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 Bundle2::storeParameters(H5::H5File& file) const {
H5::Group root = file.openGroup("/");
H5::DataSpace scalar;
H5::Attribute attr = root.createAttribute("version", H5::PredType::STD_U32LE, scalar);
attr.write(H5::PredType::NATIVE_UINT, &version_);
attr.close();
unsigned char r2 = parameters_.reduce2?1:0;
attr = root.createAttribute("reduce2", H5::PredType::STD_U8LE, scalar);
attr.write(H5::PredType::NATIVE_UCHAR, &r2);
attr.close();
attr = root.createAttribute("xROI", H5::PredType::STD_U32LE, scalar);
attr.write(H5::PredType::NATIVE_UINT, ¶meters_.xROI);
attr.close();
attr = root.createAttribute("yROI", H5::PredType::STD_U32LE, scalar);
attr.write(H5::PredType::NATIVE_UINT, ¶meters_.yROI);
attr.close();
scalar.close();
root.close();
}
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();
}
}
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;
}
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;
}
void Bundle2::closeSaveStream() {
H5::DataSpace scalar;
// Saving remaining POI information
H5::Group poiGroup = streamFile_->openGroup("/POI");
H5::Attribute attr = poiGroup.createAttribute("count", H5::PredType::STD_U64LE, scalar);
hsize_t count = poiFirstFrame_;
attr.write(H5::PredType::NATIVE_HSIZE, &count);
attr.close();
poiGroup.close();
scalar.close();
// Closing HDF5 file
streamFile_->close();
delete streamFile_;
streamFile_ = NULL;
}
void Bundle2::streamPOI(size_t frame) {
H5::DataSpace scalar;
H5::Group poiGroup = streamFile_->openGroup("/POI");
for(size_t i = poiFirstFrame_; i <= frame; ++i) {
const std::string frameGroupName = boost::str(boost::format("Frame %1$04d") % i);
H5::Group frameGroup = poiGroup.createGroup(frameGroupName);
hsize_t count = poi_[(ptrdiff_t)i - (ptrdiff_t)poiFirstFrame_].size();
H5::Attribute 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_[(ptrdiff_t)i - (ptrdiff_t)poiFirstFrame_].size(); ++camera)
poi_[(ptrdiff_t)i - (ptrdiff_t)poiFirstFrame_][camera].save(frameGroup, camera);
frameGroup.close();
}
poiGroup.close();
scalar.close();
poi_.erase(poi_.begin(), poi_.begin() + (ptrdiff_t)frame - (ptrdiff_t)poiFirstFrame_ + 1);
poiFirstFrame_ = frame + 1;
}
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();
}
void BufferedHDF2DArray<T>::Flush(int destRow) {
//
// A default writeRow of -1 implies append
//
int numDataRows;
//
// this->bufferIndex points after the end of the last data in the
// buffer (full rows), so this->bufferIndex / rowLength is the
// number of number of rows to create.
//
numDataRows = this->bufferIndex / rowLength;
if (numDataRows > 0) {
assert(fileDataSpaceInitialized);
H5::DataSpace fileSpace;
fileSpace = dataset.getSpace();
//
// Load the current size of the array on disk.
//
hsize_t fileArraySize[2], fileArrayMaxSize[2], blockStart[2];
fileSpace.getSimpleExtentDims(fileArraySize, fileArrayMaxSize);
// Save this for later to determine the offsets
blockStart[0] = fileArraySize[0];
blockStart[1] = fileArraySize[1];
//
// Calculate the number of rows to create. This is dependent
// on the current file size, the destination of where the data
// will go, and how much to write.
//
if (destRow == -1) {
fileArraySize[0] += numDataRows;
}
else {
// If the data cannot fit in the current file size, extend
// it, otherwise, do not toch the file array size.
if (destRow + numDataRows > fileArraySize[0]) {
fileArraySize[0] = destRow + numDataRows;
}
}
//
// Make room in the file for the array.
//
dataset.extend(fileArraySize);
H5::DataSpace extendedSpace = dataset.getSpace();
//
// Store the newly dimensioned dataspaces.
//
fileSpace.getSimpleExtentDims(fileArraySize, fileArrayMaxSize);
//
// Configure the proper addressing to append to the array.
//
hsize_t dataSize[2];
dataSize[0] = numDataRows;
dataSize[1] = rowLength;
hsize_t offset[2];
//
// Determine which row to write to.
//
if (destRow == -1) {
offset[0] = blockStart[0];
}
else {
offset[0] = destRow;
}
offset[1] = 0;
extendedSpace.selectHyperslab(H5S_SELECT_SET, dataSize, offset);
H5::DataSpace memorySpace(2, dataSize);
//
// Finally, write out the data.
// This uses a generic function which is specialized with
// templates later on to t
// memorySpace addresses the entire array in linear format
// fileSpace addresses the last dataLength blocks of dataset.
//
TypedWriteRow(this->writeBuffer, memorySpace, extendedSpace);
memorySpace.close();
extendedSpace.close();
fileSpace.close();
}
this->ResetWriteBuffer();
}
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(...)
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();
}
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
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, ... )
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 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();
}
// 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();
}
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, ... )
