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Merge pull request #174 from kaizu/revert-hdf5
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fix: Revert the HDF5 module
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@kozo2
kozo2 authored Apr 6, 2017
2 parents b087b07 + 5de49b2 commit d3313ac
Showing 1 changed file with 28 additions and 49 deletions.
77 changes: 28 additions & 49 deletions ecell4/core/LatticeSpaceHDF5Writer.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -29,8 +29,8 @@ struct LatticeSpaceHDF5Traits
struct h5_species_struct {
double radius;
double D;
H5std_string location;
// char location[32];
// H5std_string location;
char location[32];
uint32_t is_structure;
uint32_t dimension;
};
Expand All @@ -41,33 +41,9 @@ struct LatticeSpaceHDF5Traits
uint64_t coordinate;
};

// static H5::CompType get_property_comp()
// {
// H5::CompType property_comp_type(sizeof(h5_species_struct));
// // #define INSERT_MEMBER(member, type) \
// // property_comp_type.insertMember(#member,\
// // HOFFSET(h5_species_struct, member), type)
// #define INSERT_MEMBER(member, type) \
// H5Tinsert(property_comp_type.getId(), #member,\
// HOFFSET(h5_species_struct, member), type.getId())
// INSERT_MEMBER(radius, H5::PredType::IEEE_F64LE);
// INSERT_MEMBER(D, H5::PredType::IEEE_F64LE);
// INSERT_MEMBER(location, H5::StrType(0, H5T_VARIABLE));
// // INSERT_MEMBER(location, H5::StrType(H5::PredType::C_S1, 32));
// INSERT_MEMBER(is_structure, H5::PredType::STD_I32LE);
// INSERT_MEMBER(dimension, H5::PredType::STD_I32LE);
// #undef INSERT_MEMBER
// return property_comp_type;
// }

static H5::CompType get_voxel_comp()
{
H5::CompType voxel_comp_type(sizeof(h5_voxel_struct));
/*
#define INSERT_MEMBER(member, type) \
voxel_comp_type.insertMember(std::string(#member),\
HOFFSET(h5_voxel_struct, member), type)
*/
#define INSERT_MEMBER(member, type) \
H5Tinsert(voxel_comp_type.getId(), #member,\
HOFFSET(h5_voxel_struct, member), type.getId())
Expand All @@ -89,29 +65,25 @@ struct LatticeSpaceHDF5Traits
property.radius = mtb->radius();
property.D = mtb->D();
const VoxelPool* loc(mtb->location());
if (loc->is_vacant())
property.location = H5std_string("");
else
property.location = H5std_string(loc->species().serial().c_str());
// if (loc->is_vacant())
// std::strcpy(property.location, "");
// property.location = H5std_string("");
// else
// std::strcpy(property.location, loc->species().serial().c_str());
// property.location = H5std_string(loc->species().serial().c_str());
if (loc->is_vacant())
std::strcpy(property.location, "");
else
std::strcpy(property.location, loc->species().serial().c_str());
property.is_structure = mtb->is_structure() ? 1 : 0;
property.dimension = mtb->get_dimension();

// H5::CompType property_comp_type(get_property_comp());
// mtgroup->createAttribute("property", property_comp_type,
// H5::DataSpace(H5S_SCALAR)).write(property_comp_type, &property);
// // mtgroup->createDataSet("property", property_comp_type,
// // H5::DataSpace(H5S_SCALAR)).write(&property, property_comp_type);

mtgroup->createAttribute("radius", H5::PredType::IEEE_F64LE, H5::DataSpace(H5S_SCALAR)
).write(H5::PredType::IEEE_F64LE, &property.radius);
mtgroup->createAttribute("D", H5::PredType::IEEE_F64LE, H5::DataSpace(H5S_SCALAR)
).write(H5::PredType::IEEE_F64LE, &property.D);
mtgroup->createAttribute("location", H5::StrType(0, H5T_VARIABLE), H5::DataSpace(H5S_SCALAR)
).write(H5::StrType(0, H5T_VARIABLE), &property.location);
mtgroup->createAttribute("location", H5::StrType(H5::PredType::C_S1, 32), H5::DataSpace(H5S_SCALAR)
).write(H5::StrType(H5::PredType::C_S1, 32), &property.location);
// mtgroup->createAttribute("location", H5::StrType(0, H5T_VARIABLE), H5::DataSpace(H5S_SCALAR)
// ).write(H5::StrType(0, H5T_VARIABLE), &property.location);
mtgroup->createAttribute("is_structure", H5::PredType::STD_I32LE, H5::DataSpace(H5S_SCALAR)
).write(H5::PredType::STD_I32LE, &property.is_structure);
mtgroup->createAttribute("dimension", H5::PredType::STD_I32LE, H5::DataSpace(H5S_SCALAR)
Expand Down Expand Up @@ -170,7 +142,7 @@ struct LatticeSpaceHDF5Traits
};

template<typename Tspace_>
void save_lattice_space(const Tspace_& space, H5::Group* root, const std::string& implementation = "")
void save_lattice_space(const Tspace_& space, H5::Group* root, const std::string& impl = "")
{
typedef LatticeSpaceHDF5Traits traits_type;

Expand Down Expand Up @@ -198,16 +170,19 @@ void save_lattice_space(const Tspace_& space, H5::Group* root, const std::string
const uint32_t is_periodic(space.is_periodic()? 1 : 0);
double edge_lengths[] = {lengths[0], lengths[1], lengths[2]};

char implementation[32];
std::strcpy(implementation, impl.c_str());

#define CREATE_ATTRIBUTE(attribute, type) \
root->createAttribute(#attribute, type,\
H5::DataSpace(H5S_SCALAR)).write(type, &attribute)

CREATE_ATTRIBUTE(space_type, H5::PredType::STD_I32LE);
CREATE_ATTRIBUTE(t, H5::PredType::IEEE_F64LE);
CREATE_ATTRIBUTE(voxel_radius, H5::PredType::IEEE_F64LE);
CREATE_ATTRIBUTE(is_periodic, H5::PredType::STD_I32LE);
CREATE_ATTRIBUTE(edge_lengths, lengths_type);
CREATE_ATTRIBUTE(implementation, H5::StrType(0, H5T_VARIABLE));
// CREATE_ATTRIBUTE(impl, H5::StrType(0, H5T_VARIABLE));
CREATE_ATTRIBUTE(implementation, H5::StrType(H5::PredType::C_S1, 32));
#undef CREATE_ATTRIBUTE
}

Expand All @@ -222,22 +197,25 @@ void load_lattice_space(const H5::Group& root, Tspace_* space, const std::string
Real3 edge_lengths;
const hsize_t dims[] = {3};
uint32_t is_periodic;
std::string impl = "";
char impl_C[32];
// std::string impl = "";

#define OPEN_ATTRIBUTE(attribute, type) \
root.openAttribute(#attribute).read(type, &attribute)

OPEN_ATTRIBUTE(space_type, H5::PredType::STD_I32LE);
OPEN_ATTRIBUTE(t, H5::PredType::IEEE_F64LE);
OPEN_ATTRIBUTE(voxel_radius, H5::PredType::IEEE_F64LE);
OPEN_ATTRIBUTE(edge_lengths, H5::ArrayType(H5::PredType::NATIVE_DOUBLE, 1, dims));
OPEN_ATTRIBUTE(is_periodic, H5::PredType::STD_I32LE);
#undef OPEN_ATTRIBUTE

// if (root.attrExists("implementation"))
// root.openAttribute("implementation").read(
// H5::StrType(0, H5T_VARIABLE), impl); //XXX: '&' is not needed for HDF5std_string
if (root.attrExists("implementation"))
root.openAttribute("implementation").read(
H5::StrType(0, H5T_VARIABLE), impl); //XXX: '&' is not needed for HDF5std_string

#undef OPEN_ATTRIBUTE
H5::StrType(H5::PredType::C_S1, 32), impl_C);
const std::string impl(impl_C);

if (implementation != "" && implementation != impl)
{
Expand Down Expand Up @@ -285,7 +263,8 @@ void load_lattice_space(const H5::Group& root, Tspace_* space, const std::string

group.openAttribute("radius").read(H5::PredType::IEEE_F64LE, &property.radius);
group.openAttribute("D").read(H5::PredType::IEEE_F64LE, &property.D);
group.openAttribute("location").read(H5::StrType(0, H5T_VARIABLE), property.location); //XXX: NEVER use "&" for H5std_string when reading.
// group.openAttribute("location").read(H5::StrType(0, H5T_VARIABLE), property.location); //XXX: NEVER use "&" for H5std_string when reading.
group.openAttribute("location").read(H5::StrType(H5::PredType::C_S1, 32), property.location);
group.openAttribute("is_structure").read(H5::PredType::STD_I32LE, &property.is_structure);
group.openAttribute("dimension").read(H5::PredType::STD_I32LE, &property.dimension);

Expand Down

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