FileHDF5::FileHDF5(const string &name, FileMode mode, Compression compression, OpenFlags flags) {
if (!fileExists(name)) {
mode = FileMode::Overwrite;
}
this->mode = mode;
this->compr = compression;
//we want hdf5 to keep track of the order in which links were created so that
//the order for indexed based accessors is stable cf. issue #387
H5Object fcpl = H5Pcreate(H5P_FILE_CREATE);
fcpl.check("Could not create file creation plist");
HErr res = H5Pset_link_creation_order(fcpl.h5id(), H5P_CRT_ORDER_TRACKED|H5P_CRT_ORDER_INDEXED);
res.check("Unable to create file (H5Pset_link_creation_order failed.)");
unsigned int h5mode = map_file_mode(mode);
bool is_create = !fileExists(name) || h5mode == H5F_ACC_TRUNC;
if (is_create) {
hid = H5Fcreate(name.c_str(), h5mode, fcpl.h5id(), H5P_DEFAULT);
} else {
hid = H5Fopen(name.c_str(), h5mode, H5P_DEFAULT);
}
if (!H5Iis_valid(hid)) {
throw H5Exception("Could not open/create file");
}
openRoot();
if (is_create) {
createHeader();
} else if (!checkHeader(mode) && (flags & OpenFlags::Force) != OpenFlags::Force) {
throw nix::InvalidFile("FileHDF5::open_existing!");
}
metadata = root.openGroup("metadata");
data = root.openGroup("data");
setCreatedAt();
setUpdatedAt();
}
void LocID::deleteLink(std::string name, hid_t plist) {
HErr res = H5Ldelete(hid, name.c_str(), plist);
res.check("LocIDL::deleteLink: Could not delete link: " + name);
}
void LocID::removeAttr(const std::string &name) const {
HErr res = H5Adelete(hid, name.c_str());
res.check("LocID::removeAttr(): could not delete attribute");
}
void DataType::sign(H5T_sign_t sign) {
HErr res = H5Tset_sign(hid, sign);
res.check("DataType::sign(): H5Tset_sign failed");
}
void DataType::size(size_t t) {
HErr res = H5Tset_size(hid, t);
res.check("DataType::size: Could not set size");
}
void DataType::insert(const std::string &name, size_t offset, const DataType &dtype) {
HErr res = H5Tinsert(hid, name.c_str(), offset, dtype.hid);
res.check("DataType::insert(): H5Tinsert failed.");
}
unsigned int LocID::referenceCount() const {
H5O_info_t oInfo;
HErr res = H5Oget_info(hid, &oInfo);
res.check("LocID:referenceCount: Coud not get object info");
return oInfo.rc;
}
bool FileHDF5::flush() {
HErr err = H5Fflush(hid, H5F_SCOPE_GLOBAL);
return !err.isError();
}
