void pyne::Material::_load_comp_protocol0(H5::H5File * db, std::string datapath, int row)
{
H5::Group matgroup = (*db).openGroup(datapath);
H5::DataSet nucset;
double nucvalue;
hsize_t matG = matgroup.getNumObjs();
// Iterate over datasets in the group.
for (int matg = 0; matg < matG; matg++)
{
std::string nuckey = matgroup.getObjnameByIdx(matg);
nucset = matgroup.openDataSet(nuckey);
nucvalue = h5wrap::get_array_index<double>(&nucset, row);
if (nuckey == "Mass" || nuckey == "MASS" || nuckey == "mass")
mass = nucvalue;
else
comp[pyne::nucname::zzaaam(nuckey)] = nucvalue;
nucset.close();
};
// Set meta data
name = datapath.substr(datapath.rfind("/")+1, datapath.length());
atoms_per_mol = -1.0;
};
bool loadStackHDF5( const char* fileName, Image4DSimple& img )
{
#ifdef USE_HDF5
H5::Exception::dontPrint();
H5::H5File file( fileName, H5F_ACC_RDONLY );
for ( size_t i = 0; i < file.getObjCount(); i++ )
{
H5std_string name = file.getObjnameByIdx( i );
if ( name == "Channels" )
{
H5::Group channels = file.openGroup( name );
// Grab the attributes
H5::Attribute attr = channels.openAttribute( "width" );
H5::DataType type = attr.getDataType();
long width, height;
attr.read( type, &width );
attr.close();
attr = channels.openAttribute( "height" );
attr.read( type, &height );
attr.close();
int num_channels = 0;
// Count the number of channels
for ( size_t obj = 0; obj < channels.getNumObjs(); obj++ )
if ( channels.getObjTypeByIdx( obj ) == H5G_DATASET )
num_channels++;
int channel_idx = 0;
for ( size_t obj = 0; obj < channels.getNumObjs(); obj++ )
{
if ( channels.getObjTypeByIdx( obj ) == H5G_DATASET )
{
H5std_string ds_name = channels.getObjnameByIdx( obj );
H5::DataSet data = channels.openDataSet( ds_name );
uint8_t* buffer = new uint8_t[ data.getStorageSize() ];
data.read( buffer, data.getDataType() );
QByteArray qbarray( ( const char* )buffer, data.getStorageSize() );
data.close();
if ( !loadIndexedStackFFMpeg( &qbarray, img, channel_idx++, num_channels,
width, height ) )
{
v3d_msg( "Error happened in HDF file reading. Stop. \n", false );
return false;
}
delete [] buffer;
}
}
}
}
#endif
return true;
}
bool Bundle2::checkGeometry_(H5::H5File& file) const {
bool found = false;
H5::Group root = file.openGroup("/");
const hsize_t maxObjs = root.getNumObjs();
for(hsize_t obj = 0; obj < maxObjs; ++obj) {
string objName = root.getObjnameByIdx(obj);
if(objName == string("Geometry")) found = true;
}
root.close();
return found;
}
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);
}
}
/**
* 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;
}
/**
* @param variableNum
* @param index
* @return
*/
float HDF5FileReader::getVariableAtIndex(long variable, long index)
{
float value = std::numeric_limits<float>::min();
//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 count[1] = {1};
hsize_t offset[1] = {index};
//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_FLOAT, 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;
}
/*********************************************************
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();
}
}
void ossim_hdf5::iterateGroupForDatasetNames( H5::H5File* file,
const std::string& groupName,
std::vector<std::string>& datasetNames,
ossim_uint32& recursedCount )
{
if ( file && groupName.size() )
{
++recursedCount;
// std::cout << "iterateGroup: " << groupName << std::endl;
H5::Group* group = new H5::Group( file->openGroup(groupName) );
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 );
H5G_obj_t objType = group->getObjTypeByIdx(i);
#if 0
std::cout << "combinedName: " << combinedName
<< "\ngetObjnameByIdx[" << i << "]: " << objName
<< "\ngetObjTypeByIdx[" << i << "]: " << objType
<< std::endl;
#endif
if ( objType == H5G_GROUP )
{
// Recursive call:
if ( recursedCount < ossim_hdf5::MAX_RECURSION_LEVEL )
{
ossim_hdf5::iterateGroupForDatasetNames(
file, combinedName, datasetNames, recursedCount );
}
else
{
ossimNotify(ossimNotifyLevel_WARN)
<< "ossim_hdf5::iterateGroupForDatasetNames WARNING!"
<< "\nMax iterations reached!" << std::endl;
}
}
else if ( objType == H5G_DATASET )
{
datasetNames.push_back( combinedName );
}
else
{
ossimNotify(ossimNotifyLevel_WARN)
<< "ossim_hdf5::iterateGroupForDatasetNames WARNING!"
<< "\nUnhandled object type: " << objType << std::endl;
}
}
}
group->close();
delete group;
group = 0;
--recursedCount;
} // Matches: if ( file )
} // End: void ossim_hdf5::iterateGroupForDatasetNames
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.
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();
}