static void show (const HDF5::Object& obj, int indentLevel = 0) {
if (obj.getType () == H5I_DATASET) {
indent (indentLevel);
Core::OStream::getStdout () << "DATASET" << std::endl;
HDF5::DataSet ds = (HDF5::DataSet) obj;
HDF5::DataSetCreatePropList cp = ds.createPropList ();
HDF5::DataSetAccessPropList ap = ds.accessPropList ();
int nfilter = HDF5::Exception::check ("H5Pget_nfilters", H5Pget_nfilters (cp.handle ()));
indent (indentLevel);
Core::OStream::getStdout ().fprintf ("filters: %s\n", nfilter);
for (int j = 0; j < nfilter; j++) {
unsigned int flags;
unsigned int filter_config;
size_t cd_nelemts = 0;
char name[1024];
H5Z_filter_t filter = HDF5::Exception::check ("H5Pget_filter2", H5Pget_filter2 (cp.handle (), j, &flags, &cd_nelemts, NULL, sizeof (name) / sizeof (*name), name, &filter_config));
std::vector<unsigned int> cd_values (cd_nelemts);
filter = HDF5::Exception::check ("H5Pget_filter2", H5Pget_filter2 (cp.handle (), j, &flags, &cd_nelemts, cd_values.data (), sizeof (name) / sizeof (*name), name, &filter_config));
indent (indentLevel + 1);
Core::OStream::getStdout ().fprintf ("filter '%s' filter=%s flags=%s config=%s\n", name, filter, flags, filter_config);
BOOST_FOREACH (unsigned int value, cd_values) {
indent (indentLevel + 2);
Core::OStream::getStdout ().fprintf ("parameter %s\n", value);
}
}
MatlabObject::MatlabObject (const HDF5::Object& o) {
HDF5::Object object = o;
bool hasEmptyAttribute;
for (;;) {
isOctaveNewFormat_ = object.getType () == H5I_GROUP && object.existsAttribute ("OCTAVE_NEW_FORMAT");
if (!isOctaveNewFormat_) {
hasEmptyAttribute = object.existsAttribute ("MATLAB_empty");
break;
}
HDF5::Group grp = (HDF5::Group) object;
HDF5::DataSet typeDs = (HDF5::DataSet) grp.open ("type", setEFilePrefix ());
ASSERT (typeDs.getSpace ().getSimpleExtentType () == H5S_SCALAR);
HDF5::DataSpace s = HDF5::DataSpace::create (H5S_SCALAR);
HDF5::StringType ty = (HDF5::StringType) typeDs.getDataType ();
ASSERT (!(Exception::check ("H5Tis_variable_str", H5Tis_variable_str (ty.handle ())) != 0));
/*
const char* str = NULL;
HDF5::DataType t = getH5Type<const char*> ();
typeDs.read (&str, t, s, s);
std::string str2 (str);
typeDs.vlenReclaim (&str, t, s);
*/
size_t size = H5Tget_size (ty.handle ());
HDF5::Exception::check ("H5Tget_size", size ? 0 : -1);
std::vector<char> str (size);
typeDs.read (str.data (), ty, s, s);
std::string str2 (str.begin (), str.end ());
size_t pos = str2.find ('\0');
if (pos != std::string::npos)
str2 = str2.substr (0, pos);
if (str2 != "cell") {
hasEmptyAttribute = grp.existsAttribute ("OCTAVE_EMPTY_MATRIX");
object = grp.open ("value", setEFilePrefix ());
octaveType_ = str2;
break;
} else {
HDF5::DataSet dimsDs = (HDF5::DataSet) grp.open ("value/dims", setEFilePrefix ());
HDF5::DataSpace dimsSp = dimsDs.getSpace ();
ASSERT (dimsSp.getSimpleExtentType () == H5S_SIMPLE);
ASSERT (dimsSp.getSimpleExtentNdims () == 1);
hsize_t dim;
dimsSp.getSimpleExtentDims (&dim);
ASSERT (dim == 2);
int64_t dims[2];
dimsDs.read (dims, HDF5::getH5Type<int64_t> (), dimsSp);
ASSERT (dims[0] == 1);
ASSERT (dims[1] == 1);
object = grp.open ("value/_0", setEFilePrefix ());
}
}
H5I_type_t type = object.getType ();
if (type == H5I_DATASET) {
isStruct_ = false;
dataSet_ = (HDF5::DataSet) object;
if (hasEmptyAttribute) {
isEmpty_ = true;
isNullDataSpace_ = false;
HDF5::DataSpace dataSpace = dataSet_.getSpace ();
ASSERT (dataSpace.getSimpleExtentType () == H5S_SIMPLE);
ASSERT (dataSpace.getSimpleExtentNdims () == 1);
hsize_t ndims;
dataSpace.getSimpleExtentDims (&ndims);
ASSERT (ndims > 0);
std::vector<uint64_t> values (Core::checked_cast<size_t> (ndims));
dataSet_.read (values.data (), getH5Type<uint64_t> (), dataSpace);
bool foundZero = false;
for (size_t i = 0; i < ndims; i++)
if (!values[i])
foundZero = true;
ASSERT (foundZero);
size_.resize (Core::checked_cast<size_t> (ndims));
for (size_t i = 0; i < ndims; i++) {
ASSERT (values[i] <= std::numeric_limits<size_t>::max ());
size_[i] = Core::checked_cast<size_t> (values[i]);
}
} else {
dataSpace_ = dataSet_.getSpace ();
H5S_class_t extentType = dataSpace_.getSimpleExtentType ();
//ASSERT (extentType == H5S_SIMPLE || extentType == H5S_NULL);
ASSERT (extentType == H5S_SIMPLE || extentType == H5S_NULL || extentType == H5S_SCALAR);
if (extentType == H5S_SIMPLE) {
isNullDataSpace_ = false;
size_t dim = dataSpace_.getSimpleExtentNdims ();
size_.resize (dim);
std::vector<hsize_t> dims (dim);
dataSpace_.getSimpleExtentDims (dims.data ());
isEmpty_ = false;
for (size_t i = 0; i < dim; i++) {
ASSERT (dims[i] >= std::numeric_limits<size_t>::min () && dims[i] <= std::numeric_limits<size_t>::max ());
size_[dim - 1 - i] = Core::checked_cast<size_t> (dims[i]);
if (!dims[i])
isEmpty_ = true;
}
if (isEmpty_) {
dataSpace_ = HDF5::DataSpace ();
}
} else if (extentType == H5S_SCALAR) {
isNullDataSpace_ = false;
isEmpty_ = false;
//size_.resize (0);
size_.resize (1);
size_[0] = 1;
} else { // H5S_NULL
isEmpty_ = true;
isNullDataSpace_ = true;
size_.resize (1);
size_[0] = 0;
}
}
if (isEmpty_)
dataSet_ = HDF5::DataSet ();
} else if (type == H5I_GROUP) {
isStruct_ = true;
group_ = (HDF5::Group) object;
} else {
ABORT_MSG ("Unknown object type");
}
}
void MatlabSerializationContext::add (const SerializationKey& key, const HDF5::Object& obj) {
ASSERT (obj.isValid ());
ASSERT (ids.count (key) == 0);
ids[key] = obj;
}