bool loadStackHDF5( const char* fileName, Image4DSimple& img )
{
#ifdef USE_HDF5
H5::Exception::dontPrint();
H5::H5File file( fileName, H5F_ACC_RDONLY );
for ( size_t i = 0; i < file.getObjCount(); i++ )
{
H5std_string name = file.getObjnameByIdx( i );
if ( name == "Channels" )
{
H5::Group channels = file.openGroup( name );
// Grab the attributes
H5::Attribute attr = channels.openAttribute( "width" );
H5::DataType type = attr.getDataType();
long width, height;
attr.read( type, &width );
attr.close();
attr = channels.openAttribute( "height" );
attr.read( type, &height );
attr.close();
int num_channels = 0;
// Count the number of channels
for ( size_t obj = 0; obj < channels.getNumObjs(); obj++ )
if ( channels.getObjTypeByIdx( obj ) == H5G_DATASET )
num_channels++;
int channel_idx = 0;
for ( size_t obj = 0; obj < channels.getNumObjs(); obj++ )
{
if ( channels.getObjTypeByIdx( obj ) == H5G_DATASET )
{
H5std_string ds_name = channels.getObjnameByIdx( obj );
H5::DataSet data = channels.openDataSet( ds_name );
uint8_t* buffer = new uint8_t[ data.getStorageSize() ];
data.read( buffer, data.getDataType() );
QByteArray qbarray( ( const char* )buffer, data.getStorageSize() );
data.close();
if ( !loadIndexedStackFFMpeg( &qbarray, img, channel_idx++, num_channels,
width, height ) )
{
v3d_msg( "Error happened in HDF file reading. Stop. \n", false );
return false;
}
delete [] buffer;
}
}
}
}
#endif
return true;
}
bool exists_attribute_of_type(H5::Group const& group, string name, bool mandatory = true)
{
if (h5xx::exists_attribute(group, name)) {
return h5xx::has_type<T>(group.openAttribute(name));
}
else {
return !mandatory;
}
}
int Initialize(H5::Group &object, const std::string & attributeName) {
try {
attribute = object.openAttribute(attributeName.c_str());
}
catch (H5::Exception e) {
cout << "ERROR. Could not open attribute " << attributeName << endl;
exit(1);
}
isInitialized = true;
return 1;
}
std::string read_string_attr(H5::H5File &f, H5::Group &group, const char *name)
{
std::string strreadbuf ("");
H5::Attribute attr = group.openAttribute(name);
H5::StrType strdatatype(H5::PredType::C_S1, attr.getStorageSize());
attr.read(strdatatype, strreadbuf);
return strreadbuf;
}
void ReadAttrib(const std::string& name, T& value, const H5::DataType& dType){
//attributes are clunky in HDF5++ implementation - this is a workaround
//template is required to pass the proper value type
//access the built-in root group and create a new attribute for it.
H5::Group rootGroup = file_->openGroup("/");
H5::Attribute attrib = rootGroup.openAttribute(name);
//write the value to the attribute and close
attrib.read(dType,reinterpret_cast<void*>(&value));
attrib.close();
}
void Bundle2::loadParameters(H5::H5File& file) {
H5::Group root = file.openGroup("/");
// Checking version
unsigned int fileVersion;
H5::Attribute attr = root.openAttribute("version");
attr.read(H5::PredType::NATIVE_UINT, &fileVersion);
attr.close();
if(fileVersion != version_) throw std::runtime_error("Incompatible bundle version!");
// Reading number of cameras
hsize_t count;
H5::Group frame0Group = root.openGroup("POI/Frame 0000");
attr = frame0Group.openAttribute("count");
attr.read(H5::PredType::NATIVE_HSIZE, &count);
attr.close();
frame0Group.close();
numCameras_ = count;
// Reading parameters
unsigned char r2;
attr = root.openAttribute("reduce2");
attr.read(H5::PredType::NATIVE_UCHAR, &r2);
attr.close();
parameters_.reduce2 = (r2 == 1);
attr = root.openAttribute("xROI");
attr.read(H5::PredType::NATIVE_UINT, ¶meters_.xROI);
attr.close();
attr = root.openAttribute("yROI");
attr.read(H5::PredType::NATIVE_UINT, ¶meters_.yROI);
attr.close();
root.close();
}
void StateSet::init_from_datafile(std::string filename) {
// open other file read-only
H5::H5File otherfile;
otherfile.openFile(filename, H5F_ACC_RDONLY);
H5::Group otherroot = otherfile.openGroup("/");
// check that grid properties match
int othersx, othersy, otherN;
double otherdx;
otherroot.openAttribute("num_states").read(H5::PredType::NATIVE_INT, &otherN);
otherroot.openAttribute("grid_sizex").read(H5::PredType::NATIVE_INT, &othersx);
otherroot.openAttribute("grid_sizex").read(H5::PredType::NATIVE_INT, &othersy);
otherroot.openAttribute("grid_delta").read(H5::PredType::NATIVE_DOUBLE, &otherdx);
if (static_cast<int>(N) != otherN)
throw GeneralError("Cannot copy state data from datafile: value for num_states does not match.");
if (static_cast<int>(datalayout.sizex) != othersx)
throw GeneralError("Cannot copy state data from datafile: value for grid_sizex does not match.");
if (static_cast<int>(datalayout.sizey) != othersy)
throw GeneralError("Cannot copy state data from datafile: value for grid_sizey does not match.");
if (datalayout.dx != otherdx)
throw GeneralError("Cannot copy state data from datafile: value for grid_delta does not match.");
// copy data
H5::DataSet other_states_data = otherfile.openDataSet("/states");
other_states_data.read(state_array->get_dataptr(), other_states_data.getArrayType());
}
/**
* @param attribute
* @return
*/
bool HDF5FileReader::doesAttributeExist(const std::string& attribute)
{
bool exists = false;
H5::Group group = this->current_file->openGroup("/");
try
{
group.openAttribute(attribute);
exists = true;
} catch (H5::AttributeIException& e)
{
exists = false;
}
return exists;
}
static void attributes_append_group(Attributes &attrs, H5::Group &g, cpath basename, cpath group_path)
{
for(uint i=0;i<g.getNumObjs();i++) {
char g_name[1024];
g.getObjnameByIdx(hsize_t(i), g_name, 1024);
cpath name = group_path / g_name;
H5G_stat_t stat;
g.getObjinfo(g_name, false, stat);
if (stat.type == H5G_GROUP) {
H5::Group sub = g.openGroup(g_name);
attributes_append_group(attrs, sub, basename, name);
}
else if (stat.type == H5G_LINK)
{
//FIXME we assume soft link!
Attribute attr;
char attr_name[1024];
char link[1024];
attr.setName(remove_prefix(name, basename));
H5L_info_t info;
H5Lget_val(g.getId(), g_name, link, 1024, H5P_DEFAULT);
attr.setLink(remove_prefix(link, basename));
attrs.append(attr);
}
}
for(int i=0;i<g.getNumAttrs();i++) {
H5::Attribute h5attr = g.openAttribute(i);
Attribute attr;
BaseType type;
char name[1024];
H5Aget_name(h5attr.getId(), 1024, name);
read_attr(&attr, g, basename, group_path, name, type);
attrs.append(attr);
}
}
const std::string ReadStrAttrib(const std::string& name){
//attributes are clunky in HDF5++ implementation - this is a workaround
//template is required to pass the proper value type
std::string value;
value.resize( STRING_ATTRIB_SIZE );
H5::StrType strType(0, STRING_ATTRIB_SIZE );
//access the built-in root group and create a new attribute for it.
H5::Group rootGroup = file_->openGroup("/");
H5::Attribute attrib = rootGroup.openAttribute(name);
//write the value to the attribute and close
attrib.read(strType,value);
attrib.close();
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;
}
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();
}
/**
* @param attribute
* @return
*/
Attribute HDF5FileReader::getGlobalAttribute(const std::string& attribute)
{
//first, check if the attribute has already been requested. If so, return stored value
boost::unordered_map<std::string, Attribute>::iterator iter = gAttributes.find(attribute);
if (iter != gAttributes.end())
return (*iter).second;
// std::cout << "after search in getGlobalAttribute(const std::string& attribute)" << std::endl;
// std::cout << "attribute: " << attribute << std::endl;
H5::Group group = this->current_file->openGroup("/");
H5::Attribute h5attribute = group.openAttribute(attribute);
long attrNum = h5attribute.getId();
H5::DataType dataType = h5attribute.getDataType();
// std::cout << "attrNum after attribute: " << attrNum << std::endl;
Attribute current_attribute;
if (attrNum < 0)
{
std::cout << "attrNum: " << attrNum << " returned for " << attribute << std::endl;
}
else
{
// std::cout << "attribute: " << attribute << " attribute number: " << attrNum << std::endl;
// std::cout << "attempting to get attribute without using attribute number\n";
if (dataType.getClass() == H5T_STRING)
{
std::string attributeValue = "NULL";
h5attribute.read(dataType, attributeValue);
std::string attributeName = "";
attributeName = h5attribute.getName();
current_attribute.setAttributeName(attributeName);
//std::cout << "name: '" << attributeName << "' string attributeBuffer: '" << attributeValue << "'"<< std::endl;
current_attribute.setAttributeValue(attributeValue);
gAttributeByID[(int)attrNum] = current_attribute;
gAttributes[current_attribute.getAttributeName()] = current_attribute;
//return attribute;
} else if (dataType.getClass() == H5T_INTEGER)
{
//int attributeValue = 0.f;
int attributeBuffer;// = new int[1];
h5attribute.read(dataType, &attributeBuffer);
std::string attributeName = "";
attributeName = h5attribute.getName();
current_attribute.setAttributeName(attributeName);
//std::cout << "int attributeBuffer: '" << attributeBuffer << "'"<< std::endl;
current_attribute.setAttributeValue(attributeBuffer);
gAttributeByID[(int)attrNum] = current_attribute;
gAttributes[current_attribute.getAttributeName()] = current_attribute;
//return attribute;
} else if (dataType.getClass() == H5T_FLOAT)//CDF_FLOAT
{
//int attributeValue = 0.f;
float attributeValue;// = new int[1];
h5attribute.read(dataType, &attributeValue);
std::string attributeName = "";
attributeName = h5attribute.getName();
current_attribute.setAttributeName(attributeName);
//std::cout << "float attributeBuffer: '" << attributeValue << "'"<< std::endl;
current_attribute.setAttributeValue(attributeValue);
gAttributeByID[(int)attrNum] = current_attribute;
gAttributes[current_attribute.getAttributeName()] = current_attribute;
//return attribute;
}
}//gAttributes[attribute] = current_attribute;
return current_attribute;
// return Attribute();
}
/**
* @param i The attribute number
* @return
*/
Attribute HDF5FileReader::getGlobalAttribute(long i)
{
std::cerr << "entered " << BOOST_CURRENT_FUNCTION << " i = " << (int)i << std::endl;
H5::Group group = this->current_file->openGroup("/");
std::cout<< "group assigned\n";
H5::Attribute h5attribute = group.openAttribute((unsigned int)i);
std::cout<< "attribute opened\n";
H5::DataType dataType = h5attribute.getDataType();
std::cout<< "dataType retrieved\n";
Attribute attribute;
std::cout << "checking dataType"<<std::endl;
if (dataType.getClass() == H5T_STRING)
{
std::string attributeValue = "NULL";
h5attribute.read(dataType, attributeValue);
std::string attributeName = "";
attributeName = h5attribute.getName();
attribute.setAttributeName(attributeName);
//std::cout << "name: '" << attributeName << "' string attributeBuffer: '" << attributeValue << "'"<< std::endl;
attribute.setAttributeValue(attributeValue);
gAttributeByID[i] = attribute;
gAttributes[attribute.getAttributeName()] = attribute;
//return attribute;
} else if (dataType.getClass() == H5T_INTEGER)
{
//int attributeValue = 0.f;
int attributeBuffer;// = new int[1];
h5attribute.read(dataType, &attributeBuffer);
std::string attributeName = "";
attributeName = h5attribute.getName();
attribute.setAttributeName(attributeName);
//std::cout << "int attributeBuffer: '" << attributeBuffer << "'"<< std::endl;
attribute.setAttributeValue(attributeBuffer);
gAttributeByID[i] = attribute;
gAttributes[attribute.getAttributeName()] = attribute;
//return attribute;
} else if (dataType.getClass() == H5T_FLOAT)//CDF_FLOAT
{
//int attributeValue = 0.f;
float attributeValue;// = new int[1];
h5attribute.read(dataType, &attributeValue);
std::string attributeName = "";
attributeName = h5attribute.getName();
attribute.setAttributeName(attributeName);
//std::cout << "float attributeBuffer: '" << attributeValue << "'"<< std::endl;
attribute.setAttributeValue(attributeValue);
gAttributeByID[i] = attribute;
gAttributes[attribute.getAttributeName()] = attribute;
//return attribute;
}
//std::cout << "added: " << i << " name: '" << attribute.getAttributeName() << "'" << endl;
//std::cout << "Attribute: " << attribute.toString() << std::endl;
return attribute;
}
void load_particle_space(const H5::Group& root, Tspace_* space)
{
typedef ParticleSpaceHDF5Traits traits_type;
typedef typename traits_type::h5_species_struct h5_species_struct;
typedef typename traits_type::h5_particle_struct h5_particle_struct;
Real3 edge_lengths;
const hsize_t dims[] = {3};
const H5::ArrayType lengths_type(H5::PredType::NATIVE_DOUBLE, 1, dims);
root.openAttribute("edge_lengths").read(lengths_type, &edge_lengths);
space->reset(edge_lengths);
double t;
root.openAttribute("t").read(H5::PredType::IEEE_F64LE, &t);
space->set_t(t);
{
H5::DataSet species_dset(root.openDataSet("species"));
const unsigned int num_species(
species_dset.getSpace().getSimpleExtentNpoints());
boost::scoped_array<h5_species_struct> h5_species_table(
new h5_species_struct[num_species]);
species_dset.read(
h5_species_table.get(), traits_type::get_species_comp_type());
species_dset.close();
H5::DataSet particle_dset(root.openDataSet("particles"));
const unsigned int num_particles(
particle_dset.getSpace().getSimpleExtentNpoints());
boost::scoped_array<h5_particle_struct> h5_particle_table(
new h5_particle_struct[num_particles]);
particle_dset.read(
h5_particle_table.get(), traits_type::get_particle_comp_type());
particle_dset.close();
typedef utils::get_mapper_mf<unsigned int, Species::serial_type>::type
species_id_map_type;
species_id_map_type species_id_map;
for (unsigned int i(0); i < num_species; ++i)
{
species_id_map[h5_species_table[i].id] = h5_species_table[i].serial;
}
for (unsigned int i(0); i < num_particles; ++i)
{
space->update_particle(ParticleID(std::make_pair(h5_particle_table[i].lot, h5_particle_table[i].serial)), Particle(Species(species_id_map[h5_particle_table[i].sid]), Real3(h5_particle_table[i].posx, h5_particle_table[i].posy, h5_particle_table[i].posz), h5_particle_table[i].radius, h5_particle_table[i].D));
}
// boost::scoped_array<h5_particle_struct>
// h5_particle_table(new h5_particle_struct[num_particles]);
// for (unsigned int i(0); i < num_particles; ++i)
// {
// species_id_map_type::const_iterator
// it(species_id_map.find(particles[i].second.species_serial()));
// if (it == species_id_map.end())
// {
// species.push_back(particles[i].second.species());
// it = species_id_map.insert(
// std::make_pair(particles[i].second.species_serial(),
// species.size())).first;
// }
// h5_particle_table[i].lot = particles[i].first.lot();
// h5_particle_table[i].serial = particles[i].first.serial();
// h5_particle_table[i].sid = (*it).second;
// h5_particle_table[i].posx = particles[i].second.position()[0];
// h5_particle_table[i].posy = particles[i].second.position()[1];
// h5_particle_table[i].posz = particles[i].second.position()[2];
// h5_particle_table[i].radius = particles[i].second.radius();
// h5_particle_table[i].D = particles[i].second.D();
// }
// boost::scoped_array<h5_species_struct>
// h5_species_table(new h5_species_struct[species.size()]);
// for (unsigned int i(0); i < species.size(); ++i)
// {
// h5_species_table[i].id = i + 1;
// std::strcpy(h5_species_table[i].serial,
// species[i].serial().c_str());
// }
}
}
/*********************************************************
FunctionName:RecursiveVisitNode
FunctionDesc:递归创建Group
InputParam:
OutputParam:
Return:
Author:xiaowei.han
*********************************************************/
void RecursiveVisitNode(H5::Group& Node, Hdf5_Wrapper::LP_HDF5_DATA pData)
{
using namespace H5;
if (nullptr == pData)
{
return;
}
//获取节点名称
pData->strKeyName = Utility::UTF8ToGB2312(Node.getObjName());
//获取属性个数
int nAttrNum = static_cast<int>(Node.getNumAttrs());
for (int i = 0; i < nAttrNum; ++i)
{
auto childAttr = Node.openAttribute(i);
//解析读取属性数据
//获取数据类型
auto AttrDataType = childAttr.getDataType();
//获取数据类型大小
unsigned int nDataByte = (unsigned int)AttrDataType.getSize();
boost::scoped_ptr<CAbstractAttrHanlder> pHandler(CreateAttrHandler(childAttr.getTypeClass(), nDataByte));
if (pHandler)
{
pHandler->ReadAttr(childAttr, AttrDataType, pData->AttributeArray);
}
childAttr.close();
}
//获取节点对象个数
int nObjNum = static_cast<int>(Node.getNumObjs());
//遍历子节点信息
for (int i = 0; i < nObjNum; ++i)
{
//NECESSARY_LOG("the node name is [%s],the type is [%d].", Node.getObjnameByIdx(i).c_str(), Node.getObjTypeByIdx(i));
auto SubNodeType = Node.getObjTypeByIdx(i);
switch (SubNodeType)
{
case H5G_GROUP:
{
Hdf5_Wrapper::LP_HDF5_DATA pSubData = new Hdf5_Wrapper::HDF5_DATA;
if (nullptr != pSubData)
{
//添加进去
pData->SubDataArray.push_back(pSubData);
auto ChildGroupNode = Node.openGroup(Node.getObjnameByIdx(i));
RecursiveVisitNode(ChildGroupNode,pSubData);
ChildGroupNode.close();
}
}
break;
case H5G_DATASET:
{
auto childDataset = Node.openDataSet(Node.getObjnameByIdx(i));
Hdf5_Wrapper::LP_HDF5_DATA pSubData = new Hdf5_Wrapper::HDF5_DATA;
if (nullptr != pSubData)
{
pSubData->strKeyName = childDataset.getObjName();
//添加进去
pData->SubDataArray.push_back(pSubData);
//获取数据类型
auto ChildDataSetDataType = childDataset.getDataType();
//获取类型占用字节数
unsigned int nDataByte = (unsigned int)ChildDataSetDataType.getSize();
//判断数据类型
boost::scoped_ptr<CAbstractDataTypeHandler> pHandlder(CDataTypeHandlerFactory::CreateDataTypeHandler(childDataset.getTypeClass(),nDataByte));
if (pHandlder)
{
pHandlder->ReadDataSet(childDataset, pSubData);
}
}
}
break;
default:
break;
}
}
}
//--------------------------------------------------------------------------------------------------
///
//--------------------------------------------------------------------------------------------------
TEST(DISABLED_HDFTests, BasicFileRead)
{
std::string file_path = "D:/ResInsight/SourSim/PKMUNK_NOV_TEST_SS.sourpre.00001";
try
{
H5::Exception::dontPrint(); // Turn off auto-printing of failures to handle the errors appropriately
H5::H5File file(file_path.c_str(), H5F_ACC_RDONLY);
{
H5::Group timestep = file.openGroup("Timestep_00001");
H5::Attribute attr = timestep.openAttribute("timestep");
double timestep_value = 0.0;
H5::DataType type = attr.getDataType();
attr.read(type, ×tep_value);
//std::cout << "Timestep value " << timestep_value << std::endl;
EXPECT_NEAR(timestep_value, 1.0, 1e-1);
}
{
// Group size is not an attribute!
H5::Group GridFunctions = file.openGroup("Timestep_00001/GridParts/GridPart_00000/GridFunctions");
hsize_t group_size = GridFunctions.getNumObjs();
//std::cout << "GridFunctions group_size " << group_size << std::endl;
EXPECT_EQ(size_t(20), group_size);
/* for (hsize_t i = 0; i < group_size; i++)
{
// H5std_string node_name = GridFunctions.getObjnameByIdx(i); // crashes on VS2017 due to lib/heap/runtime differences to HDF5 VS2015 lib
std::string node_name;
node_name.resize(1024);
ssize_t slen = GridFunctions.getObjnameByIdx(i, &node_name[0], 1023);
node_name.resize(slen + 1);
std::cout << "GridFunctions sub-node name " << node_name << std::endl;
}
*/
std::string first_subnode(1024, '\0');
ssize_t slen = GridFunctions.getObjnameByIdx(0, &first_subnode[0], 1023);
first_subnode.resize(slen + 1);
EXPECT_TRUE(first_subnode.compare(0, slen, "GridFunction_00002") == 0);
}
{
H5::Group GridFunction_00002 = file.openGroup("Timestep_00001/GridParts/GridPart_00000/GridFunctions/GridFunction_00002");
H5::Attribute attr = GridFunction_00002.openAttribute("limits_max");
double limits_max = 0.0;
H5::DataType type = attr.getDataType();
attr.read(type, &limits_max);
// std::cout << "limits_max " << limits_max << std::endl;
EXPECT_NEAR(limits_max, 0.3970204292629652, 1e-10);
}
{
H5::Group GridFunction_00002 = file.openGroup("Timestep_00001/GridParts/GridPart_00000/GridFunctions/GridFunction_00002");
H5::DataSet dataset = H5::DataSet(GridFunction_00002.openDataSet("values"));
hsize_t dims[2];
H5::DataSpace dataspace = dataset.getSpace();
dataspace.getSimpleExtentDims(dims, nullptr);
std::vector<double> values;
values.resize(dims[0]);
dataset.read(values.data(), H5::PredType::NATIVE_DOUBLE);
/* for (hsize_t i = 0; i < dims[0]; i++)
{
std::cout << "value " << i << " " << values[i] << std::endl;
}
*/
EXPECT_NEAR(values[0], 0.32356910366452146, 1e-10);
EXPECT_NEAR(values[dims[0] - 1], 0.12200070891582514, 1e-10);
}
} // end of try block
catch (H5::FileIException error) // catch failure caused by the H5File operations
{
std::cout << error.getCDetailMsg();
}
catch (H5::DataSetIException error) // catch failure caused by the DataSet operations
{
std::cout << error.getCDetailMsg();
}
catch (H5::DataSpaceIException error) // catch failure caused by the DataSpace operations
{
std::cout << error.getCDetailMsg();
}
catch (H5::DataTypeIException error) // catch failure caused by the DataSpace operations
{
std::cout << error.getCDetailMsg();
}
}
int main (int argc, char * argv[])
{
long status = -1L;
H5::H5File * current_file = NULL;
try
{
current_file = new H5::H5File(argv[1], H5F_ACC_RDONLY);
}
catch(H5::Exception const& ex)
{
exit(1);
}
std::cout << "Opened file " << argv[1] << std::endl;
long counts[1];
std::vector<float>* variableData = new std::vector<float>();
std::string variable = "rho";
H5::Group group = current_file->openGroup("/");
H5::Attribute attribute = group.openAttribute()
/*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 dims_out[1];
hsize_t offset[1] = {0};
int ndims = dataspace.getSimpleExtentDims(dims_out, NULL);
std::cout << "dims_out[0]: " << dims_out[0] << " num dimensions: " << ndims << std::endl;
float * buffer = new float[dims_out[0]];
dataspace.selectHyperslab(H5S_SELECT_SET, dims_out, offset);
hsize_t dim[] = {dims_out[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(dims_out[0]);
for (int i = 0; i < dims_out[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 << "dims_out[0]: " << dims_out[0] << std::endl;
*/
return 0;
}
void ossim_hdf5::printIterative( H5::H5File* file,
const std::string& groupName,
const std::string& prefix,
ossim_uint32& recursedCount,
std::ostream& out )
{
if ( file && groupName.size() )
{
++recursedCount;
H5::Group* group = new H5::Group( file->openGroup(groupName) );
// Print attributes:
const ossim_uint32 ATTRS_COUNT = group->getNumAttrs();
for ( ossim_uint32 aIdx = 0; aIdx < ATTRS_COUNT; ++aIdx )
{
H5::Attribute attr( group->openAttribute( aIdx ) );
ossim_hdf5::printAttribute( attr, prefix, out );
attr.close();
}
const hsize_t OBJ_COUNT = group->getNumObjs();
for ( hsize_t i = 0; i < OBJ_COUNT; ++i )
{
std::string objName = group->getObjnameByIdx(i);
if ( objName.size() )
{
char separator = '/';
std::string combinedName;
combine( groupName, objName, separator, combinedName );
separator = '.';
std::string combinedPrefix;
combine( prefix, objName, separator, combinedPrefix );
H5G_obj_t objType = group->getObjTypeByIdx(i);
#if 0
std::cout << "combinedName: " << combinedName
<< "\ncombinedPrefix: " << combinedPrefix
<< "\ngetObjnameByIdx[" << i << "]: " << objName
<< "\ngetObjTypeByIdx[" << i << "]: " << objType
<< std::endl;
#endif
if ( objType == H5G_GROUP )
{
// Recursive call:
if ( recursedCount < ossim_hdf5::MAX_RECURSION_LEVEL )
{
ossim_hdf5::printIterative(
file, combinedName, combinedPrefix, recursedCount, out );
}
else
{
ossimNotify(ossimNotifyLevel_WARN)
<< "ossim_hdf5::printIterative WARNING!"
<< "\nMax iterations reached!" << std::endl;
}
}
else if ( objType == H5G_DATASET )
{
printObject( file, combinedName, combinedPrefix, out );
}
else
{
ossimNotify(ossimNotifyLevel_WARN)
<< "ossim_hdf5::printIterative WARNING!"
<< "\nUnhandled object type: " << objType << std::endl;
}
}
}
group->close();
delete group;
group = 0;
--recursedCount;
} // Matches: if ( file )
} // End: void ossim_hdf5::printIterative method.