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h5util.cpp
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h5util.cpp
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#include "error_macros.h"
#include "h5attributecloser.h"
#include "h5datasetcloser.h"
#include "h5dataspacecloser.h"
#include "h5datatypecloser.h"
#include "h5groupcloser.h"
#include "h5objectcloser.h"
#include "h5propertylistcloser.h"
#include "h5util.h"
#include "iriclib_errorcodes.h"
#include "internal/iric_logger.h"
#include <cstring>
#include <sstream>
#include <string>
using namespace iRICLib;
#define USERDEFINEDDATA_TYPE "MT"
#define USERDEFINEDDATA_LABEL "UserDefinedData_t"
#define INDEXARRAY_TYPE "I4"
#define INDEXARRAY_LABEL "IndexArray_t"
#define DATAARRAY_LABEL "DataArray_t"
namespace {
template <typename V>
int readValueT(hid_t groupId, const std::string& name, std::vector<V>* value, hid_t dataTypeNative)
{
_IRIC_LOGGER_TRACE_CALL_START("H5Dopen2");
hid_t dataSetId = H5Dopen2(groupId,name.c_str(), H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Dopen2");
if (dataSetId < 0) {
_iric_logger_error("readValueT", "H5Dopen2", dataSetId);
return IRIC_H5_CALL_ERROR;
}
H5DatasetCloser dataSetCloser(dataSetId);
_IRIC_LOGGER_TRACE_CALL_START("H5Dget_space");
hid_t dataSpaceId = H5Dget_space(dataSetId);
_IRIC_LOGGER_TRACE_CALL_END("H5Dget_space");
if (dataSpaceId < 0) {
_iric_logger_error("readValueT", "H5Dget_space", dataSpaceId);
return IRIC_H5_CALL_ERROR;
}
H5DataSpaceCloser dataSpaceCloser(dataSpaceId);
int ndims = H5Sget_simple_extent_ndims(dataSpaceId);
std::vector<hsize_t> dims(ndims);
H5Sget_simple_extent_dims(dataSpaceId, dims.data(), nullptr);
hsize_t size = 1;
for (int i = 0; i < ndims; ++i) {
size *= dims[i];
}
value->assign(size, 0);
_IRIC_LOGGER_TRACE_CALL_START("H5Dread");
herr_t status = H5Dread(dataSetId, dataTypeNative, H5S_ALL, H5S_ALL, H5P_DEFAULT, value->data());
_IRIC_LOGGER_TRACE_CALL_END("H5Dread");
if (status < 0) {
_iric_logger_error("readValueT", "H5Dread", status);
return IRIC_H5_CALL_ERROR;
}
return IRIC_NO_ERROR;
}
template <typename V>
int writeValueT(hid_t groupId, const std::string& name, const std::vector<V>& value, const std::vector<hsize_t>& dims, hid_t dataTypeInFile, hid_t dataTypeNative)
{
_IRIC_LOGGER_TRACE_CALL_START("H5Screate_simple");
hid_t dataSpaceId = H5Screate_simple(static_cast<int> (dims.size()), dims.data(), nullptr);
_IRIC_LOGGER_TRACE_CALL_END("H5Screate_simple");
if (dataSpaceId < 0) {
_iric_logger_error("writeValueT", "H5Screate_simple", dataSpaceId);
return IRIC_H5_CALL_ERROR;
}
H5DataSpaceCloser dataSpaceCloser(dataSpaceId);
_IRIC_LOGGER_TRACE_CALL_START("H5Dcreate2");
hid_t dataSetId = H5Dcreate2(groupId, name.c_str(), dataTypeInFile, dataSpaceId, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Dcreate2");
if (dataSetId < 0) {
_iric_logger_error("writeValueT", "H5Dcreate2", dataSetId);
return IRIC_H5_CALL_ERROR;
}
H5DatasetCloser dataSetCloser(dataSetId);
_IRIC_LOGGER_TRACE_CALL_START("H5Dwrite");
herr_t status = H5Dwrite(dataSetId, dataTypeNative, H5S_ALL, H5S_ALL, H5P_DEFAULT, value.data());
_IRIC_LOGGER_TRACE_CALL_END("H5Dwrite");
if (status < 0) {
_iric_logger_error("writeValueT", "H5Dwrite", status);
return IRIC_H5_CALL_ERROR;
}
return IRIC_NO_ERROR;
}
template <typename V>
int writeValueT(hid_t groupId, const std::string& name, const std::vector<V>& value, hid_t dataTypeInFile, hid_t dataTypeNative)
{
std::vector<hsize_t> dims;
dims.push_back(value.size());
_IRIC_LOGGER_TRACE_CALL_START("writeValueT");
int ier = writeValueT(groupId, name, value, dims, dataTypeInFile, dataTypeNative);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("writeValueT", ier);
RETURN_IF_ERR;
return IRIC_NO_ERROR;
}
template <typename V>
int writeValueT(hid_t groupId, const std::string& name, const V& value, hid_t dataTypeInFile, hid_t dataTypeNative)
{
std::vector<V> data;
data.push_back(value);
_IRIC_LOGGER_TRACE_CALL_START("writeValueT");
int ier = writeValueT<V>(groupId, name, data, dataTypeInFile, dataTypeNative);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("writeValueT", ier);
RETURN_IF_ERR;
return IRIC_NO_ERROR;
}
template <typename V>
int createGroupWithValuesT(hid_t groupId, const std::string& name, const std::string& label, const std::vector<V>& values, const std::vector<hsize_t>& dims, const std::string& typeAtt, hid_t dataTypeInFile, hid_t dataTypeNative, hid_t* newGroup)
{
_IRIC_LOGGER_TRACE_CALL_START("H5Pcreate");
hid_t groupCreationProperty = H5Pcreate(H5P_GROUP_CREATE);
_IRIC_LOGGER_TRACE_CALL_END("H5Pcreate");
if (groupCreationProperty < 0) {
_iric_logger_error("createGroupWithValuesT", "H5Pcreate", groupCreationProperty);
return IRIC_H5_CALL_ERROR;
}
H5PropertyListCloser groupCreationPropertyCloser(groupCreationProperty);
_IRIC_LOGGER_TRACE_CALL_START("H5Pset_link_creation_order");
H5Pset_link_creation_order(groupCreationProperty, H5P_CRT_ORDER_TRACKED | H5P_CRT_ORDER_INDEXED);
_IRIC_LOGGER_TRACE_CALL_END("H5Pset_link_creation_order");
_IRIC_LOGGER_TRACE_CALL_START("H5Gcreate2");
hid_t newGroupId = H5Gcreate2(groupId, name.c_str(), H5P_DEFAULT, groupCreationProperty, H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Gcreate2");
if (newGroupId < 0) {
_iric_logger_error("createGroupWithValuesT", "H5Gcreate2", newGroupId);
return IRIC_H5_CALL_ERROR;
}
_IRIC_LOGGER_TRACE_CALL_START("writeValueT");
int ier = writeValueT(newGroupId, " data", values, dims, dataTypeInFile, dataTypeNative);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("writeValueT", ier);
_IRIC_LOGGER_TRACE_CALL_START("H5Util::writeAttribute");
ier = H5Util::writeAttribute(newGroupId, "name", name);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("H5Util::writeAttribute", ier);
_IRIC_LOGGER_TRACE_CALL_START("H5Util::writeAttribute");
ier = H5Util::writeAttribute(newGroupId, "label", label);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("H5Util::writeAttribute", ier);
_IRIC_LOGGER_TRACE_CALL_START("H5Util::writeAttribute");
ier = H5Util::writeAttribute(newGroupId, "type", typeAtt);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("H5Util::writeAttribute", ier);
int flags = 1;
_IRIC_LOGGER_TRACE_CALL_START("H5Util::writeAttribute");
H5Util::writeAttribute(newGroupId, "flags", flags);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("H5Util::writeAttribute", ier);
if (newGroup != nullptr) {
*newGroup = newGroupId;
} else {
_IRIC_LOGGER_TRACE_CALL_START("H5Gclose");
herr_t status = H5Gclose(newGroupId);
_IRIC_LOGGER_TRACE_CALL_END("H5Gclose");
if (status < 0) {
_iric_logger_error("createGroupWithValuesT", "H5Gclose", status);
return IRIC_H5_CALL_ERROR;
}
}
return IRIC_NO_ERROR;
}
template <typename V>
int createGroupWithValuesT(hid_t groupId, const std::string& name, const std::string& label, const std::vector<V>& values, const std::string& typeAtt, hid_t dataTypeInFile, hid_t dataTypeNative, hid_t* newGroup)
{
std::vector<hsize_t> dims;
dims.push_back(values.size());
_IRIC_LOGGER_TRACE_CALL_START("createGroupWithValuesT");
int ier = createGroupWithValuesT(groupId, name, label, values, dims, typeAtt, dataTypeInFile, dataTypeNative, newGroup);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("createGroupWithValuesT", ier);
RETURN_IF_ERR;
return IRIC_NO_ERROR;
}
template <typename V>
int createGroupWithValueT(hid_t groupId, const std::string& name, const std::string& label, const V& value, const std::string& typeAtt, hid_t dataTypeInFile, hid_t dataTypeNative, hid_t* newGroup)
{
std::vector<V> values;
values.push_back(value);
_IRIC_LOGGER_TRACE_CALL_START("createGroupWithValuesT");
int ier = createGroupWithValuesT(groupId, name, label, values, typeAtt, dataTypeInFile, dataTypeNative, newGroup);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("createGroupWithValuesT", ier);
RETURN_IF_ERR;
return IRIC_NO_ERROR;
}
template <typename V>
int readGroupValueT(hid_t groupId, std::vector<V>* value, hid_t dataTypeNative)
{
_IRIC_LOGGER_TRACE_CALL_START("readValueT");
int ier = readValueT(groupId, " data", value, dataTypeNative);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("readValueT", ier);
RETURN_IF_ERR;
return IRIC_NO_ERROR;
}
template <typename V>
int updateGroupValueT(hid_t groupId, const std::vector<V>& value, const std::vector<hsize_t>& dims, hid_t dataTypeInFile, hid_t dataTypeNative)
{
_IRIC_LOGGER_TRACE_CALL_START("H5Ldelete");
herr_t status = H5Ldelete(groupId, " data", H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Ldelete");
if (status < 0) {
_iric_logger_error("updateGroupValueT", "H5Ldelete", status);
return IRIC_H5_CALL_ERROR;
}
_IRIC_LOGGER_TRACE_CALL_START("writeValueT");
int ier = writeValueT(groupId, " data", value, dims, dataTypeInFile, dataTypeNative);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("writeValueT", ier);
RETURN_IF_ERR;
return IRIC_NO_ERROR;
}
template <typename V>
int updateGroupValueT(hid_t groupId, const std::vector<V>& value, hid_t dataTypeInFile, hid_t dataTypeNative)
{
std::vector<int> dims;
dims.push_back(static_cast<int> (value.size()));
_IRIC_LOGGER_TRACE_CALL_START("updateGroupValueT");
int ier = updateGroupValueT(groupId, value, dims, dataTypeInFile, dataTypeNative);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("updateGroupValueT", ier);
RETURN_IF_ERR;
return IRIC_NO_ERROR;
}
template <typename V>
int updateGroupValueT(hid_t groupId, const V& value, hid_t dataTypeNative)
{
_IRIC_LOGGER_TRACE_CALL_START("H5Dopen2");
hid_t dataSetId = H5Dopen2(groupId, " data", H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Dopen2");
if (dataSetId < 0) {
_iric_logger_error("updateGroupValueT", "H5Dopen2", dataSetId);
return IRIC_H5_CALL_ERROR;
}
H5DatasetCloser datasetCloser(dataSetId);
_IRIC_LOGGER_TRACE_CALL_START("H5Dwrite");
herr_t status = H5Dwrite(dataSetId, dataTypeNative, H5S_ALL, H5S_ALL, H5P_DEFAULT, &value);
_IRIC_LOGGER_TRACE_CALL_END("H5Dwrite");
if (status < 0) {
_iric_logger_error("updateGroupValueT", "H5Dwrite", status);
return IRIC_H5_CALL_ERROR;
}
return IRIC_NO_ERROR;
}
template <typename V>
int updateOrCreateDataArrayT(hid_t groupId, const std::string& name, const std::vector<V>& values, const std::vector<hsize_t>& dims, const std::string& typeAtt, hid_t dataTypeInFile, hid_t dataTypeNative, std::unordered_set<std::string>* names = nullptr)
{
std::unordered_set<std::string> tmpNames;
if (names != nullptr) {
tmpNames = *names;
} else {
_IRIC_LOGGER_TRACE_CALL_START("H5Util::getGroupNames");
int ier = H5Util::getGroupNames(groupId, &tmpNames);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("H5Util::getGroupNames", ier);
RETURN_IF_ERR;
}
if (tmpNames.find(name) != tmpNames.end()) {
hid_t gId;
_IRIC_LOGGER_TRACE_CALL_START("H5Util::openGroup");
int ier = H5Util::openGroup(groupId, name, DATAARRAY_LABEL, &gId);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("H5Util::openGroup", ier);
RETURN_IF_ERR;
H5GroupCloser closer(gId);
_IRIC_LOGGER_TRACE_CALL_START("updateGroupValueT");
ier = updateGroupValueT(gId, values, dims, dataTypeInFile, dataTypeNative);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("updateGroupValueT", ier);
RETURN_IF_ERR;
} else {
_IRIC_LOGGER_TRACE_CALL_START("createGroupWithValuesT");
int ier = createGroupWithValuesT(groupId, name, DATAARRAY_LABEL, values, dims, typeAtt, dataTypeInFile, dataTypeNative, nullptr);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("createGroupWithValuesT", ier);
RETURN_IF_ERR;
tmpNames.insert(name);
if (names != nullptr) {
*names = tmpNames;
}
}
return IRIC_NO_ERROR;
}
template <typename V>
int updateOrCreateDataArrayT(hid_t groupId, const std::string& name, const std::vector<V>& values, const std::string& typeAtt, hid_t dataTypeInFile, hid_t dataTypeNative, std::unordered_set<std::string>* names = nullptr)
{
std::vector<hsize_t> dims;
dims.push_back(values.size());
_IRIC_LOGGER_TRACE_CALL_START("updateOrCreateDataArrayT");
int ier = updateOrCreateDataArrayT(groupId, name, values, dims, typeAtt, dataTypeInFile, dataTypeNative, names);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("updateOrCreateDataArrayT", ier);
RETURN_IF_ERR;
return IRIC_NO_ERROR;
}
template <typename V>
int writeAttributeT(hid_t groupId, const std::string& name, const V& value, hid_t dataTypeInFile, hid_t dataTypeNative)
{
hsize_t datalen = 1;
_IRIC_LOGGER_TRACE_CALL_START("H5Screate_simple");
hid_t dataSpaceId = H5Screate_simple(1, &datalen, nullptr);
_IRIC_LOGGER_TRACE_CALL_END("H5Screate_simple");
if (dataSpaceId < 0) {
_iric_logger_error("writeAttributeT", "H5Screate_simple", dataSpaceId);
return IRIC_H5_CALL_ERROR;
}
H5DataSpaceCloser dataSpaceCloser(dataSpaceId);
_IRIC_LOGGER_TRACE_CALL_START("H5Acreate2");
hid_t attId = H5Acreate2(groupId, name.c_str(), dataTypeInFile, dataSpaceId, H5P_DEFAULT, H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Acreate2");
if (attId < 0) {
_iric_logger_error("writeAttributeT", "H5Acreate2", attId);
return IRIC_H5_CALL_ERROR;
}
H5AttributeCloser attributeCloser(attId);
_IRIC_LOGGER_TRACE_CALL_START("H5Awrite");
herr_t status = H5Awrite(attId, dataTypeNative, &value);
_IRIC_LOGGER_TRACE_CALL_END("H5Awrite");
if (status < 0) {
_iric_logger_error("writeAttributeT", "H5Awrite", status);
return IRIC_H5_CALL_ERROR;
}
return IRIC_NO_ERROR;
}
int copyDataType(hid_t src, hid_t* tgt)
{
_IRIC_LOGGER_TRACE_CALL_START("H5Tget_size");
size_t attSize = H5Tget_size(src);
_IRIC_LOGGER_TRACE_CALL_END("H5Tget_size");
_IRIC_LOGGER_TRACE_CALL_START("H5Tcopy");
*tgt = H5Tcopy(src);
_IRIC_LOGGER_TRACE_CALL_END("H5Tcopy");
_IRIC_LOGGER_TRACE_CALL_START("H5Tset_size");
herr_t status = H5Tset_size(*tgt, attSize);
_IRIC_LOGGER_TRACE_CALL_END("H5Tset_size");
if (status < 0) {
_iric_logger_error("copyDataType", "H5Tset_size", status);
return IRIC_H5_CALL_ERROR;
}
return IRIC_NO_ERROR;
}
int copyDataSpace(hid_t src, hid_t* tgt)
{
_IRIC_LOGGER_TRACE_CALL_START("H5Scopy");
*tgt = H5Scopy(src);
_IRIC_LOGGER_TRACE_CALL_END("H5Scopy");
_IRIC_LOGGER_TRACE_CALL_START("H5Sextent_copy");
herr_t status = H5Sextent_copy(src, *tgt);
_IRIC_LOGGER_TRACE_CALL_END("H5Sextent_copy");
if (status < 0) {
_iric_logger_error("copyDataSpace", "H5Sextent_copy", status);
return IRIC_H5_CALL_ERROR;
}
return IRIC_NO_ERROR;
}
int setupBuffer(hid_t dataType, hid_t dataSpace, std::vector<char>* buffer)
{
_IRIC_LOGGER_TRACE_CALL_START("H5Tget_size");
hsize_t dtSize = H5Tget_size(dataType);
_IRIC_LOGGER_TRACE_CALL_END("H5Tget_size");
_IRIC_LOGGER_TRACE_CALL_START("H5Sget_simple_extent_ndims");
int ndims = H5Sget_simple_extent_ndims(dataSpace);
_IRIC_LOGGER_TRACE_CALL_END("H5Sget_simple_extent_ndims");
std::vector<hsize_t> dims(ndims);
_IRIC_LOGGER_TRACE_CALL_START("H5Sget_simple_extent_dims");
H5Sget_simple_extent_dims(dataSpace, dims.data(), nullptr);
_IRIC_LOGGER_TRACE_CALL_END("H5Sget_simple_extent_dims");
hsize_t dsSize = 1;
for (int i = 0; i < ndims; ++i) {
dsSize *= dims.at(i);
}
hsize_t totalSize = dtSize * dsSize;
/*
std::ostringstream ss;
ss << "In setupBuffer(), totalSize = " << totalSize;
_iric_logger_debug(ss.str());
*/
buffer->assign(totalSize, 0);
return IRIC_NO_ERROR;
}
int copyAttribute(hid_t srcId, hid_t tgtId, const std::string& name)
{
_IRIC_LOGGER_TRACE_CALL_START("H5Aopen");
hid_t srcAttId = H5Aopen(srcId, name.c_str(), H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Aopen");
if (srcAttId < 0) {
_iric_logger_error("copyAttribute", "H5Aopen", srcAttId);
return IRIC_H5_CALL_ERROR;
}
H5AttributeCloser srcAttCloser(srcAttId);
// copying datatype
_IRIC_LOGGER_TRACE_CALL_START("H5Aget_type");
hid_t srcDataTypeId = H5Aget_type(srcAttId);
_IRIC_LOGGER_TRACE_CALL_END("H5Aget_type");
if (srcDataTypeId < 0) {
_iric_logger_error("copyAttribute", "H5Aget_type", srcDataTypeId);
return IRIC_H5_CALL_ERROR;
}
H5DataTypeCloser srcDataTypeCloser(srcDataTypeId);
hid_t tgtDataTypeId;
_IRIC_LOGGER_TRACE_CALL_START("copyDataType");
int ier = copyDataType(srcDataTypeId, &tgtDataTypeId);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("copyDataType", ier);
RETURN_IF_ERR;
H5DataTypeCloser tgtDataTypeCloser(tgtDataTypeId);
// copying dataspace
_IRIC_LOGGER_TRACE_CALL_START("H5Aget_space");
hid_t srcDataSpaceId = H5Aget_space(srcAttId);
_IRIC_LOGGER_TRACE_CALL_END("H5Aget_space");
if (srcDataSpaceId < 0) {
_iric_logger_error("copyAttribute", "H5Aget_space", srcDataSpaceId);
return IRIC_H5_CALL_ERROR;
}
H5DataSpaceCloser srcDataSpaceCloser(srcDataSpaceId);
hid_t tgtDataSpaceId;
_IRIC_LOGGER_TRACE_CALL_START("copyDataSpace");
ier = copyDataSpace(srcDataSpaceId, &tgtDataSpaceId);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("copyDataSpace", ier);
RETURN_IF_ERR;
H5DataSpaceCloser tgtDataSpaceCloser(tgtDataSpaceId);
std::vector<char> buffer;
_IRIC_LOGGER_TRACE_CALL_START("setupBuffer");
ier = setupBuffer(srcDataTypeId, srcDataSpaceId, &buffer);
_IRIC_LOGGER_TRACE_CALL_END("setupBuffer");
RETURN_IF_ERR;
_IRIC_LOGGER_TRACE_CALL_START("H5Aread");
herr_t status = H5Aread(srcAttId, srcDataTypeId, buffer.data());
_IRIC_LOGGER_TRACE_CALL_END("H5Aread");
if (status < 0) {
_iric_logger_error("copyAttribute", "H5Aread", status);
return IRIC_H5_CALL_ERROR;
}
_IRIC_LOGGER_TRACE_CALL_START("H5Acreate2");
hid_t tgtAttId = H5Acreate2(tgtId, name.c_str(), tgtDataTypeId, tgtDataSpaceId, H5P_DEFAULT, H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Acreate2");
if (tgtAttId < 0) {
_iric_logger_error("copyAttribute", "H5Acreate2", tgtAttId);
return IRIC_H5_CALL_ERROR;
}
H5AttributeCloser tgtAttCloser(tgtAttId);
_IRIC_LOGGER_TRACE_CALL_START("H5Awrite");
status = H5Awrite(tgtAttId, srcDataTypeId, buffer.data());
_IRIC_LOGGER_TRACE_CALL_END("H5Awrite");
if (status < 0) {
_iric_logger_error("copyAttribute", "H5Awrite", status);
return IRIC_H5_CALL_ERROR;
}
return IRIC_NO_ERROR;
}
int copyDataset(hid_t srcId, hid_t tgtId, const std::string& name)
{
_IRIC_LOGGER_TRACE_CALL_START("H5Dopen");
hid_t srcDatasetId = H5Dopen(srcId, name.c_str(), H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Dopen");
if (srcDatasetId < 0) {
_iric_logger_error("copyDataset", "H5Dopen", srcDatasetId);
return IRIC_H5_CALL_ERROR;
}
H5DatasetCloser srcDatasetCloser(srcDatasetId);
// copying datatype
_IRIC_LOGGER_TRACE_CALL_START("H5Dget_type");
hid_t srcDataTypeId = H5Dget_type(srcDatasetId);
_IRIC_LOGGER_TRACE_CALL_END("H5Dget_type");
if (srcDataTypeId < 0) {
_iric_logger_error("copyDataset", "H5Dget_type", srcDataTypeId);
return IRIC_H5_CALL_ERROR;
}
H5DataTypeCloser srcDataTypeCloser(srcDataTypeId);
hid_t tgtDataTypeId;
_IRIC_LOGGER_TRACE_CALL_START("copyDataType");
int ier = copyDataType(srcDataTypeId, &tgtDataTypeId);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("copyDataType", ier);
RETURN_IF_ERR;
H5DataTypeCloser tgtDataTypeCloser(tgtDataTypeId);
// copying dataspace
_IRIC_LOGGER_TRACE_CALL_START("H5Dget_space");
hid_t srcDataSpaceId = H5Dget_space(srcDatasetId);
_IRIC_LOGGER_TRACE_CALL_END("H5Dget_space");
if (srcDataSpaceId < 0) {
_iric_logger_error("copyDataset", "H5Dget_space", srcDataSpaceId);
return IRIC_H5_CALL_ERROR;
}
H5DataSpaceCloser srcDataSpaceCloser(srcDataSpaceId);
hid_t tgtDataSpaceId;
_IRIC_LOGGER_TRACE_CALL_START("copyDataSpace");
ier = copyDataSpace(srcDataSpaceId, &tgtDataSpaceId);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("copyDataSpace", ier);
RETURN_IF_ERR;
H5DataSpaceCloser tgtDataSpaceCloser(tgtDataSpaceId);
std::vector<char> buffer;
_IRIC_LOGGER_TRACE_CALL_START("setupBuffer");
ier = setupBuffer(srcDataTypeId, srcDataSpaceId, &buffer);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("setupBuffer", ier);
_IRIC_LOGGER_TRACE_CALL_START("H5Dread");
herr_t status = H5Dread(srcDatasetId, srcDataTypeId,H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer.data());
_IRIC_LOGGER_TRACE_CALL_END("H5Dread");
if (status < 0) {
_iric_logger_error("copyDataset", "H5Dread", status);
return IRIC_H5_CALL_ERROR;
}
_IRIC_LOGGER_TRACE_CALL_START("H5Dcreate2");
hid_t tgtDatasetId = H5Dcreate2(tgtId, name.c_str(), tgtDataTypeId, tgtDataSpaceId, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Dcreate2");
H5DatasetCloser tgtDatasetCloser(tgtDatasetId);
_IRIC_LOGGER_TRACE_CALL_START("H5Dwrite");
status = H5Dwrite(tgtDatasetId, srcDataTypeId, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer.data());
_IRIC_LOGGER_TRACE_CALL_END("H5Dwrite");
if (status < 0) {
_iric_logger_error("copyDataset", "H5Dwrite", status);
return IRIC_H5_CALL_ERROR;
}
return IRIC_NO_ERROR;
}
int copyChildren(hid_t srcGroupId, hid_t tgtGroupId)
{
H5G_info_t info;
_IRIC_LOGGER_TRACE_CALL_START("H5Gget_info");
herr_t status = H5Gget_info(srcGroupId, &info);
_IRIC_LOGGER_TRACE_CALL_END("H5Gget_info");
if (status < 0) {
_iric_logger_error("copyChildren", "H5Gget_info", status);
return IRIC_H5_CALL_ERROR;
}
for (hsize_t i = 0; i < info.nlinks; ++i) {
_IRIC_LOGGER_TRACE_CALL_START("H5Lget_name_by_idx");
ssize_t nameLen = H5Lget_name_by_idx(srcGroupId, ".", H5_INDEX_NAME, H5_ITER_INC, i, nullptr, 0, H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Lget_name_by_idx");
if (nameLen < 0) {continue;}
std::vector<char> buffer(nameLen + 1);
_IRIC_LOGGER_TRACE_CALL_START("H5Lget_name_by_idx");
H5Lget_name_by_idx(srcGroupId, ".", H5_INDEX_NAME, H5_ITER_INC, i, buffer.data(), buffer.size(), H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Lget_name_by_idx");
std::string name = buffer.data();
_IRIC_LOGGER_TRACE_CALL_START("H5Oopen");
hid_t oid = H5Oopen(srcGroupId, name.c_str(), H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Oopen");
if (oid < 0) {continue;}
H5O_info2_t info;
_IRIC_LOGGER_TRACE_CALL_START("H5Oget_info");
status = H5Oget_info(oid, &info, H5O_INFO_BASIC);
_IRIC_LOGGER_TRACE_CALL_END("H5Oget_info");
_IRIC_LOGGER_TRACE_CALL_START("H5Oclose");
H5Oclose(oid);
_IRIC_LOGGER_TRACE_CALL_END("H5Oclose");
if (status < 0) {
_iric_logger_error("copyChildren", "H5Oget_info", status);
return IRIC_H5_CALL_ERROR;
}
if (info.type == H5O_TYPE_GROUP) {
_IRIC_LOGGER_TRACE_CALL_START("H5Gopen2");
hid_t srcChildGroupId = H5Gopen2(srcGroupId, name.c_str(), H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Gopen2");
if (srcChildGroupId < 0) {
_iric_logger_error("copyChildren", "H5Gopen2", srcChildGroupId);
return IRIC_H5_CALL_ERROR;
}
H5GroupCloser srcChildGroupCloser(srcChildGroupId);
hid_t tgtChildGroupId;
int ier = H5Util::createGroup(tgtGroupId, name, &tgtChildGroupId);
RETURN_IF_ERR;
H5GroupCloser tgtChildGroupCloser(tgtChildGroupId);
_IRIC_LOGGER_TRACE_CALL_START("H5Util::copyAttributes");
ier = H5Util::copyAttributes(srcChildGroupId, tgtChildGroupId);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("H5Util::copyAttributes", ier);
RETURN_IF_ERR;
_IRIC_LOGGER_TRACE_CALL_START("H5Util::copyGroupRecursively");
ier = H5Util::copyGroupRecursively(srcChildGroupId, tgtChildGroupId);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("H5Util::copyGroupRecursively", ier);
RETURN_IF_ERR;
} else if (info.type == H5O_TYPE_DATASET) {
_IRIC_LOGGER_TRACE_CALL_START("copyDataset");
int ier = copyDataset(srcGroupId, tgtGroupId, name);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("copyDataset", ier);
RETURN_IF_ERR;
}
}
return IRIC_NO_ERROR;
}
int getObjectNames(hid_t groupId, H5O_type_t objectType, std::vector<std::string>* names)
{
H5G_info_t info;
_IRIC_LOGGER_TRACE_CALL_START("H5Gget_info");
herr_t status = H5Gget_info(groupId, &info);
_IRIC_LOGGER_TRACE_CALL_END("H5Gget_info");
if (status < 0) {
_iric_logger_error("H5Util::getGroupNames", "H5Gget_info", status);
return IRIC_H5_CALL_ERROR;
}
for (hsize_t i = 0; i < info.nlinks; ++i) {
_IRIC_LOGGER_TRACE_CALL_START("H5Lget_name_by_idx");
ssize_t nameLen = H5Lget_name_by_idx(groupId, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, i, nullptr, 0, H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Lget_name_by_idx");
if (nameLen < 0) {continue;}
std::vector<char> buffer(nameLen + 1);
_IRIC_LOGGER_TRACE_CALL_START("H5Lget_name_by_idx");
H5Lget_name_by_idx(groupId, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, i, buffer.data(), buffer.size(), H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Lget_name_by_idx");
std::string name = buffer.data();
_IRIC_LOGGER_TRACE_CALL_START("H5Oopen");
hid_t oid = H5Oopen(groupId, name.c_str(), H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Oopen");
if (oid < 0) {
_iric_logger_error("H5Util::getGroupNames", "H5Open", oid);
return IRIC_H5_CALL_ERROR;
}
H5ObjectCloser objectCloser(oid);
H5O_info2_t info;
_IRIC_LOGGER_TRACE_CALL_START("H5Oget_info");
status = H5Oget_info(oid, &info, H5O_INFO_BASIC);
_IRIC_LOGGER_TRACE_CALL_END("H5Oget_info");
if (status < 0) {
_iric_logger_error("H5Util::getGroupNames", "H5Oget_info", status);
return IRIC_H5_CALL_ERROR;
}
if (info.type == objectType) {
names->push_back(name);
}
}
return IRIC_NO_ERROR;
}
} // namespace
std::string H5Util::indexArrayLabel()
{
return INDEXARRAY_LABEL;
}
std::string H5Util::indexArrayType()
{
return INDEXARRAY_TYPE;
}
std::string H5Util::dataArrayLabel()
{
return DATAARRAY_LABEL;
}
std::string H5Util::userDefinedDataLabel()
{
return USERDEFINEDDATA_LABEL;
}
std::string H5Util::userDefinedDataType()
{
return USERDEFINEDDATA_TYPE;
}
int H5Util::getGroupNames(hid_t groupId, std::vector<std::string>* names)
{
return getObjectNames(groupId, H5O_TYPE_GROUP, names);
}
int H5Util::getGroupNames(hid_t groupId, std::unordered_set<std::string>* names)
{
std::vector<std::string> namesVec;
int ier = getGroupNames(groupId, &namesVec);
RETURN_IF_ERR;
for (const auto& name : namesVec) {
names->insert(name);
}
return IRIC_NO_ERROR;
}
int H5Util::getGroupNamesWithLabel(hid_t groupId, const std::string& label, std::vector<std::string>* names)
{
std::vector<std::string> tmpNames;
int ier = getGroupNames(groupId, &tmpNames);
RETURN_IF_ERR;
for (const auto& name : tmpNames) {
hid_t childGroupId;
int ier = openGroup(groupId, name, label, &childGroupId, true);
if (ier != IRIC_NO_ERROR) {continue;}
H5GroupCloser closer(childGroupId);
names->push_back(name);
}
return IRIC_NO_ERROR;
}
int H5Util::getGroupNamesWithLabel(hid_t groupId, const std::string& label, std::unordered_set<std::string>* names)
{
std::vector<std::string> namesVec;
int ier = getGroupNamesWithLabel(groupId, label, &namesVec);
RETURN_IF_ERR;
for (const auto& name : namesVec) {
names->insert(name);
}
return IRIC_NO_ERROR;
}
int H5Util::getDatasetNames(hid_t groupId, std::vector<std::string>* names)
{
return getObjectNames(groupId, H5O_TYPE_DATASET, names);
}
int H5Util::getDatasetNames(hid_t groupId, std::unordered_set<std::string>* names)
{
std::vector<std::string> namesVec;
int ier = getDatasetNames(groupId, &namesVec);
RETURN_IF_ERR;
for (const auto& name : namesVec) {
names->insert(name);
}
return IRIC_NO_ERROR;
}
void H5Util::buildDimsAndBuffer(const std::vector<std::string>& value, std::vector<size_t>* dims, std::vector<char>* buffer)
{
size_t maxLen = 0;
for (const auto& v : value) {
auto len = v.length();
if (len > maxLen) {maxLen = len;}
}
maxLen += 1; // for \0
dims->clear();
dims->push_back(value.size());
dims->push_back(maxLen);
buffer->assign(maxLen * value.size(), 0);
for (size_t i = 0; i < value.size(); ++i) {
const auto& v = value.at(i);
memcpy(buffer->data() + i * maxLen, v.data(), v.length());
}
}
int H5Util::createGroup(hid_t groupId, const std::string& name, hid_t* newGroup)
{
_IRIC_LOGGER_TRACE_CALL_START("H5Pcreate");
hid_t groupCreationProperty = H5Pcreate(H5P_GROUP_CREATE);
_IRIC_LOGGER_TRACE_CALL_END("H5Pcreate");
if (groupCreationProperty < 0) {
_iric_logger_error("H5Util::createGroup", "H5Pcreate", groupCreationProperty);
return IRIC_H5_CALL_ERROR;
}
H5PropertyListCloser groupCreationPropertyCloser(groupCreationProperty);
_IRIC_LOGGER_TRACE_CALL_START("H5Pset_link_creation_order");
H5Pset_link_creation_order(groupCreationProperty, H5P_CRT_ORDER_TRACKED | H5P_CRT_ORDER_INDEXED);
_IRIC_LOGGER_TRACE_CALL_END("H5Pset_link_creation_order");
_IRIC_LOGGER_TRACE_CALL_START("H5Gcreate2");
hid_t newGroupId = H5Gcreate2(groupId, name.c_str(), H5P_DEFAULT, groupCreationProperty, H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Gcreate2");
if (newGroupId < 0) {
_iric_logger_error("H5Util::createGroup", "H5Gcreate2", newGroupId);
return IRIC_H5_CALL_ERROR;
}
*newGroup = newGroupId;
return IRIC_NO_ERROR;
}
int H5Util::createGroup(hid_t groupId, const std::string& name, const std::string& label, const std::string& type, hid_t* newGroup)
{
_IRIC_LOGGER_TRACE_CALL_START("H5Util::createGroup");
int ier = createGroup(groupId, name, newGroup);
_IRIC_LOGGER_TRACE_CALL_END("H5Util::createGroup");
RETURN_IF_ERR;
_IRIC_LOGGER_TRACE_CALL_START("H5Util::writeAttribute");
ier = H5Util::writeAttribute(*newGroup, "name", name);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("H5Util::writeAttribute", ier);
_IRIC_LOGGER_TRACE_CALL_START("H5Util::writeAttribute");
ier = H5Util::writeAttribute(*newGroup, "label", label);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("H5Util::writeAttribute", ier);
_IRIC_LOGGER_TRACE_CALL_START("H5Util::writeAttribute");
ier = H5Util::writeAttribute(*newGroup, "type", type);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("H5Util::writeAttribute", ier);
int flags = 1;
_IRIC_LOGGER_TRACE_CALL_START("H5Util::writeAttribute");
ier = H5Util::writeAttribute(*newGroup, "flags", flags);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("H5Util::writeAttribute", ier);
return IRIC_NO_ERROR;
}
int H5Util::createUserDefinedDataGroup(hid_t groupId, const std::string& name, hid_t* newGroup)
{
_IRIC_LOGGER_TRACE_CALL_START("H5Util::createGroup");
int ier = createGroup(groupId, name, USERDEFINEDDATA_LABEL, USERDEFINEDDATA_TYPE, newGroup);
_IRIC_LOGGER_TRACE_CALL_END_WITHVAL("H5Util::createGroup", ier);
RETURN_IF_ERR;
return IRIC_NO_ERROR;
}
int H5Util::openGroup(hid_t groupId, const std::string& name, const std::string& label, hid_t* childGroup, bool noErrorLog)
{
*childGroup = -1;
_IRIC_LOGGER_TRACE_CALL_START("H5Oopen");
hid_t groupId2 = H5Oopen(groupId, name.c_str(), H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Oopen");
if (groupId2 < 0) {
_iric_logger_error("H5Util::openGroup", "H5Oopen", groupId2);
return IRIC_H5_CALL_ERROR;
}
// read type info
H5O_info2_t ginfo;
_IRIC_LOGGER_TRACE_CALL_START("H5Oget_info");
herr_t status = H5Oget_info(groupId2, &ginfo, H5O_INFO_BASIC);
_IRIC_LOGGER_TRACE_CALL_END("H5Oget_info");
if (status < 0) {
_iric_logger_error("H5Util::openGroup", "H5Oget_info", status);
return IRIC_H5_CALL_ERROR;
}
if (ginfo.type != H5O_TYPE_GROUP) {
_IRIC_LOGGER_TRACE_CALL_START("H5Oclose");
H5Oclose(groupId2);
_IRIC_LOGGER_TRACE_CALL_END("H5Oclose");
if (! noErrorLog) {
std::ostringstream ss;
ss << "H5Util::openGroup(), object with name " << name << " is not a group, but the type = " << ginfo.type;
_iric_logger_error(ss.str());
}
return IRIC_NOT_GROUP;
}
// read label attribute
_IRIC_LOGGER_TRACE_CALL_START("H5Aopen");
hid_t attId = H5Aopen(groupId2, "label", H5P_DEFAULT);
_IRIC_LOGGER_TRACE_CALL_END("H5Aopen");