossimException(errMsg);
}
if ( ( lat1 > NULL_VALUE ) && ( lat2 > NULL_VALUE ) )
{
// Delta between last two latitude values.
ossim_float32 latSpacing = lat2 - lat1;
lat = lat2 + latSpacing;
}
else // Nulls in grid!
{
std::string errMsg =
"ossimH5GridModel::setGridNodes encountered nans!";
throw ossimException(errMsg);
}
#if 0 /* Please leave for debug. (drb) */
hsize_t col = x*GRID_SIZE; // Sample in image space
cout << "lat1: " << lat1 << " lat2 " << lat2
<< " lon1 " << lon1 << " lon2 " << lon2
<< "\nx,y,col,row,lat,lon:" << x << "," << y << ","
<< col << "," << row << "," << lat << "," << lon << "\n";
#endif
// Assign the latitude::
theLatGrid.setNode( x, y, lat );
// Assign the longitude.
theLonGrid.setNode( x, y, lon );
} // End sample loop.
} // Matches if ( row < imageRows ){...}else{
} // End line loop.
latDataSpace.close();
lonDataSpace.close();
if ( status )
{
theSeedFunction = ossim_hdf5::getBilinearProjection(
*latDataSet,*lonDataSet, validRect );
// Bileaner projection to handle
ossimDrect imageRect(validRect);
initializeModelParams(imageRect);
// debugDump();
}
if ( endian )
{
delete endian;
endian = 0;
}
} // Matches: if ( scalar == OSSIM_FLOAT32 )
} // Matches: if ( (latDimsOut[0] == imageRows) ...
} // Matches: if ( ( LAT_DIM_COUNT == 2 ) ...
} // Matches: if ( latDataSet && lonDataSet
return status;
} // End: bool ossimH5GridModel::setGridNodes( H5::DataSet* latDataSet, ... )
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();
}
}
};
bool ossim_hdf5::getValidBoundingRect( H5::DataSet& dataset,
const std::string& name,
ossimIrect& rect )
{
bool result = false;
H5::DataSpace imageDataspace = dataset.getSpace();
const ossim_int32 IN_DIM_COUNT = imageDataspace.getSimpleExtentNdims();
if ( IN_DIM_COUNT == 2 )
{
// Get the extents. Assuming dimensions are same for lat lon dataset.
std::vector<hsize_t> dimsOut(IN_DIM_COUNT);
imageDataspace.getSimpleExtentDims( &dimsOut.front(), 0 );
if ( dimsOut[0] && dimsOut[1] )
{
//---
// Capture the rectangle:
// dimsOut[0] is height, dimsOut[1] is width:
//---
rect = ossimIrect( 0, 0,
static_cast<ossim_int32>( dimsOut[1]-1 ),
static_cast<ossim_int32>( dimsOut[0]-1 ) );
const ossim_int32 WIDTH = rect.width();
std::vector<hsize_t> inputCount(IN_DIM_COUNT);
std::vector<hsize_t> inputOffset(IN_DIM_COUNT);
inputOffset[0] = 0;
inputOffset[1] = 0;
inputCount[0] = 1;
inputCount[1] = WIDTH;
// Output dataspace dimensions.
const ossim_int32 OUT_DIM_COUNT = 3;
std::vector<hsize_t> outputCount(OUT_DIM_COUNT);
outputCount[0] = 1; // single band
outputCount[1] = 1; // single line
outputCount[2] = WIDTH; // whole line
// Output dataspace offset.
std::vector<hsize_t> outputOffset(OUT_DIM_COUNT);
outputOffset[0] = 0;
outputOffset[1] = 0;
outputOffset[2] = 0;
ossimScalarType scalar = ossim_hdf5::getScalarType( &dataset );
if ( scalar == OSSIM_FLOAT32 )
{
// See if we need to swap bytes:
ossimEndian* endian = 0;
if ( ( ossim::byteOrder() != ossim_hdf5::getByteOrder( &dataset ) ) )
{
endian = new ossimEndian();
}
// Native type:
H5::DataType datatype = dataset.getDataType();
// Output dataspace always the same one line.
H5::DataSpace bufferDataSpace( OUT_DIM_COUNT, &outputCount.front());
bufferDataSpace.selectHyperslab( H5S_SELECT_SET,
&outputCount.front(),
&outputOffset.front() );
//---
// Dataset sample has NULL lines at the end so scan for valid rect.
// Use "<= -999" for test as per NOAA as it seems the NULL value is
// fuzzy. e.g. -999.3.
//---
const ossim_float32 NULL_VALUE = -999.0;
//---
// VIIRS Radiance data has a -1.5e-9 in the first column.
// Treat this as a null.
//---
const ossim_float32 NULL_VALUE2 = ( name == "/All_Data/VIIRS-DNB-SDR_All/Radiance" )
? -1.5e-9 : NULL_VALUE;
const ossim_float32 TOLERANCE = 0.1e-9; // For ossim::almostEqual()
// Hold one line:
std::vector<ossim_float32> values( WIDTH );
// Find the ul pixel:
ossimIpt ulIpt = rect.ul();
bool found = false;
// Line loop to find upper left pixel:
while ( ulIpt.y <= rect.lr().y )
{
inputOffset[0] = static_cast<hsize_t>(ulIpt.y);
imageDataspace.selectHyperslab( H5S_SELECT_SET,
&inputCount.front(),
&inputOffset.front() );
// Read data from file into the buffer.
dataset.read( (void*)&values.front(), datatype, bufferDataSpace, imageDataspace );
if ( endian )
{
// If the endian pointer is initialized(not zero) swap the bytes.
endian->swap( scalar, (void*)&values.front(), WIDTH );
}
// Sample loop:
ulIpt.x = rect.ul().x;
ossim_int32 index = 0;
while ( ulIpt.x <= rect.lr().x )
{
if ( !ossim::almostEqual(values[index], NULL_VALUE2, TOLERANCE) &&
( values[index] > NULL_VALUE ) )
{
found = true; // Found valid pixel.
break;
}
++ulIpt.x;
++index;
} // End: sample loop
if ( found )
{
break;
}
++ulIpt.y;
} // End line loop to find ul pixel:
// Find the lower right pixel:
ossimIpt lrIpt = rect.lr();
found = false;
// Line loop to find last pixel:
while ( lrIpt.y >= rect.ul().y )
{
inputOffset[0] = static_cast<hsize_t>(lrIpt.y);
imageDataspace.selectHyperslab( H5S_SELECT_SET,
&inputCount.front(),
&inputOffset.front() );
// Read data from file into the buffer.
dataset.read( (void*)&values.front(), datatype, bufferDataSpace, imageDataspace );
if ( endian )
{
// If the endian pointer is initialized(not zero) swap the bytes.
endian->swap( scalar, (void*)&values.front(), WIDTH );
}
// Sample loop:
lrIpt.x = rect.lr().x;
ossim_int32 index = WIDTH-1;
while ( lrIpt.x >= rect.ul().x )
{
if ( !ossim::almostEqual(values[index], NULL_VALUE2, TOLERANCE) &&
( values[index] > NULL_VALUE ) )
{
found = true; // Found valid pixel.
break;
}
--lrIpt.x;
--index;
} // End: sample loop
if ( found )
{
break;
}
--lrIpt.y;
} // End line loop to find lower right pixel.
rect = ossimIrect( ulIpt, lrIpt );
// Cleanup:
if ( endian )
{
delete endian;
endian = 0;
}
result = true;
}
else // Matches: if ( scalar == OSSIM_FLOAT32 ){...}
{
ossimNotify(ossimNotifyLevel_WARN)
<< "ossim_hdf5::getBoundingRect WARNING!"
<< "\nUnhandled scalar type: "
<< ossimScalarTypeLut::instance()->getEntryString( scalar )
<< std::endl;
}
} // Matches: if ( dimsOut...
} // Matches: if ( IN_DIM_COUNT == 2 )
imageDataspace.close();
return result;
} // End: ossim_hdf5::getBoundingRect(...)
ossimRefPtr<ossimProjection> ossim_hdf5::getBilinearProjection(
H5::DataSet& latDataSet, H5::DataSet& lonDataSet, const ossimIrect& validRect )
{
ossimRefPtr<ossimProjection> proj = 0;
// Get dataspace of the dataset.
H5::DataSpace latDataSpace = latDataSet.getSpace();
H5::DataSpace lonDataSpace = lonDataSet.getSpace();
// Number of dimensions of the input dataspace:
const ossim_int32 DIM_COUNT = latDataSpace.getSimpleExtentNdims();
if ( DIM_COUNT == 2 )
{
// Get the extents. Assuming dimensions are same for lat lon dataset.
std::vector<hsize_t> dimsOut(DIM_COUNT);
latDataSpace.getSimpleExtentDims( &dimsOut.front(), 0 );
if ( dimsOut[0] && dimsOut[1] )
{
std::vector<hsize_t> inputCount(DIM_COUNT);
std::vector<hsize_t> inputOffset(DIM_COUNT);
inputOffset[0] = 0;
inputOffset[1] = 0;
inputCount[0] = 1;
inputCount[1] = 1;
// Output dataspace dimensions.
const ossim_int32 OUT_DIM_COUNT = 3;
std::vector<hsize_t> outputCount(OUT_DIM_COUNT);
outputCount[0] = 1; // single band
outputCount[1] = 1; // single line
outputCount[2] = 1; // single sample
// Output dataspace offset.
std::vector<hsize_t> outputOffset(OUT_DIM_COUNT);
outputOffset[0] = 0;
outputOffset[1] = 0;
outputOffset[2] = 0;
ossimScalarType scalar = ossim_hdf5::getScalarType( &latDataSet );
if ( scalar == OSSIM_FLOAT32 )
{
// See if we need to swap bytes:
ossimEndian* endian = 0;
if ( ( ossim::byteOrder() != ossim_hdf5::getByteOrder( &latDataSet ) ) )
{
endian = new ossimEndian();
}
// Native type:
H5::DataType latDataType = latDataSet.getDataType();
H5::DataType lonDataType = lonDataSet.getDataType();
std::vector<ossimDpt> ipts;
std::vector<ossimGpt> gpts;
ossimGpt gpt(0.0, 0.0, 0.0); // Assuming WGS84...
ossim_float32 latValue = 0.0;
ossim_float32 lonValue = 0.0;
// Only grab every 256th value.:
const ossim_int32 GRID_SIZE = 256;
// Output dataspace always the same one pixel.
H5::DataSpace bufferDataSpace( OUT_DIM_COUNT, &outputCount.front());
bufferDataSpace.selectHyperslab( H5S_SELECT_SET,
&outputCount.front(),
&outputOffset.front() );
//---
// Dataset sample has NULL lines at the end so scan for valid rect.
// Use "<= -999" for test as per NOAA as it seems the NULL value is
// fuzzy. e.g. -999.3.
//---
const ossim_float32 NULL_VALUE = -999.0;
//---
// Get the tie points within the valid rect:
//---
ossimDpt ipt = validRect.ul();
while ( ipt.y <= validRect.lr().y )
{
inputOffset[0] = static_cast<hsize_t>(ipt.y);
// Sample loop:
ipt.x = validRect.ul().x;
while ( ipt.x <= validRect.lr().x )
{
inputOffset[1] = static_cast<hsize_t>(ipt.x);
latDataSpace.selectHyperslab( H5S_SELECT_SET,
&inputCount.front(),
&inputOffset.front() );
lonDataSpace.selectHyperslab( H5S_SELECT_SET,
&inputCount.front(),
&inputOffset.front() );
// Read data from file into the buffer.
latDataSet.read( &latValue, latDataType, bufferDataSpace, latDataSpace );
lonDataSet.read( &lonValue, lonDataType, bufferDataSpace, lonDataSpace );
if ( endian )
{
// If the endian pointer is initialized(not zero) swap the bytes.
endian->swap( latValue );
endian->swap( lonValue );
}
if ( ( latValue > NULL_VALUE ) && ( lonValue > NULL_VALUE ) )
{
gpt.lat = latValue;
gpt.lon = lonValue;
gpts.push_back( gpt );
// Add the image point subtracting the image offset.
ossimIpt shiftedIpt = ipt - validRect.ul();
ipts.push_back( shiftedIpt );
}
// Go to next point:
if ( ipt.x < validRect.lr().x )
{
ipt.x += GRID_SIZE;
if ( ipt.x > validRect.lr().x )
{
ipt.x = validRect.lr().x; // Clamp to last sample.
}
}
else
{
break; // At the end:
}
} // End sample loop.
if ( ipt.y < validRect.lr().y )
{
ipt.y += GRID_SIZE;
if ( ipt.y > validRect.lr().y )
{
ipt.y = validRect.lr().y; // Clamp to last line.
}
}
else
{
break; // At the end:
}
} // End line loop.
if ( ipts.size() )
{
// Create the projection:
ossimRefPtr<ossimBilinearProjection> bp = new ossimBilinearProjection();
// Add the tie points:
bp->setTiePoints( ipts, gpts );
// Assign to output projection:
proj = bp.get();
}
// Cleanup:
if ( endian )
{
delete endian;
endian = 0;
}
}
else // Matches: if ( scalar == OSSIM_FLOAT32 ){...}
{
ossimNotify(ossimNotifyLevel_WARN)
<< "ossim_hdf5::getBilinearProjection WARNING!"
<< "\nUnhandled scalar type: "
<< ossimScalarTypeLut::instance()->getEntryString( scalar )
<< std::endl;
}
} // Matches: if ( dimsOut...
} // Matches: if ( IN_DIM_COUNT == 2 )
latDataSpace.close();
lonDataSpace.close();
return proj;
} // End: ossim_hdf5::getBilinearProjection()
bool ossim_hdf5::crossesDateline( H5::DataSet& dataset, const ossimIrect& validRect )
{
bool result = false;
H5::DataSpace dataspace = dataset.getSpace();
// Number of dimensions of the input dataspace:
const ossim_int32 DIM_COUNT = dataspace.getSimpleExtentNdims();
if ( DIM_COUNT == 2 )
{
const ossim_uint32 ROWS = validRect.height();
const ossim_uint32 COLS = validRect.width();
// Get the extents. Assuming dimensions are same for lat lon dataset.
std::vector<hsize_t> dimsOut(DIM_COUNT);
dataspace.getSimpleExtentDims( &dimsOut.front(), 0 );
if ( (ROWS <= dimsOut[0]) && (COLS <= dimsOut[1]) )
{
std::vector<hsize_t> inputCount(DIM_COUNT);
std::vector<hsize_t> inputOffset(DIM_COUNT);
inputCount[0] = 1; // row
inputCount[1] = COLS; // col
// Output dataspace dimensions.
const ossim_int32 OUT_DIM_COUNT = 3;
std::vector<hsize_t> outputCount(OUT_DIM_COUNT);
outputCount[0] = 1; // single band
outputCount[1] = 1; // single line
outputCount[2] = COLS; // single sample
// Output dataspace offset.
std::vector<hsize_t> outputOffset(OUT_DIM_COUNT);
outputOffset[0] = 0;
outputOffset[1] = 0;
outputOffset[2] = 0;
ossimScalarType scalar = ossim_hdf5::getScalarType( &dataset );
if ( scalar == OSSIM_FLOAT32 )
{
// See if we need to swap bytes:
ossimEndian* endian = 0;
if ( ( ossim::byteOrder() != ossim_hdf5::getByteOrder( &dataset ) ) )
{
endian = new ossimEndian();
}
// Native type:
H5::DataType datatype = dataset.getDataType();
// Output dataspace always the same one line.
H5::DataSpace bufferDataSpace( OUT_DIM_COUNT, &outputCount.front());
bufferDataSpace.selectHyperslab( H5S_SELECT_SET,
&outputCount.front(),
&outputOffset.front() );
//---
// Dataset sample has NULL lines at the end so scan for valid rect.
// Use "<= -999" for test as per NOAA as it seems the NULL value is
// fuzzy. e.g. -999.3.
//---
// Buffer to hold a line:
std::vector<ossim_float32> lineBuffer(validRect.width());
// Read the first line:
inputOffset[0] = static_cast<hsize_t>(validRect.ul().y);
inputOffset[1] = static_cast<hsize_t>(validRect.ul().x);
dataspace.selectHyperslab( H5S_SELECT_SET,
&inputCount.front(),
&inputOffset.front() );
dataset.read( &(lineBuffer.front()), datatype, bufferDataSpace, dataspace );
if ( endian )
{
// If the endian pointer is initialized(not zero) swap the bytes.
endian->swap( &(lineBuffer.front()), COLS );
}
// Test the first line:
result = ossim_hdf5::crossesDateline( lineBuffer );
if ( !result )
{
// Test the last line:
inputOffset[0] = static_cast<hsize_t>(validRect.ll().y);
inputOffset[1] = static_cast<hsize_t>(validRect.ll().x);
dataspace.selectHyperslab( H5S_SELECT_SET,
&inputCount.front(),
&inputOffset.front() );
dataset.read( &(lineBuffer.front()), datatype, bufferDataSpace, dataspace );
result = ossim_hdf5::crossesDateline( lineBuffer );
}
if ( endian )
{
delete endian;
endian = 0;
}
}
else // Matches: if ( scalar == OSSIM_FLOAT32 ){...}
{
ossimNotify(ossimNotifyLevel_WARN)
<< "ossim_hdf5::crossesDateline WARNING!"
<< "\nUnhandled scalar type: "
<< ossimScalarTypeLut::instance()->getEntryString( scalar )
<< std::endl;
}
} // Matches: if ( dimsOut...
} // Matches: if ( IN_DIM_COUNT == 2 )
dataspace.close();
return result;
} // End: ossim_hdf5::crossesDateline(...)
void ossimH5ImageDataset::getTileBuf(void* buffer, const ossimIrect& rect, ossim_uint32 band)
{
static const char MODULE[] = "ossimH5ImageDataset::getTileBuf";
if ( m_dataset )
{
try
{
// Shift rectangle by the sub image offse (if any) from the m_validRect.
ossimIrect irect = rect + m_validRect.ul();
//--
// Turn off the auto-printing when failure occurs so that we can
// handle the errors appropriately
//---
// H5::Exception::dontPrint();
// NOTE: rank == array dimensions in hdf5 documentation lingo.
// Get dataspace of the dataset.
H5::DataSpace imageDataSpace = m_dataset->getSpace();
// Number of dimensions of the input dataspace.:
const ossim_int32 IN_DIM_COUNT = imageDataSpace.getSimpleExtentNdims();
// Native type:
H5::DataType dataType = m_dataset->getDataType();
std::vector<hsize_t> inputCount(IN_DIM_COUNT);
std::vector<hsize_t> inputOffset(IN_DIM_COUNT);
if ( IN_DIM_COUNT == 2 )
{
inputOffset[0] = irect.ul().y;
inputOffset[1] = irect.ul().x;
inputCount[0] = irect.height();
inputCount[1] = irect.width();
}
else
{
inputOffset[0] = band;
inputOffset[1] = irect.ul().y;
inputOffset[2] = irect.ul().x;
inputCount[0] = 1;
inputCount[1] = irect.height();
inputCount[2] = irect.width();
}
// Define hyperslab in the dataset; implicitly giving strike strike and block NULL.
imageDataSpace.selectHyperslab( H5S_SELECT_SET,
&inputCount.front(),
&inputOffset.front() );
// Output dataspace dimensions.
const ossim_int32 OUT_DIM_COUNT = 3;
std::vector<hsize_t> outputCount(OUT_DIM_COUNT);
outputCount[0] = 1; // single band
outputCount[1] = irect.height(); // lines
outputCount[2] = irect.width(); // samples
// Output dataspace offset.
std::vector<hsize_t> outputOffset(OUT_DIM_COUNT);
outputOffset[0] = 0;
outputOffset[1] = 0;
outputOffset[2] = 0;
// Output dataspace.
H5::DataSpace bufferDataSpace( OUT_DIM_COUNT, &outputCount.front());
bufferDataSpace.selectHyperslab( H5S_SELECT_SET,
&outputCount.front(),
&outputOffset.front() );
// Read data from file into the buffer.
m_dataset->read( buffer, dataType, bufferDataSpace, imageDataSpace );
if ( m_endian )
{
// If the m_endian pointer is initialized(not zero) swap the bytes.
m_endian->swap( m_scalar, buffer, irect.area() );
}
// Cleanup:
bufferDataSpace.close();
dataType.close();
imageDataSpace.close();
// memSpace.close();
// dataType.close();
// dataSpace.close();
}
catch( const H5::FileIException& error )
{
ossimNotify(ossimNotifyLevel_WARN)
<< MODULE << " caught H5::FileIException!" << std::endl;
error.printError();
}
// catch failure caused by the DataSet operations
catch( const H5::DataSetIException& error )
{
ossimNotify(ossimNotifyLevel_WARN)
<< MODULE << " caught H5::DataSetIException!" << std::endl;
error.printError();
}
// catch failure caused by the DataSpace operations
catch( const H5::DataSpaceIException& error )
{
ossimNotify(ossimNotifyLevel_WARN)
<< MODULE << " caught H5::DataSpaceIException!" << std::endl;
error.printError();
}
// catch failure caused by the DataSpace operations
catch( const H5::DataTypeIException& error )
{
ossimNotify(ossimNotifyLevel_WARN)
<< MODULE << " caught H5::DataTypeIException!" << std::endl;
error.printError();
}
catch( ... )
{
ossimNotify(ossimNotifyLevel_WARN)
<< MODULE << " caught unknown exception !" << std::endl;
}
} // Matches: if ( m_dataset )
} // End: ossimH5ImageDataset::getTileBuf