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Reads an entire array
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Ryan Pals committed Feb 7, 2020
1 parent b079046 commit bcd8c3a
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Showing 2 changed files with 66 additions and 62 deletions.
19 changes: 16 additions & 3 deletions plugins/hdf/io/Hdf5Handler.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -156,8 +156,9 @@ void Hdf5Handler::initialize(
throw error("Unkown type: " + vauge_type);
}
// m_buf = malloc(dtype.getSize() * m_chunkSize); //TODO free
m_buf = malloc(dtype.getSize() * m_chunkSize); //TODO free
// m_buf = malloc(dtype.getSize() * m_chunkSize); //TODO free
m_data.resize(m_chunkSize*dtype.getSize());
m_logger->get(LogLevel::Warning) << "m_data.size: " << m_data.size() << std::endl;
m_logger->get(LogLevel::Warning) << "Chunk offset: " << m_chunkOffset << std::endl;
// dspace.selectElements(H5S_SELECT_SET, m_chunkSize, &m_chunkOffset);
// dspace.selectHyperslab(H5S_SELECT_SET, &m_chunkSize, &m_chunkOffset);
Expand All @@ -184,12 +185,24 @@ void Hdf5Handler::close()
void *Hdf5Handler::getNextChunk() {
// m_logger->get(LogLevel::Warning) << "chunk size: " << m_chunkSize << ", chunk offset: "
// << m_chunkOffset << std::endl;
m_dspace.selectHyperslab(H5S_SELECT_SET, &m_chunkSize, &m_chunkOffset);
hsize_t elementsRemaining = m_numPoints - m_chunkOffset;
// if(elementsRemaining < m_chunkSize) {
// selectionSize = elementsRemaining;
// }
hsize_t selectionSize = std::min(elementsRemaining, m_chunkSize);

// m_logger->get(LogLevel::Warning) << "Points remainging: " << elementsRemaining;
H5::DataSpace memspace(1, &selectionSize);
m_dspace.selectHyperslab(H5S_SELECT_SET, &selectionSize, &m_chunkOffset);
m_logger->get(LogLevel::Warning) << "m_data: " << (void *)m_data.data() << std::endl;
m_logger->get(LogLevel::Warning) << "chunkOffset: " << m_chunkOffset << std::endl;
m_logger->get(LogLevel::Warning) << "chunkSize: " << selectionSize << std::endl;
m_dset.read(m_data.data(),
m_dset.getDataType(),
H5::DataSpace::ALL,
memspace,
m_dspace );
m_chunkOffset += m_chunkSize;
m_logger->get(LogLevel::Warning) << "m_data[0] = " << *((double *)m_data.data()) << std::endl;
return m_data.data();
}

Expand Down
109 changes: 50 additions & 59 deletions plugins/hdf/io/HdfReader.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -72,13 +72,53 @@ CREATE_SHARED_STAGE(HdfReader, s_info)

std::string HdfReader::getName() const { return s_info.name; }

void addField(PointViewPtr view, hdf5::DimInfo& info, PointId id, void *p) {
switch(info.pdal_type) {
case Dimension::Type::Double:
view->setField(info.id, id, * ((double *) p));
break;
case Dimension::Type::Float:
view->setField(info.id, id, * ((float *) p));
break;
case Dimension::Type::Signed8:
view->setField(info.id, id, * ((int8_t *) p));
break;
case Dimension::Type::Signed16:
view->setField(info.id, id, * ((int16_t *) p));
break;
case Dimension::Type::Signed32:
view->setField(info.id, id, * ((int32_t *) p));
break;
case Dimension::Type::Signed64:
view->setField(info.id, id, * ((int64_t *) p));
break;
case Dimension::Type::Unsigned8:
view->setField(info.id, id, * ((uint8_t *) p));
break;
case Dimension::Type::Unsigned16:
view->setField(info.id, id, * ((uint16_t *) p));
break;
case Dimension::Type::Unsigned32:
view->setField(info.id, id, * ((uint32_t *) p));
break;
case Dimension::Type::Unsigned64:
view->setField(info.id, id, * ((uint64_t *) p));
break;
default:
view->setField(info.id, id, 0);
break;
}
}

void HdfReader::addDimensions(PointLayoutPtr layout)
{
m_hdf5Handler.setLog(log());
m_hdf5Handler.initialize(m_filename, m_dimName, m_datasetName);

// layout->registerDims(dimensions());
std::cout << "HdfReader::addDimensions begin" << std::endl;
m_infos = m_hdf5Handler.getDimensionInfos();
for(int i = 0; i < m_infos.size(); i++) {
for(uint64_t i = 0; i < m_infos.size(); i++) {
// Dimension::BaseType b = Dimension::BaseType::None;
// Dimension::Type t = Dimension::Type::None;
// if(info.hdf_type == H5T_INTEGER) {
Expand Down Expand Up @@ -113,18 +153,6 @@ void HdfReader::addDimensions(PointLayoutPtr layout)

void HdfReader::ready(PointTableRef table)
{
std::cout << "HdfReader::ready" << std::endl;
m_hdf5Handler.setLog(log());
try
{
// m_hdf5Handler.initialize(m_filename, hdf5Columns);
// m_hdf5Handler.initialize(m_filename);
m_hdf5Handler.initialize(m_filename, m_dimName, m_datasetName);
}
catch (const Hdf5Handler::error& err)
{
throwError(err.what());
}
m_index = 0;
}

Expand All @@ -144,16 +172,12 @@ point_count_t HdfReader::read(PointViewPtr view, point_count_t count)
// std::unique_ptr<unsigned char>
// rawData(new unsigned char[count * point_size]);

// for(std::size_t di = 0; di < m_idlist.size(); di++) {
// Dimension::Id dimId = m_idlist[di];
// std::cout << m_idlist.size() << std::endl;
// for(auto dimId : m_idlist) {
for(auto info : m_infos) {
PointId nextId = startId;
std::cout << (unsigned)info.id << ": ";
void *buf = NULL;
// for(uint64_t pi = 0; pi < m_hdf5Handler.getNumPoints(); pi++) {
for(uint64_t pi = 0; pi < m_hdf5Handler.getNumPoints(); pi++) {
PointId nextId = startId;
void *buf = NULL;
// for(uint64_t pi = 0; pi < m_hdf5Handler.getNumPoints(); pi++) {
for(uint64_t pi = 0; pi < m_hdf5Handler.getNumPoints(); pi++) {
// for(auto info : m_infos) {
auto info = m_infos.at(0);
int bufIndex = pi % m_hdf5Handler.m_chunkSize;
if(bufIndex == 0) {
std::cout << "bufIndex: " << bufIndex <<
Expand All @@ -162,42 +186,9 @@ point_count_t HdfReader::read(PointViewPtr view, point_count_t count)
}
void *p = buf + bufIndex*point_size + info.offset;
if(pi == 0) std::cout<< Dimension::interpretationName(info.pdal_type) <<std::endl;
switch(info.pdal_type) {
case Dimension::Type::Double:
view->setField(info.id, nextId++, * ((double *) p));
break;
case Dimension::Type::Float:
view->setField(info.id, nextId++, * ((float *) p));
break;
case Dimension::Type::Signed8:
view->setField(info.id, nextId++, * ((int8_t *) p));
break;
case Dimension::Type::Signed16:
view->setField(info.id, nextId++, * ((int16_t *) p));
break;
case Dimension::Type::Signed32:
view->setField(info.id, nextId++, * ((int32_t *) p));
break;
case Dimension::Type::Signed64:
view->setField(info.id, nextId++, * ((int64_t *) p));
break;
case Dimension::Type::Unsigned8:
view->setField(info.id, nextId++, * ((uint8_t *) p));
break;
case Dimension::Type::Unsigned16:
view->setField(info.id, nextId++, * ((uint16_t *) p));
break;
case Dimension::Type::Unsigned32:
view->setField(info.id, nextId++, * ((uint32_t *) p));
break;
case Dimension::Type::Unsigned64:
view->setField(info.id, nextId++, * ((uint64_t *) p));
break;
default:
view->setField(info.id, nextId, 0);
break;
}
}
addField(view, info, nextId, p);
// }
nextId++;
}

//Not loving the position-linked data, but fine for now.
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